ORCID Profile
0000-0002-5150-7501
Current Organisation
Macquarie University
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Phylogeny and Comparative Analysis | Speciation and Extinction | Population, Ecological and Evolutionary Genetics | Evolutionary Biology
Publisher: Wiley
Date: 31-01-2008
DOI: 10.1111/J.1365-2052.2007.01683.X
Abstract: The extent and pattern of linkage disequilibrium (LD) between closely spaced markers contain information about population history, including past population size and selection history. Selection signatures can be identified by comparing the LD surrounding a putative selected allele at a locus to the putative non-selected allele. In livestock populations, locations of selection signatures identified in this way should be correlated with QTL affecting production traits, as the populations have been under strong artificial selection for these traits. We used a dense SNP map of bovine chromosome 6 to characterize the pattern of LD on this chromosome in Norwegian Red cattle, a breed which has been strongly selected for milk production. The pattern of LD was generally consistent with strong selection in regions containing QTL affecting milk production traits, including a strong selection signature in a region containing a mutation known to affect milk production. The results demonstrate that in livestock populations, the origin of selection signatures will often be QTL for livestock production traits, and illustrate the value of selection signatures in uncovering new mutations with potential effects on quantitative traits.
Publisher: Elsevier BV
Date: 02-2012
DOI: 10.1016/J.YMPEV.2011.11.005
Abstract: The rock-wallaby genus Petrogale comprises a group of habitat-specialist macropodids endemic to Australia. Their restriction to rocky outcrops, with infrequent interpopulation dispersal, has been suggested as the cause of their recent and rapid ersification. Molecular phylogenetic relationships within and among species of Petrogale were analysed using mitochondrial (cytochrome oxidase c subunit 1, cytochrome b, NADH dehydrogenase subunit 2) and nuclear (omega-globin intron, breast and ovarian cancer susceptibility gene) sequence data with representatives that encompassed the morphological and chromosomal variation within the genus, including for the first time both Petrogale concinna and Petrogale purpureicollis. Four distinct lineages were identified, (1) the brachyotis group, (2) Petrogale persephone, (3) Petrogalexanthopus and (4) the lateralis-penicillata group. Three of these lineages include taxa with the ancestral karyotype (2n=22). Paraphyletic relationships within the brachyotis group indicate the need for a focused phylogeographic study. There was support for P. purpureicollis being reinstated as a full species and P. concinna being placed within Petrogale rather than in the monotypic genus Peradorcas. Bayesian analyses of ergence times suggest that episodes of ersification commenced in the late Miocene-Pliocene and continued throughout the Pleistocene. Ancestral state reconstructions suggest that Petrogale originated in a mesic environment and dispersed into more arid environments, events that correlate with the timing of radiations in other arid zone vertebrate taxa across Australia.
Publisher: The Royal Society
Date: 10-2015
Abstract: Complex Robertsonian rearrangements, with shared arms in different fusions, are expected to prevent gene flow between hybrids through missegregation during meiosis. Here, we estimate gene flow between recently erged and chromosomally erse rock-wallabies ( Petrogale ) to test for this form of chromosomal speciation. Contrary to expectations, we observe relatively high admixture among species with complex fusions. Our results reinforce the need to consider alternative roles of chromosome change, together with genic ergence, in driving speciation.
Publisher: CSIRO Publishing
Date: 2019
DOI: 10.1071/ZO19063
Abstract: The black-footed rock-wallaby (Petrogale lateralis) is the most widespread member of the endemic Australian macropodid genus Petrogale. Considerable morphological and genetic ersity within this species has long been recognised and P. lateralis is currently ided into three described subspecies (P. lateralis lateralis, P. l. pearsoni, P. l. hacketti) and two undescribed forms (MacDonnell Ranges race, West Kimberley race). Chromosomal, morphological, genic and genomic studies have demonstrated that these five taxa are closely related but distinguishable. Here, we formally name the MacDonnell Ranges race and the West Kimberley race as subspecies of P. lateralis. Taxonomic registration: (LSID publication) rn:lsid:zoobank.org:pub:71C3B7CE-CE3D-4A78-83A6-5EB50FBBA810
Publisher: Springer Science and Business Media LLC
Date: 03-04-2012
Publisher: Springer Science and Business Media LLC
Date: 08-12-2017
Publisher: Elsevier BV
Date: 12-2016
Publisher: Elsevier BV
Date: 10-2018
DOI: 10.1016/J.YMPEV.2018.05.030
Abstract: Amongst the Australasian kangaroos and wallabies (Macropodidae) one anomalous genus, the tree-kangaroos, Dendrolagus, has secondarily returned to arboreality. Modern tree-kangaroos are confined to the wet tropical forests of north Queensland, Australia (2 species) and New Guinea (8 species). Due to their behavior, distribution and habitat most species are poorly known and our understanding of the evolutionary history and systematics of the genus is limited and controversial. We obtained tissue s les from 36 in idual Dendrolagus including representatives from 14 of the 17 currently recognised or proposed subspecies and generated DNA sequence data from three mitochondrial (3116 bp) and five nuclear (4097 bp) loci. Phylogenetic analysis of these multi-locus data resolved long-standing questions regarding inter-relationships within Dendrolagus. The presence of a paraphyletic ancestral long-footed and derived monophyletic short-footed group was confirmed. Six major lineages were identified: one in Australia (D. lumholtzi, D. bennettianus) and five in New Guinea (D. inustus, D. ursinus, a Goodfellow's group, D. mbaiso and a Doria's group). Two major episodes of ersification within Dendrolagus were identified: the first during the late Miocene/early Pliocene associated with orogenic processes in New Guinea and the second mostly during the early Pleistocene associated with the intensification of climatic cycling. All s led subspecies showed high levels of genetic ergence and currently recognized species within both the Doria's and Goodfellow's groups were paraphyletic indicating that adjustments to current taxonomy are warranted.
Publisher: MDPI AG
Date: 20-08-2019
Abstract: The recent advances in DNA sequencing technology are enabling a rapid increase in the number of genomes being sequenced. However, many fundamental questions in genome biology remain unanswered, because sequence data alone is unable to provide insight into how the genome is organised into chromosomes, the position and interaction of those chromosomes in the cell, and how chromosomes and their interactions with each other change in response to environmental stimuli or over time. The intimate relationship between DNA sequence and chromosome structure and function highlights the need to integrate genomic and cytogenetic data to more comprehensively understand the role genome architecture plays in genome plasticity. We propose adoption of the term ‘chromosomics’ as an approach encompassing genome sequencing, cytogenetics and cell biology, and present ex les of where chromosomics has already led to novel discoveries, such as the sex-determining gene in eutherian mammals. More importantly, we look to the future and the questions that could be answered as we enter into the chromosomics revolution, such as the role of chromosome rearrangements in speciation and the role more rapidly evolving regions of the genome, like centromeres, play in genome plasticity. However, for chromosomics to reach its full potential, we need to address several challenges, particularly the training of a new generation of cytogeneticists, and the commitment to a closer union among the research areas of genomics, cytogenetics, cell biology and bioinformatics. Overcoming these challenges will lead to ground-breaking discoveries in understanding genome evolution and function.
Publisher: Wiley
Date: 03-2016
DOI: 10.1111/MEC.13546
Abstract: High-throughput sequencing approaches offer opportunities to better understand the evolutionary processes driving ersification, particularly in nonmodel organisms. In particular, the 100-1000's of loci that can now be sequenced are providing unprecedented power in population, speciation and phylogenetic studies. Here, we apply an exon capture approach to generate >99% complete sequence and SNP data across >2000 loci from a tropical skink, Carlia amax, and exploit these data to identify ergent lineages and infer their relationships and demographic histories. This is especially relevant to low-dispersal tropical taxa that often have cryptic ersity and spatially dynamic histories. For C. amax, clustering of nuclear SNPs and coalescent-based species delimitation analyses identify four ergent lineages, one fewer than predicted based on geographically coherent mtDNA clades (>9.4% sequence ergence). Three of these lineages are widespread and parapatric on the mainland, whereas the most ergent is restricted to islands off the northeast Northern Territory. Tests for population expansion reject an equilibrium isolation-by-distance model for two of the three widespread lineages and infer refugial expansion sources in the relatively mesic northeast Top End and northwest Kimberley. The latter is already recognized as a hotspot of endemism, but our results also suggest that a stronger focus on the northeast Top End, and adjacent islands is warranted. More generally, our results show how genome-reduction methods such as exon capture can yield insights into the pattern and dynamics of bio ersity across complex landscapes with as yet poorly understood biogeographic history and how exon data can link between population and phylogenetic questions.
Publisher: CSIRO Publishing
Date: 2011
DOI: 10.1071/ZO12012
Publisher: Oxford University Press (OUP)
Date: 06-10-2017
Abstract: Accurate gene tree inference is an important aspect of species tree estimation in a summary-coalescent framework. Yet, in empirical studies, inferred gene trees differ in accuracy due to stochastic variation in phylogenetic signal between targeted loci. Empiricists should, therefore, examine the consistency of species tree inference, while accounting for the observed heterogeneity in gene tree resolution of phylogenomic data sets. Here, we assess the impact of gene tree estimation error on summary-coalescent species tree inference by screening ${\\sim}2000$ exonic loci based on gene tree resolution prior to phylogenetic inference. We focus on a phylogenetically challenging radiation of Australian lizards (genus Cryptoblepharus, Scincidae) and explore effects on topology and support. We identify a well-supported topology based on all loci and find that a relatively small number of high-resolution gene trees can be sufficient to converge on the same topology. Adding gene trees with decreasing resolution produced a generally consistent topology, and increased confidence for specific bipartitions that were poorly supported when using a small number of informative loci. This corroborates coalescent-based simulation studies that have highlighted the need for a large number of loci to confidently resolve challenging relationships and refutes the notion that low-resolution gene trees introduce phylogenetic noise. Further, our study also highlights the value of quantifying changes in nodal support across locus subsets of increasing size (but decreasing gene tree resolution). Such detailed analyses can reveal anomalous fluctuations in support at some nodes, suggesting the possibility of model violation. By characterizing the heterogeneity in phylogenetic signal among loci, we can account for uncertainty in gene tree estimation and assess its effect on the consistency of the species tree estimate. We suggest that the evaluation of gene tree resolution should be incorporated in the analysis of empirical phylogenomic data sets. This will ultimately increase our confidence in species tree estimation using summary-coalescent methods and enable us to exploit genomic data for phylogenetic inference. [Coalescence concatenation Cryptoblepharus exon capture gene tree phylogenomics species tree.].
Publisher: Wiley
Date: 28-01-2014
DOI: 10.1002/ECE3.954
Publisher: CSIRO Publishing
Date: 2018
DOI: 10.1071/PC18016
Abstract: Conservation uses information from genetics to assist in management decisions. However, conservation genetics typically assesses genetic ersity at the DNA level but this alone does not address all the risks associated with managing wild and captive populations. DNA is packaged into chromosomes. Differences in the number and morphology of chromosomes between species or even between populations of the same species can have important implications for management programs for threatened species. Cytogenetics, analysis of the higher molecular chromosome structure, can provide invaluable insight for the management of threatened species, where DNA alone could not address all genetic risks and threats to populations. Here we outline the important and valuable role of cytogenetics in conservation, highlighting two case studies based on threatened Australian marsupials: rock-wallabies and the Tasmanian devil. In conclusion, we summarise how cytogenetics should be better linked to conservation genetics and integrated into our management of threatened species, to ensure they have the best platform from which to persist and adapt into the future.
Publisher: Oxford University Press (OUP)
Date: 04-04-2018
Abstract: As we collect range-wide genetic data for morphologically-defined species, we increasingly unearth evidence for cryptic ersity. Delimiting this cryptic ersity is challenging, both because the ergences span a continuum and because the lack of overt morphological differentiation suggests ergence has proceeded heterogeneously. Herein, we address these challenges as we diagnose and describe species in three co-occurring species groups of Australian lizards. By integrating genomic and morphological data with data on hybridization and introgression from contact zones, we explore several approaches-and their relative benefits and weaknesses-for testing the validity of cryptic lineages. More generally, we advocate that genetic delimitations of cryptic ersity must consider whether these lineages are likely to be durable and persistent through evolutionary time.
Publisher: Queensland Museum
Date: 29-01-2018
Publisher: Springer Science and Business Media LLC
Date: 05-02-2018
Publisher: CSIRO Publishing
Date: 2019
DOI: 10.1071/RD18201
Abstract: Marsupials have unique features that make them particularly interesting to study, and sequencing of marsupial genomes is helping to understand their evolution. A decade ago, it was a huge feat to sequence the first marsupial genome. Now, the advances in sequencing technology have made the sequencing of many more marsupial genomes possible. However, the DNA sequence is only one component of the structures it is packaged into: chromosomes. Knowing the arrangement of the DNA sequence on each chromosome is essential for a genome assembly to be used to its full potential. The importance of combining sequence information with cytogenetics has previously been demonstrated for rapidly evolving regions of the genome, such as the sex chromosomes, as well as for reconstructing the ancestral marsupial karyotype and understanding the chromosome rearrangements involved in the Tasmanian devil facial tumour disease. Despite the recent advances in sequencing technology assisting in genome assembly, physical anchoring of the sequence to chromosomes is required to achieve a chromosome-level assembly. Once chromosome-level assemblies are achieved for more marsupials, we will be able to investigate changes in the packaging and interactions between chromosomes to gain an understanding of the role genome architecture has played during marsupial evolution.
Publisher: Wiley
Date: 20-08-2016
Abstract: The evolutionary histories of species are not measured directly, but estimated using genealogies inferred for particular loci. In idual loci can have discordant histories, but in general we expect to infer evolutionary histories more accurately as more of the genome is s led. High Throughput Sequencing (HTS) is now providing opportunities to incorporate thousands of loci in 'phylogenomic' studies. Here, we used target enrichment to sequence c.3000 protein-coding exons in a group of Australian skink lizards (crown group age c.80 Ma). This method uses synthetic probes to 'capture' target exons that were identified in the transcriptomes of selected probe design (PD) s les. The target exons are then enriched in s le DNA libraries prior to performing HTS. Our main goal was to study the efficacy of enrichment of targeted loci at different levels of phylogenetic ergence from the PD species. In taxa sharing a common ancestor with PD s les up to c.20 Ma, we detected little reduction in efficacy, measured here as sequencing depth of coverage. However, at around 80 Myr ergence from the PD species, we observed an approximately two-fold reduction in efficacy. A secondary goal was to develop a workflow for analysing exon capture studies of phylogenetically erse s les, while minimizing potential bias. Our approach assembles each exon in each s le separately, by first recruiting short sequencing reads having homology to the corresponding protein sequence. In sum, custom exon capture provides a complement to existing, more generic target capture methods and is a practical and robust option across low-moderate levels of phylogenetic ergence.
Publisher: Oxford University Press (OUP)
Date: 22-09-2017
Abstract: A fundamental challenge in resolving evolutionary relationships across the tree of life is to account for heterogeneity in the evolutionary signal across loci. Studies of marsupial mammals have demonstrated that this heterogeneity can be substantial, leaving considerable uncertainty in the evolutionary timescale and relationships within the group. Using simulations and a new phylogenomic data set comprising nucleotide sequences of 1550 loci from 18 of the 22 extant marsupial families, we demonstrate the power of a method for identifying clusters of loci that support different phylogenetic trees. We find two distinct clusters of loci, each providing an estimate of the species tree that matches previously proposed resolutions of the marsupial phylogeny. We also identify a well-supported placement for the enigmatic marsupial moles (Notoryctes) that contradicts previous molecular estimates but is consistent with morphological evidence. The pattern of gene-tree variation across tree-space is characterized by changes in information content, GC content, substitution-model adequacy, and signatures of purifying selection in the data. In a simulation study, we show that incomplete lineage sorting can explain the ision of loci into the two tree-topology clusters, as found in our phylogenomic analysis of marsupials. We also demonstrate the potential benefits of minimizing uncertainty from phylogenetic conflict for molecular dating. Our analyses reveal that Australasian marsupials appeared in the early Paleocene, whereas the ersification of present-day families occurred primarily during the late Eocene and early Oligocene. Our methods provide an intuitive framework for improving the accuracy and precision of phylogenetic inference and molecular dating using genome-scale data.
Publisher: Springer Science and Business Media LLC
Date: 18-04-2014
Publisher: Wiley
Date: 16-02-2018
DOI: 10.1111/CONL.12438
Publisher: CSIRO Publishing
Date: 2016
DOI: 10.1071/AM15004
Abstract: There are significant gaps in knowledge of the small terrestrial mammals ( kg) in the Northern Kimberley bioregion (NOK). There have been no known extinctions of small mammals in the NOK, despite broad-scale declines being observed across much of northern Australia. The few studies in the NOK have focussed largely on three major national parks and NOK islands and thus may not be fully representative of the region. Mammal surveys were undertaken on Doongan Station, a pastoral property adjacent to these national parks to determine the presence/absence of small mammals. Five species were found to be common (Pseudomys nanus, P. delicatulus, Rattus tunneyi, Zyzomys argurus and Sminthopsis virginiae), two species were detected less frequently (Leggadina lakedownensis and Isoodon macrourus), and four species were scarcely detected (Melomys burtoni, Hydromys chrysogaster, Planigale maculata and Dasyurus hallucatus). Two species were detected only opportunistically outside of the survey effort (Petropseudes dahli and Petaurus breviceps). The trap success was consistently low, with levels in most years being below those regarded as critically low elsewhere in northern Australia.
Publisher: Wiley
Date: 15-03-2012
Publisher: Oxford University Press (OUP)
Date: 03-12-2021
Abstract: Chromosome rearrangements can result in the rapid evolution of hybrid incompatibilities. Robertsonian fusions, particularly those with monobrachial homology, can drive reproductive isolation amongst recently erged taxa. The recent radiation of rock-wallabies (genus Petrogale) is an important model to explore the role of Robertsonian fusions in speciation. Here, we pursue that goal using an extensive s ling of populations and genomes of Petrogale from north-eastern Australia. In contrast to previous assessments using mitochondrial DNA or nuclear microsatellite loci, genomic data are able to separate the most closely related species and to resolve their ergence histories. Both phylogenetic and population genetic analyses indicate introgression between two species that differ by a single Robertsonian fusion. Based on the available data, there is also evidence for introgression between two species which share complex chromosomal rearrangements. However, the remaining results show no consistent signature of introgression amongst species pairs and where evident, indicate generally low introgression overall. X-linked loci have elevated ergence compared with autosomal loci indicating a potential role for genic evolution to produce reproductive isolation in concert with chromosome change. Our results highlight the value of genome scale data in evaluating the role of Robertsonian fusions and structural variation in ergence, speciation, and patterns of molecular evolution.
Publisher: Wiley
Date: 19-04-2022
DOI: 10.1111/MEC.16446
Abstract: Climatic and evolutionary processes are inextricably linked to conservation. Avoiding extinction in rapidly changing environments often depends upon a species' capacity to adapt in the face of extreme selective pressures. Here, we employed exon capture and high-throughput next-generation sequencing to investigate the mechanisms underlying population structure and adaptive genetic variation in the koala (Phascolarctos cinereus), an iconic Australian marsupial that represents a unique conservation challenge because it is not uniformly threatened across its range. An examination of 250 specimens representing 91 wild source locations revealed that five major genetic clusters currently exist on a continental scale. The initial ergence of these clusters appears to have been concordant with the Mid-Brunhes Transition (~430 to 300 kya), a major climatic reorganisation that increased the litude of Pleistocene glacial-interglacial cycles. While signatures of polygenic selection and environmental adaptation were detected, strong evidence for repeated, climate-associated range contractions and demographic bottleneck events suggests that geographically isolated refugia may have played a more significant role in the survival of the koala through the Pleistocene glaciation than in situ adaptation. Consequently, the conservation of genome-wide genetic variation must be aligned with the protection of core koala habitat to increase the resilience of vulnerable populations to accelerating anthropogenic threats. Finally, we propose that the five major genetic clusters identified in this study should be accounted for in future koala conservation efforts (e.g., guiding translocations), as existing management isions in the states of Queensland and New South Wales do not reflect historic or contemporary population structure.
Publisher: CSIRO Publishing
Date: 2015
DOI: 10.1071/ZO13095
Abstract: Defining taxonomic units is an important component of understanding how bio ersity has formed, and in guiding efforts to sustain it. Understanding patterns of bio ersity across the monsoonal tropics of northern Australia is limited, with molecular technology revealing deep phylogenetic structure and complex evolutionary histories. The brachyotis group of rock-wallabies (Petrogale spp.), which currently consists of three species (Petrogale brachyotis, P. burbidgei and P. concinna) distributed across north-western Australia, provides an ex le where current taxonomy does not reflect the true ersity or phylogenetic relationships within the group. We have used an integrative approach, combining morphological data, together with DNA sequences (~1000 bp mitochondrial DNA ~3000 bp nuclear DNA) to resolve relationships within P. brachyotis. Phylogenetic and morphological analyses indicated that P. brachyotis (sensu lato) represents at least two separate species: P. brachyotis (sensu stricto) from the Kimberley and western Northern Territory, and P. wilkinsi from the northern and eastern Northern Territory. Petrogale brachyotis (sensu stricto) can be separated on genetic and morphological evidence into two subspecies: P. b. brachyotis and P. b. victoriae (subsp. nov.). Distinct genetic lineages have also been identified within both P. brachyotis and P. wilkinsi, as well as within P. burbidgei and P. concinna.
Publisher: Wiley
Date: 20-09-2019
DOI: 10.1111/JBI.13698
Publisher: Wiley
Date: 21-12-2018
DOI: 10.1111/MEC.14441
Abstract: Spatial responses of species to past climate change depend on both intrinsic traits (climatic niche breadth, dispersal rates) and the scale of climatic fluctuations across the landscape. New capabilities in generating and analysing population genomic data, along with spatial modelling, have unleashed our capacity to infer how past climate changes have shaped populations, and by extension, complex communities. Combining these approaches, we uncover lineage ersity across four codistributed lizards from the Australian Monsoonal Tropics and explore how varying climatic tolerances interact with regional climate history to generate common vs. disparate responses to late Pleistocene change. We find more ergent spatial structuring and temporal demographic responses in the drier Kimberley region compared to the more mesic and consistently suitable Top End. We hypothesize that, in general, the effects of species' traits on sensitivity to climate fluctuation will be more evident in climatically marginal regions. If true, this points to the need in climatically marginal areas to craft more species-(or trait)-specific strategies for persistence under future climate change.
Publisher: Wiley
Date: 19-06-2017
DOI: 10.1111/MEC.14185
Abstract: Species endemic to the tropical regions are expected to be vulnerable to future climate change due in part to their relatively narrow climatic niches. In addition, these species are more likely to have responded strongly to past climatic change, and this can be explored through phylogeographic analyses. To test the hypothesis that tropical specialists are more sensitive to climate change than climate generalists, we generated and analyse sequence data from mtDNA and ~2500 exons to compare scales of historical persistence and population fluctuation in two sister species of Australian rainbow skinks: the tropical specialist Carlia johnstonei and the climate generalist C. triacantha. We expect the tropical specialist species to have deeper and finer-scale phylogeographic structure and stronger demographic fluctuations relative to the closely related climate generalist species, which should have had more stable populations through periods of harsh climate in the late Quaternary. Within C. johnstonei, we find that some populations from the northern Kimberley islands are highly ergent from mainland populations. In C. triacantha, one major clade occurs across the deserts and into the mesic Top End, and another occurs primarily in the Kimberley with scattered records eastwards. Where their ranges overlap in the Kimberley, both mitochondrial DNA and nuclear DNA suggest stronger phylogeographic structure and range expansion within the tropical specialist, whereas the climate generalist has minimal structuring and no evidence of recent past range expansion. These results are consistent with the hypothesis that tropical specialists are more sensitive to past climatic change.
Publisher: CSIRO Publishing
Date: 12-10-2022
DOI: 10.1071/AM22016
Abstract: The use of correct taxonomy to describe and name the earth’s bio ersity is fundamental to conservation and management. However, there are issues that need to be overcome to ensure that the described taxa and their scientific names are both appropriate and widely adopted. Obstacles to this include the use of different species definitions, taxonomic instability due to accumulation of additional specimens in analyses and the progression of science that allows better resolution of species boundaries, and the inappropriate description and naming of new taxa without adequate scientific basis in self-published journals (known as ‘taxonomic vandalism’). In an effort to manage taxonomic instability, the Australasian Mammal Taxonomy Consortium (AMTC), an affiliated body of the Australian Mammal Society, has developed several tools that include: (1) a standardised list of Australian mammal common and scientific names (2) recommendations for information that should be included in published species descriptions and (3) support for the publication of aspidonyms (i.e. a scientifically acceptable name proposed to overwrite a pre-existing unscientific name). This review discusses these issues, reaffirms the foundations for appropriate taxonomic research, and provides guidelines for those publishing taxonomic research on Australian mammals.
Publisher: CSIRO Publishing
Date: 2013
DOI: 10.1071/PC130343
Abstract: The Australian monsoonal tropics region contains one of the planet’s largest, relatively intact tropical savannas and has been continually occupied by humans for at least 50,000 years. The region, spanning Cape York Peninsula, the Top End and the Kimberley of northern Australia has long been known to host high bio ersity, but only now is the true extent of locally unique (endemic) species and genetic ersity within each of these areas becoming apparent. Though some critical regions have been included in the national reserve system, including the iconic Kakadu National Park, the ecological and evolutionary dynamics are such that large interconnected swathes of the region need to be actively managed to sustain this unique ersity in the face of escalating anthropogenic impacts and species decline. The growth in Indigenous Protected Areas and Indigenous-owned land where Traditional Owners aspire to “care for their Country” offers an opportunity to contribute to the broader conservation effort in the region. The conservation imperative is also entwined with Aboriginal cultural aspirations. Over the last few decades there has been a resurgence of effort by Aboriginal landowners to maintain their cultural responsibilities and knowledge, pursue socio-economic development opportunities, as well as to protect the bio-cultural values of their ancestral country. In the Australian monsoonal tropics, over 40% of the landscape is under some form of Aboriginal ownership or control and emerging initiatives such as the Indigenous Protected Area programme, representing a partnership of community, government and sometimes NGOs offer one (though not the only) constructive way forward. As the biological uniqueness of the landscape is uncovered, this should bolster the perceived bio ersity value and encourage further investment in protecting it, especially through programmes that promote engagement with, and employment of, Aboriginal communities. For this to be sustainable, the discovery and management of the region’s bio ersity needs to be driven increasingly by Aboriginal land owners with clear cultural and community, as well as bio ersity, benefits. This
Publisher: Proceedings of the National Academy of Sciences
Date: 18-07-2016
Abstract: Phylogeography, and its extensions into comparative phylogeography, have their roots in the layering of gene trees across geography, a paradigm that was greatly facilitated by the nonrecombining, fast evolution provided by animal mtDNA. As phylogeography moves into the era of next-generation sequencing, the specter of reticulation at several levels—within loci and genomes in the form of recombination and across populations and species in the form of introgression—has raised its head with a prominence even greater than glimpsed during the nuclear gene PCR era. Here we explore the theme of reticulation in comparative phylogeography, speciation analysis, and phylogenomics, and ask how the centrality of gene trees has fared in the next-generation era. To frame these issues, we first provide a snapshot of multilocus phylogeographic studies across the Carpentarian Barrier, a prominent biogeographic barrier iding faunas spanning the monsoon tropics in northern Australia. We find that ergence across this barrier is evident in most species, but is heterogeneous in time and demographic history, often reflecting the taxonomic distinctness of lineages spanning it. We then discuss a variety of forces generating reticulate patterns in phylogeography, including introgression, contact zones, and the potential selection-driven outliers on next-generation molecular markers. We emphasize the continued need for demographic models incorporating reticulation at the level of genomes and populations, and conclude that gene trees, whether explicit or implicit, should continue to play a role in the future of phylogeography.
Publisher: MDPI AG
Date: 31-01-2020
Abstract: Little genetic research has been undertaken on mammals across the vast expanse of the arid biome in Australia, despite continuing species decline and need for conservation management. Here, we evaluate the contemporary and historical genetic connectivity of the yellow-footed rock-wallaby, Petrogale xanthopus xanthopus, a threatened macropodid which inhabits rocky outcrops across the disconnected mountain range systems of the southern arid biome. We use 17 microsatellite loci together with mitochondrial control region data to determine the genetic ersity of populations and the evolutionary processes shaping contemporary population dynamics on which to base conservation recommendations. Our results indicate the highly fragmented populations have reduced ersity and limited contemporary gene flow, with most populations having been through population bottlenecks. Despite limited contemporary gene flow, the phylogeographic relationships of the mitochondrial control region indicate a lack of structure and suggests greater historical connectivity. This is an emerging outcome for mammals across this arid region. On the basis of our results, we recommend augmentation of populations of P. x. xanthopus, mixing populations from disjunct mountain range systems to reduce the chance of continued ersity loss and inbreeding depression, and therefore maximize the potential for populations to adapt and survive into the future.
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: Hindawi Limited
Date: 13-01-2020
DOI: 10.1111/JZS.12355
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: Informa UK Limited
Date: 02-01-2016
Publisher: Wiley
Date: 12-2013
DOI: 10.1111/MEC.12565
Abstract: Prioritization of taxa for conservation must rest on a foundation of correctly identified species boundaries, enhanced by an understanding of evolutionary history and phylogenetic relationships. Therefore, we can incorporate both evolutionary and ecological processes into efforts to sustain bio ersity. In this issue of Molecular Ecology, Malaney & Cook (2013) highlight the critical value of an evolutionary biogeographical approach, combining multilocus phylogeography with climatic niche modelling to infer phylogenetically weighted conservation priorities for evolutionary lineages of jumping mice across North America. Remarkably, they find that the Preble's meadow jumping mouse (Zapus hudsonius preblei), long debated as a threatened taxon, in fact represents the southern terminus of a relatively uniform lineage that expanded well into Alaska during the Holocene. By contrast, some other relictual and phylogenetically ergent taxa of jumping mice likely warrant greater conservation priority. This study highlights the value of integrative approaches that place current taxonomy in a broader evolutionary context to identify taxa for conservation assessment, but also highlights the challenges in maintaining potential for adaptive responses to environmental change.
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: Wiley
Date: 22-11-2018
DOI: 10.1111/EVO.13380
Abstract: Understanding the joint evolutionary and ecological underpinnings of sympatry among close relatives remains a key challenge in biology. This problem can be addressed through joint phylogenomic and phenotypic analysis of complexes of closely related lineages within, and across, species and hence representing the speciation continuum. For a complex of tropical geckos from northern Australia-Gehyra nana and close relatives-we combine mtDNA phylogeography, exon-capture sequencing, and morphological data to resolve independently evolving lineages and infer their ergence history and patterns of morphological evolution. Gehyra nana is found to include nine ergent lineages and is paraphyletic with four other species from the Kimberley region of north-west Australia. Across these 13 taxa, 12 of which are restricted to rocky habitats, several lineages overlap geographically, including on the erse Kimberley islands. Morphological evolution is dominated by body size shifts, and both body size and shape have evolved gradually across the group. However, larger body size shifts are observed among overlapping taxa than among closely related parapatric lineages of G. nana, and sympatric lineages are more ergent than expected at random. Whether elevated body size differences among sympatric lineages are due to ecological sorting or character displacement remains to be determined.
Publisher: Frontiers Media SA
Date: 10-02-2017
Start Date: 06-2022
End Date: 06-2027
Amount: $824,020.00
Funder: Australian Research Council
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