ORCID Profile
0000-0002-5448-3226
Current Organisations
Chicago Botanic Garden
,
South Australian Museum
,
St. Cloud State University
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Publisher: Australian Museum
Date: 25-11-2020
Publisher: Cold Spring Harbor Laboratory
Date: 20-02-2021
DOI: 10.1101/2021.02.20.432097
Abstract: Oenothera sect. Calylophus is a North American group of 13 recognized taxa in the evening primrose family (Onagraceae) with an evolutionary history that may include independent origins of bee pollination, edaphic endemism, and permanent translocation heterozygosity. Like other groups that radiated relatively recently and rapidly, taxon boundaries within Oenothera sect. Calylophus have remained challenging to circumscribe. In this study, we used target enrichment, flanking non-coding regions, summary coalescent methods, tests for gene flow modified for target-enrichment data, and morphometric analysis to reconstruct phylogenetic hypotheses, evaluate current taxon circumscriptions, and examine character evolution in Oenothera sect. Calylophus . Because sect. Calylophus comprises a clade with a relatively restricted geographic range, we were able to extensively s le across the range of geographic and morphological ersity in the group. We found that the combination of exons and flanking non-coding regions led to improved support for species relationships. We reconstructed potential hybrid origins of some accessions and note that if processes such as hybridization are not taken into account, the number of inferred evolutionary transitions may be artificially inflated. We recovered strong evidence for multiple origins of the evolution of bee pollination from ancestral hawkmoth pollination, the evolution of edaphic specialization on gypsum, and permanent translocation heterozygosity. This study applies newly emerging techniques alongside dense infraspecific s ling and morphological analyses to effectively address a relatively common but recalcitrant problem in evolutionary biology.
Publisher: Cold Spring Harbor Laboratory
Date: 04-03-2020
DOI: 10.1101/2020.03.03.971721
Abstract: Amphibian genomes are usually challenging to assemble due to large genome size and high repeat content. The Limnodynastidae is a family of frogs native to Australia, Tasmania and New Guinea. As an anuran lineage that successfully ersified on the Australian continent, it represents an important lineage in the hibian tree of life but lacks reference genomes. Here we sequenced and annotated the genome of the eastern banjo frog Limnodynastes dumerilii dumerilii to fill this gap. The total length of the genome assembly is 2.38 Gb with a scaffold N50 of 285.9 kb. We identified 1.21 Gb of non-redundant sequences as repetitive elements and annotated 24,548 protein-coding genes in the assembly. BUSCO assessment indicated that more than 94% of the expected vertebrate genes were present in the genome assembly and the gene set. We anticipate that this annotated genome assembly will advance the future study of anuran phylogeny and hibian genome evolution.
Publisher: Wiley
Date: 18-03-2010
DOI: 10.1111/J.1558-5646.2010.00993.X
Abstract: Late Neogene aridification in the Southern Hemisphere caused contractions of mesic biota to refugia, similar to the patterns established by glaciation in the Northern Hemisphere, but these episodes also opened up new adaptive zones that spurred range expansion and ersification in arid-adapted lineages. To understand these dynamics, we present a multilocus (nine nuclear introns, one mitochondrial gene) phylogeographic analysis of the Bynoe's gecko (Heteronotia binoei), a widely distributed complex spanning the tropical monsoon, coastal woodland, and arid zone biomes in Australia. Bayesian phylogenetic analyses, estimates of ergence times, and demographic inferences revealed episodes of ersification in the Pliocene, especially in the tropical monsoon biome, and range expansions in the Pleistocene. Ancestral habitat reconstructions strongly support recent and independent invasions into the arid zone. Our study demonstrates the varied responses to aridification in Australia, including localized persistence of lineages in the tropical monsoonal biome, and repeated invasion of and expansion through newly available arid-zone habitats. These patterns are consistent with those found in other arid environments in the Southern Hemisphere, including the South African succulent karoo and the Chilean lowlands, and highlight the erse modes of ersification and persistence of Earth's biota during the glacial cycles of the Pliocene and Pleistocene.
Publisher: Wiley
Date: 08-03-2012
Publisher: CSIRO Publishing
Date: 2004
DOI: 10.1071/ZO04045
Abstract: Blindsnakes (Typhlopidae) represent one of the least known elements of the Australian herpetofauna. Mitochondrial DNA sequence data and morphology are used here to show that a widespread species of Australian blindsnake, R hotyphlops australis, comprises two distinct species. R hotyphlops bicolor (new combination) is resurrected from synonymy with R. australis and redescriptions are provided for both species. Mitochondrial DNA sequence variation within R. australis indicates that the central and south-coast populations are more closely related to each other than either is to the morphologically distinctive populations at the northern edge of the species' range. Observed levels of differentiation suggest historical isolation of populations from the Kalbarri/Shark Bay region of the western Australian coastline. However, lack of concordance between mitochondrial haplotype phylogeny and morphology for several in iduals might reflect limited gene flow between the northern and south–central populations. We note that many taxa show restricted distributions or range disjunctions along the central Western Australian coastal margin, and we discuss possible models to explain population fragmentation in this region. Pliocene–Pleistocene sea-level fluctuations along the western Australian coast could have isolated sand plain communities in the Kalbarri/Shark Bay region from similar communities further south near Geraldton, possibly underlying the phylogeographic pattern in R. australis. Data from additional taxa will be needed to fully evaluate this hypothesis.
Publisher: Oxford University Press (OUP)
Date: 14-11-2017
Abstract: The geographic origin and migration of the brown rat (Rattus norvegicus) remain subjects of considerable debate. In this study, we sequenced whole genomes of 110 wild brown rats with a erse world-wide representation. We reveal that brown rats migrated out of southern East Asia, rather than northern Asia as formerly suggested, into the Middle East and then to Europe and Africa, thousands of years ago. Comparison of genomes from different geographical populations reveals that many genes involved in the immune system experienced positive selection in the wild brown rat.
Publisher: Magnolia Press
Date: 09-06-2014
DOI: 10.11646/ZOOTAXA.3814.2.4
Abstract: The taxonomy of central Australian populations of geckos of the genus Gehyra has been uncertain since chromosomal studies carried out in the 1970s and 1980s revealed considerable heterogeneity and apparently independent patterns of morphological and karyotypic ersity. Following detailed molecular genetic studies, species boundaries in this complex have become clearer and we here re-set the boundaries of the three named species involved, G. variegata (Duméril & Bibron, 1836), G. montium Storr, 1982, and G. nana King, 1982, and describe three new species. Two of the new species, G. moritzi and G. pulingka, include populations formerly assigned to either G. montium or G. nana Storr, 1982, while the third, G. versicolor, includes all of the eastern Australian populations formerly assigned to G. variegata.
Publisher: CSIRO Publishing
Date: 2016
DOI: 10.1071/ZO16038
Abstract: The distribution and taxonomy of varanid lizards occurring in the Bismarck Archipelago is revised on the basis of field surveys, examination of museum vouchers and molecular phylogenetic analyses. A total of four species is recorded: Varanus indicus and Varanus finschi on New Britain and some of its offshore islands, Varanus douarrha on New Ireland, Lavongai and Djaul, and Varanus semotus on Mussau Island. V. douarrha, previously mistaken for both V. indicus and V. finschi, is shown to be the only species represented on New Ireland and is here resurrected as a valid taxon based on an integrated approach combining morphological and molecular evidence. Phylogenetic analyses of two mitochondrial genes suggest that V. indicus is a relatively recent immigrant to the Bismarck Islands, whereas V. douarrha, V. finschi and V. semotus have significantly longer histories in the island group. Together with the recently described V. semotus the revalidation of V. douarrha doubles the number of species known to occur in the Bismarck region and highlights an important component of both local and regional endemism.
Publisher: CSIRO Publishing
Date: 2016
DOI: 10.1071/MF15044
Abstract: Population structure in marine teleosts is often investigated to aid conservation and fisheries management (e.g. to assess population structure to inform restocking programs). We assessed genetic population structure of the important estuary-associated marine fish, mulloway (Argyrosomus japonicus), within Australian waters and between Australia and South Africa. Genetic variation was investigated at 13 polymorphic microsatellite markers. FST values and Bayesian estimates in STRUCTURE suggested population differentiation of mulloway within Australia and confirm strong differentiation between South Africa and Australia. The 12 Australian s le sets fell into one of four spatially separated genetic clusters. Initially, a significant signal of isolation-by-distance (IBD) was evident among Australian populations. However, further investigation by decomposed-pairwise-regression (DPR) suggested five s le sets were influenced more by genetic-drift, rather than gene-flow and drift equilibrium, as expected in strong IBD cases. Cryptic oceanographic and topographical influences may isolate mulloway populations from south-western Australia. The results demonstrate that DPR is suitable to assess population structure of coastal marine species where barriers to gene flow may be less obvious than in freshwater systems. Information on the relative strengths of gene flow and genetic drift facilitates a more comprehensive understanding of the evolutionary forces that lead to population structure, which in turn informs fisheries and assists conservation management. Large-bodied predatory scale-fish may be under increasing pressure on a global scale, owing to a variety of anthropogenic reasons. In southern Australia, the iconic sciaenid A. japonicus (mulloway, jewfish or kob) is no exception. Despite the species supporting important fisheries, much of its ecology is poorly understood. It is possible that a greater understanding of their genetic population structure can help ensure a sustainable future for the only southern Australian sciaenid.
Publisher: Wiley
Date: 19-03-2015
DOI: 10.1111/CLA.12118
Publisher: Magnolia Press
Date: 20-09-2017
DOI: 10.11646/ZOOTAXA.4323.1.1
Abstract: The blindsnake genus Anilios (formerly R hotyphlops) is the largest and most erse genus of snakes in Australia with 45 currently recognized species. Recent molecular genetic studies of the genus have identified high levels of cryptic ersity within many taxa, suggesting true species ersity is greatly underestimated. Anilios leptosoma is a slender blindsnake endemic to the mid-west of Western Australia. Although morphological variation has been identified within the species in the past, the systematics and true ersity remained unstudied. Here we use recent molecular data to guide a reappraisal of morphology in order to provide a taxonomic revision of the A. leptosoma species complex. We redescribe A. leptosoma and describe two new species that occur to the south of most of true A. leptosoma’s distribution: A. systenos sp. nov. and A. obtusifrons sp. nov. Anilios systenos sp. nov. is known from the Geraldton region with the furthest record only 100 km to the north-east, a very small range for a species of snake. Anilios obtusifrons sp. nov. has an even smaller distribution, as it is only known from a small coastal area south of Kalbarri and may represent a range-restricted taxa. All species are genetically ergent from each other and can be distinguished by consistent morphological characteristics, including the shape of the snout, the termination point of the rostral cleft and number of mid-body scale rows and ventral scales.
Publisher: Oxford University Press (OUP)
Date: 12-2008
Publisher: Wiley
Date: 07-2002
Publisher: Informa UK Limited
Date: 1998
Publisher: The Royal Society
Date: 03-05-2017
Abstract: Genetic ersity is a fundamental characteristic of species and is affected by many factors, including mutation rate, population size, life history and demography. To better understand the processes that influence levels of genetic ersity across taxa, we collected genome-wide restriction-associated DNA data from more than 500 in iduals spanning 76 nominal species of Australian scincid lizards in the genus Ctenotus . To avoid potential biases associated with variation in taxonomic practice across the group, we used coalescent-based species delimitation to delineate 83 species-level lineages within the genus for downstream analyses. We then used these genetic data to infer levels of within-population genetic ersity. Using a phylogenetically informed approach, we tested whether variation in genetic ersity could be explained by population size, environmental heterogeneity or historical demography. We find that the strongest predictor of genetic ersity is a novel proxy for census population size: the number of vouchered occurrences in museum databases. However, museum occurrences only explain a limited proportion of the variance in genetic ersity, suggesting that genetic ersity might be difficult to predict at shallower phylogenetic scales.
Publisher: The Royal Society
Date: 29-07-2008
Abstract: Speciation, despite ongoing gene flow can be studied directly in nature in ring species that comprise two reproductively isolated populations connected by a chain or ring of intergrading populations. We applied three tiers of spatio-temporal analysis (phylogeny/historical biogeography, phylogeography and landscape opulation genetics) to the data from mitochondrial and nuclear genomes of eastern Australian parrots of the Crimson Rosella Platycercus elegans complex to understand the history and present genetic structure of the ring they have long been considered to form. A ring speciation hypothesis does not explain the patterns we have observed in our data (e.g. multiple genetic discontinuities, discordance in genotypic and phenotypic assignments where terminal differentiates meet). However, we cannot reject that a continuous circular distribution has been involved in the group's history or indeed that one was formed through secondary contact at the ‘ring's’ east and west however, we reject a simple ring-species hypothesis as traditionally applied, with secondary contact only at its east. We discuss alternative models involving historical allopatry of populations. We suggest that population expansion shown by population genetics parameters in one of these isolates was accompanied by geographical range expansion, secondary contact and hybridization on the eastern and western sides of the ring. Pleistocene landscape and sea-level and habitat changes then established the birds' current distributions and range disjunctions. Populations now show idiosyncratic patterns of selection and drift. We suggest that selection and drift now drive evolution in different populations within what has been considered the ring.
Publisher: CSIRO Publishing
Date: 2015
DOI: 10.1071/MF14102
Abstract: Restriction to the freshwater environment plays a dominant role in the population genetic structure of freshwater fauna. In taxa with adaptations for terrestriality, however, the restrictions on dispersal imposed by drainage ides may be overcome. We investigate the mitochondrial phylogeographic structure of the eastern long-necked turtle (Chelodina longicollis), a widespread Australian freshwater obligate with strong overland dispersa\\l capacity and specific adaptations to terrestriality. We predict that such characteristics make this freshwater species a strong candidate to test how life-history traits can drive gene flow and interbasin connectivity, overriding the constraining effects imposed by hydrological boundaries. Contrary to expectations, and similar to low-vagility freshwater vertebrates, we found two ancient mitochondrial haplogroups with clear east–west geographic partitioning either side of the Great Dividing Range. Each haplogroup is characterised by complex genetic structure, demographically stable subpopulations, and signals of isolation by distance. This pattern is overlaid with signatures of recent gene flow, likely facilitated by late Pleistocene and ongoing anthropogenic landscape change. We demonstrate that the ergent effects of landscape history can overwhelm the homogenising effects of life-history traits that connect populations, even in a highly vagile species.
Publisher: Australian Museum
Date: 25-11-2020
Publisher: Wiley
Date: 10-2008
Publisher: Wiley
Date: 20-09-2019
DOI: 10.1111/JBI.13698
Publisher: Oxford University Press (OUP)
Date: 04-02-2008
Publisher: Wiley
Date: 25-11-2017
Abstract: High-throughput sequencing methods promise to improve our ability to infer the evolutionary histories of lineages and to delimit species. These are exciting prospects for the study of Australian vertebrates, a group comprised of many globally unique lineages with a long history of isolation. The evolutionary relationships within many of these lineages have been difficult to resolve with small numbers of loci, and we now know that many lineages also exhibit substantial cryptic ersity. Here, we present a set of phylogenetically erse transcriptome resources to enable exon-based sequence capture studies of Australian vertebrates, including transcriptome sequences for four species of birds, four frogs, seven lizards and seven mammals. We also use exon data from the marsupial transcriptomes we generated to examine an approach for choosing a moderate number (dozens or hundreds) of phylogenetically informative exons based on a single transcriptome sequence, and a relatively distant reference genome.
Publisher: CSIRO Publishing
Date: 1990
DOI: 10.1071/ZO9900535
Abstract: The phylogenetic relationships of the Australian scincid lizards currently assigned to the genus Leiolopisma have been examined by quantitative micro-complement fixation (MC'F) comparisons of serum albumin. The results of these comparisons do not support the monophyly implicit in these species' current congeneric status, but suggest instead that the Australian species of Leiolopisma belong to several distinct phyletic lineages within the Eugongylus group. These findings are supported by several sets of non-biochemical characters, including features of scalation, osteology and karyotype. None of the Australian species shares a close relationship with the type-species of Leiolopisrna (L. telfairii), and so a new taxonomic arrangement is proposed which distributes them among the following genera: Bartleia, gen. nov. (jigurru) Bassiana, gen. nov. (duperreyi, platynotum and trilineata) Cautula, gen. nov. (zia) Niveoscincus, gen. nov. (coventryi, greeni, metallicus, microlepidotus, ocellatus, orocryptus, palfreymani and pretiosus) and Pseudemoia Fuhn, 1967 (baudini, entrecasteauxii Group 1 entrecasteauxii Group 2, rawlinsoni and spenceri). Preliminary comparisons suggest that other Leiolopisma species, from New Caledonia, Lord Howe I. and New Zealand, belong to phyletic lineages which are distinct from any of the Australian 'Leiolopisma' and from the type-species.
Publisher: Oxford University Press (OUP)
Date: 20-04-2012
Abstract: Presence/absence patterns of retroposon insertions at orthologous genomic loci constitute straightforward markers for phylogenetic or population genetic studies. In birds, the convenient identification and utility of these markers has so far been mainly restricted to the lineages leading to model birds (i.e., chicken and zebra finch). We present an easy-to-use, rapid, and cost-effective method for the experimental isolation of chicken repeat 1 (CR1) insertions from virtually any bird genome and potentially nonavian genomes. The application of our method to the little grebe genome yielded insertions belonging to new CR1 subfamilies that are scattered all across the phylogenetic tree of avian CR1s. Furthermore, presence/absence analysis of these insertions provides the first retroposon evidence grouping flamingos + grebes as Mirandornithes and several markers for all subsequent branching events within grebes (Podicipediformes). Five markers appear to be species-specific insertions, including the hitherto first evidence in birds for biallelic CR1 insertions that could be useful in future population genetic studies.
Publisher: Magnolia Press
Date: 11-01-2023
DOI: 10.11646/ZOOTAXA.5228.1.1
Abstract: In south-eastern Australia, the pelodryadid Litoria aurea Group (sensu Tyler & Davies 1978) comprises three species: Litoria aurea (Lesson, 1829), Litoria raniformis (Keferstein, 1867), and Litoria castanea (Steindachner, 1867). All three species have been subject to declines over recent decades and taxonomic uncertainty persists among populations on the tablelands in New South Wales. We address the systematics of the Group by analysing mitochondrial and nuclear DNA sequences to assess ergence in the Litoria raniformis from across its current range in New South Wales (NSW), Victoria, South Australia (SA) and Tasmania. We also included s les of Litoria castanea from a recently rediscovered population in the southern tablelands of NSW. Our phylogenetic and population genetic analyses show that Litoria raniformis comprises northern and southern lineages, showing deep mitochondrial DNA sequence ergence (7% net average sequence ergence) and can be diagnosed by fixed allelic differences at more than 4,000 SNP loci. S les of the northern lineage were collected from the Murray-Darling Basin while those of the southern lineage were collected from south-eastern South Australia, southern and south-eastern Victoria and Tasmania. Analysis of the morphology and bioacoustics did not unequivocally delineate the two lineages. The presence of a hybrid backcross in idual in western Victoria at the northern margin of the southern lineage, leads us to assign sub-species status to the two lineages, L. r. raniformis for the northern lineage and L. r. major for the southern lineage. Our data do not unequivocally resolve the taxonomic status of L. castanea which will require molecular genetic analyses of museum vouchers from those parts of the range where L. castanea and L. raniformis are no longer extant. Our data also suggest that human mediated movement of frogs may have occurred over the past 50 years. Our genotyping of vouchers collected in the 1970s from the Mount Lofty Ranges in South Australia detected mitochondrial haplotypes of both sub-species and SNP analysis showed that a single Tasmanian specimen was a backcross with L. r. raniformis ancestry. Movement of L. r. raniformis into Tasmania and both sub-species into the Mount Lofty Ranges are not likely due to passive movements of animals through agricultural commerce, but due to the attractiveness of the species as pets and subsequent escapes or releases, potentially of the larval life stage.
Publisher: Elsevier BV
Date: 2008
DOI: 10.1016/J.GENE.2007.10.008
Abstract: Although recent mammalian genome projects have uncovered a large part of genomic component of various groups, several repetitive sequences still remain to be characterized and classified for particular groups. The short interspersed repetitive elements (SINEs) distributed among marsupial genomes are one ex le. We have identified and characterized two new SINEs from marsupial genomes that belong to the CORE-SINE family, characterized by a highly conserved "CORE" domain. PCR and genomic dot blot analyses revealed that the distribution of each SINE shows distinct patterns among the marsupial genomes, implying different timing of their retroposition during the evolution of marsupials. The members of Mar3 (Marsupialia 3) SINE are distributed throughout the genomes of all marsupials, whereas the Mac1 (Macropodoidea 1) SINE is distributed specifically in the genomes of kangaroos. Sequence alignment of the Mar3 SINEs revealed that they can be further ided into four subgroups, each of which has diagnostic nucleotides. The insertion patterns of each SINE at particular genomic loci, together with the distribution patterns of each SINE, suggest that the Mar3 SINEs have intensively lified after the radiation of diprotodontians, whereas the Mac1 SINE has lified only slightly after the ergence of hypsiprimnodons from other macropods. By compiling the information of CORE-SINEs characterized to date, we propose a comprehensive picture of how SINE evolution occurred in the genomes of marsupials.
Publisher: Wiley
Date: 09-05-2005
Publisher: CSIRO Publishing
Date: 2006
DOI: 10.1071/ZO05038
Abstract: To date no complete phylogeny of all of the currently recognised Indo-Australian varanid species and subspecies has been published. This paper presents a comprehensive mitochondrial gene phylogeny of these lizards. A portion of the mitochondrial genome comprising part of the ND4 gene and three adjacent tRNA genes (hereafter referred to as ND4) was analysed alone and, for a subset of the taxa, combined with previously published mitochondrial data. Similar tree topologies were produced by both datasets although combining the data helped resolve some of the unresolved or weakly supported nodes in the ND4 analyses. The monophyly of the Indo-Australian group was strongly supported in all analyses. This group comprised three major lineages: the gouldii group, the Odatria group and the varius group. Mitochondrial ND4 nucleotide sequences were successfully lified from all of the Indo-Australian monitor species and subspecies currently recognised and, as such, is the first comprehensive phylogenetic study of the Australian monitor lizards published. Analysis of the tempo of ersification and evolution of preferred habitat use identified six episodes of increased net speciation rate, with two closely adjacent episodes showing the highest rates of ersification and correlating with the appearance of all preferred habitat types. The comprehensive molecular phylogenetic framework will also be useful for the identification of varanid species and traded products derived from monitors and, as such, has important applications for wildlife management and conservation.
Publisher: Elsevier BV
Date: 11-2009
DOI: 10.1016/J.YMPEV.2009.06.020
Abstract: Australian scincid lizards in the genus Ctenotus constitute the most erse vertebrate radiation in Australia. However, the evolutionary processes that have generated this ersity remain elusive, in part because both interspecific phylogenetic relationships and phylogeographic structure within Ctenotus species remain poorly known. Here we use nucleotide sequences from a mitochondrial locus and two nuclear introns to investigate broad-scale phylogeographic patterns within Ctenotus leonhardii and C. quattuordecimlineatus, two geographically widespread species of skinks that were found to have a surprisingly close genetic relationship in a previous molecular phylogenetic study. We demonstrate that the apparent close relationship between these ecologically and phenotypically distinct taxa is attributable to mitochondrial introgression from C. quattuordecimlineatus to C. leonhardii. In the western deserts, Ctenotus leonhardii in iduals carry mtDNA lineages that are derived from C. quattuordecimlineatus mtDNA lineages from that geographic region. Coalescent simulations indicate that this pattern is unlikely to have resulted from incomplete lineage sorting, implicating introgressive hybridization as the cause of this regional gene-tree discordance.
Publisher: Wiley
Date: 09-1995
Publisher: Public Library of Science (PLoS)
Date: 11-05-2015
Publisher: Public Library of Science (PLoS)
Date: 02-11-2011
Publisher: Informa UK Limited
Date: 2006
Publisher: Wiley
Date: 12-07-2011
Publisher: Elsevier BV
Date: 11-2005
DOI: 10.1016/J.YMPEV.2005.06.020
Abstract: A phylogenetic analysis of mitochondrial ND4 and adjacent tRNA sequences for a geographically extensive series of specimens reveals nine major clades within Pseudonaja, of which six are largely coincident with nominal taxa (P. affinis, P. guttata, P. inframacula, P. ingrami, P. modesta, and P. textilis). The remaining three clades are composed of specimens presently referred to P. nuchalis. Two of these clades correspond with the "Darwin" and "Southern" morphs of previous authors, while the third clade incorporates the "Orange with black head" and "Pale head, grey nape" morphs. We are unable to confirm the presence of consistent karyotypic differences between "Orange with black head" and "Pale head, grey nape" specimens, however, P. inframacula, P. textilis, and P. nuchalis "Darwin" are found to exhibit distinctive karyotypes, as previously reported. These results, in conjunction with additional observations of karyotpic and morphological variation, are consistent with nine historically-independent lineages (i.e., species) within Pseudonaja. There is strong support for a clade composed of P. affinis, P. inframacula, P. ingrami, P. textilis, and the three P. nuchalis lineages, and for the relationships (P. inframacula, P. nuchalis "Southern") and (P. nuchalis "Darwin", P. nuchalis "Orange with black head"--"Pale head, grey nape" ).
Publisher: CSIRO Publishing
Date: 2016
DOI: 10.1071/ZO16014
Abstract: Using 454 pyrosequencing and genomic enrichment techniques we developed 12 polymorphic markers for the endangered megapode, the malleefowl (Leipoa ocellata). Pyrosequencing on a 454 instrument resulted in 65 536 reads, with 3469 containing microsatellite repeats. Of these, 232 contained unique flanking sequences and had more than 8 repeat motifs. We chose 13 loci based on reliability of lification and, from these, 12 unlinked loci were selected for genotyping. In a single population (n = 19), the 12 markers were moderately polymorphic (number of alleles per locus range = 3–7) and showed moderate to high levels of heterozygosity (0.285–0.882). Nine microsatellite primer pairs developed from the brush turkey (Alectura lathami), the closest living relative of the malleefowl in the family, Megapodiidae, failed to reliably lify malleefowl DNA.
Publisher: Magnolia Press
Date: 06-07-2015
DOI: 10.11646/ZOOTAXA.3981.3.3
Abstract: The Magpie Fiddler ray, Trygonorrhina melaleuca Scott 1954, is presently South Australia's (SA) rarest fish, represented by only three museum specimens collected near Adelaide over the past 60 years and listed as Endangered in the IUCN Red List of Threatened Species. However, there is some doubt as to whether the Magpie Fiddler Ray is a different species from the widespread and common Southern Fiddler Ray, Trygonorrhina dumerilii (Castelnau 1873), resulting in two very contrasting scenarios for marine conservation. If the Magpie Fiddler Ray is a black and white patterned variant of the Southern Fiddler Ray then it will be removed from the Red List and appear as a synonym of T. dumerilii. Conversely, if it proves to be a different species then it remains SA's rarest fish species and highly data deficient. We analysed mtDNA and the largest ever nuclear gene dataset ( ,000 loci) applied to chondrichthyan species level systematics from the most recently collected Magpie Fiddler Ray specimens and a geographically representative selection of Southern Fiddler Rays to determine the species status of this enigmatic ray. We found that the Magpie Fiddler Rays share a mitochondrial haplotype with 23 Southern Fiddler Rays and are not differentiated from 35 Southern Fiddler Rays at more than 4000 SNPs derived from DArTseq data. The morphological trait values that are putatively diagnostic for the Magpie Fiddler Ray fall within the range of variation observed among Southern Fiddler Rays. Our analyses are consistent with the notion that the Magpie Fiddler Ray is a rare colour and pattern variant of the widespread and abundant Southern Fiddler Ray. We also identified two hybrids between the Eastern and Southern Fiddler Rays, only the third time that hybrids have been identified in nature in chondrichthyans. Our results provide critical guidance in the assessment of its conservation status and an ending to a 60 year old conundrum for marine conservation.
Publisher: Pensoft Publishers
Date: 23-02-2016
Publisher: The Royal Society
Date: 31-03-2010
Abstract: Worm-like snakes (scolecophidians) are small, burrowing species with reduced vision. Although largely neglected in vertebrate research, knowledge of their biogeographical history is crucial for evaluating hypotheses of snake origins. We constructed a molecular dataset for scolecophidians with detailed s ling within the largest family, Typhlopidae (blindsnakes). Our results demonstrate that scolecophidians have had a long Gondwanan history, and that their initial ersification followed a vicariant event: the separation of East and West Gondwana approximately 150 Ma. We find that the earliest blindsnake lineages, representing two new families described here, were distributed on the palaeolandmass of India+Madagascar named here as Indigascar. Their later evolution out of Indigascar involved vicariance and several oceanic dispersal events, including a westward transatlantic one, unexpected for burrowing animals. The exceptional ersification of scolecophidians in the Cenozoic was probably linked to a parallel radiation of prey (ants and termites) as well as increased isolation of populations facilitated by their fossorial habits.
Publisher: Magnolia Press
Date: 26-10-2021
DOI: 10.11646/ZOOTAXA.5057.4.1
Abstract: The hip-pocket frog (Assa darlingtoni), a small terrestrial myobatrachid frog found in mid-eastern Australia, has a highly derived, unusual, reproductive mode involving a unique form of male parental care. Males have subcutaneous pouches that open near the hip, and the developing tadpoles are carried in these pouches to post metamorphosis. It is found on several isolated mountain ranges in closed forest habitats, associated with high rainfall and temperate or sub-tropical climates. We established genetic relationships among specimens s led across the range using phylogenetic analyses of thousands of single nucleotide polymorphisms (SNPs) from the nuclear genome and mitochondrial ND2 gene nucleotide sequences. These analyses uncovered two lineages that are genetically distinct in both nDNA and mtDNA analyses and that have low levels of ergence in male advertisement calls and are morphologically cryptic. Our data support separate species status for each lineage, based on the molecular genetic data. The first, which we name as a new species, Assa wollumbin sp. nov., is restricted to a single mountain, Wollumbin (= Mount Warning), the eroded cone of an ancient shield volcano—the Tweed Volcano. The second, the nominal species A. darlingtoni, has a wider distribution in five geographically disjunct subpopulations along 430 km of the Great Dividing Range in south-eastern Queensland and north-eastern New South Wales. The distributions of the two species closely approach within 15 km of each other on the central plug and rim of the caldera of the Tweed Volcano. Assa wollumbin sp. nov. meets the conservation criteria for Critically Endangered [A3(e), B2(a,b)]. When all subpopulations of A. darlingtoni are combined the conservation assessment is Endangered [A3(e), B2(a,b)]. Because of the fragmented nature of the distribution of A. darlingtoni, combined with the genetic evidence of concordant sub-structuring, we also conducted a conservation assessment on the five subpopulations. Two were assessed as Critically Endangered (D’Aguilar Range and Conondale/Blackall Ranges), and the remainder as Endangered (Dorrigo Plateau, McPherson Ranges, and Gibraltar Ranges/Washpool).
Publisher: Wiley
Date: 16-02-2018
DOI: 10.1111/CONL.12438
Publisher: Cold Spring Harbor Laboratory
Date: 30-03-2019
DOI: 10.1101/593699
Abstract: Polyploidy has played an important role in evolution across the tree of life but it is still unclear how polyploid lineages may persist after their initial formation. While both common and well-studied in plants, polyploidy is rare in animals and generally less well-understood. The Australian burrowing frog genus Neobatrachus is comprised of six diploid and three polyploid species and offers a powerful animal polyploid model system. We generated exome-capture sequence data from 87 in iduals representing all nine species of Neobatrachus to investigate species-level relationships, the origin and inheritance mode of polyploid species, and the population genomic effects of polyploidy on genus-wide demography. We resolve the phylogenetic relationships among Neobatrachus species and provide further support that the three polyploid species have independent autotetraploid origins. We document higher genetic ersity in tetraploids, resulting from widespread gene flow specifically between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and current isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate variation on frogs with differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which in turn corresponds to population genomic estimates of demographic histories. We propose that Neobatrachus diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow into tetraploid lineages specifically. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on the evolution of adaptation in animals.
Publisher: Magnolia Press
Date: 21-06-2016
DOI: 10.11646/ZOOTAXA.4126.4.1
Abstract: The water-holding frog, Cyclorana platycephala, occurs in the Australian arid and semi-arid zones but not in the central Australian deserts. Recent inspection of morphological variation in adults and larvae suggests that the taxon comprises three regional populations: eastern, northern and western that may each represent separate species. To assess the systematic status of these populations, we documented phylogenetic relationships using mitochondrial and nuclear DNA markers, ergence in adult and larval morphology and male advertisement call. Our molecular genetic data demonstrates that the western population of C. platycephala is not the sister taxon of eastern and northern representatives of this nominate species, as the latter two are more closely related to another morphologically distinct species, C. verrucosa. Discriminant Function Analysis of 14 morphological traits in adults and 15 in larvae showed a high degree of morphological differentiation of western versus eastern/northern C. platycephala. Calls of eastern and western populations differed in duration, pulse rate, frequency and especially in litude modulation pattern across the call duration. We describe the western population as a new species, whose range is contained entirely within Western Australia. In addition, we redescribe Cyclorana platycephala, quantify morphological and genetic differences between the eastern and northern populations, and conclude that these data support recognition of a single species, Cyclorana platycephala, for populations found in New South Wales, the Barkly Tablelands and south-eastern Northern Territory, Queensland and South Australia.
Publisher: University of Chicago Press
Date: 09-2005
DOI: 10.1086/432152
Abstract: Most frog species show little resistance to evaporative water loss (EWL), but some arboreal species are known to have very high resistances. We measured EWL and cutaneous resistance to evaporation (Rc) in 25 species of frogs from northern Australia, including 17 species in the family Hylidae, six species in the Myobatrachidae, and one each in the Bufonidae and the Microhylidae. These species display a variety of ecological habits, including aquatic, terrestrial, and arboreal specialisations, with the complete range of habits displayed within just the one hylid genus, Litoria. The 25 species measured in this study have resistances that range from Rc=0 to 63.1. These include low values indistinguishable from a free water surface to high values typical of "waterproof" anuran species. There was a strong correlation between ecological habit and Rc, even taking phylogenetic relationships into account arboreal species had the highest resistance, aquatic species tended to have little or no resistance, and terrestrial species tended to have resistance between those of arboreal and aquatic frogs. For one species, Litoria rubella, we found no significant changes in EWL along a 1,500-km aridity gradient. This study represents the strongest evidence to date of a link between ecological habits and cutaneous resistance to water loss among species of frogs.
Publisher: Elsevier BV
Date: 04-2009
Publisher: Cold Spring Harbor Laboratory
Date: 05-10-2023
Publisher: Wiley
Date: 17-07-2006
DOI: 10.1111/J.1742-4658.2006.05358.X
Abstract: Five healthy adult female first-generation hybrid tree frogs were produced by interspecific breeding of closely related tree frogs Litoria splendida and L. caerulea in a cage containing large numbers of males and females of both species. Phylogenetic analysis of mitochondrial DNA sequences established the female parent to be L. splendida. The peptide profile of the hybrid frogs included the neuropeptide caerulein, four antibiotics of the caerin 1 family and several neuronal nitric oxide synthase inhibitors of the caerin 1 and 2 classes of peptides. The skin secretions of the hybrids contained some peptides common to only one parent, some produced by both parental species, and four peptides expressed by the hybrids but not the parental species.
Publisher: Oxford University Press (OUP)
Date: 25-10-2016
Abstract: The leafy seadragon (Phycodurus eques, Syngnathidae), is a charismatic endemic of Australia’s temperate coast. The species exhibits remarkable camouflage in its kelp and seagrass habitat. These habitats have been retreating throughout the range of the species, leading to concerns about the persistence of leafy seadragons. Despite being a popular aquarium display and a flagship for coastal conservation, little is known about leafy seadragon biology. We used 7 microsatellite markers and 2 mitochondrial DNA fragments to investigate the population structuring and genetic ersity of 71 in iduals. Bayesian cluster analysis identified 2 main genetic partitions, one in Western Australia and the other in South Australia. Shallower, yet significant, differentiation of mitochondrial DNA (φST) and microsatellites (FST, F′ST, D) was found on the smaller geographic scales in South Australia. Distinct groups were supported in Encounter Bay, on both shores of Gulf St Vincent, and in Spencer Gulf. S le sizes were too small in the eastern Great Australian Bight and in the westernmost locality to address genetic differentiation in these regions. Overall genetic ersity was moderate to low, but particularly low levels were found in the Western Australian cluster. This latter point needs confirmation at other sites in Western Australia. In South Australia, signatures of demographic changes were detected, which may have been caused by a population expansion due to post-glacial reflooding of the gulfs. The Western Australian and South Australian clusters appeared as demographically independent units. Conservation actions should focus on preserving genetic ersity at local scales and maintaining habitat connectivity.
Publisher: Wiley
Date: 04-2022
DOI: 10.1002/AJB2.1827
Abstract: Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree of gene-tree discordance in Solanum, one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants. A densely s led species-level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.) and nine regions (ITS, waxy, and seven plastid markers). The robustness of this topology is tested by examining a full plastome dataset with 140 species and a nuclear target-capture dataset with 39 species of Solanum (Angiosperms353 probe set). While the taxonomic framework of Solanum remained stable, gene tree conflicts and discordance between phylogenetic trees generated from the target-capture and plastome datasets were observed. The latter correspond to regions with short internodal branches, and network analysis and polytomy tests suggest the backbone is composed of three polytomies found at different evolutionary depths. The strongest area of discordance, near the crown node of Solanum, could potentially represent a hard polytomy. We argue that incomplete lineage sorting due to rapid ersification is the most likely cause for these polytomies, and that embracing the uncertainty that underlies them is crucial to understand the evolution of large and rapidly radiating lineages.
Publisher: Wiley
Date: 27-12-2012
Publisher: CSIRO Publishing
Date: 2000
DOI: 10.1071/ZO98015
Abstract: An allozyme electrophoretic analysis of the geographically widespread, southern Australian gekkonid lizard Christinus marmoratus demonstrates the presence of a hithertofore unsuspected, second species of Christinus. The second species, which was found to be syntopic with the 2n = 36 ‘race’ of C. marmoratus on the south-western side of the Nullarbor Plain, is strikingly cryptic and possesses a very similar 2n =36 karyotype. Small but consistent morphological differences between the two species allow their wider distributions to be mapped in detail. As the holotype of Phyllodactylus m. alexanderi Storr is identified as an ex le of the second species, Storr’s taxon is elevated to a full species and redefined. The geographic pattern of genetic variation within C. marmoratus crosses the distribution of the four recorded chromosome ‘races’. Reanalysis of previously reported reproductive data reveals likely differences in the timing of gametogenesis between C. alexanderi and the sympatric 2n = 36 C. marmoratus. Males of C. alexanderi show maximal testicular enlargement approximately six months before fertilisation, suggestive of oviducal sperm storage through winter, whereas the 2n = 36 C. marmoratus shows greatest testicular volumes at the presumed time of fertilisation. While females of both taxa carry eggs during September–October C. marmoratus invariably carry two eggs, but C. alexanderi have a single egg in 36% of cases.
Publisher: Elsevier BV
Date: 09-2009
DOI: 10.1016/J.YMPEV.2009.05.008
Abstract: The morphological based taxonomy of highly derived parasite groups is likely to poorly reflect their evolutionary relationships. The taxonomy of the monogenean family Capsalidae, which comprises approximately 180 species of flatworm parasites that predominantly attach to external surfaces of chondrichthyan and teleost fishes, is based mainly on six morphological characters. The phylogenetic history of the family is largely unknown. We reconstructed the phylogenetic relationships of 47 species in 20 genera from eight of the nine subfamilies, from nucleotide sequences of three unlinked nuclear genes, 28S ribosomal RNA, Histone 3 and Elongation Factor 1 alpha. Our phylogeny was well corroborated, with 75% of branches receiving strong support from both Bayesian posterior probabilities and maximum likelihood bootstrap proportions and all nodes showed positive partitioned likelihood support for each of the three genes. We found that the family was monophyletic, with the Gyrodactylidae and Udonellidae forming the sister group. The Capsalinae was monophyletic, however, our data do not support monophyly for the Benedeniinae, Entobdellinae and Trochopodinae. Monophyly was supported for Capsala, Entobdella, Listrocephalos, Neobenedenia and Tristoma, but Benedenia and Neoentobdella were polyphyletic. Comparisons of the distribution of character states for the small number of morphological characters on the molecular phylogeny show a high frequency of apparent homoplasy. Consequently the current morphological classification shows little correspondence with the phylogenetic relationships within the family.
Publisher: Walter de Gruyter GmbH
Date: 2013
DOI: 10.2478/S11686-013-0186-Y
Abstract: Dicyemid mesozoan parasites, microscopic organisms found with high intensities in the renal appendages of benthic cephalopods, have a complex, partially unknown life cycle. It is uncertain at which host life cycle stage (i.e. eggs, juvenile, adult) new infection by the dispersive infusoriform embryo occurs. As adult cephalopods have a short lifespan and die shortly after reproducing only once, and juveniles are fast-moving, we hypothesize that the eggs are the life cycle stage where new infection occurs. Eggs are abundant and sessile, allowing a huge number of new in iduals to be infected with low energy costs, and they also provide dicyemids with the maximum amount of time for survival compared with infection of juvenile and adult stages. In our study we collected giant Australian cuttlefish (Sepia apama) eggs at different stages of development and filtered seawater s les from the S. apama mass breeding aggregation area in South Australia, Australia, and tested these s les for the presence of dicyemid DNA. We did not recover dicyemid parasite cytochrome c oxidase subunit I (COI) nucleotide sequences from any of the s les, suggesting eggs are not the stage where new infection occurs. To resolve this unknown in the dicyemid life cycle, we believe experimental infection is needed.
Publisher: Magnolia Press
Date: 02-06-2023
DOI: 10.11646/ZOOTAXA.5297.3.1
Abstract: Mixophyes are large ground-dwelling myobatrachid frogs from eastern Australia and New Guinea. Several of the species found in mid-eastern and south-eastern Australia are listed as threatened, due largely to declines presumably caused by the hibian disease chytridiomycosis. Given the wide distribution of several of these species and that their distributions cross well-known biogeographic boundaries that often correspond to deep genetic breaks or species boundaries among closely related vertebrates, we undertook a molecular genetic assessment of population structure across the range of each species to determine the presence of undescribed species. Of the four species of Mixophyes subject to molecular population genetic analyses, one, the Stuttering Frog (Mixophyes balbus), showed a level of ersity consistent with the presence of two species. Morphometric, meristic and bioacoustic analyses corroborate these distinctions, and a new species is described for the populations south of the Macleay River valley in mid-eastern New South Wales to east Gippsland in Victoria. Applying the IUCN Red List threat criteria the new species meets the conservation status assessment criteria for Endangered 2B1a,b because its extent of occupancy and area of occupancy are below the threshold value and it has declined and disappeared from the southern two thirds of its distribution over the past 30 years.
Publisher: Magnolia Press
Date: 27-04-2023
DOI: 10.11646/ZOOTAXA.5271.3.3
Abstract: We describe two new species of moderate-sized (male body length 26.5–29.8 mm and 41.0 mm), predominantly green treefrogs in the genus Litoria from hill forest on the northern slopes of Papua New Guinea’s Central Cordillera. Phylogenetic analysis of mitochondrial ND4 nucleotide sequences shows that the first species is related to Litoria iris (Tyler) and its allies. It is morphologically most similar to Litoria mystax, a small green treefrog known only from the holotype that was described more than 100 years ago from the north coast of western New Guinea but differs from that species in having longer legs and a broader head. The second species is closest to Litoria gasconi, a species known only from the foothills of the Foja Mountains in Papua Province, Indonesian New Guinea, and the Prince Alexander Mountains in northern Papua New Guinea. It has a net average sequence ergence of 10% from L. gasconi and can be distinguished morphologically from it and from other pelodryadids by the presence of a striking pattern of spots and blotches on the ventral surfaces and on the hidden surfaces of the limbs. These descriptions add to the rapidly increasing known ersity of frogs in hill and lower montane forest, habitats that support the most erse frog communities on mainland New Guinea.
Publisher: Wiley
Date: 2009
Publisher: Oxford University Press (OUP)
Date: 21-02-2013
Abstract: The Australian numbat, Myrmecobius fasciatus, is the only marsupial that feeds almost exclusively on termites and that has a life following the diurnally restricted and dynamic geographical distribution of termites. The millions of years of this adaptation led to unique morphological and anatomical features, especially basicranial and dental characteristics, that make it difficult to identify a clear phylogenetic affiliation to other marsupials. From DNA sequence analyses, the family Myrmecobiidae is placed within the dasyuromorph marsupials, but the exact position varies from study to study, and support values are mostly rather modest. Here, we report the recovery and analysis of approximately 110,000 quasifossilized traces of mobile element insertions into the genome of a dasyurid marsupial (Tasmanian devil), 25 of which are phylogenetically informative for early dasyuromorphial evolution. Fourteen of these ancient retroposon insertions are shared by the 16 Dasyuromorphia species analyzed, including the numbat, but are absent in the outgroups. An additional 11 other insertions are present in all Dasyuridae but are absent in the numbat. These findings place numbats as the sister group to all living Dasyuridae and show that the investigated Dasyuromorphia, including the Myrmecobiidae, constitutes a monophyletic group that is separated from Peramelemorphia, Notoryctemorphia, and other marsupials.
Publisher: Wiley
Date: 26-12-2014
DOI: 10.1111/SYEN.12051
Publisher: Elsevier BV
Date: 12-2011
Publisher: The Royal Society
Date: 18-09-2007
Abstract: The disparity in species richness among groups of organisms is one of the most pervasive features of life on earth. A number of studies have addressed this pattern across higher taxa (e.g. ‘beetles’), but we know much less about the generality and causal basis of the variation in ersity within evolutionary radiations at lower taxonomic scales. Here, we address the causes of variation in species richness among major lineages of Australia's most erse vertebrate radiation, a clade of at least 232 species of scincid lizards. We use new mitochondrial and nuclear intron DNA sequences to test the extent of ersification rate variation in this group. We present an improved likelihood-based method for estimating per-lineage ersification rates from combined phylogenetic and taxonomic (species richness) data, and use the method in a hypothesis-testing framework to localize ersification rate shifts on phylogenetic trees. We soundly reject homogeneity of ersification rates among members of this radiation, and find evidence for a dramatic rate increase in the common ancestor of the genera Ctenotus and Lerista . Our results suggest that the evolution of traits associated with climate tolerance may have had a role in shaping patterns of ersity in this group.
Publisher: Magnolia Press
Date: 05-04-2023
DOI: 10.11646/ZOOTAXA.5263.2.1
Abstract: New Guinea has the most erse insular frog fauna in the world, and rates of species discovery and description have increased rapidly in the last two decades. Pelodryadid treefrogs are the second most erse family of anurans on the island but their taxonomy, relationships, and especially ecology remain poorly documented. Based on differences in morphology, advertisement calls (where available) and phylogenetic analyses of a 787 base pair alignment from the mitochondrial ND4 gene and flanking tRNA, we describe five new species of small treefrogs from hill and lower montane forests in the high rainfall belt that straddles the southern versant of Papua New Guinea’s Central Cordillera. Three of these species are known only from forest growing on karst substrates, adding to the growing number of herpetofauna species currently known only from the extensive karst habitats of Papua New Guinea’s South-fold Mountains. We also describe the arboreal breeding strategies of two of the new species, and report obligate treehole (phytotelm) breeding in New Guinean frogs for the first time. The new phytotelm–breeding species has juveniles with colour and patterning that closely resemble bird droppings, suggesting defensive mimicry or masquerade. A preliminary phylogeny suggests that arboreal-breeding frogs do not form a monophyletic group and that arboreal breeding has evolved multiple times within the New Guinean pelodryadid radiation. A further striking feature of the phylogeny is poor support for most basal nodes in the most erse radiation of Melanesian Pelodryadidae, suggesting rapid ecological ersification and speciation, potentially following colonisation from Australia and/or mountain uplift. These new taxa and observations highlight previously unrecognised ecological and reproductive ersity in the Melanesian Pelodryadidae.
Publisher: Elsevier BV
Date: 09-2010
DOI: 10.1016/J.IJPARA.2010.02.017
Abstract: Relationships between the three classes of Neodermata (parasitic Platyhelminthes) are much debated and restrict our understanding of the evolution of parasitism and contingent adaptations. The historic view of a sister relationship between Cestoda and Monogenea (Cercomeromorphae larvae bearing posterior hooks) has been dismissed and the weight of evidence against monogenean monophyly has mounted. We present the nucleotide sequence of the complete mitochondrial (mt) genome of Benedenia seriolae (Monogenea: Monopisthocotylea: Capsalidae), the first complete non-gyrodactylid monopisthocotylean mt genome to be reported. We also include nucleotide sequence data for some mt protein coding genes for a second capsalid, Neobenedenia sp. Analyses of the new mt genomes with all available platyhelminth mt genomes provide new phylogenetic hypotheses, which strongly influence perspectives on the evolution of diet in the Neodermata. Our analyses do not support monogenean monophyly but confirm that the Digenea and Cestoda are each monophyletic and sister groups. Epithelial feeding monopisthocotyleans on fish hosts are basal in the Neodermata and represent the first shift to parasitism from free-living ancestors. The next evolutionary step in parasitism was a dietary change from epithelium to blood. The common ancestor of Digenea+Cestoda was monogenean-like and most likely sanguinivorous. From this ancestral condition, adult digeneans and cestodes independently evolved dietary specialisations to suit their erse microhabitats in their final vertebrate hosts. These improved perspectives on relationships fundamentally enhance our understanding of the evolution of parasitism in the Neodermata and in particular, the evolution of diet.
Publisher: CSIRO Publishing
Date: 1990
DOI: 10.1071/ZO9900033
Abstract: The standard and C-banded (four species) karyotypes of six species of the family Petauridae (Gymnobelideus leadbeateri, Petaurus australis, P. breviceps, P. norfolcensis, Dactylopsila trivirgata and Dactylonax palpator) are described. The G-banded karyotype of P. norfolcensis is also described. Gymnobelideus and Petaurus have diploid chromosome number of 22. All three species of Petaurus have a similar karyotype, consisting of biarmed autosomes and very small sex chromosomes, which differs from Gymnobelideus by a minimum of one chromosomal rearrangement of each autosome. Dactylopsila and Dactylonax have similar karyotypes with diploid chromosome numbers of 18. The relationship of these two genera to Petaurus is still uncertain but all members of this family differ from Pseudocheiridae in the small size of the sex chromosomes.
Publisher: Magnolia Press
Date: 30-09-2020
DOI: 10.11646/ZOOTAXA.4858.2.3
Abstract: Population declines and range contractions among Australian frogs that commenced in the early 1980s continue in some species that were once widespread. The generality of this pattern has been difficult to discern, especially for those species that are encountered rarely because they have restricted periods of calling activity with poorly defined habitat preferences, and are not common. Several lines of evidence indicate that Litoria littlejohni is such a species. This frog was once known from mid-eastern New South Wales to eastern Victoria, and evidence from wildlife atlas databases and targeted searches indicate that it has declined in large portions of its former range, leaving several populations that are isolated, in some cases restricted in distribution, and of small size. We investigated the relationships among populations using mitochondrial ND4 nucleotide sequences and single nucleotide polymorphisms (SNPs) from the nuclear genome. We found that northern and southern populations form two highly ergent genetic groups whose distributions abut at the southern margin of the Sydney Basin Bioregion and these genetic groups also show ergence in morphology and male advertisement calls. Here we describe the populations to the south of the Sydney Basin Bioregion as a new species and provide information on its distribution and ecology. In light of the apparent isolation and small size of known populations of the new species and the consequent restriction of the range of L. littlejohni, we assessed the conservation status of both species.
Publisher: CSIRO Publishing
Date: 2004
DOI: 10.1071/ZO02069
Abstract: Allozyme variation at 36 loci was screened in 179 in iduals of the Litoria lesueuri species group from 33 locations from across the species' range in eastern Australia. We identified three genetic groups, with discrete and disjunct distributions, that we consider to be separate species. The northernmost group, L.�jungguy, sp. nov., had a distinctive standard and C-band karyotype, while the karyotypes of the two southern groups, L. lesueuri (Duméril & Bibron, 1841) and L. wilcoxii Gunther, 1864, differed only in minor details of their C-band patterns. Stepwise discriminant function analysis of morphometric variation among 13 meristic variables was able to discriminate L. lesueuri and L. wilcoxii in 100% of cases but discrimination between L. wilcoxii and L. jungguy was less successful, with 75% and 56% of each group respectively being correctly classified. Locations with inter-group hybrids were identified in the Australian Capital Territory, mid-east Queensland and two localities in far north Queensland. However, each of the groups has a large geographic range within which there was relative allozyme and karyotype uniformity. On the basis of the genetic data, each group is herein elevated to species status. Existing types were assigned to their respective genetic groups on the basis of a discriminant function analysis. Formal taxonomic accounts are provided. The closely related L. booroolongensis (Moore, 1961), sole member of the L.�booroolongensis species group, differed allozymically from all three species of the L. lesueuri species group but only from the northern species in its karyotype. Small genetic distances between L.�booroolongensis and members of the L. lesueuri species group indicate a close relationship for the two species groups.
Publisher: Wiley
Date: 28-08-2012
DOI: 10.1002/ECE3.352
Publisher: Elsevier BV
Date: 07-2013
DOI: 10.1016/J.YMPEV.2013.03.007
Abstract: Recent conceptual and methodological advances have increased the ability to apply multifaceted approaches to species delimitation, which is particularly useful in delimiting recently ersified species where single lines of evidence lead to incorrect species delimitation or assignment of in iduals to species (e.g. cryptic, morphological species and paraphyletic, hybridizing species). Species of the Australian Gehyra gecko radiation have historically proven difficult to delimit due the group's uniform, almost continent-wide geographic distribution and conservative morphology, contrasting high chromosomal and genetic ersity. Using an integrated approach to species delimitation taking advantage of morphological, geographic distributional and multi-locus genetic data, we investigate the ersity within three Gehyra species from the Australian arid zone. Our results show that these species represent eight distinct phylogenetic lineages, which display different patterns of morphological distinction and reproductive isolation. Using a recently developed Bayesian species delimitation method, we also find different levels of support for putative species dependent on priors for population size and timing of ersification assumed. Our results show that the current taxonomy does not adequately account for the ersity of the group. Discrepancies between lines of evidence indicate that ersification of the group is recent and ongoing, thus posing challenges for both species concepts and delimitation.
Publisher: Oxford University Press (OUP)
Date: 18-05-2022
Publisher: Wiley
Date: 10-2009
Publisher: Springer Science and Business Media LLC
Date: 13-07-2012
Publisher: Elsevier BV
Date: 08-1998
Abstract: Phylogenetic relationships among the venomous Australo-Papuan elapid snake radiation remain poorly resolved, despite the application of erse data sets. To examine phylogenetic relationships among this enigmatic group, portions of the cytochrome b and 16S rRNA mitochondrial DNA genes were sequenced from 19 of the 20 terrestrial Australian genera and 6 of the 7 terrestrial Melanesian genera, plus a sea krait (Laticauda) and a true sea snake (Hydrelaps). These data clarify several significant issues in elapid phylogeny. First, Melanesian elapids form sister groups to Australian species, indicating that the ancestors of the Australian radiation came via Asia, rather than representing a relict Gondwanan radiation. Second, the two major groups of sea snakes (sea kraits and true sea snakes) represent independent invasions of the marine environment. Third, the radiation of viviparous Australian elapids is much older than has been suggested from immunological data. Parsimony analyses were unable to resolve relationships among the Australian radiation, a problem previously encountered with analyses of other (morphological, electrophoretic, karyotypic, immunological) data sets on these species. These data suggest that the reason for this continued difficulty lies in the timing of speciation events: the elapids apparently underwent a spectacular adaptive radiation soon after reaching Australia, such that ergences are ancient even within genera. Indeed, intrageneric ergences are almost as large as intergeneric ergences. Although this timing means that our sequence data cannot fully resolve phylogenetic relationships among the Australian elapids, the data suggest a close relationship of the following clades: Pseudonaja with Oxyuranus Ogmodon with Toxicocalamus Demansia with Aspidomorphus Echiopsis with Denisonia the "Notechis" lineage with Drysdalia coronoides and Rhinoplocephalus and Suta with Drysdalia coronata. At least two of the Australian genera (Drysdalia and Simoselaps) appear to be paraphyletic. These sequence data support many of the conclusions reached by earlier studies using other types of data, but additional information will be needed before the phylogeny of the Australian elapids can be fully resolved.
Publisher: Elsevier BV
Date: 10-1998
Abstract: Phylogenetic reconstruction in molecular systematics has largely been achieved using mitochondrial gene sequences and less frequently sequences of nuclear ribosomal RNA genes. At present few other nuclear genes have been identified that could be used to test these phylogenies. C-mos, a single-copy nuclear oncogene, has been identified as a candidate nuclear marker. Data are presented on the usefulness of c-mos sequences in the phylogenetic analysis of squamate reptile families. We obtained partial sequences of c-mos from 13 squamate reptile families and outgroup representatives from the orders Rhynchocephalia, Chelonia, and Crocodylia. Phylogenetic analysis reveals a high degree of phylogenetic information contained within the sequence for both the synonymous and nonsynonymous substitutions. Phylogenetic resolution was present at both the deepest and shallower ergences but relationships among the major squamate lineages were not resolved, possibly because rapid cladogenesis may have led to the ersification of these lineages.
Publisher: Elsevier BV
Date: 04-2003
DOI: 10.1016/S1055-7903(02)00396-2
Abstract: Green pythons, which are regionally variable in colour patterns, are found throughout the lowland rainforest of New Guinea and adjacent far northeastern Australia. The species is popular in commercial trade and management of this trade and its impacts on natural populations could be assisted by molecular identification tools. We used mitochondrial nucleotide sequences and a limited allozyme data to test whether significantly differentiated populations occur within the species range. Phylogenetic analysis of mtDNA sequences revealed hierarchal phylogeographic structure both within New Guinea and between New Guinea and Australia. Strongly supported reciprocally monophyletic mitochondrial lineages, northern and southern, were found either side of the central mountain range that runs nearly the length of New Guinea. Limited allozyme data suggest that population differentiation is reflected in the nuclear as well as the mitochondrial genome. A previous morphological analysis did not find any phenotypic concordance with the pattern of differentiation observed in the molecular data. The southern mitochondrial lineage includes all of the Australian haplotypes, which form a single lineage, nested among the southern New Guinean haplotypes.
Publisher: Public Library of Science (PLoS)
Date: 17-03-2014
Publisher: Elsevier BV
Date: 06-2012
DOI: 10.1016/J.YMPEV.2012.03.003
Abstract: The Cotesia flavipes complex of parasitoid wasps (Hymenoptera: Braconidae) are economically important for the biological control of lepidopteran stemboring pests associated with gramineous crops. Some members of the complex successfully parasitize numerous stemborer pest species, however certain geographic populations have demonstrated variation in the range of hosts that they parasitize. In addition, the morphology of the complex is highly conserved and considerable confusion surrounds the identity of species and host-associated biotypes. We generated nucleotide sequence data for two mtDNA genes (COI, 16S) and three anonymous nuclear loci (CfBN, CfCN, CfEN) for the C. flavipes complex. To analyze genetic variation and relationships among populations we used (1) concatenated mtDNA and nDNA data, (2) a nDNA multilocus network approach, and (3) two species tree inference methods, i.e. Bayesian estimation of species trees (BEST) and Bayesian inference of species trees from multilocus data with (*)BEAST. All phylogenetic analyses provide strong support for monophyly of the complex and the presence of at least four species, C. chilonis (from China and Japan), C. sesamiae (from Africa), C. flavipes (originating from the Indo-Asia region but introduced into Africa and the New World), and C. nonagriae (from Australia and Papua New Guinea). Haplotype ersity of geographic populations relates to historical biogeographic barriers and biological control introductions, and reflects previous reports of ecological variation in these species. Strong discordance was found between the mitochondrial and nuclear markers in the Papua New Guinea haplotypes, which may be an outcome of hybridization and introgression of C. flavipes and C. nonagriae. The position of Cotesia flavipes from Japan was not well supported in any analysis and was the sister taxon to C. nonagriae (mtDNA, (*)BEAST), C. flavipes (nDNA) or C. flavipes+C. nonagriae (BEST) and, may represent a cryptic species. The concatenated five gene phylogenetic analyses did not support the overall separation and monophyly of clades associated with different host species, although some clades did show specific host associations, possibly due to localized host availability, rather than host specificity. Our results provide a framework for assessing whether distinct lineages represent cryptic species, and for examining parasitoid-host evolution and compatibility more generally. Given the limitations of morphological based identification for members of this complex, molecular identification is recommended prior to any biological control introductions.
Publisher: Elsevier BV
Date: 12-2016
Publisher: Wiley
Date: 03-10-2007
Publisher: The Royal Society
Date: 22-05-1991
Publisher: CSIRO Publishing
Date: 2011
DOI: 10.1071/ZO11062
Abstract: Of the three species of taipan, Oxyuranus temporalis is the least known, being described only recently from a single juvenile specimen. We redescribe the species based on additional adult specimens from the Great Victoria Desert. Molecular genetic variation between the three localities from which the species is known was low, suggesting a single widespread population or recent radiation. Limited analysis of faecal material and gut contents suggested solely mammalian prey. The additional specimens suggest the possibility of a considerable distribution across sandy deserts of the central and western interior of Australia. Further studies and fieldwork are required to more accurately determine its geographic range, quantify the toxicity of the venom and assess the suitability of available antivenoms.
Publisher: GigaScience Press
Date: 07-2020
DOI: 10.46471/GIGABYTE.2
Abstract: Amphibian genomes are usually challenging to assemble due to their large genome size and high repeat content. The Limnodynastidae is a family of frogs native to Australia, Tasmania and New Guinea. As an anuran lineage that successfully ersified on the Australian continent, it represents an important lineage in the hibian tree of life but lacks reference genomes. Here we sequenced and annotated the genome of the eastern banjo frog Limnodynastes dumerilii dumerilii to fill this gap. The total length of the genome assembly is 2.38 Gb with a scaffold N50 of 285.9 kb. We identified 1.21 Gb of non-redundant sequences as repetitive elements and annotated 24,548 protein-coding genes in the assembly. BUSCO assessment indicated that more than 94% of the expected vertebrate genes were present in the genome assembly and the gene set. We anticipate that this annotated genome assembly will advance the future study of anuran phylogeny and hibian genome evolution.
Publisher: Magnolia Press
Date: 22-11-2021
DOI: 10.11646/ZOOTAXA.5071.1.1
Abstract: The bleating tree frog (Litoria dentata) is one of the more prominent pelodryadid frogs of eastern Australia by virtue of its extremely loud, piercing, male advertisement call. A member of the Litoria rubella species group, L. dentata has a broad latitudinal distribution and is widespread from coastal and subcoastal lowlands through to montane areas. A recent mitochondrial DNA analysis showed a deep phylogeographic break between populations of L. dentata on the mid-north coast of New South Wales. Here we extended the mitochondrial survey with more geographically comprehensive s ling and tested the systematic implications of our findings with nuclear genome wide single-nucleotide polymorphism, morphological and male advertisement call datasets. While similar in appearance and in male advertisement call, our integrative analysis demonstrates the presence of three species which replace each other in a north-south series. We redescribe Litoria dentata, which is restricted to coastal north-eastern New South Wales, and formally describe Litoria balatus sp. nov., from south-eastern Queensland, and Litoria quiritatus sp. nov., from the mid-coast of New South Wales to north-eastern Victoria.
Publisher: Inter-Research Science Center
Date: 08-09-2016
DOI: 10.3354/MEPS11840
Publisher: Informa UK Limited
Date: 02-1992
Publisher: CSIRO Publishing
Date: 2004
DOI: 10.1071/ZO03030
Abstract: The genus Liasis comprises two groups of pythons, the olive python, Liasis olivaceus, and the water pythons L. fuscus and L. mackloti. We used partial mitochondrial control region DNA sequences to examine (a) the phylogeography of water pythons from five Indonesian Lesser Sunda islands, New Guinea, and northern Australia, (b) the relationships of the two subspecies of olive pythons, and (c) the relationship of the Papuan python, Apodora papuana, with the species of Liasis. Maximum likelihood, parsimony and distance analyses showed that A. papuana is the sister lineage to all Liasis and that Liasis fuscus/L. mackloti and L. olivaceus are separate lineages. There is also support for the reciprocal monophyly of the two olive python subspecies, L. olivaceus barroni and L. o. olivaceus, and for distinction of island populations described previously as L. mackloti dunni from Wetar and L. mackloti savuensis from Sawu. These two island populations are as equally distinct as the populations from the island cluster of Babar/Semau/Timor. There is strong support for the recognition of two lineages ('eastern' and 'western') of water pythons in Australia. We propose that the drier interior of the Plio-Pleistocene land bridge between Australia and New Guinea acted as a barrier to gene flow, influencing the genetic ergence between the 'eastern' and 'western' lineages of the semi-aquatic water pythons.
Publisher: Elsevier BV
Date: 08-2014
Publisher: Informa UK Limited
Date: 06-2009
DOI: 10.1071/MU07011
Publisher: Wiley
Date: 15-03-2007
Publisher: Wiley
Date: 24-01-2012
DOI: 10.1111/J.1420-9101.2012.02460.X
Abstract: Body size affects life history, the ecological niche of an organism and its interactions with other organisms. Resultantly, marked differences in body size between related organisms are often an indication of a species boundary. This is particularly evident in the Gehyra variegata species complex of geckos, which displays differential body sizes between genetically ergent species, but high levels of intraspecific morphological conservatism. We report on a Gehyra population that displays extraordinary body size differentiation in comparison with other G. variegata species. We used morphological and environmental data to show this population is phenotypically and ecologically distinct from its parapatric congener Gehyra lazelli and that morphology and ecology are significantly correlated. Contrastingly, mtDNA analysis indicates paraphyly between the two groups, and allele frequencies at six microsatellite loci show no population structure concordant with morpho-/ecotype. These results suggest either ecological speciation or environmentally induced phenotypic polymorphism, in an otherwise morphologically conservative group.
Publisher: Oxford University Press (OUP)
Date: 04-07-2013
DOI: 10.1111/BIJ.12132
Publisher: Elsevier BV
Date: 03-2018
Publisher: Springer Science and Business Media LLC
Date: 31-07-2008
Abstract: Understanding the dispersal and genetic structure of invasive insects across islands is important for designing management plans that are appropriate at spatial and temporal scales. For invasive parasites, population dynamics are largely determined by the distribution and density of their host species. The introduced parasitic fly, Philornis downsi , parasitises nestlings of endemic birds on all major islands of the Galápagos archipelago. The fly's high mortality and fitness impacts are of conservation concern for vulnerable and declining species of Darwin's finches. Using microsatellite data in Bayesian clustering and landscape genetic analyses, we examine gene flow and dispersal in P. downsi between three islands and across habitats (highlands, lowlands) and examine for the presence of population bottlenecks. We also examine variation at the mitochondrial gene CO1 across islands to establish if cryptic species were present. Both the mitochondrial and microsatellite data were consistent with there being a single species across islands. We found low genetic differentiation between islands and strong evidence for inter-island gene flow, or shared recent ancestry among in iduals. Landscape genetic analysis identified two genetic clusters: one encompassing Santa Cruz and Isabela, and one on Floreana Island. There was no evidence of genetic differentiation between habitats and molecular variance was mainly attributable to within in iduals. The combined P. downsi population was found to have undergone a population bottleneck. Philornis downsi populations have high connectivity within and between islands, with low levels of genetic differentiation between Floreana and the other two islands examined. The genetic bottleneck found across islands suggests there was a small founding population or few introduction events of P. downsi . The high dispersal capacity and wide habitat use of P. downsi highlights the significant threat that this parasite poses to the Galápagos avifauna. Our findings are relevant for assessing the viability of methods to control P. downsi on Galápagos, such as the sterile insect technique.
Publisher: Biology Centre, AS CR
Date: 06-08-2014
DOI: 10.14411/FP.2014.034
Publisher: Springer Science and Business Media LLC
Date: 12-06-2007
DOI: 10.1007/S00239-006-0083-1
Abstract: Maximum-likelihood models of codon and amino acid substitution were used to analyze the lung-specific surfactant protein C (SP-C) from terrestrial, semi-aquatic, and ing mammals to identify lineages and amino acid sites under positive selection. Site models used the nonsynonymous/synonymous rate ratio (omega) as an indicator of selection pressure. Mechanistic models used physicochemical distances between amino acid substitutions to specify nonsynonymous substitution rates. Site models strongly identified positive selection at different sites in the polar N-terminal extramembrane domain of SP-C in the three ing lineages: site 2 in the cetaceans (whales and dolphins), sites 7, 9, and 10 in the pinnipeds (seals and sea lions), and sites 2, 9, and 10 in the sirenians (dugongs and manatees). The only semi-aquatic contrast to indicate positive selection at site 10 was that including the polar bear, which had the largest body mass of the semi-aquatic species. Analysis of the biophysical properties that were influential in determining the amino acid substitutions showed that isoelectric point, chemical composition of the side chain, polarity, and hydrophobicity were the crucial determinants. Amino acid substitutions at these sites may lead to stronger binding of the N-terminal domain to the surfactant phospholipid film and to increased adsorption of the protein to the air-liquid interface. Both properties are advantageous for the repeated collapse and reinflation of the lung upon ing and resurfacing and may reflect adaptations to the high hydrostatic pressures experienced during ing.
Publisher: Springer Science and Business Media LLC
Date: 04-1991
DOI: 10.1007/BF00126228
Publisher: Wiley
Date: 23-11-2012
DOI: 10.1111/JBI.12045
Publisher: Springer Science and Business Media LLC
Date: 04-1991
DOI: 10.1007/BF00126227
Publisher: Wiley
Date: 05-2008
DOI: 10.1111/J.1471-8286.2007.02006.X
Abstract: We isolated 15 polymorphic microsatellite loci for the Baw Baw frog, Philoria frosti, from a genomic library enriched for (AAC)(n) and (AAAG)(n) repetitive elements. The number of alleles ranges from two to 14 per locus with the observed heterozygosity ranging from 0.04 to 0.96.
Publisher: Wiley
Date: 11-2003
DOI: 10.1111/J.0014-3820.2003.TB01504.X
Abstract: Molecular data derived from allozymes and mitochondrial nucleotide sequences, in combination with karyotypes, sex ratios, and inheritance data, have revealed the widespread Australian lizard Menetia greyii to be a complex of sexual and triploid unisexual taxa. Three sexual species, three presumed parthenogenetic lineages, and one animal of uncertain status were detected amongst 145 animals examined from south-central Australia, an area representing less than one-seventh of the total distribution of the complex. Parthenogenesis appears to have originated via interspecific hybridization, although presumed sexual ancestors could only be identified in two cases. The allozyme and mtDNA data reveal the presence of many distinct clones within the presumed parthenogenetic lineages. This new instance of vertebrate parthenogenesis is a first for the Scincidae and only the second definitive case of unisexuality in an indigenous Australian vertebrate.
Publisher: Springer Science and Business Media LLC
Date: 11-2003
Publisher: Springer Science and Business Media LLC
Date: 12-06-2014
DOI: 10.1007/S12024-014-9573-4
Abstract: In this paper we report on the identification of a section of mitochondrial DNA that can be used to identify the species of protected and illegally traded pythons of the genus Morelia. Successful enforcement of wildlife laws requires forensic tests that can identify the species nominated in the relevant legislation. The potentially degraded state of evidentiary s les requires that forensic investigation using molecular genetic species identification is optimized to interrogate small fragments of DNA. DNA was isolated from 35 s les of Morelia spilota from which the complete cytochrome b was sequenced. The ND6 gene was also sequenced in 32 of these s les. Additional DNA sequences were generated from 9 additional species of Morelia. The sequences were aligned by Geneious and imported into MEGA to create phylogenetic trees based on the entire complex of approximately 1,706 base pairs (bp). To mimic degraded DNA, which is usually found in forensic cases, short sub-sections of the full alignment were used to generate phylogenetic trees. The sub-sections that had the greatest DNA sequence information were in parts of the cytochrome b gene. Our results highlight that legislation is presently informed by inadequate taxonomy. We demonstrated that a 278 bp region of the cytochrome b gene recovered the topology of the phylogenetic tree found with the entire gene sequence and correctly identified species of Morelia with a high degree of confidence. The locus described in this report will assist in the successful prosecution of alleged illegal trade in python species.
Publisher: The Royal Society
Date: 18-07-2012
Abstract: Monitor lizards are emblematic reptiles that are widely distributed in the Old World. Although relatively well studied in vertebrate research, their biogeographic history is still controversial. We constructed a molecular dataset for 54 anguimorph species, including representatives of all families with detailed s ling of the Varanidae (38 species). Our results are consistent with an Asian origin of the Varanidae followed by a dispersal to Africa 41 (49–33) Ma, possibly via an Iranian route. Another major event was the dispersal of monitors to Australia in the Late Eocene–Oligocene 32 (39–26) Ma. This ergence estimate adds to the suggestion that Australia was colonized by several squamate lineages prior to the collision of the Australian plate with the Asian plate starting 25 Ma.
Publisher: Oxford University Press (OUP)
Date: 02-1993
Publisher: Wiley
Date: 16-02-2016
DOI: 10.1111/MEC.13511
Abstract: Multilocus phylogeography can uncover taxonomically unrecognized lineage ersity across complex biomes. The Australian monsoonal tropics include vast, ecologically intact savanna-woodland plains interspersed with ancient sandstone uplands. Although recognized in general for its high species richness and endemism, the bio ersity of the region remains underexplored due to its remoteness. This is despite a high rate of ongoing species discovery, especially in wetter regions and for rock-restricted taxa. To provide a baseline for ongoing comparative analyses, we tested for phylogeographic structure in an ecologically generalized and widespread taxon, the gecko Heteronotia binoei. We apply coalescent analyses to multilocus sequence data (mitochondrial DNA and eight nuclear DNA introns) from in iduals s led extensively and at fine scale across the region. The results demonstrate surprisingly deep and geographically nested lineage ersity. Several intra-specific clades previously shown to be endemic to the region were themselves found to contain multiple, short-range lineages. To infer landscapes with concentrations of unique phylogeographic ersity, we probabilistically estimate the ranges of lineages from point data and then, combining these estimates with the nDNA species tree, estimate phyloendemism across the region. Highest levels of phyloendemism occur in northern Top End, especially on islands, across the topographically complex Arnhem escarpment, and across the sandstone ranges of the western Gulf region. These results drive home that deep phylogeographic structure is prevalent in tropical low-dispersal taxa, even ones that are ubiquitous across geography and habitats.
Publisher: American Museum of Natural History (BioOne sponsored)
Date: 03-2006
Publisher: Elsevier BV
Date: 03-2006
DOI: 10.1016/J.YMPEV.2005.09.004
Abstract: Current knowledge of the evolutionary relationships amongst the wolf spiders (Araneae: Lycosidae) is based on assessment of morphological similarity or phylogenetic analysis of a small number of taxa. In order to enhance the current understanding of lycosid relationships, phylogenies of 70 lycosid species were reconstructed by parsimony and Bayesian methods using three molecular markers the mitochondrial genes 12S rRNA, NADH1, and the nuclear gene 28S rRNA. The resultant trees from the mitochondrial markers were used to assess the current taxonomic status of the Lycosidae and to assess the evolutionary history of sheet-web construction in the group. The results suggest that a number of genera are not monophyletic, including Lycosa, Arctosa, Alopecosa, and Artoria. At the subfamilial level, the status of Pardosinae needs to be re-assessed, and the position of a number of genera within their respective subfamilies is in doubt (e.g., Hippasa and Arctosa in Lycosinae and Xerolycosa, Aulonia and Hygrolycosa in Venoniinae). In addition, a major clade of strictly Australasian taxa may require the creation of a new subfamily. The analysis of sheet-web building in Lycosidae revealed that the interpretation of this trait as an ancestral state relies on two factors: (1) an asymmetrical model favoring the loss of sheet-webs and (2) that the suspended silken tube of Pirata is directly descended from sheet-web building. Paralogous copies of the nuclear 28S rRNA gene were sequenced, confounding the interpretation of the phylogenetic analysis and suggesting that a cautionary approach should be taken to the further use of this gene for lycosid phylogenetic analysis.
Publisher: Magnolia Press
Date: 09-08-2021
DOI: 10.11646/ZOOTAXA.5016.4.1
Abstract: The rarely encountered giant burrowing frog, Heleioporus australiacus, is distributed widely in a variety of sclerophyll forest habitats east of the Great Dividing Range in south-eastern Australia. Analyses of variation in nucleotide sequences of the mitochondrial ND4 gene and thousands of nuclear gene SNPs revealed the presence of two deeply ergent lineages. Multivariate morphological comparisons show the two lineages differ in body proportions with 91% of in iduals being correctly classified in DFA. The two lineages differ in the number and size of spots on the lateral surfaces and the degree by which the cloaca is surrounded by colour patches. The mating calls are significantly different in number of pulses in the note. The presence of a F2 hybrid in the area where the distribution of the two taxa come into closest proximity leads us to assign subspecies status to the lineages, as we have not been able to assess the extent of potential genetic introgression. In our s ling, the F2 hybrid s le sits within an otherwise uns led gap of ~90km between the distributions of the two lineages. The nominate northern sub-species is restricted to the Sydney Basin bioregion, while the newly recognised southern subspecies occurs from south of the Kangaroo Valley in the mid-southern coast of New South Wales to near Walhalla in central Gippsland in Victoria. The habitat of the two subspecies is remarkably similar. Adults spend large portions of their lives on the forest floor where they forage and burrow in a variety of vegetation communities. The southern subspecies occurs most commonly in dry sclerophyll forests with an open understory in the south and in open forest and heath communities with a dense understory in the north of its distribution. The northern subspecies is also found in dry open forests and heaths in association with eroded sandstone landscapes in the Sydney Basin bioregion. Males of both taxa call from both constructed burrows and open positions on small streams, differing from the five Western Australian species of Heleioporus where males call only from constructed burrows. Using the IUCN Red List process, we found that the extent of occupancy and area of occupancy along with evidence of decline for both subspecies are consistent with the criteria for Endangered (A2(c)B2(a)(b)).
Publisher: Oxford University Press (OUP)
Date: 11-03-2014
DOI: 10.1111/BIJ.12221
Publisher: CSIRO Publishing
Date: 1991
DOI: 10.1071/ZO9910387
Abstract: The potential value of rapid sequencing of the srRNA molecule for phylogenetic reconstruction of the higher vertebrates was investigated. The study involved partial sequencing of 19 taxa that, along with 6 sequences from the literature, covered all of the major groups of higher vertebrates. The results show that sequencing of the srRNA molecule is not suitable at this taxonomic level because: (i) there is insufficient nucleotide sequence variation (ii) expansion segments, although common, have a high probability of convergence for both their position and their sequence and (iii) the phylogenetic branching of the higher vertebrates has been mainly 'bush-like' rather than 'tree-like'.
Publisher: Wiley
Date: 07-02-2011
Publisher: Oxford University Press (OUP)
Date: 28-03-2014
Abstract: The correlation between species ersification and morphological evolution has long been of interest in evolutionary biology. We investigated the relationship between these processes during the radiation of 250+scincid lizards that constitute Australia's most species-rich clade of terrestrial vertebrates. We generated a time-calibrated phylogenetic tree for the group that was more than 85% complete at the species level and collected multivariate morphometric data for 183 species. We reconstructed the dynamics of species ersification and trait evolution using a Bayesian statistical framework (BAMM) that simultaneously accounts for variation in evolutionary rates through time and among lineages. We extended the BAMM model to accommodate time-dependent phenotypic evolution, and we describe several new methods for summarizing and visualizing macroevolutionary rate heterogeneity on phylogenetic trees. Two major clades (Lerista, Ctenotus >90 spp. each) are associated with high rates of species ersification relative to the background rate across Australian sphenomorphine skinks. The Lerista clade is characterized by relatively high lability of body form and has undergone repeated instances of limb reduction, but Ctenotus is characterized by an extreme deceleration in the rate of body shape evolution. We estimate that rates of phenotypic evolution decreased by more than an order of magnitude in the common ancestor of the Ctenotus clade. These results provide evidence for a modal shift in phenotypic evolutionary dynamics and demonstrate that major axes of morphological variation can be decoupled from species ersification. More generally, the Bayesian framework described here can be used to identify and characterize complex mixtures of dynamic processes on phylogenetic trees. [Bayesian ersification evolvability lizard macroevolution, punctuated equilibrium, speciation.].
Publisher: Society for the Study of Amphibians and Reptiles
Date: 06-2013
DOI: 10.1670/11-234
Publisher: Wiley
Date: 03-2017
DOI: 10.1111/J.1471-8286.2007.01987.X
Abstract: Despite long-term study, the mechanism explaining the parapatric distribution of two Australian reptile tick species is not understood. We describe the development of primers lifying 10 microsatellite Bothriocroton hydrosauri loci, for the study of population structure and dispersal patterns of this tick. The numbers of alleles per locus ranged from two to seven in ticks from the study site, and the observed heterozygosity between 0.28 and 0.69. Pedigree analysis indicates that one locus is inherited in a non-Mendelian manner in three families, which was not explained by null allele presence.
Publisher: Oxford University Press (OUP)
Date: 12-2003
Publisher: Wiley
Date: 11-2010
Publisher: Magnolia Press
Date: 02-10-2023
Publisher: The Royal Society
Date: 22-02-1995
Publisher: Springer Science and Business Media LLC
Date: 09-11-2014
Publisher: Elsevier BV
Date: 11-2008
DOI: 10.1016/J.REGPEP.2008.06.004
Abstract: The skin secretions of Crinia signifera, C. riparia and C. deserticola contain bioactive disulfide-containing peptides. Signiferin 1 (RLCIPYIIPC-OH) from C. signifera and C. deserticola) contracts smooth muscle at a concentration of 10(-9) M, and effects proliferation of lymphocytes at 10(-6) M. In contrast, riparin 1.1 (RLCIPVIFC-OH) and riparin 1.2 (FLPPCAYKGTC-OH) from C. riparia show lymphocyte activity but do not contract smooth muscle. The lymphocyte and smooth muscle activities involve CCK2R. 3D structures of signiferin 1 and riparin 1.1 have been established using 2D NMR methods: these studies show significant differences in the shapes of the disulfide rings and with the orientations of the N-terminal residues. cDNA cloning establishes that the pre sections of the precursor pre-pro-riparin 1.4-1.6 peptides are different from the conserved pre regions of disulfide-containing antimicrobial peptides from species of the genus Rana found in the northern hemisphere and caerin antimicrobial peptides isolated from Australian tree frogs of the genus Litoria. This suggests that (i) either that riparins 1 have converged to similar structure and function to the ranid and hyloid prepropeptides which were lost initially from the myobatrachid lineage, or (ii) the prepropeptides in all three groups were derived from a single ancestral form that has remained relatively conserved in the hyloid and ranoid lineages but has undergone substantial ergent evolution in the myobatrachids.
Publisher: Elsevier BV
Date: 08-2014
DOI: 10.1016/J.YMPEV.2014.03.026
Abstract: Scincid lizards in the genus Ctenotus represent one of Australia's most species-rich vertebrate clades, with more than 100 recognized species. Formal diagnoses of many species have relied on qualitative assessments of adult color pattern, but the validity of many such species has not been tested in a phylogenetic framework. We used mitochondrial and nuclear DNA to perform the first phylogenetic analysis of species in the Ctenotus inornatus group, a complex of at least 11 nominal forms that are distributed widely across the Australian continent. Mitochondrial and nuclear gene phylogenies support the presence of multiple species in the group, but these clades largely fail to match species boundaries as currently defined. Multivariate analyses of color pattern indicate that extreme intraspecific morphological variation in this character has created a significant impediment to understanding taxonomic ersity in the group. Our results suggest that nearly all species in the C. inornatus group require substantial taxonomic revision, and several geographically widespread forms ("C. saxatilis" and "C. robustus") appear to be polyphyletic taxa drawn from phenotypically similar but genetically distinct lineages. We describe one new species and provide redescriptions for three additional species. We synonymize names applied to a number of genetically incoherent or otherwise poorly-defined forms. The results of our study highlight an acute need for population genetic studies of species boundaries in Australian skinks, many of which are recognized by morphological traits that vary greatly within and between populations.
Publisher: Oxford University Press (OUP)
Date: 12-04-2016
Publisher: Cold Spring Harbor Laboratory
Date: 25-03-2021
DOI: 10.1101/2021.03.25.436973
Abstract: Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree of gene-tree discordance in Solanum, one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants. A densely s led species-level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.) and nine regions (ITS, waxy , and seven plastid markers). The robustness of this topology is tested by examining a full plastome dataset with 140 species and a nuclear target-capture dataset with 39 species of Solanum (Angiosperms353 probe set). While the taxonomic framework of Solanum remained stable, gene tree conflicts and discordance between phylogenetic trees generated from the target-capture and plastome datasets were observed. The latter correspond to regions with short internodal branches, and network analysis and polytomy tests suggest the backbone is composed of three polytomies found at different evolutionary depths. The strongest area of discordance, near the crown node of Solanum, could potentially represent a hard polytomy. We argue that incomplete lineage sorting due to rapid ersification is the most likely cause for these polytomies, and that embracing the uncertainty that underlies them is crucial to understand the evolution of large and rapidly radiating lineages.
Publisher: Oxford University Press (OUP)
Date: 30-05-2014
Abstract: Marsupials exhibit great ersity in ecology and morphology. However, compared with their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species. This tree allows us to analyze the evolution of habitat preference and geographic distributions of marsupial species through time. We found a pattern of mesic-adapted lineages evolving to use more arid and open habitats, which is broadly consistent with regional climate and environmental change. However, contrary to the general trend, several lineages subsequently appear to have reverted from drier to more mesic habitats. Biogeographic reconstructions suggest that current views on the connectivity between Australia and New Guinea/Wallacea during the Miocene and Pliocene need to be revised. The antiquity of several endemic New Guinean clades strongly suggests a substantially older period of connection stretching back to the Middle Miocene and implies that New Guinea was colonized by multiple clades almost immediately after its principal formation.
Publisher: Springer Science and Business Media LLC
Date: 12-2017
Publisher: Magnolia Press
Date: 19-02-2021
DOI: 10.11646/ZOOTAXA.4933.2.3
Abstract: We show that the Wotjulum frog, Litoria watjulumensis (Copland, 1957), comprises two deeply ergent mitochondrial DNA lineages that are also reciprocally monophyletic for a nuclear gene locus and have discrete distributions. The taxa are differentiated in multivariate analysis of shape but show no appreciable differences in colour and pattern. The two taxa differ substantially in the degree of female biased sexual size dimorphism, with the western taxon showing considerably more pronounced dimorphism. We subsequently resurrect Litoria (Hyla) spaldingi (Hosmer, 1964) for populations from east of the Daly River system in the Northern Territory through to western Queensland and restrict L. watjulumensis to populations from the Kimberley region of north-western Australia and the Victoria River system of the western Northern Territory. The complex advertisement call of L. spaldingi is described for the first time.
Publisher: Cambridge University Press (CUP)
Date: 16-04-2015
DOI: 10.1017/S0031182015000384
Abstract: Dicyemids, poorly known parasites of benthic cephalopods, are one of the few phyla in which mitochondrial (mt) genome architecture departs from the typical ~16 kb circular metazoan genome. In addition to a putative circular genome, a series of mt minicircles that each comprises the mt encoded units (I–III) of the cytochrome c oxidase complex have been reported. Whether the structure of the mt minicircles is a consistent feature among dicyemid species is unknown. Here we analyse the complete cytochrome c oxidase subunit I ( COI ) minicircle molecule, containing the COI gene and an associated non-coding region (NCR), for ten dicyemid species, allowing for first time comparisons between species of minicircle architecture, NCR function and inferences of minicircle replication. Divergence in COI nucleotide sequences between dicyemid species was high (average net ergence = 31·6%) while within species ersity was lower (average net ergence = 0·2%). The NCR and putative 5′ section of the COI gene were highly ergent between dicyemid species (average net nucleotide ergence of putative 5′ COI section = 61·1%). No tRNA genes were found in the NCR, although palindrome sequences with the potential to form stem-loop structures were identified in some species, which may play a role in transcription or other biological processes.
Publisher: Genetics Society of Japan
Date: 2006
DOI: 10.1266/GGS.81.181
Abstract: Australidelphia is the cohort, originally named by Szalay, of all Australian marsupials and the South American Dromiciops. A lot of mitochondria and nuclear genome studies support the hypothesis of a monophyly of Australidelphia, but some familial relationships in Australidelphia are still unclear. In particular, the familial relationships among the order Diprotodontia (koala, wombat, kangaroos and possums) are ambiguous. These Diprotodontian families are largely grouped into two suborders, Vombatiformes, which contains Phascolarctidae (koala) and Vombatidae (wombat), and Phalangerida, which contains Macropodidae, Potoroidae, Phalangeridae, Petauridae, Pseudocheiridae, Acrobatidae, Tarsipedidae and Burramyidae. Morphological evidence and some molecular analyses strongly support monophyly of the two families in Vombatiformes. The monophyly of Phalangerida as well as the phylogenetic relationships of families in Phalangerida remains uncertain, however, despite searches for morphological synapomorphy and mitochondrial DNA sequence analyses. Moreover, phylogenetic relationships among possum families (Phalangeridae, Petauridae, Pseudocheiridae, Acrobatidae, Tarsipedidae and Burramyidae) as well as a sister group of Macropodoidea (Macropodidae and Potoroidae) remain unclear. To evaluate familial relationships among Dromiciops and Australian marsupials as well as the familial relationships in Diprotodontia, we determined the complete mitochondrial sequence of six Diprotodontian species. We used Maximum Likelihood analyses with concatenated amino acid and codon sequences of 12 mitochondrial protein genomes. Our analysis of mitochondria amino acid sequence supports monophyly of Australian marsupials+Dromiciops and monophyly of Phalangerida. The close relatedness between Macropodidae and Phalangeridae is also weakly supported by our analysis.
Publisher: Elsevier BV
Date: 12-2015
Publisher: Elsevier BV
Date: 05-2015
DOI: 10.1016/J.FSIGEN.2014.12.002
Abstract: Python snake species are often encountered in illegal activities and the question of species identity can be pertinent to such criminal investigations. Morphological identification of species of pythons can be confounded by many issues and molecular examination by DNA analysis can provide an alternative and objective means of identification. Our paper reports on the development and validation of a PCR primer pair that lifies a segment of the mitochondrial cytochrome b gene that has been suggested previously as a good candidate locus for differentiating python species. We used this DNA region to perform species identification of pythons, even when the template DNA was of poor quality, as might be the case with forensic evidentiary items. Validation tests are presented to demonstrate the characteristics of the assay. Tests involved the cross-species lification of this marker in non-target species, minimum amount of DNA template required, effects of degradation on product lification and a blind trial to simulate a casework scenario that provided 100% correct identity. Our results demonstrate that this assay performs reliably and robustly on pythons and can be applied directly to forensic investigations where the presence of a species of python is in question.
Publisher: Magnolia Press
Date: 25-02-2022
DOI: 10.11646/ZOOTAXA.5104.2.3
Abstract: The six species of mountain frogs (Philoria: Limnodynastidae: Anura) are endemic to south-eastern Australia. Five species occur in headwater systems in mountainous north-eastern New South Wales (NSW) and south-eastern Queensland (Qld), centred on the Gondwana Rainforests of Australia World Heritage Area. A previous molecular genetic analysis identified ergent genetic lineages in the central and western McPherson Ranges region of Qld and NSW, but s ling was inadequate to test the species status of these lineages. With more comprehensive geographic s ling and examination of the nuclear genome using SNP analysis, we show that an undescribed species, P. knowlesi sp. nov., occurs in the central and western McPherson Ranges (Levers Plateau and Mount Barney complex). The new species is not phylogenetically closely related to P. loveridgei in the nuclear data but is related to one of two ergent lineages within P. loveridgei in the mtDNA data. We postulate that the discordance between the nuclear and mtDNA outcomes is due to ancient introgression of the mtDNA genome from P. loveridgei into the new species. Male advertisement calls and multivariate morphological analyses do not reliably distinguish P. knowlesi sp. nov. from any of the Philoria species in northeast NSW and southeast Qld. The genetic comparisons also enable us to define further the distributions of P. loveridgei and P. kundagungan. S les from the Lamington Plateau, Springbrook Plateau, Wollumbin (Mt Warning National Park), and the Nightcap Range, are all P. loveridgei, and its distribution is now defined as the eastern McPherson Ranges and Tweed caldera. Philoria kundagungan is distributed from the Mistake Mountains in south-eastern Qld to the Tooloom Scrub on the Koreelah Range, southwest of Woodenbong, in NSW, with two subpopulations identified by SNP analysis. We therefore assessed the IUCN threat category of P. loveridgei and P. kundagungan and undertook new assessments for each of its two subpopulations and for the new taxon P. knowlesi sp. nov., using IUCN Red List criteria. Philoria loveridgei, P. kundagungan (entire range and northern subpopulation separately) and P. knowlesi sp. nov. each meet criteria for “Endangered” (EN B2(a)(b)[i, iii]). The southern subpopulation of P. kundagungan, in the Koreelah Range, meets criteria for “Critically Endangered” (CE B2(a)(b)[i, iii]). These taxa are all highly threatened due to the small number of known locations, the restricted nature of their breeding habitat, and direct and indirect threats from climate change, and the potential impact of the hibian disease chytridiomycosis. Feral pigs are an emerging threat, with significant impacts now observed in Philoria breeding habitat in the Mistake Mountains.
Publisher: Elsevier BV
Date: 2011
DOI: 10.1016/J.PEPTIDES.2010.09.019
Abstract: Host defense peptides of 35 species of Australian frogs from the hylids Cyclorana and Litoria, and the myobatrachids Crinia, Limnodynastes and Uperoleia have been identified. The biological activities of the majority of these peptides have been determined and include hormones, neuropeptides, opioids, immunomodulators, membrane active peptides [including antimicrobial, anticancer, antiviral (enveloped viruses like HIV and Herpes) and antifungal peptides], neuronal nitric oxide synthase inhibitors, pheromones and in idual peptides with other specific activities. The host defense peptide skin profile can be diagnostic at both the species and higher taxonomic levels for ex le, species of Crinia, Litoria and Uperoleia each produce quite different types of peptides. Species of Cyclorana and Limnodynastes are more difficult to characterize by skin peptides alone: species of both genera produce similar peptides with no apparent activity. The skin peptide profiles of frogs from the genera Crinia, Litoria and Uperoleia may be used together with morphological and cognate methods, to differentiate between sub-species and even different population clusters of the same species. Nucleotide sequencing of cDNAs of precursors (pre-pro peptides) of bioactive peptides from the skin glands of various species of the genus Litoria show that the majority of these peptides originated from a single ancestor gene before the break away of Australia from Gondwana. The exceptions are the caerulein neuropeptides {e.g. caerulein [pEQDY(SO(3)H)TGWMDF(NH(2))]} which have a different origin to that of other Litoria peptides. Disulfide containing peptides from skin glands of species of Crinia show a different evolutionary route to peptides from species of Litoria.
Publisher: Informa UK Limited
Date: 31-01-2018
Publisher: Wiley
Date: 20-04-2009
DOI: 10.1111/J.1755-0998.2009.02572.X
Abstract: The New Holland honeyeater (Phylidonyris novaehollandiae) plays a significant role in the pollination and sustainability of Australia's endemic flora, and hence fauna. Despite this key ecosystem function, knowledge of P. novaehollandiae life-history traits and population dynamics remain poorly understood. We describe the development of primers lifying 22 P. novaehollandiae microsatellite loci. Fifteen of the loci were found to be polymorphic, with observed heterozygosity between 0.500 and 1.000, and from four to 17 alleles per locus in adult birds from the study site.
Publisher: Magnolia Press
Date: 22-08-2013
DOI: 10.11646/ZOOTAXA.3701.5.1
Abstract: We present an assessment of the systematic status of populations currently assigned to Eremiascincusfasciolatus across Australia using morphological data. Our analyses show that these populations actually comprise four species: a large and robust, narrow-banded taxon from eastern Queensland and three slender, desert-dwelling taxa from the western, northern, and south-eastern Australian arid zone respectively. These data necessitate: 1) the redescription of E.fasciolatus, a species endemic to the dry forests of eastern Queensland, 2) the resurrection of E. pallidus for the western taxon, 3) the resurrection of E. intermedius for the northern taxon, and 4) the description of the south-eastern desert-dwelling taxon, which largely occurs in the Lake Eyre Basin, as a new species. The new species, Eremiascincusphantasmus sp. nov., can be distinguished from congeners by its large size, pale color, depressed snout, and small circular ear opening, as well as by several scale characteristics. Body proportions, a depressed snout, small ear opening, and pale color suggest that this species is fossorial and predominantly occurs in habitats with loose substrate, such as dune systems and sandy plains. A synopsis of each species and a key to the narrow-banded species of Eremiascincus are provided.
Publisher: Oxford University Press (OUP)
Date: 20-04-2005
Abstract: Eucalyptus leucoxylon is a widespread woodland tree species found in southeastern Australia that has suffered from, and continues to be, threatened by the impacts of habitat clearance and degradation. Populations now consist predominantly of scattered in iduals, and their conservation status is of increasing concern. We report the development and characterization of a set of eight highly polymorphic microsatellite loci for E. leucoxylon. The loci can be lified in three PCR multiplexes and electrophoresed in a single lane, allowing rapid throughput of large numbers of s les. A total of 111 alleles were detected in 68 in iduals with an average of 12.3 alleles per locus, a mean expected heterozygosity of 0.83, and a mean observed heterozygosity of 0.72. The combined probabilities of identity and probabilities of paternity exclusion allow an extremely precise level of in idual identification, indicating that these microsatellite markers will be ideal for population genetic and parentage-type studies in E. leucoxylon. The markers also exhibited an average of 76% conservation within the subgenus Symphyomyrtus, to which E. leucoxylon belongs, and 53% conservation across other subgenera of Eucalyptus, demonstrating the potential of these markers in ecological and breeding studies in a wide range of Eucalyptus species.
Publisher: Elsevier BV
Date: 06-2007
DOI: 10.1016/J.CBD.2007.02.003
Abstract: The pulmonary surfactant system of heterothermic mammals must be capable of dealing with the effect of low body temperatures on the physical state of the lipid components. We have shown previously that there is a modest increase in surfactant cholesterol during periods of torpor, however these changes do not fully explain the capacity of surfactant to function under the wide range of physical conditions imposed by torpor. Here we examine indirectly the role of surfactant protein C (SP-C) in adapting to variable body temperatures by testing for the presence of positive (adaptive) selection during evolutionary transitions between heterothermy and homeothermy. We sequenced SP-C from genomic DNA of 32 mammalian species from groups of closely related heterothermic and homeothermic species (contrasts). We used phylogenetic analysis by maximum likelihood estimates of rates of non-synonymous to synonymous substitutions and fully Bayesian inference of these sequences to determine whether the mode of body temperature regulation exerts a selection pressure driving the molecular adaptation of SP-C. The protein sequence of SP-C is highly conserved with synonymous or highly conservative amino acid substitutions being predominant. The evolution of SP-C among mammals is characterised by high codon usage bias and high rates of transition/transversion. The only contrast to show evidence of positive selection was that of the bears (Ursus americanus and U. maritimus). The significance of this result is unclear. We show that SP-C is under strong evolutionary constraints, driven by purifying selection, presumably to maintain protein function despite variation in the mode of body temperature regulation.
Publisher: American Society of Ichthyologists and Herpetologists (ASIH)
Date: 03-2014
DOI: 10.1643/CI-11-162
Publisher: Springer Science and Business Media LLC
Date: 19-03-2014
DOI: 10.1038/HDY.2014.6
Publisher: Elsevier BV
Date: 08-2001
DOI: 10.1016/S0379-0738(01)00426-1
Abstract: The applicability of mitochondrial DNA (mtDNA) sequencing was investigated for the identification of the following forensically important species of blowflies from southeastern Australia: Calliphora albifrontalis, C. augur, C. dubia, C. hilli hilli, C. maritima, C. stygia, C. vicina, Chrysomya rufifacies, Ch. varipes and Onesia tibialis. All breed in carrion except O. tibialis, which is an earthworm parasitoid. Emphasis was placed on Calliphora species because they predominate among the carrion-breeding blowfly fauna of southern Australia and their immatures are difficult to identify morphologically. A partial sequence of the mitochondrial COII gene was determined for all species and for COI for C. albifrontalis, C. augur, C. dubia and C. stygia only. Five other species of blowflies, Chrysomya albiceps, Ch. rufifacies, Protophormia terraenovae, Lucilia illustris and L. sericata, for which sequence data were already available, were also included. Analysis of the COI and COII sequences revealed abundant phylogenetically informative nucleotide substitutions that could identify blowfly species to species group. In contrast, because of the low level of sequence ergence of sister species, the data could not distinguish among taxa from the same species group, i.e. the species within the C. augur and C. stygia groups. The molecular data support the existing species group separation of the taxa within Calliphora. Because of the speed and accuracy of current nucleotide sequencing technology and the abundant apomorphic substitutions available from mtDNA sequences, this approach, with the analysis of additional taxa and genes, is likely to enable the reliable identification of carrion-breeding blowflies in Australia.
Publisher: Wiley
Date: 17-05-2012
DOI: 10.1002/ECE3.84
Location: United States of America
No related grants have been discovered for Stephen Donnellan.