ORCID Profile
0000-0002-3081-6700
Current Organisation
University of Guelph
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Publisher: Springer Science and Business Media LLC
Date: 12-1999
DOI: 10.1007/PL00006599
Abstract: The extracellular hemoglobins of cladocerans derive from the aggregation of 12 two-domain globin subunits that are apparently encoded by four genes. This study establishes that at least some of these genes occur as a tandem array in both Daphnia magna and Daphnia exilis. The genes share a uniform structure a bridge intron separates two globin domains which each include three exons and two introns. Introns are small, averaging just 77 bp, but a longer sequence (2.2-3.2 kb) separates adjacent globin genes. A survey of structural ersity in globin genes from other daphniids revealed three independent cases of intron loss, but exon lengths were identical, excepting a 3-bp insertion in exon 5 of Simocephalus. Heterogeneity in the extent of nucleotide ergence was marked among exons, largely as a result of the pronounced ersification of the terminal exon. This variation reflected, in part, varying exposure to concerted evolution. Conversion events were frequent in exons 1-4 but were absent from exons 5 and 6. Because of this difference, the results of phylogenetic analyses were strongly affected by the sequences employed in this construction. Phylogenies based on total nucleotide ergence in exons 1-4 revealed affinities among all genes isolated from a single species, reflecting the impact of gene conversion events. In contrast, phylogenies based on total nucleotide ergence in exons 5 and 6 revealed affinities among orthologous genes from different taxa.
Publisher: Elsevier BV
Date: 12-2003
Publisher: Wiley
Date: 10-1996
Publisher: Pensoft Publishers
Date: 16-08-2023
DOI: 10.3897/ZOOKEYS.1175.105068
Abstract: The parasitoid wasp genus Alphomelon Mason, 1981 is revised, based on a combination of basic morphology (dichotomous key and brief diagnostic descriptions), DNA barcoding, biology (host data and wasp cocoons), and distribution data. A total of 49 species is considered the genus is almost entirely Neotropical (48 species recorded from that region), but three species reach the Nearctic, with one of them extending as far north as 45° N in Canada. Alphomelon parasitizes exclusively Hesperiinae caterpillars (Lepidoptera: Hesperiidae), mostly feeding on monocots in the families Arecaceae, Bromeliaceae, Cannaceae, Commelinaceae, Heliconiaceae, and Poaceae. Most wasp species parasitize either on one or very few (2–4) host species, usually within one or two hesperiine genera but some species can parasitize several hosts from up to nine different hesperiine genera. Among species with available data for their cocoons, roughly half weave solitary cocoons (16) and half are gregarious (17) cocoons tend to be surrounded by a rather distinctive, coarse silk (especially in solitary species, but also distinguishable in some gregarious species). Neither morphology nor DNA barcoding alone was sufficient on its own to delimit all species properly by integrating all available evidence (even if incomplete, as available data for every species is different) a foundation is provided for future studies incorporating more specimens, especially from South America. The following 30 new species are described: cruzi , itatiaiensis , and palomae , authored by Shimbori & Fernandez-Triana and adrianguadamuzi , amazonas , andydeansi , calixtomoragai , carolinacanoae , christerhanssoni , diniamartinezae , duvalierbricenoi , eldaarayae , eliethcantillanoae , gloriasihezarae , guillermopereirai , hazelcambroneroae , josecortesi , keineraragoni , luciarosae , manuelriosi , mikesharkeyi , osvaldoespinozai , paramelanoscelis , paranigriceps , petronariosae , ricardocaleroi , rigoi , rostermoragai , sergioriosi , and yanayacu , authored by Fernandez-Triana & Shimbori.
Publisher: Springer Science and Business Media LLC
Date: 08-10-2008
Publisher: Oxford University Press (OUP)
Date: 06-1999
DOI: 10.2307/2640718
Publisher: Springer Science and Business Media LLC
Date: 07-1984
DOI: 10.1007/BF00016601
Publisher: Springer Science and Business Media LLC
Date: 1981
DOI: 10.1007/BF00540595
Publisher: Wiley
Date: 09-04-2012
DOI: 10.1111/J.1755-0998.2012.03143.X
Abstract: The enormous cytochrome oxidase subunit I (COI) sequence database being assembled from the various DNA barcoding projects as well as from independent phylogenetic studies constitutes an almost unprecedented amount of data for molecular systematics, in addition to its role in species identification and discovery. As part of a study of the potential of this gene fragment to improve the accuracy of phylogenetic reconstructions, and in particular, exploring the effects of dense taxon s ling, we have assembled a data set for the hyper erse, cosmopolitan parasitic wasp superfamily Ichneumonoidea, including the release of 1793 unpublished sequences. Of approximately 84 currently recognized Ichneumonoidea subfamilies, 2500 genera and 41,000 described species, barcoding 5'-COI data were assembled for 4168 putative species-level terminals (many undescribed), representing 671 genera and all but ten of the currently recognized subfamilies. After the removal of identical and near-identical sequences, the 4174 initial sequences were reduced to 3278. We show that when subjected to phylogenetic analysis using both maximum likelihood and parsimony, there is a broad correlation between taxonomic congruence and number of included sequences. We additionally present a new measure of taxonomic congruence based upon the Simpson ersity index, the Simpson dominance index, which gives greater weight to morphologically recognized taxonomic groups (subfamilies) recovered with most representatives in one or a few contiguous groups or subclusters.
Publisher: Springer Science and Business Media LLC
Date: 11-1993
DOI: 10.1038/HDY.1993.168
Publisher: Canadian Science Publishing
Date: 08-2003
DOI: 10.1139/G03-040
Abstract: Cytological and organismal characteristics associated with cellular DNA content underpin most adaptionist interpretations of genome size variation. Since fishes are the only group of vertebrate for which relationships between genome size and key cellular parameters are uncertain, the cytological correlates of genome size were examined in this group. The cell and nuclear areas of erythrocytes showed a highly significant positive correlation with each other and with genome size across 22 cartilaginous and 201 ray-finned fishes. Regressions remained significant at all taxonomic levels, as well as among different fish lineages. However, the results revealed that cartilaginous fishes possess higher cytogenomic ratios than ray-finned fishes, as do cold-water fishes relative to their warm-water counterparts. Increases in genome size owing to ploidy shifts were found to influence cell and nucleus size in an immediate and causative manner, an effect that persists in ancient polyploid lineages. These correlations with cytological parameters known to have important influences on organismal phenotypes support an adaptive interpretation for genome size variation in fishes.Key words: evolution, genome size, DNA content, cell size, erythrocyte size, fishes, nucleotypic effect.
Publisher: Wiley
Date: 25-02-2013
Abstract: Although nematodes are one of the most erse metazoan phyla, species identification through morphology is difficult. Several genetic markers have been used for their identification, but most do not provide species-level resolution in all groups, and those that do lack primer sets effective across the phylum, precluding high-throughput processing. This study describes a cocktail of three novel primer pairs that overcome this limitation by recovering cytochrome c oxidase I (COI) barcodes from erse nematode lineages parasitic on vertebrates, including members of three orders and eight families. Its effectiveness across a broad range of nematodes enables high-throughput processing.
Publisher: Oxford University Press (OUP)
Date: 1985
DOI: 10.2307/2408534
Publisher: Oxford University Press (OUP)
Date: 11-1998
Publisher: Proceedings of the National Academy of Sciences
Date: 08-1993
Abstract: Allozyme, morphological, and PCR-generated mtDNA markers were used to analyze hybrid parentage and introgression between the neighboringly sympatric crustaceans Daphnia galeata mendotae and Daphnia rosea. mtDNA analysis of D. galeata mendotae from 15 lakes and of D. rosea from 8 lakes revealed species-specific fragment patterns resulting from TaqI and RsaI digestion. No in iduals of one parent species possessed the typical mtDNA of the other parent species, suggesting that mtDNA introgression is rare or nonexistent. Hybrids from 18 lakes possessed either the mtDNA patterns of D. rosea or of D. galeata mendotae, indicating that reciprocal hybridization occurs. The mtDNA genome of the dominant parent species in a lake was overrepresented in the hybrids, suggesting that hybridization most often involves females of the common species and males of the rare species. Such a pattern is consistent with the differing importance of density to the environmental induction of males and sexual eggs in Daphnia. For the assessment of nuclear gene flow, eight sympatric populations of each parental taxon and seven allopatric populations of D. galeata were analyzed for allozyme variation at nine polymorphic loci. Our results provided evidence for asymmetric interspecific gene flow involving alleles at six loci that are unlikely to be convergent or symplesiomorphic. This reticulate evolution accounted for much of the genetic ergence between European and North American populations of D. galeata.
Publisher: Public Library of Science (PLoS)
Date: 10-07-2013
Publisher: Oxford University Press (OUP)
Date: 10-2005
Publisher: Public Library of Science (PLoS)
Date: 10-09-2015
Publisher: Elsevier BV
Date: 03-2009
DOI: 10.1016/J.YMPEV.2008.11.026
Abstract: Molecular studies have enlightened our understanding of freshwater zooplankton biogeography, yet questions remain regarding the scale and commonality of geographic speciation. Here, we present a mtDNA-based phylogenetic hypothesis for 92 Daphnia species from all seven continents, with a focus on North and South America, Europe, and Australia, and use it to explore the frequency, scale, and geographical orientation of allopatric ergence events. Allopatric speciation can conservatively account for at least 42% of cladogenetic events among the species included in our study most of these involve intercontinental splits. Closely related species pairs are concentrated in the circumarctic region and between northern and southern continents, aligned with bird migration routes, suggesting recent dispersal. By contrast, deeper phylogenetic patterns are consistent with vicariance scenarios linked to continental fragmentation. The possible reasons for the puzzling persistence of these ancient patterns in light of the eroding force of dispersal are considered. Our results demonstrate the high frequency and complex pattern of allopatric speciation in this ancient, passively dispersed genus.
Publisher: American Society of Parasitologists
Date: 06-2013
DOI: 10.1645/GE-3138.1
Publisher: Elsevier BV
Date: 06-2000
DOI: 10.1016/S1383-5742(00)00004-1
Abstract: The conservation of genetic ersity has emerged as one of the central issues in conservation biology. Although researchers in the areas of evolutionary biology, population management, and conservation biology routinely investigate genetic variability in natural populations, only a handful of studies have addressed the effects of chemical contamination on population genetics. Chemical contamination can cause population reduction by the effects of somatic and heritable mutations, as well as non-genetic modes of toxicity. Stochastic processes in small populations, increased mutation load, and the phenomenon of mutational meltdown are compounding factors that cause reduced fitness and accelerate the process of population extirpation. Although the original damage caused by chemical contaminants is at the molecular level, there are emergent effects at the level of populations, such as the loss of genetic ersity, that are not predictable based solely on knowledge of the mechanism of toxicity of the chemical contaminants. Therefore, the study of evolutionary toxicology, which encompasses the population-genetic effects of environmental contaminants, should be an important focus of ecotoxicology. This paper reviews the issues surrounding the genetic effects of pollution, summarizes the technical approaches that can be used to address these issues, and provides ex les of studies that have addressed some of them.
Publisher: Elsevier BV
Date: 05-1986
Publisher: Proceedings of the National Academy of Sciences
Date: 26-08-2008
Abstract: We DNA barcoded 2,597 parasitoid wasps belonging to 6 microgastrine braconid genera reared from parapatric tropical dry forest, cloud forest, and rain forest in Area de Conservación Guanacaste (ACG) in northwestern Costa Rica and combined these data with records of caterpillar hosts and morphological analyses. We asked whether barcoding and morphology discover the same provisional species and whether the biological entities revealed by our analysis are congruent with wasp host specificity. Morphological analysis revealed 171 provisional species, but barcoding exposed an additional 142 provisional species 95% of the total is likely to be undescribed. These 313 provisional species are extraordinarily host specific more than 90% attack only 1 or 2 species of caterpillars out of more than 3,500 species s led. The most extreme case of overlooked ersity is the morphospecies Apanteles leucostigmus . This minute black wasp with a distinctive white wing stigma was thought to parasitize 32 species of ACG hesperiid caterpillars, but barcoding revealed 36 provisional species, each attacking one or a very few closely related species of caterpillars. When host records and/or within-ACG distributions suggested that DNA barcoding had missed a species-pair, or when provisional species were separated only by slight differences in their barcodes, we examined nuclear sequences to test hypotheses of presumptive species boundaries and to further probe host specificity. Our iterative process of combining morphological analysis, ecology, and DNA barcoding and reiteratively using specimens maintained in permanent collections has resulted in a much more fine-scaled understanding of parasitoid ersity and host specificity than any one of these elements could have produced on its own.
Publisher: Entomological Society of Washington
Date: 2013
Publisher: Springer Science and Business Media LLC
Date: 2013
Publisher: Public Library of Science (PLoS)
Date: 23-11-2011
Publisher: Wiley
Date: 12-1991
Publisher: Springer Science and Business Media LLC
Date: 02-1993
DOI: 10.1038/HDY.1993.24
Publisher: Wiley
Date: 04-1996
Publisher: Public Library of Science (PLoS)
Date: 26-07-2011
Publisher: Springer Science and Business Media LLC
Date: 02-1987
DOI: 10.1007/BF02530280
Publisher: Public Library of Science (PLoS)
Date: 17-04-2014
Publisher: Springer Science and Business Media LLC
Date: 12-1974
DOI: 10.1038/HDY.1974.99
Abstract: A 28-year-old woman with severe mitral stenosis underwent percutaneous mitral valvuloplasty at 26 weeks' gestation. Balloon dilation using a double 18-18 mm balloon resulted in improvement in mean mitral pressure gradient (32 to 8 mmHg) and in calculated mitral valve area (0.9 to 2.4 cm2) without complications and any evidence of fetal distress during procedures with an estimated radiation exposure to the fetus of 0.13 rem. This procedure resulted in the disappearance of symptoms of congestive heart failure and allowed for normal full term spontaneous delivery of a 3.51 Kg boy without any complication.
Publisher: Wiley
Date: 07-07-2006
Publisher: Springer Science and Business Media LLC
Date: 2013
Publisher: Wiley
Date: 12-01-2007
Publisher: Wiley
Date: 04-1987
Publisher: Elsevier BV
Date: 05-2010
DOI: 10.1016/J.YMPEV.2009.12.008
Abstract: The copepod family Centropagidae is widely distributed and occurs in marine, estuarine, freshwater, and inland saline settings. Molecular phylogenies based upon the 16S and 28S genes demonstrate a complex biogeographic history, involving at least five independent invasions of continental waters from the sea. The first colonization was ancient, likely into part of Gondwanaland, and resulted in an inland radiation in southern genera via both vicariance and subsequent habitat shifting among different types of continental waters. Species occupying saline lakes are nested within freshwater clades, indicating invasion of these habitats via fresh waters rather than directly from the ocean or from epicontinental seas. In contrast with the great southern clade, all of the remaining continental invasions are northern, species poor, and quite recent, perhaps even Pleistocene. Long-lived evolutionary euryhalinity, a high propensity for inland invasion, continental vicariance, and in situ radiation within single continents have all played major roles in the ersification of the centropagids.
Publisher: Public Library of Science (PLoS)
Date: 16-04-2020
Publisher: Springer Science and Business Media LLC
Date: 02-1987
DOI: 10.1007/BF02530279
Publisher: Springer Science and Business Media LLC
Date: 05-2008
Publisher: BMJ
Date: 06-2022
DOI: 10.1136/BMJPO-2022-001444
Abstract: Children have been relatively spared from the direct effects of COVID-19 globally, but there are significant concerns about indirect effects on the most vulnerable children’s well-being. Nigeria is the largest African nation, but little is known about children’s experience of the COVID-19 pandemic. Our aims were to determine children’s knowledge of COVID-19 and their mental health responses to the pandemic. Children aged 6–17 years living in Calabar, Nigeria, were surveyed using a combination of online data collection assisted by parents and on-site data collection at schools. Parents filled out sociodemographic details, while children answered questions about COVID-19 knowledge and preventive measures. An adapted version of the ‘Perceived Stress Scale for Children’ was used to assess stress with additional free text space for expression of views and experiences of COVID-19. A total of 265 children completed questionnaires, mean age was 12.5 years, 52.1% were girls. All children knew about the virus and over two-thirds (67.8%) had good knowledge of COVID-19 transmission. Children identified television (60.8%), parents (44.2%) and social media (32.8%), as main sources of COVID-19 information. The overall mean stress score among the children was 20.47. Children mentioned the following as stressors: fear of the COVID-19 disease, effect of pandemic restrictions on schooling and social interactions as well as home/family tensions. Parental love and support were overwhelmingly reported as strengths. Nigerian children in this study had good knowledge and understanding of the COVID-19 pandemic and preventive measures to counter the virus. Children had high stress levels and expressed pandemic-related concerns but parental love and support were mitigating factors. Government and child health service providers need to tailor health and support services in response to children’s needs and concerns.
Publisher: Springer Science and Business Media LLC
Date: 2012
Publisher: Wiley
Date: 14-11-2006
Publisher: The Royal Society
Date: 22-11-1993
Publisher: Wiley
Date: 11-12-2013
Publisher: University of Chicago Press
Date: 08-1983
DOI: 10.1086/284134
Publisher: Public Library of Science (PLoS)
Date: 28-03-2011
Publisher: Canadian Science Publishing
Date: 04-1996
DOI: 10.1139/Z96-073
Abstract: Although the establishment of species boundaries in the genus Daphnia is complicated by the prevalence of interspecific hybrids and by phenotypic plasticity, genetic studies can resolve these complexities. This investigation employed allozyme analyses to critically assess species boundaries in members of the Daphnia pulex group from the south-central United States and Mexico. These studies demonstrated the occurrence of three common Nearctic species (obtusa, pulex, pulicaria), but also revealed the occurrence of three previously unrecognized taxa (cheraphila, pileata, prolata). All of these newly described species have their distributional centroid in this region of North America and are restricted to clay-water habitats. F 1 hybrids were detected between three pairs of species (cheraphila × prolata, obtusa × pileata, pulex × pulicaria), but only the latter hybrids were common. The discovery of daphniid taxa endemic to this region of North America contrasts with the results of a broader survey of sites in Canada, and suggests that additional species await description from other unglaciated regions of North America.
Publisher: Elsevier BV
Date: 06-1996
Abstract: Although members of the crustacean genus Daphnia have been the target of much research, there is little understanding of the group's evolutionary history. We addressed this gap by inferring a phylogeny for one of the major species groups (longispina) using nucleotide sequence variation of a 525-bp segment of the mitochondrial 12S rDNA and allozyme variation at 21 loci. We identified the major lineages and their relationships, assessed the phylogenetic utility of the few morphological characters in the group, and examined Daphnia phylogeography. Nuclear and mtDNA phylogenies were generally concordant in recognizing the same four species complexes. An exception was the position of Daphnia galeata mendotae. The allozyme tree paired this species with the Daphnia rosea lineage, whereas the mtDNA trees grouped D. g. mendotae with Daphnia galeata galeata. This discordance was consistent with the reticulate evolution of nuclear genes supporting the hypothesis that D. g. mendotae represents a case of homoploid hybrid speciation. Striking morphological stasis in the longispina group was evidenced by its very limited morphological ergence over an estimated 100 MY, and by the unusual transitional saturation of the conservative 12S rRNA gene within a species group. Phylogenetic inference also provided evidence that similarities in cephalic crest shape likely resulted from convergent or parallel evolution among species. Endemism at the continental level was indicated for previously cosmopolitan species, but the estimated times of these isions were inconsistent with vicariance events suggesting recent dispersal among continents. A significant role for ergent selection in new habitats during speciation was suggested by the neighboringly sympatric distributions of four sister species pairs over broad geographic areas.
Publisher: Public Library of Science (PLoS)
Date: 07-04-2015
Publisher: JSTOR
Date: 07-1989
DOI: 10.2307/2425683
Publisher: No publisher found
Date: 1978
Publisher: American Chemical Society (ACS)
Date: 23-09-2009
DOI: 10.1021/JF901618Z
Abstract: The present study investigated the ability of DNA barcoding to reliably identify the seven commercially important salmon and trout species (genera Oncorhynchus and Salmo ) in North America. More than 1000 salmonid reference s les were collected from a wide geographic range. DNA extracts from these s les were sequenced for the standard 650 bp barcode region of the cytochrome c oxidase subunit I gene (COI). DNA barcodes showed low intraspecies ergences (mean, 0.26% range, 0.04-1.09%), and the mean congeneric ergence was 32-fold greater, at 8.22% (range, 3.42-12.67%). The minimum interspecies ergence was always greater than the maximum intraspecies ergence, indicating that these species can be reliably differentiated using DNA barcodes. Furthermore, several shorter barcode regions (109-218 bp), termed "mini-barcodes", were identified in silico that can differentiate all eight species, providing a potential means for species identification in heavily processed products.
Publisher: Public Library of Science (PLoS)
Date: 29-04-2015
Publisher: Oxford University Press (OUP)
Date: 12-1994
DOI: 10.2307/2410513
Publisher: Springer Science and Business Media LLC
Date: 1997
Publisher: JSTOR
Date: 06-1980
DOI: 10.2307/4266
Publisher: Springer Science and Business Media LLC
Date: 27-03-2008
DOI: 10.1007/S00239-008-9088-2
Abstract: Mitochondrial genomes show wide variation in their GC content. This study examines the correlations between mitochondrial genome-wide shifts in this feature and a fragment of the cytochrome c oxidase subunit I (COI) gene in animals, plants, and fungi. Because this approach utilizes COI as a sentinel, analyzing sequences from repositories such as GenBank and the Barcode of Life Data System (BOLD) can provide rapid insights into nucleotide usage. With this approach we probe nucleotide composition in a variety of taxonomic groups and establish the degree to which mitochondrial GC content varies among them. We then focus on two groups in particular, the classes Insecta and Aves, which possess the highest and lowest GC content, respectively. We establish that the sentinel approach provides strong indicators of mitochondrial GC content within ergent phyla (R values = 0.86-0.95, p < 0.001, in test cases) and provide evidence that selective pressures acting on GC content extend to noncoding regions of the plant and fungal mitochondrial genomes. We demonstrate that there is considerable variation in GC content of the mitochondrial genome within phyla and at each taxonomic level, leading to a substantial overlap zone in GC content between chordates and invertebrates. Our results provide a novel insight into the mitochondrial genome composition of animals, plants, and fungi and advocate this sentinel technique for the detection of rapid alterations in nucleotide usage as a measure of mitochondrial genome bio ersity.
Publisher: Oxford University Press (OUP)
Date: 05-1979
Publisher: Wiley
Date: 05-1992
Publisher: Springer Science and Business Media LLC
Date: 06-1976
DOI: 10.1038/HDY.1976.40
Abstract: Genotypic frequencies were analysed for two years in a permanent population of the cladoceran crustacean, Daphnia magna, which was polymorphic for an esterase and for malate dehydrogenase. Large temporal changes in genotypic frequencies occurred at both loci. There was no evidence of a seasonal pattern in the frequency changes. In most s les, genotypes at the two enzyme loci were non-randomly associated these associations showed temporal changes. On some occasions marked spatial heterogeneity in genotypic frequencies existed within the population. Genotypic differences in parthenogenetic and sexual egg production were observed. In a primarily parthenogenetically reproducing population, non-random associations between genotypes of structural and regulatory loci will be the rule. The allozyme variants themselves may or may not be under selection. The relevance of these observations to ecological studies on Daphnia is considered.
Publisher: Springer Science and Business Media LLC
Date: 12-09-2012
Publisher: Public Library of Science (PLoS)
Date: 08-07-2013
Publisher: Wiley
Date: 10-1983
Publisher: Springer Science and Business Media LLC
Date: 06-1987
DOI: 10.1038/HDY.1987.67
Publisher: Canadian Science Publishing
Date: 02-1991
DOI: 10.1139/Z91-063
Abstract: The bivalve mollusc Dreissena polymorpha colonized Lake St. Clair in 1986 as a result of ballast water discharge. The present study shows that since initiating reproduction in 1988, its population density at all of the sites originally colonized has increased more than a 1000-fold. The species has, as well, expanded its range in Lake St. Clair dramatically. The density and range increase is not yet complete, as populations at most sites remain dominated by juveniles. Densities in excess of 5000 in iduals/m 2 seem likely to be achieved at most sites in Lake St. Clair within 5 years. It appears likely that D. polymorpha will have a significant impact on composition of the benthos. Shells of in idual unionids carry in excess of 10 000 D. polymorpha, and lipid reserves of such unionids are only half those of unaffected in iduals. Aside from direct interactions with benthic organisms, the filtering activity of D. polymorpha populations may be sufficient to result in a significant impact on the turbidity of water exiting Lake St. Clair.
Publisher: Wiley
Date: 08-1992
DOI: 10.2307/1940690
Publisher: Wiley
Date: 02-1987
DOI: 10.2307/1938819
Publisher: Public Library of Science (PLoS)
Date: 25-03-2014
Publisher: Wiley
Date: 21-10-2013
Abstract: Although their functional importance in ecosystems is increasingly recognized, soil-dwelling micro-arthropods are usually poorly known in comparison with their above-ground counterparts. Collembola constitute a significant and species-rich component of the soil bio ersity, but it remains a woefully understudied group because of the taxonomic impediment. The ever-increasing use of molecular taxonomic tools, such as DNA barcoding, provides a possible solution. Here, we test the use of this approach through a ersity survey of Collembola from the vicinity of Churchill, Manitoba, Canada, and compare the results with previous surveys in the same area and in other sub-Arctic regions. The systematic barcoding c aign at Churchill revealed a erse collembolan fauna consisting of 97 species-level MOTUs in six types of habitats. If all these MOTUs are confirmed as species, this richness would be far higher than prior records for Arctic Canada and could lead to reconsider the actual ersity of the group in Arctic environments.
Publisher: MDPI AG
Date: 03-10-2023
DOI: 10.3390/F14101991
Publisher: Wiley
Date: 21-04-2009
DOI: 10.1111/J.1755-0998.2009.02646.X
Abstract: Frequently, the ersity of umbrella taxa is invoked to predict patterns of other, less well-known, life. However, the utility of this strategy has been questioned. We tested whether a phylogenetic ersity (PD) analysis of CO1 DNA barcodes could act as a proxy for standard methods of determining s ling efficiency within and between sites, namely that an accumulation curve of barcode ersity would be similar to curves generated using morphology or nuclear genetic markers. Using taxa at the forefront of the taxonomic impediment - parasitoid wasps (Ichneumonidae, Braconidae, Cynipidae and Diapriidae), contrasted with a taxon expected to be of low ersity (Formicidae) from an area where total ersity is expected to be low (Churchill, Manitoba), we found that barcode accumulation curves based on PD were significantly different in both slope and scale from curves generated using names based on morphological data, while curves generated using nuclear genetic data were only different in scale. We conclude that these differences clearly identify the taxonomic impediment within the strictly morphological alpha-taxonomy of these hyper erse insects. The absence of an asymptote within the barcode PD trend of parasitoid wasps reflects the as yet incomplete s ling of the site (and more accurately its total ersity), while the morphological analysis asymptote represents a collision with the taxonomic impediment rather than complete s ling. We conclude that a PD analysis of standardized DNA barcodes can be a transparent and reproducible triage tool for the management and conservation of species and spaces.
Publisher: Wiley
Date: 12-09-2012
Publisher: Springer Science and Business Media LLC
Date: 13-06-2007
Publisher: Canadian Science Publishing
Date: 07-1986
DOI: 10.1139/F86-175
Abstract: On the basis of intensive collections of Microcrustacea (Cladocera, Copepoda, Anostraca, and Notostraca) from 11 sites in the Canadian arctic archipelago, patterns of species richness, distribution, and community composition were evaluated. Microcrustacean communities of pond habitats in the high arctic of Canada are much less erse than communities at more mesic, subarctic sites. There is both a marked decline in species richness and a dramatic change in the composition of pond communities with increasing latitude and decreasing summer temperatures. Ponds in the low arctic have 3–4 times as many species as those in the high arctic and are dominated by calanoid copepods, a group largely absent from the high arctic. Sites with similar climatic conditions in Alaska have microcrustacean communities with higher species richness, a phenomenon correlated partially with the presence of glacial refuges throughout the Pleistocene. The failure of certain zooplankton taxa, especially calanoids, to colonize areas in the Canadian arctic remote from refuges in the 7000 yr since deglaciation suggests that their dispersal rates are low. Reestablishment of complete zooplankton communities in glaciated terrain with severe environmental conditions apparently requires long periods, although initial colonization by a few pioneer species may be rapid.
Publisher: Wiley
Date: 06-04-2010
DOI: 10.1111/J.1755-0998.2009.02799.X
Abstract: The capuchinos are a group of birds in the genus Sporophila that has apparently radiated recently, as evidenced by their lack of mitochondrial genetic ersity. We obtained cytochrome c oxidase I (COI) sequences (or DNA barcodes) for the 11 species of the group and various outgroups. We compared the patterns of COI variability of the capuchinos with those of the largest barcode data set from neotropical birds currently available (500 species representing 51% of avian richness in Argentina), and subjected COI sequences to neighbour-joining, maximum parsimony and Bayesian phylogenetic analyses as well as statistical parsimony network analysis. A clade within the capuchinos, the southern capuchinos, showed higher intraspecific and lower interspecific ergence than the remaining Argentine species. As most of the southern capuchinos shared COI haplotypes and pairwise distances within species were in many cases higher than distances between them, the phylogenetic affinities within the group remained unresolved. The observed genetic pattern is consistent with both incomplete lineage sorting and gene flow between species. The southern capuchinos constitute the only large group of species among the neotropical birds barcoded so far that are inseparable when using DNA barcodes, and one of few multispecies avian groups known to lack reciprocal monophyly. Extending the analysis to rapidly evolving nuclear and mitochondrial markers will be crucial to understanding this radiation. Apart from giving insights into the evolution of the capuchinos, this study shows how DNA barcoding can rapidly flag species or groups of species worthy of deeper study.
Publisher: JSTOR
Date: 10-1989
DOI: 10.2307/3565340
Publisher: Wiley
Date: 21-04-2009
DOI: 10.1111/J.1755-0998.2009.02629.X
Abstract: Building a global library of DNA barcodes will require efficient logistics of pre-laboratory specimen processing and seamless interfacing with molecular protocols. If not addressed properly, the task of aggregating specimens may become the biggest bottleneck in the analytical chain. Three years of experience in developing a collection management system to facilitate high-throughput DNA barcoding have allowed the Canadian Centre for DNA Barcoding to recognize and resolve the most common logistical obstacles. Dealing with these challenges on a larger scale will be an important step towards building a solid collection-based foundation for the international DNA barcoding effort.
Publisher: Wiley
Date: 22-05-2009
Publisher: Proceedings of the National Academy of Sciences
Date: 02-03-2010
Abstract: Comparative population genetics of ecological guilds can reveal generalities in patterns of differentiation bearing on hypotheses regarding the origin and maintenance of community ersity. Contradictory estimates of host specificity and beta ersity in tropical Lepidoptera (moths and butterflies) from New Guinea and the Americas have sparked debate on the role of host-associated ergence and geographic isolation in explaining latitudinal ersity gradients. We s led haplotypes of mitochondrial cytochrome c oxidase I from 28 Lepidoptera species and 1,359 in iduals across four host plant genera and eight sites in New Guinea to estimate population ergence in relation to host specificity and geography. Analyses of molecular variance and haplotype networks indicate varying patterns of genetic structure among ecologically similar sympatric species. One-quarter lacked evidence of isolation by distance or host-associated differentiation, whereas 21% exhibited both. Fourteen percent of the species exhibited host-associated differentiation without geographic isolation, 18% showed the opposite, and 21% were equivocal, insofar as analyses of molecular variance and haplotype networks yielded incongruent patterns. Variation in dietary breadth among community members suggests that speciation by specialization is an important, but not universal, mechanism for ersification of tropical Lepidoptera. Geographically widespread haplotypes challenge predictions of vicariance biogeography. Dispersal is important, and Lepidoptera communities appear to be highly dynamic according to the various phylogeographic histories of component species. Population genetic comparisons among herbivores of major tropical and temperate regions are needed to test predictions of ecological theory and evaluate global patterns of bio ersity.
Publisher: Wiley
Date: 18-01-2007
Publisher: Wiley
Date: 20-04-2009
DOI: 10.1111/J.1755-0998.2008.02393.X
Abstract: Dracunculus insignis is a nematode parasite that infects the subcutaneous tissues of mammals such as raccoon (Procyon lotor), mink (Neovison vison) and fisher (Martes pennanti). D. lutrae, a morphologically similar species, has only been recovered from the otter (Lontra canadensis). Species identification of these two North American guinea worms has only been achieved by morphology of males and host identity. As a result, where only female specimens are present, accurate identifications are not possible. To date, specimens recovered from otter have been assumed to be D. lutrae, while those from all other hosts are assumed to be D. insignis. This study uses DNA barcoding to differentiate between these two North American dracunculoids. Our results show that D. insignis is a 'true' generalist, showing little sequence ergence regardless of host association, although our studies did validate its occurrence in a new host - the otter. Interestingly, specimens of the host specialist, D. lutrae, showed some sequence ergence, although it was low. The finding of D. insignis in otter substantiates the need to supplement morphology-based methods in providing species identifications for certain dracunculoids.
Publisher: Springer Science and Business Media LLC
Date: 10-1988
DOI: 10.1007/BF00026331
Publisher: Canadian Science Publishing
Date: 09-1982
DOI: 10.1139/Z82-274
Abstract: Even when provided with abundant food and grown in isolation, Daphnia magna from arctic Canada responds to declining photoperiods by producing male and then ephippial offspring. In contrast, clones of English origin do not alter their reproductive behaviour when exposed to photoperiod shifts. Hybrid clones show an intermediate response in terms of ephippial egg production, but a variable response in male production. The results indicate that variation exists at gene loci controlling sexual behaviour in local populations as well as between distant populations. The significance of this variation is discussed in relation to the environmental heterogeneity encountered by D. magna over its extensive range.
Publisher: The Royal Society
Date: 22-09-2000
Publisher: Proceedings of the National Academy of Sciences
Date: 29-04-2008
Abstract: DNA barcodes can be used to identify cryptic species of skipper butterflies previously detected by classic taxonomic methods and to provide first clues to the existence of yet other cryptic species. A striking case is the common geographically and ecologically widespread neotropical skipper butterfly Perichares philetes (Lepidoptera, Hesperiidae), described in 1775, which barcoding splits into a complex of four species in Area de Conservación Guanacaste (ACG) in northwestern Costa Rica. Three of the species are new, and all four are described. Caterpillars, pupae, and foodplants offer better distinguishing characters than do adults, whose differences are mostly average, subtle, and blurred by intraspecific variation. The caterpillars of two species are generalist grass-eaters of the other two, specialist palm-eaters, each of which feeds on different genera. But all of these cryptic species are more specialized in their diet than was the morphospecies that held them. The four ACG taxa discovered to date belong to a panneotropical complex of at least eight species. This complex likely includes still more species, whose exposure may require barcoding. Barcoding ACG hesperiid morphospecies has increased their number by nearly 10%, an unexpectedly high figure for such relatively well known insects.
Publisher: Canadian Science Publishing
Date: 05-1993
DOI: 10.1139/Z93-119
Abstract: Allozyme analysis of 28 populations of Daphnia similis s.l. from the western United States and Canada indicated the presence of three different species. One taxon, D. salina, is newly described and a second species, D. exilis, previously synonymized with D. similis, is also shown to be distinct. Species recognition is not solely reliant on allozyme analysis, as morphological differences among the species are conspicuous. Daphnia salina is a halophile, while the other two species occur in habitats of lower but variable salinity. All three taxa appear to reproduce by cyclic parthenogenesis, although levels of genetic ersity were so low in D. salina that determination of its breeding system was tentative. Genetic distance analysis suggested that D. salina erged from the other two species some 27 million years ago, whereas D. exilis and D. similis separated 9 million years ago.
Publisher: Canadian Science Publishing
Date: 03-2005
DOI: 10.1139/Z05-026
Abstract: Our paper on spiders provides an early demonstration of the power of DNA barcoding we believe that its conclusions will prove scalable to all eukaryotes. We further anticipate that the "Barcode of Life" movement will soon lead to automated systems for species identification and discovery. However, we emphasize that these systems will operate within a Linnaean framework and that collaborations between molecular and morphological taxonomists are critical.
Publisher: Elsevier BV
Date: 11-1994
DOI: 10.1016/0169-5347(94)90127-9
Abstract: In the quest to ascertain the selective agents sustaining sex, much effort has been directed to studies of the origin and fate of asexuals. Ostracod crustaceans are of particular importance to this work, as they appear to show the highest incidence of transitions to parthenogenesis of any animal group. In addition, their excellent fossil record provides a historical perspective, suggesting that some parthenogenetic ostracods have outmanoeuvered the Red Queen for at least 70 million years. Genetic studies are now probing the basis of such persistence and are providing new direction for experimental work examining this frequent abandonment of sex.
Publisher: Wiley
Date: 06-04-2007
Publisher: Canadian Science Publishing
Date: 03-2005
DOI: 10.1139/Z05-024
Abstract: With almost 40 000 species, the spiders provide important model systems for studies of sociality, mating systems, and sexual dimorphism. However, work on this group is regularly constrained by difficulties in species identification. DNA-based identification systems represent a promising approach to resolve this taxonomic impediment, but their efficacy has only been tested in a few groups. In this study, we demonstrate that sequence ersity in a standard segment of the mitochondrial gene coding for cytochrome c oxidase I (COI) is highly effective in discriminating spider species. A COI profile containing 168 spider species and 35 other arachnid species correctly assigned 100% of subsequently analyzed specimens to the appropriate species. In addition, we found no overlap between mean nucleotide ergences at the intra- and inter-specific levels. Our results establish the potential of COI as a rapid and accurate identification tool for bio ersity surveys of spiders.
Publisher: University of Chicago Press
Date: 02-1983
DOI: 10.2307/1541196
Publisher: Wiley
Date: 30-12-2013
Abstract: In this study, we evaluated the efficacy of various primers for the purpose of DNA barcoding old, pinned museum specimens of blackflies (Diptera: Simuliidae). We analysed 271 pinned specimens representing two genera and at least 36 species. Due to the age of our material, we targeted overlapping DNA fragments ranging in size from 94 to 407 bp. We were able to recover valid sequences from 215 specimens, of which 18% had 500- to 658-bp barcodes, 36% had 201- to 499-bp barcodes and 46% had 65- to 200-bp barcodes. Our study demonstrates the importance of choosing suitable primers when dealing with older specimens and shows that even very short sequences can be diagnostically informative provided that an appropriate gene region is used. Our study also highlights the lack of knowledge surrounding blackfly taxonomy, and we briefly discuss the need for further phylogenetic studies in this socioeconomically important family of insects.
Publisher: Wiley
Date: 12-2006
DOI: 10.1111/J.1365-2915.2006.00653.X
Abstract: A short fragment of mt DNA from the cytochrome c oxidase 1 (CO1) region was used to provide the first CO1 barcodes for 37 species of Canadian mosquitoes (Diptera: Culicidae) from the provinces Ontario and New Brunswick. Sequence variation was analysed in a 617-bp fragment from the 5' end of the CO1 region. Sequences of each mosquito species formed barcode clusters with tight cohesion that were usually clearly distinct from those of allied species. CO1 sequence ergences were, on average, nearly 20 times higher for congeneric species than for members of a species ergences between congeneric species averaged 10.4% (range 0.2-17.2%), whereas those for conspecific in iduals averaged 0.5% (range 0.0-3.9%).
Publisher: Wiley
Date: 1992
Publisher: Wiley
Date: 08-09-2011
Publisher: Springer Science and Business Media LLC
Date: 2009
Publisher: Wiley
Date: 02-03-2011
Publisher: Wiley
Date: 08-2005
Publisher: Elsevier BV
Date: 18-11-1996
DOI: 10.1016/0048-9697(96)05169-8
Abstract: This review aims both to identify the potential risks to animal populations as a consequence of exposure to genotoxins and to identify the techniques most useful in assessing these risks. These evaluations are complicated by the fact that contaminant exposure acts both to restructure naturally occurring genetic ersity and, when contaminants have mutagenic activity, to enhance the rate of introduction of new variation. There is now evidence that contaminant exposure often leads to change in the genetic attributes of natural populations. Short-lived organisms often develop resistance to contaminants, with only modest impacts on ersity in the balance of the genome, although massive mortality occurs during the gene replacement. Resistance is, however, less likely to evolve in species with small population size, such as many wildlife species. Such species will experience population declines or extinction as the impact of contaminants on physiological systems is not counteracted by gene replacements. Even when adaptation to exposure occurs, populations may suffer diminished fitness as a consequence of the mutagenic effects of contaminants. The expression of these effects range from an increase in the incidence of developmental abnormalities to shifts in chromosomal and gene structure. The assessment of this broad range of impacts can only be accomplished with a spectrum of analytical approaches. However, recent advances in molecular and developmental genetics are now making possible the detailed assessment of these mutagenic impacts in natural populations.
Publisher: Public Library of Science (PLoS)
Date: 31-12-2020
DOI: 10.1371/JOURNAL.PNTD.0008867
Abstract: Aedes aegypti mosquito-borne viruses including Zika (ZIKV), dengue (DENV), yellow fever (YFV), and chikungunya (CHIKV) have emerged and re-emerged globally, resulting in an elevated burden of human disease. Aedes aegypti is found worldwide in tropical, sub-tropical, and temperate areas. The characterization of mosquito blood meals is essential to understand the transmission dynamics of mosquito-vectored pathogens. Here, we report Ae . aegypti and Culex quinquefasciatus host feeding patterns and arbovirus transmission in Northern Mexico using a metabarcoding-like approach with next-generation deep sequencing technology. A total of 145 Ae . aegypti yielded a blood meal analysis result with 107 (73.8%) for a single vertebrate species and 38 (26.2%) for two or more. Among the single host blood meals for Ae . aegypti , 28.0% were from humans, 54.2% from dogs, 16.8% from cats, and 1.0% from tortoises. Among those with more than one species present, 65.9% were from humans and dogs. For Cx . quinquefasciatus , 388 in iduals yielded information with 326 (84%) being from a single host and 63 (16.2%) being from two or more hosts. Of the single species blood meals, 77.9% were from dogs, 6.1% from chickens, 3.1% from house sparrows, 2.4% from humans, while the remaining 10.5% derived from other 12 host species. Among those which had fed on more than one species, 11% were from dogs and humans, and 89% of other host species combinations. Forage ratio analysis revealed dog as the most over-utilized host by Ae . aegypti (= 4.3) and Cx . quinquefasciatus (= 5.6) and the human blood index at 39% and 4%, respectively. A total of 2,941 host-seeking female Ae . aegypti and 3,536 Cx . quinquefasciatus mosquitoes were collected in the surveyed area. Of these, 118 Ae . aegypti pools and 37 Cx . quinquefasciatus pools were screened for seven arboviruses (ZIKV, DENV 1–4, CHIKV, and West Nile virus (WNV)) using qRT-PCR and none were positive (point prevalence = 0%). The 95%-exact upper limit confidence interval was 0.07% and 0.17% for Ae . aegypti and Cx . quinquefasciatus , respectively The low human blood feeding rate in Ae . aegypti , high rate of feeding on mammals by Cx . quinquefasciatus , and the potential risk to transmission dynamics of arboviruses in highly urbanized areas of Northern Mexico is discussed.
Publisher: Canadian Science Publishing
Date: 1997
Publisher: Springer Science and Business Media LLC
Date: 2009
Publisher: Oxford University Press (OUP)
Date: 12-1998
DOI: 10.2307/2411338
Publisher: Geological Society of America
Date: 2008
Publisher: Wiley
Date: 08-1978
Publisher: The Royal Society
Date: 05-09-2016
Abstract: Prologue ‘As the study of natural science advances, the language of scientific description may be greatly simplified and abridged. This has already been done by Linneaus and may be carried still further by other invention. The descriptions of natural orders and genera may be reduced to short definitions, and employment of signs, somewhat in the manner of algebra, instead of long descriptions. It is more easy to conceive this, than it is to conceive with what facility, and in how short a time, a knowledge of all the objects of natural history may ultimately be acquired and that which is now considered learning and science, and confined to a few specially devoted to it, may at length be universally possessed in every civilized country and in every rank of life’. J. C. Louden 1829. Magazine of natural history , vol. 1 . This article is part of the themed issue ‘From DNA barcodes to biomes’.
Publisher: University of Chicago Press
Date: 03-1982
DOI: 10.1086/283921
Publisher: Elsevier BV
Date: 04-1988
Publisher: Public Library of Science (PLoS)
Date: 15-04-2011
Publisher: Springer Science and Business Media LLC
Date: 24-02-2004
Publisher: The Royal Society
Date: 22-04-1996
Abstract: Holocyclic clones of the aphid Rhopalosiphum padi (L.) reproduce by cyclic parthenogenesis, whereas anholocyclic in iduals are obligate parthenogens. Mitochondrial DNA and (mtDNA) and random lified polymorphic DNA markers in R. padi as well as plasmid DNA markers of its bacterial endosymbiont, Buchnera aphidicola, were examined to determine the extent of genetic ergence between clones with these differing breeding systems. These analyses revealed that cyclically parthenogenetic lineages possessed differing mtDNA and plasmid haplotypes than most obligately asexual clones. The extent of sequence ergence between the maternally inherited molecules suggest a relatively ancient origin of asexuality. Our work also identified a random lified polymorphic DNA marker linked to the life-cycle variation in R. padi. This marker not only permits the rapid diagnosis of breeding system but sets the stage for studies to identify the gene(s) controlling this variation in mode of reproduction.
Publisher: Public Library of Science (PLoS)
Date: 14-07-2011
Publisher: Springer Science and Business Media LLC
Date: 1997
Publisher: Public Library of Science (PLoS)
Date: 21-07-2009
Publisher: Pensoft Publishers
Date: 24-02-2014
Publisher: MDPI AG
Date: 29-09-2020
Abstract: Lipolexis is a small genus in the subfamily Aphidiinae represented by one species in Europe (Lipolexis gracilis Förster) and by four in Asia (Lipolexis wuyiensis Chen, L. oregmae Gahan, L. myzakkaiae Pramanik and Raychaudhuri and L. pseudoscutellaris Pramanik and Raychaudhuri). Although L. oregmae is employed in biological control programs against pest aphids, the last morphological study on the genus was completed over 50 years ago. This study employs an integrative approach (morphology and molecular analysis (COI barcode region)), to examine Lipolexis specimens that were s led worldwide, including specimens from BOLD database. These results establish that two currently recognized species of Lipolexis (L. gracilis, L. oregmae) are actually a species complex and also reveal phylogenetic relationships within the genus. Six new species are described and a global key for the identification of Lipolexis species is provided.
Publisher: Wiley
Date: 02-1997
Publisher: Elsevier BV
Date: 07-1999
DOI: 10.1016/S0921-8777(99)00030-0
Abstract: The discrimination of recent mutational derivatives from ancestral variation is a critical antecedent to any effort which aims to identify the factors modulating the rates of origin and persistence of new mutants. We propose that newly arisen mtDNA variants, which we designate as terminal branch haplotypes (TBHs), can be recognized by joint sequencing and phylogenetic analysis. This study examined mtDNA ersity in natural populations of the brown bullhead (Ameiurus nebulosus) from four heavily contaminated sites and three relatively pristine locations. While sequence analysis of the mtDNA D-loop region revealed that TBHs were prevalent in these populations, contaminant exposure appeared to play a minor role in their generation. Instead, most TBHs likely arose due to spontaneous mutations with variation in their incidence among sites reflecting the impact of demographic factors.
Publisher: Canadian Science Publishing
Date: 08-2015
Publisher: Entomological Society of Washington
Date: 03-02-2014
Publisher: The Royal Society
Date: 05-09-2016
Abstract: Recent estimates suggest that the global insect fauna includes fewer than six million species, but this projection is very uncertain because taxonomic work has been limited on some highly erse groups. Validation of current estimates minimally requires the investigation of all lineages that are erse enough to have a substantial impact on the final species count. This study represents a first step in this direction it employs DNA barcoding to evaluate patterns of species richness in 27 orders of Canadian insects. The analysis of over one million specimens revealed species counts congruent with earlier results for most orders. However, Diptera and Hymenoptera were unexpectedly erse, representing two-thirds of the 46 937 barcode index numbers (=species) detected. Correspondence checks between known species and barcoded taxa showed that s ling was incomplete, a result confirmed by extrapolations from the barcode results which suggest the occurrence of at least 94 000 species of insects in Canada, a near doubling from the prior estimate of 54 000 species. One dipteran family, the Cecidomyiidae, was extraordinarily erse with an estimated 16 000 species, a 10-fold increase from its predicted ersity. If Canada possesses about 1% of the global fauna, as it does for known taxa, the results of this study suggest the presence of 10 million insect species with about 1.8 million of these taxa in the Cecidomyiidae. If so, the global species count for this fly family may exceed the combined total for all 142 beetle families. If extended to more geographical regions and to all hyper erse groups, DNA barcoding can rapidly resolve the current uncertainty surrounding a species count for the animal kingdom. A newly detailed understanding of species ersity may illuminate processes important in speciation, as suggested by the discovery that the most erse insect lineages in Canada employ an unusual mode of reproduction, haplodiploidy. This article is part of the themed issue ‘From DNA barcodes to biomes’.
Publisher: Springer Science and Business Media LLC
Date: 04-1986
DOI: 10.1007/BF00006537
Publisher: Entomological Society of Washington
Date: 03-02-2014
Publisher: Springer Science and Business Media LLC
Date: 09-07-2010
Abstract: DNA barcoding uses a 650 bp segment of the mitochondrial cytochrome c oxidase I (COI) gene as the basis for an identification system for members of the animal kingdom and some other groups of eukaryotes. PCR lification of the barcode region is a key step in the analytical chain, but it sometimes fails because of a lack of homology between the standard primer sets and target DNA. Two forward PCR primers were developed following analysis of all known arthropod mitochondrial genome arrangements and sequence alignment of the tRNA-W gene which was usually located within 200 bp upstream of the COI gene. These two primers were combined with a standard reverse primer (LepR1) to produce a cocktail which generated a barcode licon from 125 of 141 species that included representatives of 121 different families of Hexapoda. High quality sequences were recovered from 79% of the species including groups, such as scale insects, that invariably fail to lify with standard primers. A cocktail of two tRNA-W forward primers coupled with a standard reverse primer lifies COI for most hexapods, allowing characterization of the standard barcode primer binding region in COI 5' as well as the barcode segment. The current results show that primers designed to bind to highly conserved gene regions upstream of COI will aid the lification of this gene region in species where standard primers fail and provide valuable information to design a primer for problem groups.
Publisher: Springer Science and Business Media LLC
Date: 10-1991
DOI: 10.1038/HDY.1991.83
Publisher: Wiley
Date: 16-12-2009
DOI: 10.1111/J.1755-0998.2009.02671.X
Abstract: Although the genus Sycophila has broad host preferences, some species are specifically associated with figs as nonpollinator wasps. Because of their sexual dimorphism, morphological plasticity, cryptic mating behaviour and poorly known biology, species identifications are often uncertain. It is particularly difficult to match conspecific females and males. In this study, we employed two molecular markers, mitochondrial COI and nuclear ITS2, to identify Sycophila from six Chinese fig species. Morphological studies revealed 25 female and male morphs, while sequence results for both genes were consistent in supporting the presence of 15 species, of which 13 were host specialists and two used dual hosts. A single species of Sycophila was respectively found on four fig species, but six species were isolated from Ficus benjamina and a same number was reared from Ficus microcarpa. Sequence results revealed three male morphs in one species and detected two species that were overlooked by morphological analysis.
Publisher: Oxford University Press (OUP)
Date: 08-1994
DOI: 10.2307/2410390
Publisher: Wiley
Date: 21-08-2002
Publisher: Universidad de Costa Rica
Date: 24-08-2023
Publisher: Public Library of Science (PLoS)
Date: 05-02-2009
Publisher: Springer Science and Business Media LLC
Date: 07-1995
DOI: 10.1038/HDY.1995.102
Publisher: Springer Science and Business Media LLC
Date: 12-1980
DOI: 10.1038/HDY.1980.74
Abstract: Fifteen populations of the cladoceran crustacean, Daphnia carinata, were examined for allozyme variation at sixteen gene loci. In iduals of this cyclic parthenogen were heterozygous at only 2.1 per cent of their loci. Large differences in gene frequencies existed among the populations. Within populations genotypic frequencies were in good agreement with Hardy-Weinberg expectations, and remained stable during annual cycles of population growth. Strong linkage disequilibrium was observed between the allelic variants at two leucine aminopeptidase loci in certain populations, suggesting that the loci are tightly linked and that populations of D. carinata are founded from few in iduals.
Publisher: Wiley
Date: 19-03-2007
Publisher: Oxford University Press (OUP)
Date: 31-01-2007
Publisher: Wiley
Date: 11-05-2015
DOI: 10.1111/REC.12225
Publisher: Proceedings of the National Academy of Sciences
Date: 06-03-2007
Abstract: DNA barcoding systems employ a short, standardized gene region to identify species. A 648-bp segment of mitochondrial cytochrome c oxidase 1 ( CO1 ) is the core barcode region for animals, but its utility has not been tested in fungi. This study began with an examination of patterns of sequence ergences in this gene region for 38 fungal taxa with full CO1 sequences. Because these results suggested that CO1 could be effective in species recognition, we designed primers for a 545-bp fragment of CO1 and generated sequences for multiple strains from 58 species of Penicillium subgenus Penicillium and 12 allied species. Despite the frequent literature reports of introns in fungal mitochondrial genomes, we detected introns in only 2 of 370 Penicillium strains. Representatives from 38 of 58 species formed cohesive assemblages with distinct CO1 sequences, and all cases of sequence sharing involved known species complexes. CO1 sequence ergences averaged 0.06% within species, less than for internal transcribed spacer nrDNA or β-tubulin sequences ( BenA ). CO1 ergences between species averaged 5.6%, comparable to internal transcribed spacer, but less than values for BenA (14.4%). Although the latter gene delivered higher taxonomic resolution, the lification and alignment of CO1 was simpler. The development of a barcoding system for fungi that shares a common gene target with other kingdoms would be a significant advance.
Publisher: Springer Science and Business Media LLC
Date: 12-05-2008
Abstract: The goal of DNA barcoding is to develop a species-specific sequence library for all eukaryotes. A 650 bp fragment of the cytochrome c oxidase 1 (CO1) gene has been used successfully for species-level identification in several animal groups. It may be difficult in practice, however, to retrieve a 650 bp fragment from archival specimens, (because of DNA degradation) or from environmental s les (where universal primers are needed). We used a bioinformatics analysis using all CO1 barcode sequences from GenBank and calculated the probability of having species-specific barcodes for varied size fragments. This analysis established the potential of much smaller fragments, mini-barcodes, for identifying unknown specimens. We then developed a universal primer set for the lification of mini-barcodes. We further successfully tested the utility of this primer set on a comprehensive set of taxa from all major eukaryotic groups as well as archival specimens. In this study we address the important issue of minimum amount of sequence information required for identifying species in DNA barcoding. We establish a novel approach based on a much shorter barcode sequence and demonstrate its effectiveness in archival specimens. This approach will significantly broaden the application of DNA barcoding in bio ersity studies.
Publisher: Proceedings of the National Academy of Sciences
Date: 03-06-2020
Publisher: Public Library of Science (PLoS)
Date: 13-07-2010
Publisher: Wiley
Date: 04-1996
Publisher: Hindawi Limited
Date: 19-04-2011
Publisher: Springer Science and Business Media LLC
Date: 12-1995
DOI: 10.1038/HDY.1995.175
Publisher: Canadian Science Publishing
Date: 05-1990
DOI: 10.1139/F90-113
Abstract: Mitochondrial DNA (mtDNA) was isolated from five species of the genus Salvelinus (alpinus, confluentus, fontinalis, malma, and namaycush) and from the closely related taxon, Hucho hucho. Restriction sites recognized by 14 endonucleases were mapped for each of the species and percent sequence ergence estimated between species pairs. A phylogeny of Savelinus based on restriction analysis of mtDNA, using Hucho as an outgroup, readily resolved the three subgenera: Baione, Cristivomer, and Salvelinus. Within Baione, no differences were detected between the mtDNA of brook (S. fontinalis fontinalis) and aurora (S. f. timagamiensis) trout. However, members of the subgenus Salvelinus were more variable such that two groups were resolved, one consisting of S. alpinus alpinus, S. a. oquassa, and S. malma, and the other of S. a. stagnalis and S. confluentus. A composite distance phenogram representing the phylogeny of the subfamily Salmoninae was constructed using the sequence ergence data obtained in the current study in conjunction with data from three other salmonid mtDNA studies. Estimates of ergence time between the major taxa of this group suggest that the salmonine genera originated in the late-Miocene to early-Pliocene, while extant species originated during the late-Pliocene to early-Pleistocene.
Publisher: Public Library of Science (PLoS)
Date: 04-11-2013
Publisher: Oxford University Press (OUP)
Date: 08-1989
DOI: 10.2307/2409582
Publisher: Springer Science and Business Media LLC
Date: 24-07-2015
DOI: 10.1038/SREP12395
Abstract: How common are cryptic species - those overlooked because of their morphological similarity? Despite its wide-ranging implications for biology and conservation, the answer remains open to debate. Butterflies constitute the best-studied invertebrates, playing a similar role as birds do in providing models for vertebrate biology. An accurate assessment of cryptic ersity in this emblematic group requires meticulous case-by-case assessments, but a preview to highlight cases of particular interest will help to direct future studies. We present a survey of mitochondrial genetic ersity for the butterfly fauna of the Iberian Peninsula with unprecedented resolution (3502 DNA barcodes for all 228 species), creating a reliable system for DNA-based identification and for the detection of overlooked ersity. After compiling available data for European butterflies (5782 sequences, 299 species), we applied the Generalized Mixed Yule-Coalescent model to explore potential cryptic ersity at a continental scale. The results indicate that 27.7% of these species include from two to four evolutionary significant units (ESUs), suggesting that cryptic bio ersity may be higher than expected for one of the best-studied invertebrate groups and regions. The ESUs represent important units for conservation, models for studies of evolutionary and speciation processes and sentinels for future research to unveil hidden ersity.
Publisher: No publisher found
Date: 2015
Publisher: Springer Science and Business Media LLC
Date: 06-1989
DOI: 10.1038/HDY.1989.53
Publisher: Wiley
Date: 14-11-2019
DOI: 10.1111/ZSC.12390
Publisher: Wiley
Date: 02-2001
DOI: 10.1046/J.1365-294X.2001.01188.X
Abstract: Phylogeographic analyses have revealed the importance of Pleistocene vicariance events in shaping the distribution of genetic ersity in freshwater fishes. However, few studies have examined the patterning of variation in freshwater organisms with differing dispersal syndromes and life histories. The present investigation addresses this gap, examining the phylogeography of Sida crystallina, a species whose production of diapausing eggs capable of passive dispersal was thought to constrain its regional genetic differentiation. By contrast, the present analysis has revealed deep allozyme and cytochrome oxidase I mitochondrial DNA ergence between populations from North America and Europe. Moreover, North American populations are separated into four allopatric assemblages, whose distribution suggests their derivation from different Pleistocene refugia. These lineages show higher haplotype ersity and deeper sequence ergence than those of any fish from temperate North America. Its distinctive life history traits have evidently sheltered lineages of Sida from extinction, contributing to a remarkably comprehensive and high resolution phylogeographic record.
Publisher: Canadian Science Publishing
Date: 02-2007
DOI: 10.1139/F07-008
Abstract: The ability of a 650 base pair section of the mitochondrial cytochrome c oxidase I (COI) gene to provide species-level identifications has been demonstrated for large taxonomic assemblages of animals such as insects, birds, and fishes, but not for the subphylum Crustacea, one of the most erse groups of arthropods. In this study, we test the ability of COI to provide identifications in this group, examining two disparate levels in the taxonomic hierarchy — orders and species. The first phase of our study involved the development of a sequence profile for 23 dominant crustacean orders, based upon the analysis of 150 species, each belonging to a different family. The COI amino acid data placed these taxa into cohesive assemblages whose membership coincided with currently accepted boundaries at the order, superorder, and subclass levels. Species-level resolution was subsequently examined in an assemblage of Decapoda and in representatives of the genera Daphnia (Cladocera) and Gammarus (Amphipoda). These studies revealed that levels of nucleotide sequence ergence were from 19 to 48 times greater between congeneric species than between in iduals of a species. We conclude that sequence variation in the COI barcode region will be very effective for discriminating species of Crustacea.
Publisher: Oxford University Press (OUP)
Date: 12-1974
DOI: 10.2307/2407280
Publisher: Oxford University Press (OUP)
Date: 08-1989
DOI: 10.2307/2409581
Publisher: Oxford University Press (OUP)
Date: 02-2004
Publisher: Wiley
Date: 21-04-2009
DOI: 10.1111/J.1755-0998.2009.02630.X
Abstract: Although devices combining microfluidic and advanced sequencing technologies promise a future where one can generate a DNA barcode in minutes, current analytical regimes typically involve workflows that extend over 2 days. Here we describe simple protocols enabling the advance from a specimen to barcode-based identification in less than 2 h. The protocols use frozen or lyophilized reagents that can be prepackaged into 'kits' and support barcode analysis across the animal kingdom. The analytical procedure allows 5 min for DNA extraction, 25 min for polymerase chain reaction lification of the barcode region, 25 min for cycle-sequencing, 10 min for cleanup, 45 min for capillary sequencing and 5 min for trace file analysis to complete DNA-based identification. This study involved the comparison of varied DNA preservation and extraction methods, and evaluated Taq polymerases with high processivity and resistance to inhibitors.
Publisher: Canadian Science Publishing
Date: 2000
DOI: 10.1139/CJZ-78-5-794
Publisher: Wiley
Date: 07-2020
Publisher: Public Library of Science (PLoS)
Date: 03-09-2010
Publisher: Wiley
Date: 15-01-2015
Abstract: This study presents DNA barcode records for 4118 specimens representing 561 species of bees belonging to the six families of Apoidea (Andrenidae, Apidae, Colletidae, Halictidae, Megachilidae and Melittidae) found in Central Europe. These records provide fully compliant barcode sequences for 503 of the 571 bee species in the German fauna and partial sequences for 43 more. The barcode results are largely congruent with traditional taxonomy as only five closely allied pairs of species could not be discriminated by barcodes. As well, 90% of the species possessed sufficiently deep sequence ergence to be assigned to a different Barcode Index Number (BIN). In fact, 56 species (11%) were assigned to two or more BINs reflecting the high levels of intraspecific ergence among their component specimens. Fifty other species (9.7%) shared the same Barcode Index Number with one or more species, but most of these species belonged to a distinct barcode cluster within a particular BIN. The barcode data contributed to clarifying the status of nearly half the examined taxonomically problematic species of bees in the German fauna. Based on these results, the role of DNA barcoding as a tool for current and future taxonomic work is discussed.
Publisher: Springer Science and Business Media LLC
Date: 12-1986
DOI: 10.1038/HDY.1986.134
Publisher: Public Library of Science (PLoS)
Date: 26-08-2015
Publisher: University of Chicago Press
Date: 08-1985
DOI: 10.2307/1541394
Publisher: Wiley
Date: 29-10-2008
DOI: 10.1111/J.1755-0998.2008.02297.X
Abstract: A 658-bp fragment of mitochondrial DNA from the 5' region of the mitochondrial cytochrome c oxidase 1 (COI) gene has been adopted as the standard DNA barcode region for animal life. In this study, we test its effectiveness in the discrimination of over 300 species of aphids from more than 130 genera. Most (96%) species were well differentiated, and sequence variation within species was low, averaging just 0.2%. Despite the complex life cycles and parthenogenetic reproduction of aphids, DNA barcodes are an effective tool for identification.
Publisher: Wiley
Date: 11-06-2010
DOI: 10.1111/J.1755-0998.2009.02822.X
Abstract: Species identification of earthworms is usually achieved by careful observation of morphological features, often sexual characters only present in adult specimens. Consequently, juveniles or cocoons are often impossible to identify, creating a possible bias in studies that aim to document species richness and abundance. DNA barcoding, the use of a short standardized DNA fragment for species identification, is a promising approach for species discrimination. When a reference library is available, DNA-based identification is possible for all life stages. In this study, we show that DNA barcoding is an unrivaled tool for high volume identification of juvenile earthworms. To illustrate this advance, we generated DNA barcodes for specimens of Lumbricus collected from three temperate grasslands in western France. The analysis of genetic distances between in iduals shows that juvenile sequences unequivocally match DNA barcode clusters of previously identified adult specimens, demonstrating the potential of DNA barcoding to provide exhaustive specimen identification for soil ecological research.
Publisher: Proceedings of the National Academy of Sciences
Date: 27-02-2006
Abstract: Insect parasitoids are a major component of global bio ersity and affect the population dynamics of their hosts. However, identification of insect parasitoids is often difficult, and they are suspected to contain many cryptic species. Here, we ask whether the cytochrome c oxidase I DNA barcode could function as a tool for species identification and discovery for the 20 morphospecies of Belvosia parasitoid flies (Diptera: Tachinidae) that have been reared from caterpillars (Lepidoptera) in Area de Conservación Guanacaste (ACG), northwestern Costa Rica. Barcoding not only discriminates among all 17 highly host-specific morphospecies of ACG Belvosia , but it also raises the species count to 32 by revealing that each of the three generalist species are actually arrays of highly host-specific cryptic species. We also identified likely hybridization among Belvosia by using a variable internal transcribed spacer region 1 nuclear rDNA sequence as a genetic covariate in addition to the strategy of overlaying barcode clusters with ecological information. If general, these results will increase estimates of global species richness and imply that tropical conservation and host–parasite interactions may be more complex than expected.
Publisher: Pensoft Publishers
Date: 29-08-2013
Publisher: Cold Spring Harbor Laboratory
Date: 30-03-2022
DOI: 10.1101/2022.03.29.486224
Abstract: Wild silkmoths (Saturniidae) are one of the most emblematic and most studied families of moths. Yet, the absence of a robust phylogenetic framework based on a comprehensive taxonomic s ling impedes our understanding of their evolutionary history. We analyzed 1,024 ultraconserved elements (UCEs) and their flanking regions to infer the relationships among 338 species of Saturniidae representing all described subfamilies, tribes, and genera. We investigated systematic biases in genomic data and performed dating and historical biogeographic analyses to reconstruct the evolutionary history of wild silkmoths in space and time. Using Gene Genealogy Interrogation, we showed that saturation of nucleotide sequence data blurred our understanding of early ergences and first biogeographic events. Our analyses support a Neotropical origin of saturniids, shortly after the Cretaceous-Paleogene extinction event ( ca 64.0 [stem] - 52.0 [crown] Ma), and two independent colonization events of the Old World during the Eocene, presumably through the Bering Land Bridge. Early ergences strongly shaped the distribution of extant subfamilies as they showed very limited mobility across biogeographical regions, except for Saturniinae, a subfamily now present on all continents but Antarctica. Overall, our results provide a framework for in-depth investigations into the spatial and temporal dynamics of all saturniid lineages and for the integration of their evolutionary history into further global studies of bio ersity and conservation. Rather unexpectedly for a taxonomically well-known family such as Saturniidae, the proper alignment of taxonomic isions and ranks with our phylogenetic results leads us to propose substantial rearrangements of the family classification, including the description of one new subfamily and two new tribes.
Publisher: Wiley
Date: 12-1991
Publisher: CSIRO Publishing
Date: 2012
DOI: 10.1071/IS12029
Abstract: Interspecific hybridisation is a rare but widespread phenomenon identified as a potential complicating factor for the identification of species through DNA barcoding. Hybrids can, however, also deceive morphology-based taxonomy, resulting in the description of invalid species based on hybrid specimens. As the result of an unexpected case of discordance between barcoding results and current morphology-based taxonomy, we discovered an ex le of such a hybrid ‘species’ in hawkmoths. By combining barcodes, morphology and a nuclear marker, we show that Gnathothlibus collardi Haxaire, 2002 is actually an F1 hybrid between two closely related species that co-occur on Tahiti. In accordance with the International Code of Zoological Nomenclature, the taxon G. collardi is thus invalid as a species. This study demonstrates the potential of DNA barcodes to detect overlooked hybrid taxa. With the growth of sequence libraries, we anticipate that more unsuspected hybrid species will be detected, particularly among those taxa that are very rare, such as those known from only the type specimen.
Publisher: Public Library of Science (PLoS)
Date: 27-07-2011
Publisher: Canadian Science Publishing
Date: 08-2002
DOI: 10.1139/Z02-145
Abstract: Haploid genome sizes (C-values) were estimated for 12 species of freshwater oligochaetes (families Naididae and Tubificidae) and 15 species of earthworms (families Lumbricidae and Megascolecidae). Aquatic worms ranged in genome size from about 0.8 to 7.6 pg, while earthworms varied from approximately 0.4 to 1.2 pg. Interspecific differences in nuclear DNA content did not appear to be linked to variation in chromosome number, but there was evidence of cryptopolyploidy in the aquatic worms. No correlations were found between genome size and either body size or life-history traits, although there may be an association between higher DNA content and parthenogenetic reproduction in earthworms.
Publisher: Public Library of Science (PLoS)
Date: 14-05-2014
Publisher: Canadian Science Publishing
Date: 2001
Publisher: Oxford University Press (OUP)
Date: 24-02-2005
Abstract: A complete DNA-based inventory of the Earth's present biota using large-scale high-throughput DNA sequencing of signature region(s) (DNA barcoding) is an ambitious proposal rivaling the Human Genome Project. We examine whether this approach will also enable us to assess the past ersity of the earth's biota. To test this, we sequenced the 5' terminus of the mitochondrial cytochrome c oxidase I (COI) gene of in iduals belonging to a group of extinct ratite birds, the moa of New Zealand. Moa comprised a large number of taxa that radiated in isolation on this oceanic landmass. Using a phylogenetic approach based on a large data set including protein coding and 12S DNA sequences as well as morphology, we now have precise information about the number of moa species that once existed. We show that each of the moa species detected using this extensive data set has a unique COI barcode(s) and that they all show low levels of within-species COI variation. Consequently, we conclude that COI sequences accurately identify the species discovered using the larger data set. Hence, more generally, this study suggests that DNA barcoding might also help us detect other extinct animal species and that a large-scale inventory of ancient life is possible.
Publisher: Springer Science and Business Media LLC
Date: 04-1995
DOI: 10.1038/HDY.1995.52
Publisher: The Royal Society
Date: 22-11-1994
Publisher: Wiley
Date: 20-12-2014
Abstract: Beetles are the most erse group of animals and are crucial for ecosystem functioning. In many countries, they are well established for environmental impact assessment, but even in the well-studied Central European fauna, species identification can be very difficult. A comprehensive and taxonomically well-curated DNA barcode library could remedy this deficit and could also link hundreds of years of traditional knowledge with next generation sequencing technology. However, such a beetle library is missing to date. This study provides the globally largest DNA barcode reference library for Coleoptera for 15 948 in iduals belonging to 3514 well-identified species (53% of the German fauna) with representatives from 97 of 103 families (94%). This study is the first comprehensive regional test of the efficiency of DNA barcoding for beetles with a focus on Germany. Sequences ≥500 bp were recovered from 63% of the specimens analysed (15 948 of 25 294) with short sequences from another 997 specimens. Whereas most specimens (92.2%) could be unambiguously assigned to a single known species by sequence ersity at CO1, 1089 specimens (6.8%) were assigned to more than one Barcode Index Number (BIN), creating 395 BINs which need further study to ascertain if they represent cryptic species, mitochondrial introgression, or simply regional variation in widespread species. We found 409 specimens (2.6%) that shared a BIN assignment with another species, most involving a pair of closely allied species as 43 BINs were involved. Most of these taxa were separated by barcodes although sequence ergences were low. Only 155 specimens (0.97%) show identical or overlapping clusters.
Publisher: Public Library of Science (PLoS)
Date: 16-08-2011
Publisher: Canadian Science Publishing
Date: 08-1991
DOI: 10.1139/F91-168
Abstract: Geographic distributions of major fish species resident in Lake St. Clair, field assessments of their seasonal thermal distributions, and laboratory determinations of their median and maximum final temperature preferenda were compared with their catchability at different temperatures. Fish catchability at various temperatures was estimated (regression analysis) during the fall pound net set survey (1977–88) using number of fish caught per 24-h net set as the dependent variable. Swimming activity was expected to be higher at temperatures closest to the species' preferred temperature, thereby increasing catchability. Maximum final temperature preferendum was the best predictor of observed fish temperature preferences. Geographic distributions and median final temperature preferenda were better predictors than summer or fall seasonal thermal distributions. Acute temperature preferenda were also good predictors of fish catchability at different temperatures. Of the 22 species examined, the catchability of Centrarchidae (five of six species), Catostomidae (two of five species), Clupeidae (one species), Ictaluridae (two species), and Percichthyidae (two species) was greater in warmer water, while the catchability of Amiidae (one species), Cyprinidae (one species), Catostomidae (three of five species), Esocidae (one species), Percidae (two species), and Sciaenidae (one species) increased in colder water. Temperature significantly accounted for differences in catchability among most species (14 of 22).
Publisher: Wiley
Date: 21-04-2009
DOI: 10.1111/J.1755-0998.2009.02649.X
Abstract: With more than 15 000 described marine species, fishes are a conspicuous, erse and increasingly threatened component of marine life. It is generally accepted that most large-bodied fishes have been described, but this conclusion presumes that current taxonomic systems are robust. DNA barcoding, the analysis of a standardized region of the cytochrome c oxidase 1 gene (COI), was used to examine patterns of sequence ergence between populations of 35 fish species from opposite sides of the Indian Ocean, chosen to represent differing lifestyles from inshore to offshore. A substantial proportion of inshore species showed deep ergences between populations from South African and Australian waters (mean = 5.10%), a pattern which also emerged in a few inshore/offshore species (mean = 0.84%), but not within strictly offshore species (mean = 0.26%). Such deep ergences, detected within certain inshore and inshore/offshore taxa, are typical of ergences between congeneric species rather than between populations of a single species, suggesting that current taxonomic systems substantially underestimate species ersity. We estimate that about one third of the 1000 fish species thought to bridge South African and Australian waters actually represent two taxa.
Publisher: Wiley
Date: 20-06-2002
DOI: 10.1046/J.1365-294X.2002.01517.X
Abstract: It has long been known that polyploid organisms are more prevalent in arctic than in temperate environments. Past explanations for this geographical trend have focused on the role of glacial cycles in generating polyploids and the influence of abiotic factors in favouring polyploidy in the north. In combination, these mechanisms probably suffice to explain the observed geographical cline in ploidy levels in members of the Daphnia pulex complex in the Holarctic. While only diploid members of the D. pulex complex are found in the temperate regions of North America and Europe, allozyme and DNA quantification analyses indicate that the southern Argentine pulex-complex fauna is dominated by polyploids. Indeed, the present study is the first to document the presence of polyploid members of the D. pulex complex in any temperate climate. The results of phylogeographic analyses suggest that this difference in polyploid distribution between the northern and southern hemispheres is based more on ecological and historical contingencies than direct selection for polyploidy. Specifically, competition with diploid relatives probably limits the lower latitudinal range of polyploids in the north, but appears not to have occurred in Argentina. Because of these differences, the present study provides important insights into the erse factors that determine the distributions and evolutionary fates of polyploid organisms.
Publisher: Wiley
Date: 12-2009
Publisher: Proceedings of the National Academy of Sciences
Date: 20-03-2007
Abstract: Many species of tachinid flies are viewed as generalist parasitoids because what is apparently a single species of fly has been reared from many species of caterpillars. However, an ongoing inventory of the tachinid flies parasitizing thousands of species of caterpillars in Area de Conservación Guanacaste, northwestern Costa Rica, has encountered species of specialist tachinids with only a few generalists. We DNA-barcoded 2,134 flies belonging to what appeared to be the 16 most generalist of the reared tachinid morphospecies and encountered 73 mitochondrial lineages separated by an average of 4% sequence ergence. These lineages are supported by collateral ecological information and, where tested, by independent nuclear markers (28S and ITS1), and we therefore view these lineages as provisional species. Each of the 16 apparently generalist species dissolved into one of four patterns: ( i ) a single generalist species, ( ii ) a pair of morphologically cryptic generalist species, ( iii ) a complex of specialist species plus a generalist, or ( iv ) a complex of specialists with no remaining generalist. In sum, there remained 9 generalist species among the 73 mitochondrial lineages we analyzed, demonstrating that a generalist lifestyle is possible for a tropical caterpillar parasitoid fly. These results reinforce the emerging suspicion that estimates of global species richness are likely underestimates for parasitoids (which may constitute as much as 20% of all animal life) and that the strategy of being a tropical generalist parasitic fly may be yet more unusual than has been envisioned for tachinids.
Publisher: Wiley
Date: 08-1978
Publisher: Wiley
Date: 16-01-2003
DOI: 10.1046/J.1365-294X.2003.01728.X
Abstract: Numerous molecular studies have identified morphologically cryptic, freshwater invertebrate species, but have not suggested possible mechanisms for their phenotypic stasis. The hipod crustacean genus Hyalella contains numerous morphologically cryptic species in the H. azteca complex, as well as a small number of morphologically very ergent, narrowly endemic taxa. One such taxon, Hyalella montezuma, is the sole planktonic filter-feeder within the North American hipod fauna, and is known only from Montezuma Well, a fishless travertine spring mound in Arizona, USA. In this study, we conduct a phylogenetic analysis of mtDNA sequence data using likelihood, Bayesian and cladistic approaches to determine both the relationship of H. montezuma to the H. 'azteca' species complex, and to ascertain if its morphological and ecological differentiation have been comparatively recent. The results show that H. montezuma has a very close phylogenetic affiliation with one lineage in the H. azteca complex, indicating that its origin has been recent. We present evidence suggesting that fish predation is an important ecological factor, which constrains morphological and ecological ersification within the genus Hyalella, and that Montezuma Well has provided a relaxation on this constraint.
Publisher: Oxford University Press (OUP)
Date: 12-2001
Publisher: University of Chicago Press
Date: 12-1988
DOI: 10.1086/284892
Publisher: Wiley
Date: 12-06-2022
DOI: 10.1111/APA.16422
Abstract: Critically review research methods used to elicit children and young people's views and experiences in the first year of COVID‐19, using an ethical and child rights lens. A systematic search of peer‐reviewed literature on children and young people's perspectives and experiences of COVID‐19. LEGEND ( Let Evidence Guide Every New Decision ) tools were applied to assess the quality of included studies. The critical review methodology addressed four ethical parameters: (1) Duty of care (2) Children and young people's consent (3) Communication of findings and (4) Reflexivity. Two phases of searches identified 8131 studies 27 studies were included for final analysis, representing 43,877 children and young people's views. Most studies were from high‐income countries. Three major themes emerged: (a) Whose voices are heard (b) How are children and young people heard and (c) How do researchers engage in reflexivity and ethical practice? Online surveys of children and young people from middle‐class backgrounds dominated the research during COVID‐19. Three studies actively involved children and young people in the research process two documented a rights‐based framework. There was limited attention paid to some ethical issues, particularly the lack of inclusion of children and young people in research processes. There are equity gaps in accessing the experiences of children and young people from disadvantaged settings. Most children and young people were not involved in shaping research methods by soliciting their voices.
Publisher: Wiley
Date: 04-1994
Abstract: Among insects, the epidermal cell cycle pattern is related to the type of ontogenetic development. In taxa undergoing complete metamorphosis, cells are commonly maintained in the G2 stage of interphase between bouts of cell ision. In crustaceans, as in insects exhibiting incomplete metamorphosis, it is believed that cells ordinarily remain in G1 for much of the intermoult, with DNA replication occurring late in the moult cycle followed closely by cell ision. The present study reveals a differing pattern of epidermal cell ision in two distantly related members of the cladoceran crustacean genus Daphnia. Cell cycle kinetics were examined in the last juvenile instar of each species using DNA content determinations and estimates of mitotic frequency. These analyses confirm that each epidermal cell possessed the diploid DNA amount, completed a single cell cycle, and remained in G1 for the majority of the instar. However, DNA replication occurred shortly after moulting and was followed by intense mitotic activity so that cell proliferation was restricted to a short period soon after ecdysis. Cell densities during the instar increased by approximately 60 and 100% for D. pulex and D. magna, respectively.
Publisher: Public Library of Science (PLoS)
Date: 17-12-2013
Publisher: CSIRO Publishing
Date: 2010
DOI: 10.1071/MF09222
Abstract: Barcoding has proven a useful tool in the rapid identification of all life stages of fish species. Such information is of critical importance for fisheries management and conservation, especially in high- ersity regions, such as Mexico’s marine waters, where more than 2200 species occur. The present study reports the barcode analysis of 1392 specimens from the Yucatan Peninsula, corresponding to 610 adults and juveniles, 757 larvae and 25 eggs, representing 181 species (179 teleosts and 2 rays), 136 genera and 74 families. Barcoding results revealed major range extensions and overlooked taxa, including three sympatric species of Albula (one likely undescribed) and a new taxon of Floridichthys. In total, six species of eggs and 34 species of larvae were identified through their barcode match with adults. These cases enabled the first discrimination of the larvae of four species of Eucinostomus, and new information about spawning locality and time was obtained from egg records for the hogfish, Lachnolaimus maximus, which is one of the most commercially important species in the Mexican Caribbean. Also, barcodes revealed mistakes in species recognition during a sport-fish contest. In the future, barcodes will help avoid similar errors and protect rare or endangered species, and will aid regulation of fisheries quotas.
Publisher: Wiley
Date: 21-04-2009
DOI: 10.1111/J.1755-0998.2009.02628.X
Abstract: Inventory of the caterpillars, their food plants and parasitoids began in 1978 for today's Area de Conservacion Guanacaste (ACG), in northwestern Costa Rica. This complex mosaic of 120 000 ha of conserved and regenerating dry, cloud and rain forest over 0-2000 m elevation contains at least 10 000 species of non-leaf-mining caterpillars used by more than 5000 species of parasitoids. Several hundred thousand specimens of ACG-reared adult Lepidoptera and parasitoids have been intensively and extensively studied morphologically by many taxonomists, including most of the co-authors. DNA barcoding - the use of a standardized short mitochondrial DNA sequence to identify specimens and flush out undisclosed species - was added to the taxonomic identification process in 2003. Barcoding has been found to be extremely accurate during the identification of about 100 000 specimens of about 3500 morphologically defined species of adult moths, butterflies, tachinid flies, and parasitoid wasps. Less than 1% of the species have such similar barcodes that a molecularly based taxonomic identification is impossible. No specimen with a full barcode was misidentified when its barcode was compared with the barcode library. Also as expected from early trials, barcoding a series from all morphologically defined species, and correlating the morphological, ecological and barcode traits, has revealed many hundreds of overlooked presumptive species. Many but not all of these cryptic species can now be distinguished by subtle morphological and/or ecological traits previously ascribed to 'variation' or thought to be insignificant for species-level recognition. Adding DNA barcoding to the inventory has substantially improved the quality and depth of the inventory, and greatly multiplied the number of situations requiring further taxonomic work for resolution.
Publisher: Oxford University Press (OUP)
Date: 1988
DOI: 10.2307/2409123
Publisher: Canadian Science Publishing
Date: 09-1989
DOI: 10.1139/F89-202
Abstract: Dreissena polymorpha, a bivalve mollusc endemic to Europe, has established a population in Lakes St. Clair and Erie, likely as a result of ballast water discharge. Allozyme studies showed that the Lake St. Clair population was polymorphic at 73.9% of the loci examined and that in idual heterozygosities averaged 31.6%. This high level of genotypic ersity indicated that the population was founded from a substantial number of in iduals and did not undergo a bottleneck subsequent to founding. The population is reproducing with peak densities in excess of 200 in iduals∙m −2 . Juvenile settlement occurs in late July and August with veliger larvae preferentially settling on the shells of live mussels. The species appears likely to become a dominant member of the shallow water benthos throughout the lower Great Lakes.
Publisher: Canadian Science Publishing
Date: 1997
Publisher: Canadian Science Publishing
Date: 2002
DOI: 10.1139/Z01-903
Publisher: The Royal Society
Date: 11-08-2010
Abstract: DNA barcoding aims to accelerate species identification and discovery, but performance tests have shown marked differences in identification success. As a consequence, there remains a great need for comprehensive studies which objectively test the method in groups with a solid taxonomic framework. This study focuses on the 180 species of butterflies in Romania, accounting for about one third of the European butterfly fauna. This country includes five eco-regions, the highest of any in the European Union, and is a good representative for temperate areas. Morphology and DNA barcodes of more than 1300 specimens were carefully studied and compared. Our results indicate that 90 per cent of the species form barcode clusters allowing their reliable identification. The remaining cases involve nine closely related species pairs, some whose taxonomic status is controversial or that hybridize regularly. Interestingly, DNA barcoding was found to be the most effective identification tool, outperforming external morphology, and being slightly better than male genitalia. Romania is now the first country to have a comprehensive DNA barcode reference database for butterflies. Similar barcoding efforts based on comprehensive s ling of specific geographical regions can act as functional modules that will foster the early application of DNA barcoding while a global system is under development.
Publisher: Canadian Science Publishing
Date: 06-1982
DOI: 10.1139/Z82-176
Abstract: The predation rates of the rhabdocoel Mesostoma ehrenbergii were determined on a number of cladoceran species. Two means of capturing prey are employed by the flatworm but only active predation was explored in these experiments. It was found that this flatworm is a size-dependent predator with a preference for prey of about 1.2 mm. It was also observed that prey behavior was not an important factor in determining susceptibility to predation. M. ehrenbergii is a voracious predator in iduals consume more than 10 prey/day.
Publisher: Elsevier BV
Date: 10-2000
Publisher: Springer Science and Business Media LLC
Date: 10-06-2008
Publisher: Oxford University Press (OUP)
Date: 05-1991
DOI: 10.2307/2409923
Publisher: Springer Science and Business Media LLC
Date: 15-01-2015
Publisher: Pensoft Publishers
Date: 12-06-2023
DOI: 10.3897/ZOOKEYS.1166.105589
Abstract: Two new genera and one new species of the Braconinae tribe Adeshini are described and illustrated: Crenuladesha Ranjith & Quicke, gen. nov. , type species Adesha narendrani Ranjith, 2017, comb. nov. from India, and Protadesha Quicke & Butcher, gen. nov. , type species Protadesha intermedia Quicke & Butcher, sp. nov. from South Africa. The former lacks the mid-longitudinal propodeal carina characteristic of the tribe, and the latter displays less derived fore wing venation with two distinct abscissae of vein 2CU. A molecular phylogenetic analysis is included to confirm their correct placement. Since neither of the two new genera displays all of the characters given in the original diagnosis of the Adeshini a revised diagnosis is provided, as well as an illustrated key to the genera.
Publisher: Wiley
Date: 08-2009
DOI: 10.1890/07-1852.1
Abstract: Ecological linkages between species ersity in communities and genetic ersity in populations have potential to influence the assembly of communities in habitats recovering from human disturbance, but few studies have attempted to synthesize relationships between these levels of biological organization, especially for locally adapted species. No such studies have been done in freshwater ecosystems despite the plethora of environmental stressors plaguing aquatic communities around the world. We present the first study to test (1) whether ersity and dissimilarity among communities and populations of a locally adapted species are correlated and (2) whether communities and population haplotypes respond differently to environmental selection and spatial structure of habitats. We used a fragment of mitochondrial DNA (mtDNA) belonging to the gene cytochrome oxidase subunit I (COI) as a neutral tag to discriminate among different population haplotype variants. In boreal lakes with different histories of exposure to anthropogenic acidification, ersity and dissimilarity metrics for crustacean zooplankton communities and locally adapted populations of an abundant and broadly distributed calanoid copepod species, Leptodiaptomus minutus, did not correlate. This discord was likely because zooplankton communities responded more strongly to acidity and acidity-related environmental variables than spatial structure of lakes, whereas the distribution of L. minutus haplotypes was more strongly governed by spatial structure of lakes than environmental selection. Although spatial structure was the dominant driver of haplotype structure among L. minutus lake populations, there were similarities in the types of environmental variables that influenced the distributions of species in communities and haplotypes in populations. How haplotype ersity among populations relates to community ersity depends on the relative influence of spatial structure of habitats and selection at each of these scales of biological organization.
Publisher: The Royal Society
Date: 29-03-1996
Abstract: Despite extensive studies on the ecology and evolution of the freshwater microcrustacean Daphnia , there is little understanding of the evolutionary history of the genus. Past attempts at reconstructing phylogenetic relationships among Daphnia species have been highly controversial, mainly because of the poor taxonomy of the genus. However, following a revised taxonomy of the daphniid fauna of North America, we conducted a comprehensive appraisal of systematic relationships within the genus through the analysis of sequence ersity in 503 b.p. of the 12S rRNA gene of the mtDNA. The large sequence ergence among its 34 North American members indicates that the genus Daphnia originated during the Mesozoic, even though many lineages exhibit extreme morphological stasis. Results from both cladistic and phenetic analyses indicate the presence of three subgenera comprised of 15 species complexes. Only four of these lineages have shown active speciation over the past 3 Ma, suggesting that cladogenesis in the genus has been constrained. Our study also reveals that interspecific hybridization occurs between taxa which show very large sequence ergence (up to 14%), suggesting that reproductive isolation within the genus evolves slowly.
Publisher: Wiley
Date: 2002
Publisher: Elsevier BV
Date: 07-1999
DOI: 10.1016/S0921-8777(99)00029-4
Abstract: Investigations of intrain idual sequence ersity in mtDNA are a key step in exploring the linkage between somatic mutations in mtDNA and mitochondrial genome evolution. This paper reports a directional cloning procedure enabling the isolation of multiple copies of the D-loop region of the mitochondrial genome from the fish Ameiurus nebulosus. Sequence analysis of 708 D-loop molecules revealed eight mutants, an average intrain idual mutation frequency of 1.12%. Three different types of mutations were detected but each derived from a single mutational event. By contrasting the spectrum of nucleotide variation at multiple biological levels, one can investigate the effects of spontaneous mutations on genome evolution. Such hierarchical analysis suggested shifts in the type and distribution of mtDNA (mitochondrial DNA) mutations at different biological levels, indicating the need to recognize three different rates of mtDNA sequence change from the cellular to population level.
Publisher: Public Library of Science (PLoS)
Date: 02-11-2012
Publisher: Canadian Science Publishing
Date: 07-2002
DOI: 10.1139/F02-091
Abstract: Using freshwater cladocerans as an ex le, this paper explores the contributions that genetic analyses are making to the field of invasion biology. Most importantly, this approach enables a quantification of the incidence of both recent and past invasions. By determining genetic ergence between European and North American lineages of cladocerans, it is possible to estimate the natural incidence of past exchange between these continents. The results of this analysis establish that the current pace of species invasions is extraordinary present rates are nearly 50 000 times higher than historical levels. Genetic studies can also exploit molecular markers to localize the points of origin of invaders. Finally, genetic studies are poised to play an important role in monitoring invasions the DNA bar-coding of life is now simple and rapid enough to enable the development of molecular identification systems.
Publisher: University of Chicago Press
Date: 03-2011
DOI: 10.1899/10-010.1
Publisher: Wiley
Date: 11-2007
Publisher: Canadian Science Publishing
Date: 08-1997
DOI: 10.1139/Z97-148
Abstract: Despite the importance of Daphnia in freshwater zooplankton assemblages, species boundaries in the genus are unclear. This study verifies the taxonomic validity of D. catawba by establishing its genetic ergence from other species of Daphnia that occur in eastern North America. In addition, it reveals the presence of a second, closely allied species, D. minnehaha, which had previously been placed in synonomy with D. pulex. Daphnia catawba and D. minnehaha share a preference for acidic habitats and are restricted to the deciduous and boreal forest regions of the eastern portion of the continent, where D. catawba is restricted to lakes, while D. minnehaha occurs in ponds. Both species reproduce by cyclic parthenogenesis and, based on the extent of their allozyme differentiation, last had a common ancestor more than 7 million years ago. Populations of D. minnehaha fall into two genetic clades those from the Great Lakes watershed are morphologically ergent and have much lower levels of genotypic ersity than those from eastern Canada and the New England states.
Publisher: IOP Publishing
Date: 15-05-2014
Publisher: Springer Science and Business Media LLC
Date: 09-2003
Publisher: Springer Science and Business Media LLC
Date: 03-1996
DOI: 10.1038/HDY.1996.44
Publisher: CSIRO Publishing
Date: 1977
DOI: 10.1071/ZO9770371
Abstract: The taxonomy of Daphnia in south-eastern Australia has been revised on the basis of conventional morphological studies supplemented by electrophoretic analysis. Ten species are recognized of these five have not previously been described and three others have been treated as forms of Daphnia carinata. Detailed descriptions, with figures of the females of all species and of the males of eight species, are included as well as a key to the adult females. Comment is made on the ecology and distribution of the species and on the zoogeographical relationship of Australian Daphnia.
Publisher: Oxford University Press (OUP)
Date: 18-10-2006
Publisher: Springer Science and Business Media LLC
Date: 11-2009
Publisher: Wiley
Date: 24-07-2006
Publisher: Springer Science and Business Media LLC
Date: 08-1998
Publisher: Elsevier BV
Date: 2017
DOI: 10.1016/J.FOODCHEM.2016.07.077
Abstract: Honey is generated by various bee species from erse plants, and because the value of different types of honey varies more than 100-fold, it is a target for fraud. This paper describes a protocol that employs DNA metabarcoding of three gene regions (ITS2, rbcLa, and COI) to provide an inexpensive tool to simultaneously deliver information on the botanical and entomological origins of honey. This method was used to examine seven varieties of honey: light, medium, dark, blended, pasteurized, creamed, and meliponine. Plant and insect sources were identified in five s les, but only the botanical or insect source could be identified in the other two. Two s les were found to be misrepresented. Although this method was generally successful in determining both plant and insect sources, honeys rich in polyphenolic compounds or subject to crystallization were recalcitrant to analysis, so further research is required to combat honey adulteration and mislabeling.
Publisher: Wiley
Date: 09-1990
DOI: 10.1046/J.1420-9101.1990.3050391.X
Abstract: The crustacean subclass Ostracoda shows an exceptionally high incidence of transitions from sexual to asexual reproduction, whose cause remains uncertain. In the current study, patterns of allozymic variation were examined in 12 species of asexual ostracodes at a low arctic site. Populations of 11 species had genotypic frequencies consistent with apomixis, having gross departures from Hardy‐Weinberg expectations and non‐random associations between loci. Allozyme phenotypes suggest that polyploidy is common in most asexual ostracode species in arctic ponds. Although most species had low clonal ersity, 3 had unusually high ersity, with a maximum of 18 clones detected per pond. Asexual species belonging to genera with sexual relatives had higher clonal ersities than those from genera without sexuals, suggesting that sexuals may serve as the source of this clonal ersity.
Publisher: Pensoft Publishers
Date: 29-07-2009
Publisher: Springer Science and Business Media LLC
Date: 09-1975
DOI: 10.1038/257161A0
Publisher: Public Library of Science (PLoS)
Date: 28-09-2004
Publisher: Wiley
Date: 04-1999
DOI: 10.1046/J.1365-294X.1999.00583.X
Abstract: As French populations of the aphid Sitobion avenae exhibit a range of reproductive modes, this species provides a good opportunity for studying the evolution of breeding system variation. The present analysis combined ecological and genetic investigations into the spatial distribution of variation in reproductive mode. Reproductive mode was characterized in 277 lineages of S. avenae from France, and these aphids were scored for five microsatellite loci. The analyses revealed strong geographical partitioning of breeding systems, with obligate asexuals mostly restricted to the south of France, while lineages producing sexual forms were more common in the north. Contrary to what might be anticipated for organisms with frequent parthenogenesis, there was substantial genic and genotypic ersity, even in the obligately asexual lineages. More than 120 different genotypes were detected among the 277 aphid lineages, with an average of 5.9 alleles per locus (range four to 16) and heterozygosity of 56.7%. As with previous studies of allozyme variation in aphids, most loci showed heterozygote deficits, and disequilibrium was common among allelic variants at different loci, even after removal of replicate copies of genotypes that might have been derived through clonal reproduction. Our results suggest that selection is important in structuring reproductive systems and genetic variation in French S. avenae. Canonical correspondence analysis was employed to examine the associations between genotypic and phenotypic variables, enabling the identification of alleles correlated with life-history traits.
Publisher: Entomological Society of Washington
Date: 12-06-2015
Publisher: Springer Science and Business Media LLC
Date: 07-10-2017
Publisher: MDPI AG
Date: 02-03-0001
Abstract: Members of the Monoctonina subtribe have long been neglected in applied studies of the subfamily Aphidiinae, due to their low economic importance, as they do not parasitize pests of cultivated plants. Consequently, data about this group are scarce, including its taxonomy and phylogeny. In the present study, we explore inter- and intraspecific genetic variation of Monoctonina species, including genera Monoctonus Haliday 1833, Monoctonia Starý 1962, Falciconus Mackauer 1959 and Harkeria Cameron 1900. We employ two molecular markers, the barcode region of the mitochondrial cytochrome c oxidase subunit I (COI) and the D2 region of the 28S nuclear gene (28S rDNA), to analyze genetic structuring and phylogeny of all available Monoctonina species, and combine them with morphological data for an integrative approach. We report one new species, and three potentially new species which can be formally described when further specimens are available. Analysis of phylogenetic relationships within the subtribe shows a basal position for the genera Falciconus and Monoctonia, and the close relatedness of Harkeria and Monoctonus.
Publisher: Canadian Science Publishing
Date: 05-1986
DOI: 10.1139/Z86-171
Abstract: Secondary sex ratios of the cyclic parthenogen Daphnia magna were studied in habitats near Churchill, Manitoba. Daphnia magna is believed to possess an environmentally mediated sex-determining system. Throughout the season females produced broods that were predominantly unisexual. The proportion of male offspring was low early in the season but rose to a value near 50% in each of four populations. It is hypothesized that after they have an initial series of female broods, in idual females begin to alternate the sexes of their broods in response to an environmental cue. Such an alternation of brood sexes would explain the population sex-ratio pattern observed and would satisfy theoretical requirements for population and in idual secondary sex ratios of 1:1. In studies on cladocerans, environmental cues inducing the sex-ratio response must be distinguished from cues with a sex-determining effect.
Publisher: Springer Science and Business Media LLC
Date: 23-10-2010
Publisher: Springer Science and Business Media LLC
Date: 08-2001
DOI: 10.1046/J.1365-2540.2001.00885.X
Abstract: Studies on the biogeographical patterning of reproductive systems promise to extend understanding of the factors which modulate breeding system transitions. Two closely allied cladoceran crustaceans, Daphnia pulex and D. pulicaria, show varied modes of reproduction, with populations reproducing by either cyclic or obligate parthenogenesis. Prior studies have provided a detailed understanding of their breeding system ersity in the polar and cold temperate regions of North America. The present investigation extends this analysis, characterizing breeding systems and clonal ersity at sites throughout the United States and Mexico. Genotypic ersity in these southern areas was high, but only diploids were detected, indicating that polyploids are restricted to the north. F(1) hybrids and their two parental species were present in most areas, although their frequencies varied geographically. Hybrids invariably reproduced by obligate asexuality, but both parental taxa showed regional shifts in their breeding system. The complexity of these latter patterns suggests that they reflect the interplay of historical factors and selection.
Publisher: Springer Science and Business Media LLC
Date: 2013
Publisher: JSTOR
Date: 10-1984
DOI: 10.2307/3226469
Publisher: Wiley
Date: 12-08-2009
DOI: 10.1111/J.1755-0998.2009.02577.X
Abstract: DNA barcoding employs short, standardized gene regions (5' segment of mitochondrial cytochrome oxidase subunit I for animals) as an internal tag to enable species identification. Prior studies have indicated that it performs this task well, because interspecific variation at cytochrome oxidase subunit I is typically much greater than intraspecific variation. However, most previous studies have focused on local faunas only, and critics have suggested two reasons why barcoding should be less effective in species identification when the geographical coverage is expanded. They suggested that many recently erged taxa will be excluded from local analyses because they are allopatric. Second, intraspecific variation may be seriously underestimated by local studies, because geographical variation in the barcode region is not considered. In this paper, we analyse how adding a geographical dimension affects barcode resolution, examining 353 butterfly species from Central Asia. Despite predictions, we found that geographically separated and recently erged allopatric species did not show, on average, less sequence differentiation than recently erged sympatric taxa. Although expanded geographical coverage did substantially increase intraspecific variation reducing the barcoding gap between species, this did not decrease species identification using neighbour-joining clustering. The inclusion of additional populations increased the number of paraphyletic entities, but did not impede species-level identification, because paraphyletic species were separated from their monophyletic relatives by substantial sequence ergence. Thus, this study demonstrates that DNA barcoding remains an effective identification tool even when taxa are s led from a large geographical area.
Publisher: Springer Science and Business Media LLC
Date: 08-1983
DOI: 10.1038/HDY.1983.40
Publisher: Springer Science and Business Media LLC
Date: 08-1991
DOI: 10.1007/BF02193629
Publisher: The Royal Society
Date: 15-09-2005
Abstract: Two hundred and seven species of fish, mostly Australian marine fish, were sequenced (barcoded) for a 655 bp region of the mitochondrial cytochrome oxidase subunit I gene ( cox1 ). Most species were represented by multiple specimens, and 754 sequences were generated. The GC content of the 143 species of teleosts was higher than the 61 species of sharks and rays (47.1% versus 42.2%), largely due to a higher GC content of codon position 3 in the former (41.1% versus 29.9%). Rays had higher GC than sharks (44.7% versus 41.0%), again largely due to higher GC in the 3rd codon position in the former (36.3% versus 26.8%). Average within-species, genus, family, order and class Kimura two parameter (K2P) distances were 0.39%, 9.93%, 15.46%, 22.18% and 23.27%, respectively. All species could be differentiated by their cox1 sequence, although single in iduals of each of two species had haplotypes characteristic of a congener. Although DNA barcoding aims to develop species identification systems, some phylogenetic signal was apparent in the data. In the neighbour-joining tree for all 754 sequences, four major clusters were apparent: chimaerids, rays, sharks and teleosts. Species within genera invariably clustered, and generally so did genera within families. Three taxonomic groups—dogfishes of the genus Squalus , flatheads of the family Platycephalidae, and tunas of the genus Thunnus —were examined more closely. The clades revealed after bootstrapping generally corresponded well with expectations. In iduals from operational taxonomic units designated as Squalus species B through F formed in idual clades, supporting morphological evidence for each of these being separate species. We conclude that cox1 sequencing, or ‘barcoding’, can be used to identify fish species.
Publisher: The Royal Society
Date: 14-09-2005
Abstract: By facilitating bioliteracy, DNA barcoding has the potential to improve the way the world relates to wild bio ersity. Here we describe the early stages of the use of cox1 barcoding to supplement and strengthen the taxonomic platform underpinning the inventory of thousands of sympatric species of caterpillars in tropical dry forest, cloud forest and rain forest in northwestern Costa Rica. The results show that barcoding a biologically complex biota unambiguously distinguishes among 97% of more than 1000 species of reared Lepidoptera. Those few species whose barcodes overlap are closely related and not confused with other species. Barcoding also has revealed a substantial number of cryptic species among morphologically defined species, associated sexes, and reinforced identification of species that are difficult to distinguish morphologically. For barcoding to achieve its full potential, (i) ability to rapidly and cheaply barcode older museum specimens is urgent, (ii) museums need to address the opportunity and responsibility for housing large numbers of barcode voucher specimens, (iii) substantial resources need be mustered to support the taxonomic side of the partnership with barcoding, and (iv) hand-held field-friendly barcorder must emerge as a mutualism with the taxasphere and the barcoding initiative, in a manner such that its use generates a resource base for the taxonomic process as well as a tool for the user.
Publisher: Pensoft Publishers
Date: 17-05-2010
Publisher: The Royal Society
Date: 08-09-2005
Abstract: The role of DNA barcoding as a tool to accelerate the inventory and analysis of ersity for hyper erse arthropods is tested using ants in Madagascar. We demonstrate how DNA barcoding helps address the failure of current inventory methods to rapidly respond to pressing bio ersity needs, specifically in the assessment of richness and turnover across landscapes with hyper erse taxa. In a comparison of inventories at four localities in northern Madagascar, patterns of richness were not significantly different when richness was determined using morphological taxonomy (morphospecies) or sequence ergence thresholds (Molecular Operational Taxonomic Unit(s) MOTU). However, sequence-based methods tended to yield greater richness and significantly lower indices of similarity than morphological taxonomy. MOTU determined using our molecular technique were a remarkably local phenomenon—indicative of highly restricted dispersal and/or long-term isolation. In cases where molecular and morphological methods differed in their assignment of in iduals to categories, the morphological estimate was always more conservative than the molecular estimate. In those cases where morphospecies descriptions collapsed distinct molecular groups, sequence ergences of 16% (on average) were contained within the same morphospecies. Such high ergences highlight taxa for further detailed genetic, morphological, life history, and behavioral studies.
Publisher: Oxford University Press (OUP)
Date: 11-1987
DOI: 10.2307/2409098
Publisher: Canadian Science Publishing
Date: 10-1993
DOI: 10.1139/F93-239
Abstract: Seasonal, within-lake, and among-lake variation in helmet size and shape has been reported for Daphnia galeata mendotae. The genetic component of this variation was assessed by an allozyme and morphological reanalysis of nine previously studied sites. Genetic associations with morphological variation were found, but all were attributed to D. galeata mendotae × Daphnia rosea hybridization or to taxonomic confusion with D. rosea. The existence of hybrids accounted for spatial polymorphism both within and among lakes. In addition, hybrids contributed to seasonal variation as they increased in abundance from summer to winter. Nevertheless, cyclomorphosis in D. galeata mendotae s.s was real and due largely to phenotypic plasticity. Local hybridization between D. galeata mendotae and D. rosea was widespread from the midwestern states to Vermont. The distributions and habitat associations of D. galeata mendotae and D. rosea indicated that ecological segregation at the lake level acts as an important reproductive isolating mechanism. Reinterpretation of previous studies, however, suggests that disturbance followed by one or a few hybridization events often leads to hybrid domination of a lake.
Publisher: PeerJ
Date: 13-04-2022
DOI: 10.7717/PEERJ.13049
Abstract: Located in the central region of northern Nigeria, the Jos Plateau covers approximately 9,400 km² with an average altitude of 1,280 m and constitutes a unique terrestrial ecoregion known as the Jos Plateau forest-grassland mosaic. The biota of the Jos Plateau include endemic elements, but very limited information is available on its ichthyofauna. This is despite the fact that the ancient plateau contributes to several large rivers spanning multiple major drainage systems including the Niger and Benue Rivers, and Lake Chad. This study provides the first species list for the fishes of the Jos Plateau based mainly on 175 DNA barcoded museum voucher specimens representing 20 species, and another three species without a DNA barcode. In total, 23 species from eight families and 17 genera were collected from the Jos Plateau including five putatively new species, four in the family Cyprinidae and one in the Clariidae. With ten species, the Cyprinidae is the most erse fish family on the Jos Plateau, followed by Clariidae and Cichlidae, each with three species. The study also provides data on species distribution and habitat parameters including information on water chemistry that strongly suggests that selected water bodies are heavily impacted by anthropogenic activities. Urgent management steps are required to preserve the unique and erse fish communities of the Jos Plateau and their habitats.
Publisher: Public Library of Science (PLoS)
Date: 14-02-2011
Publisher: Wiley
Date: 1990
DOI: 10.1046/J.1420-9101.1990.3010065.X
Abstract: Members of the crustacean subclass Ostracoda show a high incidence of transitions from sexual to asexual reproduction. The cause of these shifts remains uncertain, perhaps because there have been few genetic studies on the group. The present study examined sex ratios and allozyme variation in 7 sexual species of ostracodes from ponds at a low Arctic site. Sex ratios in most species were strongly female‐biased. Detailed study of Cyprinotus glaucus indicated that sex ratios were heterogeneous among populations, but stable during juvenile‐adult development. Among 6 species, the proportion of polymorphic loci ranged from 0–33 %, and in idual heterozygosities 0–14 %. Genotypic frequencies at polymorphic loci conformed to Hardy‐Weinberg expectations in all species, but gene frequency differences among local populations of C. glaucus suggest restricted gene flow for this passively‐dispersed species. Averaged over 5 species, approximately 27 % of the polymorphic loci were sex‐linked. Linkage relationships were variable, with an in idual locus being sex‐linked in some species and autosomal in others.
Publisher: Wiley
Date: 09-01-1999
Publisher: Springer Science and Business Media LLC
Date: 11-1974
DOI: 10.1038/252389A0
Publisher: Elsevier BV
Date: 04-2007
DOI: 10.1016/J.TIG.2007.02.001
Abstract: DNA barcoding aims to provide an efficient method for species-level identifications and, as such, will contribute powerfully to taxonomic and bio ersity research. As the number of DNA barcode sequences accumulates, however, these data will also provide a unique 'horizontal' genomics perspective with broad implications. For ex le, here we compare the goals and methods of DNA barcoding with those of molecular phylogenetics and population genetics, and suggest that DNA barcoding can complement current research in these areas by providing background information that will be helpful in the selection of taxa for further analyses.
Publisher: Springer Science and Business Media LLC
Date: 28-05-2004
Publisher: University of Chicago Press
Date: 05-1981
DOI: 10.1086/283761
Publisher: The Royal Society
Date: 16-12-2009
Abstract: This study reports DNA barcodes for more than 1300 Lepidoptera species from the eastern half of North America, establishing that 99.3 per cent of these species possess diagnostic barcode sequences. Intraspecific ergences averaged just 0.43 per cent among this assemblage, but most values were lower. The mean was elevated by deep barcode ergences (greater than 2%) in 5.1 per cent of the species, often involving the sympatric occurrence of two barcode clusters. A few of these cases have been analysed in detail, revealing species overlooked by the current taxonomic system. This study also provided a large-scale test of the extent of regional ergence in barcode sequences, indicating that geographical differentiation in the Lepidoptera of eastern North America is small, even when comparisons involve populations as much as 2800 km apart. The present results affirm that a highly effective system for the identification of Lepidoptera in this region can be built with few records per species because of the limited intra-specific variation. As most terrestrial and marine taxa are likely to possess a similar pattern of population structure, an effective DNA-based identification system can be developed with modest effort.
Publisher: Canadian Science Publishing
Date: 09-2004
DOI: 10.1139/F04-106
Abstract: Fishes possess both the largest and smallest vertebrate genomes, but the evolutionary significance of this variation is unresolved. The present study provides new genome-size estimates for more than 500 species, with a focus on the cartilaginous and ray-finned fishes. These results confirm that genomes are smaller in ray-finned than in cartilaginous fishes, with the exception of polyploids, which account for much genome-size variation in both groups. Genome-size ersity in ray-finned fishes is not related to metabolic rate, but is positively correlated with egg diameter, suggesting linkages to the evolution of parental care. Freshwater and other eurybiotic fishes have larger genomes than their marine and stenobiotic counterparts. Although genome-size ersity among the fishes appears less clearly linked to any single biological correlate than in the birds, mammals, or hibians, this study highlights several particularly variable taxa that are suitable for further study.
Publisher: Wiley
Date: 11-12-2012
Abstract: Microgastrine wasps are among the most species-rich and numerous parasitoids of caterpillars (Lepidoptera). They are often host-specific and thus are extensively used in biological control efforts and figure prominently in trophic webs. However, their extraordinary ersity coupled with the occurrence of many cryptic species produces a significant taxonomic impediment. We present and release the results of 8 years (2004-2011) of DNA barcoding microgastrine wasps. Currently they are the best represented group of parasitoid Hymenoptera in the Barcode of Life Data System (BOLD), a massive barcode storage and analysis data management site for the International Barcoding of Life (iBOL) program. There are records from more than 20 000 specimens from 75 countries, including 50 genera (90% of the known total) and more than 1700 species (as indicated by Barcode Index Numbers and 2% MOTU). We briefly discuss the importance of this DNA data set and its collateral information for future research in: (1) discovery of cryptic species and description of new taxa (2) estimating species numbers in bio ersity inventories (3) clarification of generic boundaries (4) biological control programmes (5) molecular studies of host-parasitoid biology and ecology (6) evaluation of shifts in species distribution and phenology and (7) fostering collaboration at national, regional and world levels. The integration of DNA barcoding with traditional morphology-based taxonomy, host records, and other data has substantially improved the accuracy of microgastrine wasp identifications and will significantly accelerate further studies on this group of parasitoids.
Publisher: Springer Science and Business Media LLC
Date: 11-2003
Publisher: Wiley
Date: 28-03-2003
DOI: 10.1046/J.1365-294X.2003.01801.X
Abstract: The Black, Azov, Caspian and Aral Seas, remnants of the intracontinental Paratethys basin, are home to a spectacular ersity of crustaceans. This study examines the past history of the Ponto-Caspian fauna through comparative phylogeographical studies on both benthic and planktonic taxa, based on an examination of nucleotide ersity in the mitochondrial, cytochrome c oxidase subunit 1 (COI) gene. The COI data reveal a striking ex le of phylogeographical concordance. All species analysed, three hipods and three cladocerans, are characterized by two monophyletic clades corresponding to the Black and Caspian regions. However, this phylogeographical partition is, on average, four times deeper for the benthic hipods than for the planktonic cladocerans. Based on standard molecular clocks, the Black and Caspian lineages of benthic crustaceans erged at varied intervals from 1 to 8 million years ago. By contrast, planktonic lineages are more recent with their ergence occurring in the last million years. Levels of intraspecific polymorphisms are variable and generally lower in planktonic than benthic taxa. The mechanisms responsible for the high ersity of crustaceans in the Ponto-Caspian region are discussed on the basis of these results.
Publisher: University of Chicago Press
Date: 04-1989
DOI: 10.2307/1541582
Publisher: Wiley
Date: 03-2008
DOI: 10.1111/J.1471-8286.2007.01964.X
Abstract: Although a mitochondrial DNA barcode has been shown to be of great utility for species identification and discovery in an increasing number of erse taxa, caution has been urged with its application to one of the most taxonomically erse vertebrate groups - the hibians. Here, we test three of the perceived shortcomings of a CO1 DNA barcode's utility with a group of Holarctic hibians: primer fit, sequence variability and overlapping intra- and interspecific variability. We found that although the CO1 DNA barcode priming regions were variable, we were able to reliably lify a CO1 fragment from degenerate primers and primers with G-C residues at the 3' end. Any overlap between intra- and interspecific variation in our taxonomic s ling was due to introgressive hybridization (Bufo/Anaxyrus), complex genetics (Ambystoma) or incomplete taxonomy (Triturus). Rates of hybridization and species discovery are not expected to be greater for hibians than for other vertebrate groups, and thus problems with the utility of using a single mitochondrial gene for species identification will not be specific to hibians. Therefore, we conclude that there is greater potential for a CO1 barcode's use with hibians than has been reported to date. A large-scale effort to barcode the hibians of the world, using the same primary barcode region of CO1, will yield important findings for science and conservation.
Publisher: Canadian Science Publishing
Date: 08-1996
DOI: 10.1139/Z96-153
Abstract: The genetic characterization of more than 1500 populations belonging to the Daphnia pulex group from the United States and Mexico revealed nine previously unrecognized species. Three of these taxa, showing morphological and genetic affinities, are newly described in this paper and are assigned membership in a new species complex. These species share a unique configuration of P 3 sensilla and a triangular ephippial shape which differs from that of other members of the genus Daphnia. All three species are large-bodied forms showing distinctive setulation of the internal margin of the ventral carapace. All these members of the complex appear to be narrow endemics, restricted to temporary ponds in semi-arid areas of the Pacific Northwest.
Publisher: Crustacean Society
Date: 05-2003
Publisher: Public Library of Science (PLoS)
Date: 25-09-2014
Publisher: Proceedings of the National Academy of Sciences
Date: 21-01-2014
Abstract: Understanding the interaction structure of ecological assemblages is the basis for understanding how they vary in space and time. To reconstruct interactions in the High Arctic, we draw on three sources of information: two based on DNA sequence data and one on the rearing of parasitoids from their hosts. Overall, we show that a combination of all three techniques will not only provide high resolution for describing feeding associations among in idual species, but also rev our view of the overall structure of the target network. Thus, our findings suggest that combining several types of information will fundamentally change our impression of both how local interaction webs are structured, and how biotic interactions are patterned across the globe.
Publisher: Oxford University Press (OUP)
Date: 2022
DOI: 10.1093/GIGASCIENCE/GIAC040
Abstract: Traditional biomonitoring approaches have delivered a basic understanding of bio ersity, but they cannot support the large-scale assessments required to manage and protect entire ecosystems. This study used DNA metabarcoding to assess spatial and temporal variation in species richness and ersity in arthropod communities from 52 protected areas spanning 3 Canadian ecoregions. This study revealed the presence of 26,263 arthropod species in the 3 ecoregions and indicated that at least another 3,000–5,000 await detection. Results further demonstrate that communities are more similar within than between ecoregions, even after controlling for geographical distance. Overall α- ersity declined from east to west, reflecting a gradient in habitat disturbance. Shifts in species composition were high at every site, with turnover greater than nestedness, suggesting the presence of many transient species. Differences in species composition among their arthropod communities confirm that ecoregions are a useful synoptic for biogeographic patterns and for structuring conservation efforts. The present results also demonstrate that metabarcoding enables large-scale monitoring of shifts in species composition, making it possible to move beyond the biomass measurements that have been the key metric used in prior efforts to track change in arthropod communities.
Publisher: The Royal Society
Date: 07-02-2003
Publisher: The Royal Society
Date: 08-09-2005
Abstract: Large-scale DNA barcoding projects are now moving toward activation while the creation of a comprehensive barcode library for eukaryotes will ultimately require the acquisition of some 100 million barcodes. To satisfy this need, analytical facilities must adopt protocols that can support the rapid, cost-effective assembly of barcodes. In this paper we discuss the prospects for establishing high volume DNA barcoding facilities by evaluating key steps in the analytical chain from specimens to barcodes. Alliances with members of the taxonomic community represent the most effective strategy for provisioning the analytical chain with specimens. The optimal protocols for DNA extraction and subsequent PCR lification of the barcode region depend strongly on their condition, but production targets of 100K barcode records per year are now feasible for facilities working with compliant specimens. The analysis of museum collections is currently challenging, but PCR cocktails that combine polymerases with repair enzyme(s) promise future success. Barcode analysis is already a cost-effective option for species identification in some situations and this will increasingly be the case as reference libraries are assembled and analytical protocols are simplified.
Publisher: Public Library of Science (PLoS)
Date: 30-05-2012
Publisher: Springer Science and Business Media LLC
Date: 04-1989
DOI: 10.1038/HDY.1989.30
Publisher: Wiley
Date: 04-1990
Publisher: PeerJ
Date: 14-01-2021
DOI: 10.7717/PEERJ.10420
Abstract: Natural history collections are a valuable resource for molecular taxonomic studies and for examining patterns of evolutionary ersification, particularly in the case of rare or extinct species. However, the recovery of sequence information is often complicated by DNA degradation. This article describes use of the Sequel platform (Pacific Biosciences) to recover the 658 bp barcode region of the mitochondrial cytochrome c oxidase I (COI) gene from 380 butterflies with an average age of 50 years. Nested multiplex PCR was employed for library preparation to facilitate sequence recovery from extracts with low concentrations of highly degraded DNA. By employing circular consensus sequencing (CCS) of short licons (circa 150 bp), full-length barcodes could be assembled without a reference sequence, an important advance from earlier protocols which required reference sequences to guide contig assembly. The Sequel protocol recovered COI sequences (499 bp on average) from 318 of 380 specimens (84%), much higher than for Sanger sequencing (26%). Because each read derives from a single molecule, it was also possible to quantify the incidence of substitutions arising from DNA damage. In agreement with past work on sequence changes induced by DNA degradation, the transition C/G → T/A was the most prevalent category of change, but its rate of occurrence (4.58E−4) was so low that it did not impede the recovery of reliable sequences. Because the current protocol recovers COI sequence from most museum specimens, and because sequence fidelity is unaffected by nucleotide misincorporations, large-scale sequence characterization of museum specimens is feasible.
Publisher: Canadian Science Publishing
Date: 05-2004
DOI: 10.1139/Z04-041
Abstract: We evaluated sequence ersity in the mitochondrial cytochrome-c oxidase I (COI EC 1.9.3.1) gene as a tool for resolving differences among species of Arctic springtails. The Collembola examined in this analysis were collected from Igloolik, Cornwallis, and Somerset islands and included representatives from all major families found in the Arctic. Members of 13 genera and 19 species were examined, including 4 species of the genus Folsomia and 3 species of the genus Hypogastrura. In all cases, species were successfully discriminated. Sequence ergences within species were generally less than 1%, whereas ergences between species were greater than 8% in all cases. Divergences among in iduals of one species of Folsomia were much higher (up to 13%), but this likely represents the presence of an undescribed sibling species. We conclude that DNA barcoding is a powerful tool for identifying species of Collembola and should regularly be useful as a complement to traditional, morphological taxonomy.
Publisher: CSIRO Publishing
Date: 2012
DOI: 10.1071/IS12038
Abstract: Bio ersity of tropical Saturniidae, as measured through traditionally described and catalogued species, strongly risks pooling cryptic species under one name. We examined the DNA barcodes, morphology, habitus and ecology of 32 ‘well known’ species of dry forest saturniid moths from Area de Conservacion Guanacaste (ACG) in north-western Costa Rica and found that they contain as many as 49 biological entities that are probably separate species. The most prominent splitting of traditional species – Eacles imperialis, Automeris zugana, Automeris tridens, Othorene verana, Hylesia dalina, Dirphia avia, Syssphinx molina, Syssphinx colla, and Syssphinx quadrilineata – is where one species was believed to breed in dry forest and rain forest, but is found to be two biological entities variously distinguishable by DNA barcodes and morphology, habitus, and/or microecological distribution. This implies that ‘standard’ biological information about each traditional species may be an unconscious mix of interspecific information, and begs renewed DNA barcoding, closer attention to so-called intraspecific variation, and increased museum collection and curation of specimens from more in idual and ecologically characterised sites – as well as eventually more species descriptions. Simultaneously, this inclusion of sibling species as in idual entities in bio ersity studies, rather than pooled under one traditional name, reduces the degree of ecological and evolutionary generalisation perceived by the observer.
Publisher: Wiley
Date: 18-11-2010
Publisher: Wiley
Date: 25-08-2012
Publisher: Public Library of Science (PLoS)
Date: 29-08-2011
Publisher: Wiley
Date: 29-01-2009
DOI: 10.1111/J.1095-8649.2008.02080.X
Abstract: FISH-BOL, the Fish Barcode of Life c aign, is an international research collaboration that is assembling a standardized reference DNA sequence library for all fishes. Analysis is targeting a 648 base pair region of the mitochondrial cytochrome c oxidase I (COI) gene. More than 5000 species have already been DNA barcoded, with an average of five specimens per species, typically vouchers with authoritative identifications. The barcode sequence from any fish, fillet, fin, egg or larva can be matched against these reference sequences using BOLD the Barcode of Life Data System (www.barcodinglife.org). The benefits of barcoding fishes include facilitating species identification, highlighting cases of range expansion for known species, flagging previously overlooked species and enabling identifications where traditional methods cannot be applied. Results thus far indicate that barcodes separate c. 98 and 93% of already described marine and freshwater fish species, respectively. Several specimens with ergent barcode sequences have been confirmed by integrative taxonomic analysis as new species. Past concerns in relation to the use of fish barcoding for species discrimination are discussed. These include hybridization, recent radiations, regional differentiation in barcode sequences and nuclear copies of the barcode region. However, current results indicate these issues are of little concern for the great majority of specimens.
Publisher: Public Library of Science (PLoS)
Date: 02-07-2014
Publisher: Springer Science and Business Media LLC
Date: 11-1994
DOI: 10.1038/HDY.1994.154
Publisher: Cambridge University Press (CUP)
Date: 28-01-2011
DOI: 10.1017/S0007485310000714
Abstract: Although DNA barcode coverage has grown rapidly for many insect orders, there are some groups, such as scale insects, where sequence recovery has been difficult. However, using a recently developed primer set, we recovered barcode records from 373 specimens, providing coverage for 75 species from 31 genera in two families. Overall success was % for mealybugs and % for armored scale species. The G·C content was very low in most species, averaging just 16.3%. Sequence ergences (K2P) between congeneric species averaged 10.7%, while intra-specific ergences averaged 0.97%. However, the latter value was inflated by high intra-specific ergence in nine taxa, cases that may indicate species overlooked by current taxonomic treatments. Our study establishes the feasibility of developing a comprehensive barcode library for scale insects and indicates that its construction will both create an effective system for identifying scale insects and reveal taxonomic situations worthy of deeper analysis.
Publisher: Elsevier BV
Date: 07-1996
Publisher: Springer Science and Business Media LLC
Date: 11-1994
DOI: 10.1038/HDY.1994.152
Publisher: Wiley
Date: 18-06-2023
DOI: 10.1002/EAP.2890
Abstract: Outbreaks of the spongy moth Lymantria dispar can have devastating impacts on forest resources and ecosystems. Lepidoptera‐specific insecticides, such as Bacillus thuringiensis var. kurstaki (BTK) and tebufenozide, are often deployed to prevent heavy defoliation of the forest canopy. While it has been suggested that using BTK poses less risk to non‐target Lepidoptera than leaving an outbreak untreated, in situ testing of this assumption has been impeded by methodological challenges. The trade‐offs between insecticide use and outbreaks have yet to be addressed for tebufenozide, which is believed to have stronger side effects than BTK. We investigated the short‐term trade‐offs between tebufenozide treatments and no‐action strategies for the non‐target herbivore community in forest canopies. Over 3 years, Lepidoptera and Symphyta larvae were s led by canopy fogging in 48 oak stands in southeast Germany during and after a spongy moth outbreak. Half of the sites were treated with tebufenozide and changes in canopy cover were monitored. We contrasted the impacts of tebufenozide and defoliator outbreaks on the abundance, ersity, and functional structure of chewing herbivore communities. Tebufenozide treatments strongly reduced Lepidoptera up to 6 weeks after spraying. Populations gradually converged back to control levels after 2 years. Shelter‐building species dominated caterpillar assemblages in treated plots in the post‐spray weeks, while flight‐dimorphic species were slow to recover and remained underrepresented in treated stands 2 years post‐treatment. Spongy moth outbreaks had minor effects on leaf chewer communities. Summer Lepidoptera decreased only when severe defoliation occurred, whereas Symphyta declined 1 year after defoliation. Polyphagous species with only partial host plant overlap with the spongy moth were absent from heavily defoliated sites, suggesting greater sensitivity of generalists to defoliation‐induced plant responses. These results demonstrate that both tebufenozide treatments and spongy moth outbreaks alter canopy herbivore communities. Tebufenozide had a stronger and longer lasting impact, but it was restricted to Lepidoptera, whereas the outbreak affected both Lepidoptera and Symphyta. These results are tied to the fact that only half of the outbreak sites experienced severe defoliation. This highlights the limited accuracy of current defoliation forecast methods, which are used as the basis for the decision to spray insecticides.
Publisher: Elsevier BV
Date: 02-1995
Publisher: Public Library of Science (PLoS)
Date: 11-10-2012
Publisher: Oxford University Press (OUP)
Date: 09-1988
DOI: 10.2307/2408918
Publisher: Wiley
Date: 26-11-2003
DOI: 10.1046/J.1365-294X.2003.02024.X
Abstract: The morphological stasis of many freshwater crustaceans has resulted in the prior delineation of cosmopolitan species and has been explained by their capacity for long-distance dispersal. This study examines the phylogeography of Daphnia obtusa, a cladoceran thought to be widespread in North America. However, sequence variation of the mitochondrial cytochrome c oxidase subunit I gene indicates that this taxon is composed of two morphologically cryptic species, designated D. obtusa NA1 and NA2. NA2 is restricted to the east, whereas NA1 is broadly distributed across the United States, and is sub ided into four phylogroups that show weak genetic differentiation over broad geographical areas, which likely reflects recent long-distance dispersal. The current distributions of the four phylogroups in NA1 can be explained by recent range expansion from different refugia following the last Pleistocene glacial advance. Interestingly, the mitochondrial phylogroups identified in this study do not correspond to lineages detected in a previous allozyme analysis. However, the latter groups are associated with a habitat shift suggesting that natural selection may have played a role in their ergence. The results of this and previous studies illustrate the complicated biogeographical history of freshwater cladocerans.
Publisher: Wiley
Date: 10-1973
Abstract: This perspective aims at underlining the usefulness of event-related potentials (ERP) to better understand the brain correlates of Korsakoff's syndrome (KS), a neuropsychiatric disease characterized by severe memory impairment and most frequently resulting as a neurological complication of alcohol-dependence (AD). While ERP have been broadly used in AD, it has up to now been very little applied in KS or in the comparison of KS and AD. Within the framework of dual-process models, an influential theory postulating that addictive states result from an imbalance between under-activated reflective system and over-activated automatic-affective one, this paper proposes: (1) a brief synthesis of the main results of ERP studies in AD and KS, and (2) new research avenues using ERP to identify the electrophysiological correlates of cognitive and emotional dysfunction in KS. These experimental perspectives aim at exploring the continuity hypothesis, which postulates a gradient of impairments from AD to KS. We conclude on the possibility of developing neuropsychological strategies with electrophysiological follow-up to ensure KS diagnosis and test the efficacy of patient's neurocognitive rehabilitation.
Publisher: Canadian Science Publishing
Date: 03-2005
DOI: 10.1139/F04-210
Abstract: A spectacular adaptive radiation of crustaceans has occurred in the Black, Caspian, and Aral seas. This study tests several evolutionary scenarios based on the extent of genetic differentiation and the phylogenetic relationships among endemic mysids and gammarid hipods from the Black and Caspian seas. Molecular phylogenies for these taxa were based on two mitochondrial genes: cytochrome c oxidase subunit I and the large ribosomal RNA subunit (16S), and one nuclear gene, the large ribosomal RNA subunit (28S). The results support the monophyly of the PontoCaspian gammarids (genera Dikerogammarus, Echinogammarus, Obesogammarus, and Pontogammarus), suggesting their origin from one colonization event. By contrast, several colonization events preceded the radiation of the PontoCaspian mysids (genera Limnomysis and Paramysis). Levels of intraspecific ergence were variable, with mysids showing either no geographic structure or deep genetic splits reflecting a long history of reproductive isolation between populations in marine settings and those in fresh waters. These findings suggest that the ersity of the PontoCaspian crustaceans has been underestimated and that species regarded as euryhaline are often composed of distinct evolutionary groups whose taxonomic status should be reevaluated.
Publisher: Oxford University Press (OUP)
Date: 03-1998
Abstract: We describe a novel PCR-based method that allows the generation of nested termination fragments by integrating both selective DNA lification and directed chain termination into a single PCR reaction. These termination fragments can be examined for sequence variation in either denaturing or non-denaturing polyacrylamide gels. This method provides a one-step and highly effective approach for the detection of both insertions/deletions and single base pair substitutions in sequences up to 1 kb in length.
Publisher: Wiley
Date: 05-2008
DOI: 10.1111/J.1471-8286.2007.01998.X
Abstract: The performance of DNA barcoding as a tool for fast taxonomic verification in ecological assessment projects of small mammals was evaluated during a collecting trip to a lowland tropical rainforest site in Suriname. We also compared the performance of tissue s ling onto FTA CloneSaver cards vs. liquid nitrogen preservation. DNA barcodes from CloneSaver cards were recovered from 85% of specimens, but DNA degradation was apparent, because only 36% of sequence reads were long (over 600 bp). In contrast, cryopreserved tissue delivered 99% barcode recovery (97% > 600 bp). High humidity, overs ling or tissue type may explain the poor performance of CloneSaver cards. Comparison of taxonomic assignments made in the field and from barcode results revealed inconsistencies in just 3.4% of cases and most of the discrepancies were due to field misidentifications (3%) rather than s ling/analytical error (0.5%). This result reinforces the utility of DNA barcoding as a tool for verification of taxonomic identifications in ecological surveys, which is especially important when the collection of voucher specimens is not possible.
Publisher: Wiley
Date: 07-07-2006
Publisher: JSTOR
Date: 06-1977
DOI: 10.2307/3819
Publisher: University of Chicago Press
Date: 09-2010
DOI: 10.1899/09-121.1
Publisher: Wiley
Date: 24-06-2013
Publisher: Wiley
Date: 08-07-2011
Publisher: The Royal Society
Date: 07-08-2003
Publisher: Proceedings of the National Academy of Sciences
Date: 10-2004
Abstract: Astraptes fulgerator , first described in 1775, is a common and widely distributed neotropical skipper butterfly (Lepidoptera: Hesperiidae). We combine 25 years of natural history observations in northwestern Costa Rica with morphological study and DNA barcoding of museum specimens to show that A. fulgerator is a complex of at least 10 species in this region. Largely sympatric, these taxa have mostly different caterpillar food plants, mostly distinctive caterpillars, and somewhat different ecosystem preferences but only subtly differing adults with no genitalic ergence. Our results add to the evidence that cryptic species are prevalent in tropical regions, a critical issue in efforts to document global species richness. They also illustrate the value of DNA barcoding, especially when coupled with traditional taxonomic tools, in disclosing hidden ersity.
Publisher: Springer Science and Business Media LLC
Date: 16-09-2015
DOI: 10.1038/SREP14188
Abstract: The study analyzes sequence variation of two mitochondrial genes (COI, cytb) in Pediculus humanus from three countries (Egypt, Pakistan, South Africa) that have received little prior attention and integrates these results with prior data. Analysis indicates a maximum K2P distance of 10.3% among 960 COI sequences and 13.8% among 479 cytb sequences. Three analytical methods (BIN, PTP, ABGD) reveal five concordant OTUs for COI and cytb. Neighbor-Joining analysis of the COI sequences confirm five clusters three corresponding to previously recognized mitochondrial clades A, B, C and two new clades, “D” and “E”, showing 2.3% and 2.8% ergence from their nearest neighbors (NN). Cytb data corroborate five clusters showing that clades “D” and “E” are both 4.6% ergent from their respective NN clades. Phylogenetic analysis supports the monophyly of all clusters recovered by NJ analysis. Divergence time estimates suggest that the earliest split of P. humanus clades occured slightly more than one million years ago (MYa) and the latest about 0.3 MYa. Sequence ergences in COI and cytb among the five clades of P. humanus are 10X those in their human host, a difference that likely reflects both rate acceleration and the acquisition of lice clades from several archaic hominid lineages.
Publisher: PeerJ
Date: 25-04-2022
DOI: 10.7717/PEERJ.13267
Abstract: Although Pakistan has rich bio ersity, many groups are poorly known, particularly insects. To address this gap, we employed DNA barcoding to survey its insect ersity. Specimens obtained through erse collecting methods at 1,858 sites across Pakistan from 2010–2019 were examined for sequence variation in the 658 bp barcode region of the cytochrome c oxidase 1 (COI) gene. Sequences from nearly 49,000 specimens were assigned to 6,590 Barcode Index Numbers (BINs), a proxy for species, and most (88%) also possessed a representative image on the Barcode of Life Data System (BOLD). By coupling morphological inspections with barcode matches on BOLD, every BIN was assigned to an order (19) and most (99.8%) were placed to a family (362). However, just 40% of the BINs were assigned to a genus (1,375) and 21% to a species (1,364). Five orders (Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera) accounted for 92% of the specimens and BINs. More than half of the BINs (59%) are so far only known from Pakistan, but others have also been reported from Bangladesh (13%), India (12%), and China (8%). Representing the first DNA barcode survey of the insect fauna in any South Asian country, this study provides the foundation for a complete inventory of the insect fauna in Pakistan while also contributing to the global DNA barcode reference library.
Publisher: Biology Centre, AS CR
Date: 26-09-2022
Publisher: Proceedings of the National Academy of Sciences
Date: 17-01-2006
Abstract: Although central to much biological research, the identification of species is often difficult. The use of DNA barcodes, short DNA sequences from a standardized region of the genome, has recently been proposed as a tool to facilitate species identification and discovery. However, the effectiveness of DNA barcoding for identifying specimens in species-rich tropical biotas is unknown. Here we show that cytochrome c oxidase I DNA barcodes effectively discriminate among species in three Lepidoptera families from Area de Conservación Guanacaste in northwestern Costa Rica. We found that 97.9% of the 521 species recognized by prior taxonomic work possess distinctive cytochrome c oxidase I barcodes and that the few instances of interspecific sequence overlap involve very similar species. We also found two or more barcode clusters within each of 13 supposedly single species. Covariation between these clusters and morphological and/or ecological traits indicates overlooked species complexes. If these results are general, DNA barcoding will significantly aid species identification and discovery in tropical settings.
Publisher: Springer Science and Business Media LLC
Date: 11-1994
DOI: 10.1038/HDY.1994.147
Publisher: Elsevier BV
Date: 06-1994
Publisher: Canadian Science Publishing
Date: 08-2003
DOI: 10.1139/Z03-126
Abstract: Little information is available on genome size ersity among insects, even in otherwise well-studied groups such as the Lepidoptera. In fact, only six lepidopteran species have been studied to date. The present study therefore represents the first attempt to survey genome size variation in this group, giving estimates for more than 50 species and increasing the coverage of the order to 15 families. Based on this expanded data set, some interesting patterns of variation can be observed, albeit only in a preliminary way. By providing the first large survey of lepidopteran genome sizes, as well as some methodological guidelines and highlights of interesting future work, it is hoped that this study will stimulate further analysis of this erse group of insects.
Publisher: MDPI AG
Date: 12-01-2022
Abstract: Determining the size of the German insect fauna requires better knowledge of several mega erse families of Diptera and Hymenoptera that are taxonomically challenging. This study takes the first step in assessing these “dark taxa” families and provides species estimates for four challenging groups of Diptera (Cecidomyiidae, Chironomidae, Phoridae, and Sciaridae). These estimates are based on more than 48,000 DNA barcodes (COI) from Diptera collected by Malaise traps that were deployed in southern Germany. We assessed the fraction of German species belonging to 11 fly families with well-studied taxonomy in these s les. The resultant ratios were then used to estimate the species richness of the four “dark taxa” families (DT families hereafter). Our results suggest a surprisingly high proportion of undetected bio ersity in a supposedly well-investigated country: at least 1800–2200 species await discovery in Germany in these four families. As this estimate is based on collections from one region of Germany, the species count will likely increase with expanded geographic s ling.
Publisher: The Royal Society
Date: 07-10-2009
Abstract: Population genetic surveys approximately 25 years apart examined the distribution and abundance of asexual clones of the freshwater zooplankter Daphnia pulex complex in rock pools near Churchill, Manitoba, Canada. In 1984–1985, melanic members of this species complex were present in 131 rock pools at this site, but were only detected in 90 of these pools in 2007–2008. Allozymic surveys conducted during these two time periods revealed that 59 per cent of these populations showed unchanged clonal composition. Total clonal replacement occurred in 8 per cent of the populations, while the others (33%) included a mixture of ‘resident’ clones and new ‘colonists’. We discuss these changes in light of shifts in biotic and abiotic factors. We also discuss the use of rock pool habitats as ‘sentinel’ systems for examining long-term environmental changes in the ecological genetics of aquatic organisms in the Arctic.
Publisher: Springer Science and Business Media LLC
Date: 1999
Publisher: The Royal Society
Date: 28-09-2016
Abstract: Global change is causing drastic changes in the pollinator communities of the Arctic. While arctic flowers are visited by a wide range of insects, flies in family Muscidae have been proposed as a pollinator group of particular importance. To understand the functional outcome of current changes in pollinator community composition, we examined the role of muscids in the pollination of a key plant species, the mountain avens ( Dryas ). We monitored the seed set of Dryas across 15 sites at Zackenberg, northeast Greenland, and used sticky flower mimics and DNA barcoding to describe the flower-visiting community at each site. To evaluate the consequences of shifts in pollinator phenology under climate change, we compared the flower visitors between the early and the late season. Our approach revealed a erse community of insects visiting Dryas , including two-thirds of all insect species known from the area. Even against this erse background, the abundance of muscid flies emerged as a key predictor for seed set in Dryas , whereas overall insect abundance and species richness had little or no effect. With muscid flies as the main drivers of the pollinating function in the High Arctic, a recently observed decline in their abundances offers cause for concern.
Publisher: Wiley
Date: 29-01-2009
DOI: 10.1111/J.1095-8649.2008.02077.X
Abstract: The freshwater fish fauna of Mexico and Guatemala is exceptionally erse with >600 species, many endemic. In this study, patterns of sequence ergence were analysed in representatives of this fauna using cytochrome c oxidase subunit 1 (COI) DNA barcodes for 61 species in 36 genera. The average ergence among conspecific in iduals was 0.45%, while congeneric taxa showed 5.1% ergence. Three species of Poblana, each occupying a different crater lake in the arid regions of Central Mexico, have had a controversial taxonomic history but are usually regarded as endemics to a single lake. They possess identical COI barcodes, suggesting a very recent history of isolation. Representatives of the Cichlidae, a complex and poorly understood family, were well discriminated by barcodes. Many species of Characidae seem to be young, with low ergence values (<2%), but nevertheless, clear barcode clusters were apparent in the Bramocharax-Astyanax complex. The symbranchid, Opisthernon aenigmaticum, has been regarded as a single species ranging from Guatemala to Mexico, but it includes two deeply ergent barcode lineages, one a possible new endemic species. Aside from these special cases, the results confirm that DNA barcodes will be highly effective in discriminating freshwater fishes from Central America and that a comprehensive analysis will provide new important insights for understanding ersity of this fauna.
Publisher: Springer Science and Business Media LLC
Date: 02-2000
DOI: 10.1046/J.1365-2540.2000.00661.X
Abstract: Genome and body sizes were measured in 38 species of turbellarian flatworms and 16 species of copepod crustaceans. Significant positive relationships existed between genome size and body size in both groups. The slopes of these regressions indicated that increases in cell volume are reinforced by increased cell numbers, or that cell volumes show positive allometric variation with genome size. Genome sizes appear to vary in a discontinuous fashion among congeneric species in both groups, indicating that such changes have occurred rapidly, and with potentially profound effects on important morphological characters.
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Paul Hebert.