ORCID Profile
0000-0001-6665-3395
Current Organisations
University of Adelaide
,
South Australian Museum
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Population, Ecological and Evolutionary Genetics | Genetics | Evolutionary Impacts of Climate Change | Host-Parasite Interactions | Genetic Immunology | Ecology | Molecular Evolution | Molecular evolution | Behavioural ecology | Environmental Science and Management | Conservation and Biodiversity | Host-parasite interactions | Animal behaviour | Biological adaptation | Genomics and transcriptomics | Genetics | Biological Adaptation
ANZSRC Socio-Economic Objective (SEO)
Sparseland, Permanent Grassland and Arid Zone Flora, Fauna and Biodiversity | Expanding Knowledge in the Biological Sciences | Climate Change Mitigation Strategies |
Related Links
Publications
Molecular systematics and biodiversity of oniscidean isopods in the groundwater calcretes of Central Western Australia
Publisher: Elsevier BV
Date: 11-2016
DOI: 10.1016/J.YMPEV.2016.07.026
Abstract: Groundwater calcrete aquifers of central Western Australia have been shown to contain a high ersity of stygobiont (subterranean aquatic) invertebrates, with each species confined to an in idual calcrete and the entire system resembling a 'subterranean archipelago' containing hundreds of isolated calcretes. Here, we utilised alternative s ling techniques above the water table and uncovered a significant fauna of subterranean terrestrial oniscidean isopods from the calcretes. We explored the ersity and evolution of this fauna using molecular analyses based on one mitochondrial gene, Cytochrome C Oxidase Subunit I (COI), two Ribosomal RNA genes (28S and 18S), and one protein coding nuclear gene, Lysyl-tRNA Synthetase (LysRS). The results from 12 calcretes showed the existence of 36 ergent DNA lineages belonging to four oniscidean families (Paraplatyarthridae, Armadillidae, Stenoniscidae and Philosciidae). Using a combination of phylogenetic and species delimitation methods, we hypothesized the occurrence of at least 27 putative new species of subterranean oniscideans, of which 24 taxa appeared to be restricted to an in idual calcrete, lending further support to the "subterranean island hypothesis". Three paraplatyarthrid species were present on adjacent calcretes and these exceptions possessed more ommatidia and body pigments compared with the calcrete-restricted taxa, and are likely to represent troglophiles. The occurrence of stenoniscid isopods in the calcretes of central Western Australia, a group previously only known from the marine littoral zone, suggests a link to the marine inundation of the Eucla basin during the Late Eocene. The current oniscidean subterranean fauna consists of groups known to be subtropical, littoral and benthic, reflecting different historical events that have shaped the evolution of the fauna in the calcretes.
Rise of the machines - recommendations for ecologists when using next generation sequencing for microsatellite development
Publisher: Wiley
Date: 16-06-2011
DOI: 10.1111/J.1755-0998.2011.03037.X
Abstract: Next generation sequencing is revolutionizing molecular ecology by simplifying the development of molecular genetic markers, including microsatellites. Here, we summarize the results of the large-scale development of microsatellites for 54 nonmodel species using next generation sequencing and show that there are clear differences amongst plants, invertebrates and vertebrates for the number and proportion of motif types recovered that are able to be utilized as markers. We highlight that the heterogeneity within each group is very large. Despite this variation, we provide an indication of what number of sequences and consequent proportion of a 454 run are required for the development of 40 designable, unique microsatellite loci for a typical molecular ecological study. Finally, to address the challenges of choosing loci from the vast array of microsatellite loci typically available from partial genome runs (average for this study, 2341 loci), we provide a microsatellite development flowchart as a procedural guide for application once the results of a partial genome run are obtained.
A draft genome assembly of the eastern banjo frog Limnodynastes dumerilii dumerilii (Anura: Limnodynastidae)
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.
Panmixia supports divergence with gene flow in Darwin's small ground finch, Geospiza fuliginosa, on Santa Cruz, Galápagos Islands
Publisher: Wiley
Date: 08-03-2012
Development of eight microsatellite loci from the Green and Golden Bell Frog (Litoria aurea) through GS-FLX pyrosequencing and cross-amplification with other species of the Litoria aurea species group
Publisher: Springer Science and Business Media LLC
Date: 13-07-2012
DNA profiling reveals Neobenedenia girellae as the primary parasitic monogenean in global fisheries and aquaculture
Publisher: Elsevier BV
Date: 12-2018
DOI: 10.1016/J.YMPEV.2018.05.012
Abstract: Accurate identification of parasite species and strains is crucial to mitigate the risk of epidemics and emerging disease. Species of Neobenedenia are harmful monogenean ectoparasites that infect economically important bony fishes in aquaculture worldwide, however, the species boundaries between two of the most notorious taxa, N. melleni and N. girellae, has been a topic of contention for decades. Historically, identifications of Neobenedenia isolates have overwhelmingly been attributed to N. melleni, and it has been proposed that N. girellae is synonymous with N. melleni. We collected 33 Neobenedenia isolates from 22 host species spanning nine countries and lified three genes including two nuclear (Histone 3 and 28S rDNA) and one mitochondrial (cytochrome b). Four major clades were identified using Maximum Likelihood and Bayesian inference analyses clades A-D corresponding to N. girellae, N. melleni, N. longiprostata and N. pacifica, respectively. All unidentified isolates and the majority of Neobenedenia sequences from GenBank fell into clade A. The results of this study indicate that N. girellae is a separate species to N. melleni, and that a large proportion of previous s les identified as N. melleni may be erroneous and a revision of identifications is needed. The large ersity of host species that N. girellae is able to infect as determined in this study and the geographic range in which it is present (23.8426°S and 24.1426°N) makes it a globally cosmopolitan species and a threat to aquaculture industries around the world.
Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies
Publisher: Public Library of Science (PLoS)
Date: 14-03-2018
A draft genome assembly of the eastern banjo frog Limnodynastes dumerilii dumerilii (Anura: Limnodynastidae)
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.
Subtle genetic clustering among South Australian colonies of little penguins (Eudyptula minor)
Publisher: Springer Science and Business Media LLC
Date: 10-06-2020
MHC in a monogamous lizard – Characterization of class I MHC genes in the Australian skink Tiliqua rugosa
Publisher: Elsevier BV
Date: 12-2015
DOI: 10.1016/J.DCI.2015.07.012
Abstract: The major histocompatibility complex (MHC) is a highly variable region of vertebrate genomes that encodes cellular proteins involved in the immune response. In addition to the benefits of MHC research in understanding the genetic basis of host resistance to disease, the MHC is an ideal candidate for studying genetic ersity under strong natural selection. However, the MHC of many non-model vertebrate taxa are poorly characterized, hindering an understanding of disease resistance and its application to conservation genetics in these groups. Squamates (lizards and snakes) remain particularly underrepresented despite their being the most erse order of non-avian sauropsids. We characterized MHC class I sequence ersity from an Australian skink, the sleepy lizard (Tiliqua rugosa), using both cDNA and genomic sequence data and also present genomic class I sequences from the related skinks Tiliqua adelaidensis and Egernia stokesii. Phylogenetic analysis of Tiliqua and other published sqamate MHC class I sequences suggest that MHC erged very early in Tiliqua compared with the other studied squamates. We identified at least 4 classical MHC class I loci in T. rugosa and also shared polymorphism among T. rugosa, T. adelaidensis and E. stokesii in the sequences encoding peptide-binding α1 and α2 domains.
<p><strong>A new species of Near-shore Marine Goby (Pisces: Gobiidae: <em>Nesogobius</em>) </strong><strong>from Kangaroo Island, Australia</strong></p>
Publisher: Magnolia Press
Date: 11-12-2015
DOI: 10.11646/ZOOTAXA.4057.3.4
Abstract: Nesogobius is one of two goby genera with all species wholly restricted to temperate Australian waters. Described here is a new member of the genus discovered during near-shore marine and estuarine fish s ling along the central southern Australian coastline. The tiger sandgoby Nesogobius tigrinus sp. nov. is distinguished from other congeners by a combination of colouration including four prominent vertical black bars on males morphological characters involving body scales (large), head scales (naked), body depth (slender) and gill opening (wide) meristic counts including a lack of second dorsal and anal fin spines and mitochondrial DNA sequence ergence. The species appears to be a narrow range endemic, restricted to specific sub-tidal habitat in the unique sheltered embayments of northeast Kangaroo Island. This study forms part of ongoing investigations to more fully describe the bio ersity and conservation requirements of the regional ichthyofauna.
Stingray diversification across the end-Cretaceous extinctions
Publisher: Museums Victoria
Date: 2016
Species boundaries in carp gudgeons (Eleotrididae : Hypseleotris) from the River Murray, South Australia: evidence for multiple species and extensive hybridization
Publisher: CSIRO Publishing
Date: 2000
DOI: 10.1071/MF00039
Abstract: Allozyme analyses of carp gudgeons (Hypseleotris) from five sites in the lower River Murray revealed three distinctive taxa designated HA, HB and HC, diagnosable from one another by fixed differences at 3–5 loci, and three apparent F 1 hybrid forms, HA& yen HB, HA& yen HX and HB& yen HX, where HX denotes a taxon not s led in its ‘pure’ form. Of all fish s led, 25% were hybrids, although only one hybrid form was found at any one site, and never in company with both parental taxa. No hybrids involving HC were found, although this was the most common taxon, and no HA& yen HB hybrids were present at the one site of demonstrated sympatry between the parental taxa. Morphological analysis and the lack of introgression confirm that HA, HB, and HC are distinct biological species. Partial meristic data suggest that HC corresponds to H. klunzingeri s.l., ‘Midgley’s carp gudgeon’ is a composite of HA, HB and HA& yen HB hybrids, and ‘Lake’s carp gudgeon’ may be a composite of HX and one of its hybrids (HB& yen HX). We speculate that one or more of the hybrid classes may be ‘unisexual lineages’ (clonally reproducing, usually all-female forms derived from hybridization between congeners).
Systematic and conservation implications of mitochondrial DNA diversity in emu-wrens, Stipiturus (Aves : Maluridae)
Publisher: Informa UK Limited
Date: 06-2009
DOI: 10.1071/MU07011
The critical thermal maximum of diving beetles (Coleoptera: Dytiscidae): a comparison of subterranean and surface-dwelling species
Publisher: Elsevier BV
Date: 2021
Parallel decay of vision genes in subterranean water beetles
Publisher: Elsevier BV
Date: 08-2022
DOI: 10.1016/J.YMPEV.2022.107522
Abstract: In the framework of neutral theory of molecular evolution, genes specific to the development and function of eyes in subterranean animals living in permanent darkness are expected to evolve by relaxed selection, ultimately becoming pseudogenes. However, definitive empirical evidence for the role of neutral processes in the loss of vision over evolutionary time remains controversial. In previous studies, we characterized an assemblage of independently-evolved water beetle (Dytiscidae) species from a subterranean archipelago in Western Australia, where parallel vision and eye loss have occurred. Using a combination of transcriptomics and exon capture, we present evidence of parallel coding sequence decay, resulting from the accumulation of frameshift mutations and premature stop codons, in eight phototransduction genes (arrestins, opsins, ninaC and transient receptor potential channel genes) in 32 subterranean species in contrast to surface species, where these genes have open reading frames. Our results provide strong evidence to support neutral evolutionary processes as a major contributing factor to the loss of phototransduction genes in subterranean animals, with the ultimate fate being the irreversible loss of a light detection system.
The tuatara genome: insights into vertebrate evolution from the sole survivor of an ancient reptilian order
Publisher: Cold Spring Harbor Laboratory
Date: 08-12-2019
DOI: 10.1101/867069
Abstract: The tuatara ( Sphenodon punctatus ), the only living member of the archaic reptilian order Rhynchocephalia (Sphenodontia) once widespread across Gondwana, is an iconic and enigmatic terrestrial vertebrate endemic to New Zealand. A key link to the now extinct stem reptiles from which dinosaurs, modern reptiles, birds and mammals evolved, the tuatara provides exclusive insights into the ancestral amniotes. The tuatara genome, at ∼5 Gbp, is among the largest vertebrate genomes assembled. Analysis of this genome and comparisons to other vertebrates reinforces the uniqueness of the tuatara. Phylogenetic analyses indicate tuatara erged from the snakes and lizards ∼250 MYA. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Genome sequence analysis identifies expansions of protein, non-protein-coding RNA families, and repeat elements, the latter of which show an extraordinary amalgam of reptilian and mammalian features. Sequencing of this genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. It also provides important insights into both the technical challenges and the cultural obligations associated with genome sequencing.
Detection of Prunus necrotic ringspot virus in almond: effect of sampling time on the efficiency of serological and biological indexing methodologies
Publisher: CSIRO Publishing
Date: 2002
DOI: 10.1071/EA01064
Abstract: The reliability of enzyme-linked immunosorbent assay (ELISA) and indexing methodologies for the detection of Prunus necrotic ringspot virus (PNRSV) in almond was assessed under local conditions. Thirteen field-grown almond trees were s led fortnightly throughout the growing season. Petal and leaf homogenates were used for ELISA and to inoculate herbaceous indicator species, while buds collected from October onwards were budded to woody indicators. ELISA reliably detected PNRSV in petals and young leaves from bud-break until the cessation of stem elongation. While herbaceous indexing was not as reliable as ELISA, woody indicators could differentiate positive from negative s les reliably throughout the testing period. However, for mass screening of foundation plantings, nursery stock and elite germplasm, woody indexing is too costly and slow to give results. The use of ELISA can overcome these limitations but the timing of s le collection is critical. Petal or leaf tissue collected early in the season will yield the most reliable results.
Differential transcriptomic responses to heat stress in surface and subterranean diving beetles
Publisher: Cold Spring Harbor Laboratory
Date: 13-12-2021
DOI: 10.1101/2021.12.12.470823
Abstract: Subterranean habitats are generally very stable environments, and as such evolutionary transitions of organisms from surface to subterranean lifestyles may cause considerable shifts in physiology, particularly with respect to thermal tolerance. In this study we compared responses to heat shock at the molecular level in a geographically widespread, surface-dwelling water beetle to a congeneric subterranean species restricted to a single aquifer (Dytiscidae: Hydroporinae). The obligate subterranean beetle Paroster macrosturtensis is known to have a lower thermal tolerance compared to surface lineages (CT max 38°C cf . 42-46 °C), but the genetic basis of this physiological difference has not been characterized. We experimentally manipulated the thermal environment of 24 in iduals to demonstrate that both species can mount a heat shock response at high temperatures (35°C), as determined by comparative transcriptomics. However, genes involved in these responses differ between species and a far greater number were differentially expressed in the surface taxon, suggesting it can mount a more robust heat shock response these data may underpin its higher thermal tolerance compared to subterranean relatives. In contrast, the subterranean species examined not only differentially expressed fewer genes in response to increasing temperatures, but also in the presence of the experimental setup employed here alone. Our results suggest P. macrosturtensis may be comparatively poorly equipped to respond to both thermally induced stress and environmental disturbances more broadly. The molecular findings presented here have conservation implications for P. macrosturtensis and contribute to a growing narrative concerning weakened thermal tolerances in obligate subterranean organisms at the molecular level.
Positive selection in the N-terminal extramembrane domain of lung surfactant protein C (SP-C) in marine mammals
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.
Comparison of Reptilian Genomes Reveals Deletions Associated with the Natural Loss of γδ T Cells in Squamates
Publisher: The American Association of Immunologists
Date: 15-04-2022
Abstract: T lymphocytes or T cells are key components of the vertebrate response to pathogens and cancer. There are two T cell classes based on their TCRs, αβ T cells and γδ T cells, and each plays a critical role in immune responses. The squamate reptiles may be unique among the vertebrate lineages by lacking an entire class of T cells, the γδ T cells. In this study, we investigated the basis of the loss of the γδ T cells in squamates. The genome and transcriptome of a sleepy lizard, the skink Tiliqua rugosa, were compared with those of tuatara, Sphenodon punctatus, the last living member of the Rhynchocephalian reptiles. We demonstrate that the lack of TCRγ and TCRδ transcripts in the skink are due to large deletions in the T. rugosa genome. We also show that tuataras are on a growing list of species, including sharks, frogs, birds, alligators, and platypus, that can use an atypical TCRδ that appears to be a chimera of a TCR chain with an Ab-like Ag-binding domain. Tuatara represents the nearest living relative to squamates that retain γδ T cells. The loss of γδTCR in the skink is due to genomic deletions that appear to be conserved in other squamates. The genes encoding the αβTCR chains in the skink do not appear to have increased in complexity to compensate for the loss of γδ T cells.
LINEs between Species: Evolutionary Dynamics of LINE-1 Retrotransposons across the Eukaryotic Tree of Life
Publisher: Oxford University Press (OUP)
Date: 03-10-2016
DOI: 10.1093/GBE/EVW243
Taxonomic revision of south-eastern Australian giant burrowing frogs (Anura: Limnodynastidae: Heleioporus Gray)
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)).
Unravelling the taxonomy and identification of a problematic group of benthic fishes from tropical rivers (Gobiidae: Glossogobius)
Publisher: Wiley
Date: 22-06-2021
DOI: 10.1111/JFB.14701
Abstract: Flathead gobies (genus Glossogobius ) include c . 40 small‐ to medium‐sized benthic fishes found primarily in freshwater habitats across the Indo‐Pacific, having bio ersity value as well as cultural and economic value as food fishes, especially in developing countries. To help resolve considerable confusion regarding the identification of some of the larger‐growing Glossogobius species, a systematic framework was established using nuclear genetic markers, mitochondrial DNA barcoding and phenotypic evidence for a geographically widespread collection of in iduals from the waterways of tropical northern Australia. Species boundaries and distribution patterns were discordant with those previously reported, most notably for the tank goby Glossogobius giuris , which included a cryptic species. Genetic ergence was matched with accompanying unique visual characters that aid field identification. Additional taxonomic complexity was also evident, by comparison with DNA barcodes from international locations, suggesting that the specific names applicable for two of the candidate species in Australia remain unresolved due to confusion surrounding type specimens. Although flathead gobies are assumed to be widespread and common, this study demonstrates that unrealised taxonomic and ecological complexity is evident, and this will influence assessments of tropical bio ersity and species conservation. This study supports the need for taxonomic studies of freshwater fishes to underpin management in areas subject to significant environmental change.
Anonymous nuclear loci in non-model organisms: making the most of high-throughput genome surveys
Publisher: Oxford University Press (OUP)
Date: 11-05-2012
DOI: 10.1093/BIOINFORMATICS/BTS284
Abstract: Motivation: When working with non-model organisms, few if any species-specific markers are available for phylogenetic, phylogeographic and population studies. Therefore, researchers often try to adapt markers developed in distantly related taxa, resulting in poor lification and ascertainment bias in their target taxa. Markers can be developed de novo and anonymous nuclear loci (ANL) are proving to be a boon for researchers seeking large numbers of fast-evolving, independent loci. However, the development of ANL can be laboratory intensive and expensive. A workflow is described to identify suitable low-copy anonymous loci from high-throughput shotgun sequences, dramatically reducing the cost and time required to develop these markers and produce robust multilocus datasets. Results: By successively removing repetitive and evolutionary conserved sequences from low coverage shotgun libraries, we were able to isolate thousands of potential ANL. Empirical testing of loci developed from two reptile taxa confirmed that our methodology yields markers with comparable lification rates and nucleotide ersities to ANLs developed using other methodologies. Our approach capitalizes on next-generation sequencing technologies to enable the development of phylogenetic, phylogeographic and population markers for taxa lacking suitable genomic resources. Contact: terry.bertozzi@samuseum.sa.gov.au
Horizontal transfer of BovB and L1 retrotransposons in eukaryotes
Publisher: Springer Science and Business Media LLC
Date: 09-07-2018
Incidence on Polypogon monspeliensis of Clavibacter toxicus and Anguina sp., the organisms associated with 'flood plain staggers' in South Australia
Publisher: CSIRO Publishing
Date: 1995
DOI: 10.1071/EA9950567
Abstract: During 1991-92, a survey was conducted in South Australia to determine the distribution of the nematode Anguina sp. and bacterium Clavibacter toxicus associated with 'flood plain staggers'. Polypogon monspeliensis (annual beardgrass) was examined at 265 sites in flood-prone areas in the South East. Seed-galls produced by Anguina sp. were observed at 96 sites, and at 78 of these, seed heads infected with C. toxicus were observed. Infected sites were observed throughout the survey area, with the greatest concentration between Naracoorte and Kingston. No infected Agrostis avenacea (annual blowngrass) was found in the South East or along the flood plains of the Murray River.
Stressed out underground?: Illuminating the genomic response to heat stress in surface and subterranean predaceous diving beetles
Publisher: Pensoft Publishers
Date: 14-07-2022
DOI: 10.3897/ACA.5.E90170
Abstract: Subterranean realms possess high environmental stability with respect to light levels, temperature, and humidity. The transition to a subterranean lifestyle can therefore cause massive shifts in a species’ biology. How does the colonisation of these habitats affect the thermal tolerance of an organism? Past studies demonstrate species in extremely stable environments might lose the ability to mount a heat shock response, which involves the expression of heat shock proteins to remediate misfolded or denaturing proteins as a result of heat stress. Such organisms might therefore be at particular risk of decline in the face of climate change. However, similarly robust data are limited for subterranean organisms. To help address this knowledge gap, here we compared the heat-shock response of a surface-dwelling and subterranean species of predaceous ing beetle (Dytiscidae, Hydroporinae), Paroster nigroadumbratus and P. macrosturtensis, the latter of which is restricted to a single groundwater aquifer in the Yilgarn region of Western Australia. Though P. macrosturtensis is able to survive warmer conditions than it encounters in nature based on past survival experiments, it is nonetheless less robust in the face of temperature extremes compared to surface-dwelling relatives the genomic basis of this difference is unknown. By sequencing transcriptomes of experimentally heat-shocked in iduals we demonstrate both species can indeed mount a heat shock response at high temperatures (35ºC). However, the genes involved in these responses differ and a far greater number are differentially expressed in the surface species, including those involved in remediating oxidative stress, which might explain its more robust response to heat stress. In contrast, the subterranean species significantly upregulated a heat shock protein gene under conditions it encounters in nature, suggesting it is far more sensitive to ambient stressors. These findings have conservation implications for P. macrosturtensis and contribute to a growing narrative concerning weakened thermal tolerances in obligate subterranean organisms at the molecular level.
Opsin transcripts of predatory diving beetles: a comparison of surface and subterranean photic niches.
Publisher: The Royal Society
Date: 2015
DOI: 10.1098/RSOS.140386
Abstract: The regressive evolution of eyes has long intrigued biologists yet the genetic underpinnings remain opaque. A system of discrete aquifers in arid Australia provides a powerful comparative means to explore trait regression at the genomic level. Multiple surface ancestors from two tribes of ing beetles (Dytiscidae) repeatedly invaded these calcrete aquifers and convergently evolved eye-less phenotypes. We use this system to assess transcription of opsin photoreceptor genes among the transcriptomes of two surface and three subterranean dytiscid species and test whether these genes have evolved under neutral predictions. Transcripts for UV , long-wavelength and ciliary-type opsins were identified from the surface beetle transcriptomes. Two subterranean beetles showed parallel loss of all opsin transcription, as expected under ‘neutral’ regressive evolution. The third species Limbodessus palmulaoides retained transcription of a long-wavelength opsin ( lwop ) orthologue, albeit in an aphotic environment. Tests of selection on lwop indicated no significant differences between transcripts derived from surface and subterranean habitats, with strong evidence for purifying selection acting on L. palmulaoides lwop . Retention of sequence integrity and the lack of evidence for neutral evolution raise the question of whether we have identified a novel pleiotropic role for lwop , or an incipient phase of pseudogene development.
Telomere length and age in pinnipeds: The endangered Australian sea lion as a case study
Publisher: Wiley
Date: 07-02-2011
Publisher Correction: The tuatara genome reveals ancient features of amniote evolution
Publisher: Springer Science and Business Media LLC
Date: 18-08-2020
DOI: 10.1038/S41586-020-2661-6
Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Characterisation of major histocompatibility complex class I transcripts in an Australian dragon lizard
Publisher: Elsevier BV
Date: 07-2018
DOI: 10.1016/J.DCI.2018.02.012
Abstract: Characterisation of squamate major histocompatibility complex (MHC) genes has lagged behind other taxonomic groups. MHC genes encode cell-surface glycoproteins that present self- and pathogen-derived peptides to T cells and play a critical role in pathogen recognition. Here we characterise MHC class I transcripts for an agamid lizard (Ctenophorus decresii) and investigate the evolution of MHC class I in Iguanian lizards. An iterative assembly strategy was used to identify six full-length C. decresii MHC class I transcripts, which were validated as likely to encode classical class I MHC molecules. Evidence for exon shuffling recombination was uncovered for C. decresii transcripts and Bayesian phylogenetic analysis of Iguanian MHC class I sequences revealed a pattern expected under a birth-and-death mode of evolution. This work provides a stepping stone towards further research on the agamid MHC class I region.
Development of 15 microsatellite loci from mulloway, Argyrosomus japonicus (Pisces: Sciaenidae) using next generation sequencing and an assessment of their cross amplification in other sciaenids
Publisher: Springer Science and Business Media LLC
Date: 09-11-2014
The tuatara genome reveals ancient features of amniote evolution
Publisher: Springer Science and Business Media LLC
Date: 05-08-2020
DOI: 10.1038/S41586-020-2561-9
Abstract: The tuatara ( Sphenodon punctatus )—the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana 1,2 —is an iconic species that is endemic to New Zealand 2,3 . A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes 2,4 . Here we analyse the genome of the tuatara, which—at approximately 5 Gb—is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage erged from that of snakes and lizards around 250 million years ago. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Our genome sequence analysis identifies expansions of proteins, non-protein-coding RNA families and repeat elements, the latter of which show an amalgam of reptilian and mammalian features. The sequencing of the tuatara genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. Our study also provides important insights into both the technical challenges and the cultural obligations that are associated with genome sequencing.
Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus)
Publisher: Public Library of Science (PLoS)
Date: 17-09-2021
DOI: 10.1371/JOURNAL.PONE.0256861
Abstract: Transcriptome-based exon capture approaches, along with next-generation sequencing, are allowing for the rapid and cost-effective production of extensive and informative phylogenomic datasets from non-model organisms for phylogenetics and population genetics research. These approaches generally employ a reference genome to infer the intron-exon structure of targeted loci and preferentially select longer exons. However, in the absence of an existing and well-annotated genome, we applied this exon capture method directly, without initially identifying intron-exon boundaries for bait design, to a group of highly erse Haloniscus (Philosciidae), paraplatyarthrid and armadillid isopods, and examined the performance of our methods and bait design for phylogenetic inference. Here, we identified an isopod-specific set of single-copy protein-coding loci, and a custom bait design to capture targeted regions from 469 genes, and analysed the resulting sequence data with a mapping approach and newly-created post-processing scripts. We effectively recovered a large and informative dataset comprising both short ( bp) and longer ( bp) exons, with high uniformity in sequencing depth. We were also able to successfully capture exon data from up to 16-year-old museum specimens along with more distantly related outgroup taxa, and efficiently pool multiple s les prior to capture. Our well-resolved phylogenies highlight the overall utility of this methodological approach and custom bait design, which offer enormous potential for application to future isopod, as well as broader crustacean, molecular studies.
Isolation and characterisation of 12 polymorphic microsatellite loci for the threatened mound-building malleefowl, Leipoa ocellata (Aves:Megapodiidae)
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.
Fiddling with the proof: the Magpie Fiddler Ray is a colour pattern variant of the common Southern Fiddler Ray (Rhinobatidae: Trygonorrhina)
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.
First comparative insight into the architecture of COI mitochondrial minicircle molecules of dicyemids reveals marked inter-species variation
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.
DNA barcoding of microgastrine parasitoid wasps (Hymenoptera: Braconidae) using high‐throughput methods more than doubles the number of species known for Australia
Publisher: Wiley
Date: 11-06-2018
Abstract: The Microgastrinae are a hugely erse subfamily of endoparasitoid wasps of lepidopteran caterpillars. They are important in agriculture as biological control agents and play a significant ecological role in the regulation of caterpillar populations. Whilst the group has been the focus of intensive rearing and DNA barcoding studies in the Northern Hemisphere, the Australian fauna has received little attention. In total, 99 species have been described from or have been introduced into Australia, but the real species ersity for the region is clearly much larger than this. In this study, museum ethanol s les and recent field collections were mined for hundreds of specimens of microgastrine wasps, which were then barcoded for the COI region, ITS2 ribosomal spacer and the wingless nuclear genes, using a pooled sequencing approach on an Illumina Miseq system. Full COI sequences were obtained for 525 in iduals which, when combined with 162 publicly available sequences, represented 417 haplotypes, and a total of 236 species were delimited using a consensus approach. By more than doubling the number of known microgastrine wasp species in Australia, our study highlights the value of DNA barcoding in the context of employing high-throughput sequencing methods of bulk ethanol museum collections for bio ersity assessment.
Regeneration of almond from immature seed cotyledons
Publisher: Springer Science and Business Media LLC
Date: 2001
A new species of Philoria (Anura: Limnodynastidae) from the uplands of the Gondwana Rainforests World Heritage Area of eastern Australia
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.
Host-defence peptide profiles of the skin secretions of interspecific hybrid tree frogs and their parents, female Litoria splendida and male Litoria caerulea
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.
Random non-coding fragments of lizard DNA: anonymous nuclear loci for the Australian skink, Tiliqua rugosa, and their utility in other Egernia-group species
Publisher: CSIRO Publishing
Date: 2014
DOI: 10.1071/ZO14085
Abstract: We report the development of 48 anonymous nuclear loci from the Australian skink Tiliqua rugosa using 454 sequencing. These loci lified across a Western Australian lineage (47 loci), a ‘northern’ lineage (48 loci) and a ‘southern’ lineage (46 loci). We further tested lification for the related T. adelaidensis and Egernia stokesii where 37 and 34 loci lified respectively. The loci showed variability within T. rugosa (22 polymorphic loci) and at least 27 loci also exhibited variation among the three species, highlighting the usefulness of these markers for phylogenetic, phylogeographic and population genetic analyses in T. rugosa and related species.
Looks can deceive: molecular phylogeny of a family of flatworm ectoparasites (Monogenea: Capsalidae) does not reflect current morphological classification
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.
A new species of barred frog, Mixophyes (Anura: Myobatrachidae) from south-eastern Australia identified by molecular genetic analyses
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.
Comparison of ELISA and RT-PCR for the detection of Prunus necrotic ring spot virus and prune dwarf virus in almond (Prunus dulcis)
Publisher: Elsevier BV
Date: 12-2003
DOI: 10.1016/J.JVIROMET.2003.08.014
Abstract: A technique based on the reverse transcriptase-polymerase chain reaction (RT-PCR) has been developed to detect the presence of Prunus necrotic ringspot virus (PNRSV) and prune dwarf virus (PDV) simultaneously in almond. This paper presents the results of a 3-year study comparing both enzyme-linked immunosorbent assay (ELISA) and RT-PCR for the detection of PNRSV and PDV using 175 almond leaf s les. Multiplex RT-PCR was found to be more sensitive than ELISA, especially when followed by nested PCR for the detection of PDV. The RT-PCR technique has the added advantage that plant material can be tested at any time throughout the growing season.
Variation in Telomere Length of the Common Carp, Cyprinus carpio (Cyprinidae), in Relation to Body Length
Publisher: American Society of Ichthyologists and Herpetologists (ASIH)
Date: 03-2014
DOI: 10.1643/CI-11-162
Multilocus phylogeny and recent rapid radiation of the viviparous sea snakes (Elapidae: Hydrophiinae)
Publisher: Elsevier BV
Date: 03-2013
DOI: 10.1016/J.YMPEV.2012.09.021
Abstract: The viviparous sea snakes (Hydrophiinae: Hydrophiini) comprise a young but morphologically and ecologically erse clade distributed throughout the Indo-Pacific. Despite presenting a very promising model for marine ersification studies, many relationships among the 62 species and 16 genera in Hydrophiini remain unresolved. Here, we extend previous taxonomic and genomic s ling for Hydrophiini using three mitochondrial fragments and five nuclear loci for multiple in iduals of 39 species in 15 genera. Our results highlight many of the impediments to inferring phylogenies in recent rapid radiations, including low variation at all five nuclear markers, and conflicting relationships supported by mitochondrial and nuclear trees. However, concatenated Bayesian and likelihood analyses, and a multilocus coalescent tree, recovered concordant support for primary clades and several previously unresolved inter-specific groupings. The Aipysurus group is monophyletic, with egg-eating specialists forming separate, early- erging lineages. All three monotypic semi-aquatic genera (Ephalophis, Parahydrophis and Hydrelaps) are robustly placed as early erging lineages along the branch leading to the Hydrophis group, with Ephalophis recovered as sister to Parahydrophis. The molecular phylogeny implies extensive evolutionary convergence in feeding adaptations within the Hydrophis group, especially the repeated evolution of small-headed (microcephalic) forms. Microcephalophis (Hydrophis) gracilis is robustly recovered as a relatively distant sister lineage to all other s led Hydrophis group species, here termed the 'core Hydrophis group'. Within the 'core Hydrophis group', Hydrophis is recovered as broadly paraphyletic, with several other genera nested within it (Pelamis, Enhydrina, Astrotia, Thalassophina, Acalyptophis, Kerilia, Lapemis, Disteira). Instead of erecting multiple new genera, we recommend dismantling the latter (mostly monotypic) genera and recognising a single genus, Hydrophis Latreille 1802, for the core Hydrophis group. Estimated ergence times suggest that all Hydrophiini last shared a common ancestor ∼6million years ago, but that the majority of extant lineages ersified over the last ∼3.5million years. The core Hydrophis group is a young and rapidly speciating clade, with 26 s led species and 9 genera and dated at only ∼1.5-3million years old.
Re-evaluating inheritance in genome evolution: widespread transfer of LINEs between species
Publisher: Cold Spring Harbor Laboratory
Date: 08-02-2017
DOI: 10.1101/106914
Abstract: Transposable elements (TEs) are mobile DNA sequences, colloquially known as ‘jumping genes’ because of their ability to replicate to new genomic locations. Given a vector of transfer (e.g. tick or virus), TEs can jump further: between organisms or species in a process known as horizontal transfer (HT). Here we propose that LINE-1 (L1) and Bovine-B (BovB), the two most abundant TE families in mammals, were initially introduced as foreign DNA via ancient HT events. Using a 503-genome dataset, we identify multiple ancient L1 HT events in eukaryotes and provide evidence that L1s infiltrated the mammalian lineage after the monotreme-therian split. We also extend the BovB paradigm by increasing the number of estimated transfer events compared to previous studies, finding new potential blood-sucking parasite vectors and occurrences in new lineages (e.g. bats, frog). Given that these TEs make up nearly half of the genome sequence in today’s mammals, our results provide the first evidence that HT can have drastic and long-term effects on the new host genomes. This revolutionizes our perception of genome evolution to consider external factors, such as the natural introduction of foreign DNA. With the advancement of genome sequencing technologies and bioinformatics tools, we anticipate our study to be the first of many large-scale phylogenomic analyses exploring the role of HT in genome evolution. LINE-1 (L1) elements occupy about half of most mammalian genomes (1), and they are believed to be strictly vertically inherited (2). Mutagenic L1 insertions are thought to account for approximately 1 of every 1000 random, disease-causing insertions in humans (4-7). Our research indicates that the very presence of L1s in humans, and other therian mammals, is due to an ancient transfer event – which has drastic implications for our perception of genome evolution. Using a machina analyses over 503 genomes, we trace the origins of L1 and BovB retrotransposons across the tree of life, and provide evidence of their long-term impact on eukaryotic evolution.
Evaluating evolutionary history in the face of high gene tree discordance in Australian Gehyra (Reptilia: Gekkonidae)
Publisher: Springer Science and Business Media LLC
Date: 19-03-2014
DOI: 10.1038/HDY.2014.6
Genetic and morphological divergence in island and mainland birds: informing conservation priorities
Publisher: Elsevier BV
Date: 12-2011
Widespread horizontal transfer of retrotransposons
Publisher: Proceedings of the National Academy of Sciences
Date: 31-12-2013
Abstract: In higher organisms such as vertebrates, it is generally believed that lateral transfer of genetic information does not readily occur, with the exception of retroviral infection. However, horizontal transfer (HT) of protein coding repetitive elements is the simplest way to explain the patchy distribution of BovB, a long interspersed element (LINE) about 3.2 kb long, that has been found in ruminants, marsupials, squamates, monotremes, and African mammals. BovB sequences are a major component of some of these genomes. Here we show that HT of BovB is significantly more widespread than believed, and we demonstrate the existence of two plausible arthropod vectors, specifically reptile ticks. A phylogenetic tree built from BovB sequences from species in all of these groups does not conform to expected evolutionary relationships of the species, and our analysis indicates that at least nine HT events are required to explain the observed topology. Our results provide compelling evidence for HT of genetic material that has transformed vertebrate genomes.
Species boundaries in the Rana arfaki group (Anura: Ranidae) and phylogenetic relationships to other New Guinean Rana
Publisher: Magnolia Press
Date: 07-06-2010
DOI: 10.11646/ZOOTAXA.2496.1.3
Abstract: Allozyme electrophoresis is used to explore molecular genetic relationships within the Rana arfaki group and between this group and selected lineages of New Guinean Rana. Rana jimiensis is confirmed as a species distinct from R. arfaki and its range in Papua New Guinea is extended to the Southern Highlands Province and the north-coastal ranges in Sandaun Province. Rana arfaki and R. jimiensis show a high level of genetic differentiation maintained across a wide geographic area and show consistent morphological differences in head shape, tympanum size, degree of digital disc dilation and extent of sexual dimorphism. The two species occur syntopically on the Papuan Plateau, Southern Highlands Province, and are regionally sympatric in Sandaun Province. The observed level of genetic differentiation is equivalent to that reported previously between regionally sympatric members of the Rana papua group. Populations of R. jimiensis from north and south of the central cordillera show no obvious morphological and only minor genetic differentiation. In contrast, R. arfaki shows considerable geographic variation in both morphology and allozymes and may include two or more regionally distinctive forms.
Allozyme analysis of Australian isolates of Dilophospora alopecuri
Publisher: Elsevier BV
Date: 03-1998
Closing the mitochondrial circle on paraphyly of the Monogenea (Platyhelminthes) infers evolution in the diet of parasitic flatworms
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.
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