ORCID Profile
0000-0002-1165-4427
Current Organisation
Museum & Art Gallery of the Northern Territory
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Phylogeny and Comparative Analysis | Speciation and Extinction | Population, Ecological and Evolutionary Genetics | Evolutionary Biology
Expanding Knowledge in the Biological Sciences | Flora, Fauna and Biodiversity at Regional or Larger Scales |
Publisher: Oxford University Press (OUP)
Date: 19-06-2021
Abstract: Color polymorphism—two or more heritable color phenotypes maintained within a single breeding population—is an extreme type of intraspecific ersity widespread across the tree of life. Color polymorphism is hypothesized to be an engine for speciation, where morph loss or ergence between distinct color morphs within a species results in the rapid evolution of new lineages, and thus, color polymorphic lineages are expected to display elevated ersification rates. Multiple species in the lizard family Lacertidae are color polymorphic, making them an ideal group to investigate the evolutionary history of this trait and its influence on macroevolution. Here, we produce a comprehensive species-level phylogeny of the lizard family Lacertidae to reconstruct the evolutionary history of color polymorphism and test if color polymorphism has been a driver of ersification. Accounting for phylogenetic uncertainty with multiple phylogenies and simulation studies, we estimate an ancient origin of color polymorphism (111 Ma) within the Lacertini tribe (subfamily Lacertinae). Color polymorphism most likely evolved few times in the Lacertidae and has been lost at a much faster rate than gained. Evolutionary transitions to color polymorphism are associated with shifts in increased net ersification rate in this family of lizards. Taken together, our empirical results support long-standing theoretical expectations that color polymorphism is a driver of ersification.[Color polymorphism Lacertidae state-dependent speciation extinction models trait-dependent ersification.]
Publisher: Cold Spring Harbor Laboratory
Date: 12-09-2017
DOI: 10.1101/187534
Abstract: High-throughput DNA sequencing allows efficient discovery of thousands of single nucleotide polymorphisms (SNPs) in non-model species. Population genetic theory predicts that this large number of independent markers should provide detailed insights into population structure, even when only a few in iduals are s led. Still, s ling design can have a strong impact on such inferences. Here, we use simulations and empirical SNP data to investigate the impacts of s ling design on estimating genetic differentiation among populations that represent three species of Galápagos giant tortoises ( Chelonoidis spp.). Though microsatellite and mitochondrial DNA analyses have supported the distinctiveness of these species, a recent study called into question how well these markers matched with data from genomic SNPs, thereby questioning decades of studies in non-model organisms. Using ,000 genome-wide SNPs from 30 in iduals from three Galápagos giant tortoise species, we find distinct structure that matches the relationships described by the traditional genetic markers. Furthermore, we confirm that accurate estimates of genetic differentiation in highly structured natural populations can be obtained using thousands of SNPs and 2-5 in iduals, or hundreds of SNPs and 10 in iduals, but only if the units of analysis are delineated in a way that is consistent with evolutionary history. We show that the lack of structure in the recent SNP-based study was likely due to unnatural grouping of in iduals and erroneous genotype filtering. Our study demonstrates that genomic data enable patterns of genetic differentiation among populations to be elucidated even with few s les per population, and underscores the importance of s ling design. These results have specific implications for studies of population structure in endangered species and subsequent management decisions. “Modern molecular techniques provide unprecedented power to understand genetic variation in natural populations. Nevertheless, application of this information requires sound understanding of population genetics theory.” - Fred Allendorf (2017, p. 420)
Publisher: Wiley
Date: 05-06-2013
DOI: 10.1111/EVO.12159
Abstract: Tests of the genetic structure of empirical populations typically focus on the correlative relationships between population connectivity and geographic and/or environmental factors in landscape genetics. However, such tests may overlook or misidentify the impact of candidate factors on genetic structure, especially when connectivity patterns differ between past and present populations because of shifting environmental conditions over time. Here we account for the underlying demographic component of population connectivity associated with a temporarily dynamic landscape in tests of the factors structuring population genetic variation in an Australian lizard, Lerista lineopunctulata, from 24 nuclear loci. Correlative tests did not support significant effect from factors associated with a static contemporary landscape. However, spatially explicit demographic modeling of genetic differentiation shows that changes in environmental conditions (as estimated from paleoclimatic data) and corresponding distributional shifts from the past to present landscape significantly structures genetic variation. Results from model-based inference (i.e., from an integrative modeling approach that generates spatially explicit expectations that are tested with approximate Bayesian computation) contrasts with those from correlative analyses, highlighting the importance of expanding the landscape genetic perspective to tests the links between pattern and process, revealing how factors shape patterns of genetic variation within species.
Publisher: Springer Science and Business Media LLC
Date: 12-06-2014
Publisher: Elsevier BV
Date: 2013
Publisher: Springer Science and Business Media LLC
Date: 13-09-2017
DOI: 10.1038/S41598-017-11516-2
Abstract: Species are being lost at an unprecedented rate due to human-driven environmental changes. The cases in which species declared extinct can be revived are rare. However, here we report that a remote volcano in the Galápagos Islands hosts many giant tortoises with high ancestry from a species previously declared as extinct: Chelonoidis elephantopus or the Floreana tortoise. Of 150 in iduals with distinctive morphology s led from the volcano, genetic analyses revealed that 65 had C. elephantopus ancestry and thirty-two were translocated from the volcano’s slopes to a captive breeding center. A genetically informed captive breeding program now being initiated will, over the next decades, return C. elephantopu s tortoises to Floreana Island to serve as engineers of the island’s ecosystems. Ironically, it was the haphazard translocations by mariners killing tortoises for food centuries ago that created the unique opportunity to revive this “lost” species today.
Publisher: Wiley
Date: 05-02-2013
DOI: 10.1111/JBI.12077
Publisher: Society for the Study of Amphibians and Reptiles
Date: 12-2011
DOI: 10.1670/10-115.1
Publisher: Elsevier BV
Date: 09-2022
Publisher: Cold Spring Harbor Laboratory
Date: 28-08-2020
DOI: 10.1101/2020.08.27.270207
Abstract: Color polymorphism – two or more heritable color phenotypes maintained within a single breeding population – is an extreme type of intra-specific ersity widespread across the tree of life but rarely studied in a comparative framework. Color polymorphism is thought to be an engine for speciation, where morph loss or ergence between distinct color morphs within a species results in the rapid evolution of new lineages, and thus, color polymorphic lineages are expected to display elevated ersification rates. Lizards of the family Lacertidae have evolved multiple lineages with color polymorphism, but lack of a complete and robust phylogeny for the group has made comparative analysis difficult. Here, we produce a comprehensive species-level phylogeny of the lizard family Lacertidae to reconstruct the evolutionary history of color polymorphism and test if color polymorphism has been a driver of ersification. Accounting for phylogenetic uncertainty, we estimate an ancient macroevolutionary origin of color polymorphism within the Lacertini tribe (subfamily Lacertinae). Color polymorphism most likely evolved several times in the Lacertidae and has been lost at a much faster rate than gained. Evolutionary transitions to color polymorphism are associated with shifts in increased net ersification rate in this family of lizards. Taken together, our empirical results support long-standing theoretical expectations that color polymorphism is a driver of ersification.
Publisher: Elsevier BV
Date: 05-2003
Publisher: PeerJ
Date: 05-11-2020
DOI: 10.7717/PEERJ.10284
Abstract: Color polymorphism defies evolutionary expectations as striking phenotypic variation is maintained within a single species. Color and other traits mediate social interactions, and stable polymorphism within a population is hypothesized to be related to correlational selection of other phenotypic traits among color morphs. Here, we report on a previously unknown throat color polymorphism in the Aegean Wall Lizard ( Podarcis erhardii ) and examine morph-correlated differences in traits important to social behavior and communication: maximum bite force capacity and chemical signal profile. We find that both sexes of P. erhardii have three color morphs: orange, yellow, and white. Moreover, orange males are significantly larger and tend to bite harder than yellow and white males. Although the established color polymorphism only partially matches the observed intraspecific variation in chemical signal signatures, the chemical profile of the secretions of orange males is significantly ergent from that of white males. Our findings suggest that morph colors are related to differences in traits that are crucial for social interactions and competitive ability, illustrating the need to look beyond color when studying polymorphism evolution.
Publisher: Wiley
Date: 04-10-2014
DOI: 10.1111/MEC.12919
Abstract: Although many classic radiations on islands are thought to be the result of repeated lineage splitting, the role of past fusion is rarely known because during these events, purebreds are rapidly replaced by a swarm of admixed in iduals. Here, we capture lineage fusion in action in a Galápagos giant tortoise species, Chelonoidis becki, from Wolf Volcano (Isabela Island). The long generation time of Galápagos tortoises and dense s ling (841 in iduals) of genetic and demographic data were integral in detecting and characterizing this phenomenon. In C. becki, we identified two genetically distinct, morphologically cryptic lineages. Historical reconstructions show that they colonized Wolf Volcano from Santiago Island in two temporally separated events, the first estimated to have occurred ~199 000 years ago. Following arrival of the second wave of colonists, both lineages coexisted for approximately ~53 000 years. Within that time, they began fusing back together, as microsatellite data reveal widespread introgressive hybridization. Interestingly, greater mate selectivity seems to be exhibited by purebred females of one of the lineages. Forward-in-time simulations predict rapid extinction of the early arriving lineage. This study provides a rare ex le of reticulate evolution in action and underscores the power of population genetics for understanding the past, present and future consequences of evolutionary phenomena associated with lineage fusion.
Publisher: Wiley
Date: 30-05-2012
Publisher: Wiley
Date: 25-06-2021
DOI: 10.1111/JEB.13881
Abstract: Understanding the relative importance of sexual and natural selection in shaping morphological traits is a long‐standing goal of evolutionary ecology. Male‐biased sexual size dimorphism (SSD) is typically associated with male–male competition. Similarly, male polymorphisms are considered a consequence of competitive social interactions. This classic paradigm overlooks the fact that environmental factors mediate social interactions and can lead to ecological adaptations. Common side‐blotched lizards, Uta stansburiana , are a model system for this paradigm due to well‐known rock‐paper‐scissors social dynamics between male morphs. SSD in this species has been considered primarily a consequence of social interactions, with male size resulting from the number of morphs in each population and female size being constrained through fecundity benefits. We test if the environment explains intraspecific variation in SSD and number of male morphs in U. stansburiana . By compiling data from 49 populations, we show that environmental variables are stronger predictors of SSD than the number of male morphs. Similarly, we show that the environment mediates SSD and potentially contributes to morph loss in colder environments. We propose that the environment favours smaller males in areas of high seasonality. Our results demonstrate the importance of the environment as a mediator of SSD.
Publisher: CSIRO Publishing
Date: 2011
DOI: 10.1071/ZO11005
Abstract: Outlining the distribution of genetic variation, patterns of gene flow and clarifying the biogeographic processes underlying population history are critical components of a comprehensive conservation strategy for endangered or vulnerable species. We provide this information for the vulnerable sunset frog (Spicospina flammocaerulea) using a comprehensive genetic dataset (ND2) with s les from 17 of 22 geographic localities where this species has been found. From genetic, biogeographic and coalescent-based analyses, we document the existing genetic variation, likely movement patterns and explore the biogeographic history of S. flammocaerulea. While catchment-based genetic variation is well documented in other high-rainfall taxa in south-western Australia, a much more complex scenario including dispersal across ridge lines between catchments better explains the distribution of genetic variation and observed patterns of gene flow in S. flammocaerulea. The population history of S. flammocaerulea is strongly indicative of recent population contraction and expansion, which may be related to late Pleistocene climate fluctuations. This suggests that this species can adapt or move in response to fluctuating climates provided suitable habitats or expansion areas are available. However, like many other endemic taxa with limited geographic ranges in south-western Australia, the potential to shift distributions is h ered by being land-locked within an agricultural landscape, limiting management options in the face of climate change.
Publisher: Springer Science and Business Media LLC
Date: 12-03-2018
DOI: 10.1038/S41598-018-22519-Y
Abstract: A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Publisher: Wiley
Date: 23-10-2017
DOI: 10.1111/EVA.12551
Abstract: High‐throughput DNA sequencing allows efficient discovery of thousands of single nucleotide polymorphisms ( SNP s) in nonmodel species. Population genetic theory predicts that this large number of independent markers should provide detailed insights into population structure, even when only a few in iduals are s led. Still, s ling design can have a strong impact on such inferences. Here, we use simulations and empirical SNP data to investigate the impacts of s ling design on estimating genetic differentiation among populations that represent three species of Galápagos giant tortoises ( Chelonoidis spp.). Though microsatellite and mitochondrial DNA analyses have supported the distinctiveness of these species, a recent study called into question how well these markers matched with data from genomic SNP s, thereby questioning decades of studies in nonmodel organisms. Using ,000 genomewide SNP s from 30 in iduals from three Galápagos giant tortoise species, we find distinct structure that matches the relationships described by the traditional genetic markers. Furthermore, we confirm that accurate estimates of genetic differentiation in highly structured natural populations can be obtained using thousands of SNP s and 2–5 in iduals, or hundreds of SNP s and 10 in iduals, but only if the units of analysis are delineated in a way that is consistent with evolutionary history. We show that the lack of structure in the recent SNP ‐based study was likely due to unnatural grouping of in iduals and erroneous genotype filtering. Our study demonstrates that genomic data enable patterns of genetic differentiation among populations to be elucidated even with few s les per population, and underscores the importance of s ling design. These results have specific implications for studies of population structure in endangered species and subsequent management decisions.
Publisher: Public Library of Science (PLoS)
Date: 06-2021
DOI: 10.1371/JOURNAL.PBIO.3001210
Abstract: Global bio ersity loss is a profound consequence of human activity. Disturbingly, bio ersity loss is greater than realized because of the unknown number of undocumented species. Conservation fundamentally relies on taxonomic recognition of species, but only a fraction of bio ersity is described. Here, we provide a new quantitative approach for prioritizing rigorous taxonomic research for conservation. We implement this approach in a highly erse vertebrate group—Australian lizards and snakes. Of 870 species assessed, we identified 282 (32.4%) with taxonomic uncertainty, of which 17.6% likely comprise undescribed species of conservation concern. We identify 24 species in need of immediate taxonomic attention to facilitate conservation. Using a broadly applicable return-on-investment framework, we demonstrate the importance of prioritizing the fundamental work of identifying species before they are lost.
Publisher: Magnolia Press
Date: 09-2017
DOI: 10.11646/ZOOTAXA.4317.1.5
Abstract: The Dotted-Line Robust Slider, Lerista lineopunctulata (Duméril & Bibron, 1839), is widely distributed along the western coast of Western Australia. An investigation of ersity within this taxon showed a clear split between northern and southern populations in the vicinity of Jurien. Accordingly, Lerista lineopunctulata is restricted to the southern population while the northern is recognised as Lerista miopus (Günther, 1867). Both taxa are redescribed and diagnosed and a neotype for L. miopus is designated.
Publisher: University of Chicago Press
Date: 12-2015
DOI: 10.1086/683658
Abstract: Species ersification often results from ergent evolution of ecological or social signaling traits. Theoretically, a combination of the two may promote speciation, however, empirical ex les studying how social signal and ecological ergence might be involved in ersification are rare in general and typically do not consider range overlap as a contributing factor. We show that ecologically distinct lineages within the Australian sand dragon species complex (including Ctenophorus maculatus, Ctenophorus fordi, and Ctenophorus femoralis) have ersified recently, erging in ecologically relevant and social signaling phenotypic traits as arid habitats expanded and differentiated. Diversification has resulted in repeated and independent invasion of distinct habitat types, driving convergent evolution of similar phenotypes. Our results suggest that parapatry facilitates ersification in visual signals through reinforcement as a hybridization-avoidance mechanism. We show that particularly striking variation in visual social signaling traits is better explained by the extent of lineage parapatry relative to ecological or phylogenetic ergence, suggesting that these traits reinforce ergence among lineages initiated by ecologically adaptive evolution. This study provides a rare empirical ex le of a repeated, intricate relationship between ecological and social signal evolution during ersification driven by ecological ergence and the evolution of new habitats, thereby supporting emergent theories regarding the importance of both ecological and social trait evolution throughout speciation.
Publisher: Public Library of Science (PLoS)
Date: 21-10-2015
Publisher: Wiley
Date: 24-01-2012
DOI: 10.1111/J.1420-9101.2012.02460.X
Abstract: Body size affects life history, the ecological niche of an organism and its interactions with other organisms. Resultantly, marked differences in body size between related organisms are often an indication of a species boundary. This is particularly evident in the Gehyra variegata species complex of geckos, which displays differential body sizes between genetically ergent species, but high levels of intraspecific morphological conservatism. We report on a Gehyra population that displays extraordinary body size differentiation in comparison with other G. variegata species. We used morphological and environmental data to show this population is phenotypically and ecologically distinct from its parapatric congener Gehyra lazelli and that morphology and ecology are significantly correlated. Contrastingly, mtDNA analysis indicates paraphyly between the two groups, and allele frequencies at six microsatellite loci show no population structure concordant with morpho-/ecotype. These results suggest either ecological speciation or environmentally induced phenotypic polymorphism, in an otherwise morphologically conservative group.
Publisher: Oxford University Press (OUP)
Date: 06-04-2018
Abstract: Empirical population genetic studies generally rely on s ling subsets of the population(s) of interest and of the nuclear or organellar genome targeted, assuming each is representative of the whole. Violations of these assumptions may impact population-level parameter estimation and lead to spurious inferences. Here, we used targeted capture to sequence the full mitochondrial genome from 123 in iduals of the Galapagos giant tortoise endemic to Pinzón Island (Chelonoidis duncanensis) s led at 2 time points pre- and postbottleneck (circa 1906 and 2014) to explicitly assess differences in ersity estimates and demographic reconstructions based on subsets of the mitochondrial genome versus the full sequences and to evaluate potential biases associated with ersity estimates and demographic reconstructions from postbottlenecked s les alone. Haplotypic ersities were equal between the temporal s les based on the full mitochondrial genome, but single gene estimates suggested either decreases or increases in ersity depending upon the region. Demographic reconstructions based on the full sequence were more similar between the temporal s les than those based on the control region alone, or a subset of 3 regions, where the trends in population size changes shifted in magnitude and direction between the temporal s les. In all cases, the estimated coalescent point was more distant for the historical than contemporary s le. In summary, our results empirically demonstrate the influence of s ling bias when interpreting population genetic patterns and punctuate the need for careful consideration of potentially conflicting evolutionary signal across the mitochondrial genome.
Publisher: Wiley
Date: 25-06-2007
Publisher: Wiley
Date: 03-2010
Publisher: Elsevier BV
Date: 11-2007
DOI: 10.1016/J.YMPEV.2007.05.023
Abstract: Within the southwestern Australian bio ersity hotspot, the Shark Bay region displays high levels of plant and animal endemism, particularly in the herpetofauna. The region has been subjected to dramatic climatic fluctuations and has been geologically active from the Late Miocene to the present. The myobatrachid frog Arenophryne rotunda, a Shark Bay endemic, provides an ideal opportunity to examine the relative effects of fluctuating climates and geological activity on the biota of Shark Bay. A comprehensive phylogeographic analysis of A. rotunda, based on data comprising 1154 bp of the mitochondrial gene ND2, is presented. My results demonstrate a major genetic break that ides this species at the northern edge of the Victorian Plateau into northern and southern species lineages, dating to the Late Miocene, with a further ision of the southern species lineage across the Murchison Gorge dating to the Plio-Pleistocene border. Both of these periods are related to prominent geological activity and climatic shifts in the Shark Bay region. Interpretation of phylogeographic results point to the prominent role of fluctuating Pleistocene climates and associated coastal landscape evolution in the generation of phylogeographic structure within the distinct A. rotunda species lineages. Similar processes have been invoked to explain the ersity of other Shark Bay biota.
Publisher: Oxford University Press (OUP)
Date: 07-07-2018
Abstract: Genome-wide assessments allow for fuller characterization of genetic ersity, finer-scale population delineation, and better detection of demographically significant units to guide conservation compared with those based on "traditional" markers. Galapagos giant tortoises (Chelonoidis spp.) have long provided a case study for how evolutionary genetics may be applied to advance species conservation. Ongoing efforts to bolster tortoise populations, which have declined by 90%, have been informed by analyses of mitochondrial DNA sequence and microsatellite genotypic data, but could benefit from genome-wide markers. Taking this next step, we used double-digest restriction-site associated DNA sequencing to collect genotypic data at >26000 single nucleotide polymorphisms (SNPs) for 117 in iduals representing all recognized extant Galapagos giant tortoise species. We then quantified genetic ersity, population structure, and compared results to estimates from mitochondrial DNA and microsatellite loci. Our analyses detected 12 genetic lineages concordant with the 11 named species as well as previously described structure within one species, C. becki. Furthermore, the SNPs provided increased resolution, detecting admixture in 4 in iduals. SNP-based estimates of ersity and differentiation were significantly correlated with those derived from nuclear microsatellite loci and mitochondrial DNA sequences. The SNP toolkit presented here will serve as a resource for advancing efforts to understand tortoise evolution, species radiations, and aid conservation of the Galapagos tortoise species complex.
Publisher: Springer Science and Business Media LLC
Date: 31-08-2015
Publisher: CSIRO Publishing
Date: 28-09-2020
DOI: 10.1071/ZO21017
Abstract: Australian lizards are a erse group distributed across the continent and inhabiting a wide range of environments. Together, they exhibit a remarkable ersity of reproductive morphologies, physiologies, and behaviours that is broadly representative of vertebrates in general. Many reproductive traits exhibited by Australian lizards have evolved independently in multiple lizard lineages, including sociality, complex signalling and mating systems, viviparity, and temperature-dependent sex determination. Australian lizards are thus outstanding model organisms for testing hypotheses about how reproductive traits function and evolve, and they provide an important basis of comparison with other animals that exhibit similar traits. We review how research on Australian lizard reproduction has contributed to answering broader evolutionary and ecological questions that apply to animals in general. We focus on reproductive traits, processes, and strategies that are important areas of current research, including behaviours and signalling involved in courtship mechanisms involved in mating, egg production, and sperm competition nesting and gestation sex determination and finally, birth in viviparous species. We use our review to identify important questions that emerge from an understanding of this body of research when considered holistically. Finally, we identify additional research questions within each topic that Australian lizards are well suited for reproductive biologists to address.
Publisher: The Royal Society
Date: 22-02-2014
Abstract: Statistical species delimitation usually relies on singular data, primarily genetic, for detecting putative species and in idual assignment to putative species. Given the variety of speciation mechanisms, singular data may not adequately represent the genetic, morphological and ecological ersity relevant to species delimitation. We describe a methodological framework combining multivariate and clustering techniques that uses genetic, morphological and ecological data to detect and assign in iduals to putative species. Our approach recovers a similar number of species recognized using traditional, qualitative taxonomic approaches that are not detected when using purely genetic methods. Furthermore, our approach detects groupings that traditional, qualitative taxonomic approaches do not. This empirical test suggests that our approach to detecting and assigning in iduals to putative species could be useful in species delimitation despite varying levels of differentiation across genetic, phenotypic and ecological axes. This work highlights a critical, and often overlooked, aspect of the process of statistical species delimitation—species detection and in idual assignment. Irrespective of the species delimitation approach used, all downstream processing relies on how in iduals are initially assigned, and the practices and statistical issues surrounding in idual assignment warrant careful consideration.
Publisher: Public Library of Science (PLoS)
Date: 15-03-2017
Publisher: Wiley
Date: 15-09-2008
Publisher: Cold Spring Harbor Laboratory
Date: 27-05-2017
DOI: 10.1101/143131
Abstract: Species are being lost at an unprecedented rate due to human-driven environmental changes. The cases in which species declared extinct can be revived are rare. However, here we report that a remote volcano in the Galápagos Islands hosts many giant tortoises with high ancestry from a species previously declared as extinct: Chelonoidis elephantopus or the Floreana tortoise. Of 150 in iduals with distinctive morphology s led from the volcano, genetic analyses revealed that 65 had C. elephantopus ancestry and thirty-two were translocated from the volcano’s slopes to a captive breeding center. A genetically informed captive breeding program now being initiated will, over the next decades, return C. elephantopu s tortoises to Floreana Island to serve as engineers of the island’s ecosystems. Ironically, it was the haphazard translocations by mariners killing tortoises for food centuries ago that created the unique opportunity to revive this “lost” species today.
Publisher: Springer Science and Business Media LLC
Date: 03-12-2018
DOI: 10.1038/S41559-018-0733-X
Abstract: Giant tortoises are among the longest-lived vertebrate animals and, as such, provide an excellent model to study traits like longevity and age-related diseases. However, genomic and molecular evolutionary information on giant tortoises is scarce. Here, we describe a global analysis of the genomes of Lonesome George—the iconic last member of Chelonoidis abingdonii —and the Aldabra giant tortoise ( Aldabrachelys gigantea ). Comparison of these genomes with those of related species, using both unsupervised and supervised analyses, led us to detect lineage-specific variants affecting DNA repair genes, inflammatory mediators and genes related to cancer development. Our study also hints at specific evolutionary strategies linked to increased lifespan, and expands our understanding of the genomic determinants of ageing. These new genome sequences also provide important resources to help the efforts for restoration of giant tortoise populations.
Publisher: The Royal Society
Date: 05-09-2008
Abstract: The Pacific iguanas of the Fijian and Tongan archipelagos are a biogeographic enigma in that their closest relatives are found only in the New World. They currently comprise two genera and four species of extinct and extant taxa. The two extant species, Brachylophus fasciatus from Fiji, Tonga, and Vanuatu and Brachylophus vitiensis from western Fiji, are of considerable conservation concern with B. vitiensis listed as critically endangered. A recent molecular study has shown that Brachylophus comprised three evolutionarily significant units. To test these conclusions and to reevaluate the phylogenetic and biogeographic relationships within Brachylophus , we generated an mtDNA dataset consisting of 1462 base pairs for 61 in iduals from 13 islands, representing both Brachylophus species. Unweighted parsimony analyses and Bayesian analyses produced a well-resolved phylogenetic hypothesis supported by high bootstrap values and posterior probabilities within Brachylophus . Our data reject the monophyly of specimens previously believed to comprise B. fasciatus . Instead, our data demonstrate that living Brachylophus comprise three robust and well-supported clades that do not correspond to current taxonomy. One of these clades comprises B. fasciatus from the Lau group of Fiji and Tonga (type locality for B. fasciatus ), while a second comprises putative B. fasciatus from the central regions of Fiji, which we refer to here as B . n. sp. Animals in this clade form the sister group to B. vitiensis rather than other B. fasciatus . We herein describe this clade as a new species of Brachylophus based on molecular and morphological data. With only one exception, every island is home to one or more unique haplotypes. We discuss alternative biogeographic hypotheses to explain their distribution in the Pacific and the difficulties of distinguishing these. Together, our molecular and taxonomic results have important implications for future conservation initiatives for the Pacific iguanas.
Publisher: Wiley
Date: 13-08-2018
DOI: 10.1111/EVA.12682
Publisher: Springer Science and Business Media LLC
Date: 25-02-2022
DOI: 10.1038/S41437-022-00510-8
Abstract: The Galapagos Archipelago is recognized as a natural laboratory for studying evolutionary processes. San Cristóbal was one of the first islands colonized by tortoises, which radiated from there across the archipelago to inhabit 10 islands. Here, we sequenced the mitochondrial control region from six historical giant tortoises from San Cristóbal (five long deceased in iduals found in a cave and one found alive during an expedition in 1906) and discovered that the five from the cave are from a clade that is distinct among known Galapagos giant tortoises but closely related to the species from Española and Pinta Islands. The haplotype of the in idual collected alive in 1906 is in the same clade as the haplotype in the contemporary population. To search for traces of a second lineage in the contemporary population on San Cristóbal, we closely examined the population by sequencing the mitochondrial control region for 129 in iduals and genotyping 70 of these for both 21 microsatellite loci and ,000 genome-wide single nucleotide polymorphisms [SNPs]. Only a single mitochondrial haplotype was found, with no evidence to suggest substructure based on the nuclear markers. Given the geographic and temporal proximity of the two deeply ergent mitochondrial lineages in the historical s les, they were likely sympatric, raising the possibility that the lineages coexisted. Without the museum s les, this important discovery of an additional lineage of Galapagos giant tortoise would not have been possible, underscoring the value of such collections and providing insights into the early evolution of this iconic radiation.
Publisher: Wiley
Date: 15-08-2014
DOI: 10.1111/BRV.12132
Abstract: The south-western land ision of Western Australia (SWWA), bordering the temperate Southern and Indian Oceans, is the only global bio ersity hotspot recognised in Australia. Renowned for its extraordinary ersity of endemic plants, and for some of the largest and most botanically significant temperate heathlands and woodlands on Earth, SWWA has long fascinated biogeographers. Its flat, highly weathered topography and the apparent absence of major geographic factors usually implicated in biotic ersification have challenged attempts to explain patterns of biogeography and mechanisms of speciation in the region. Botanical studies have always been central to understanding the bio ersity values of SWWA, although surprisingly few quantitative botanical analyses have allowed for an understanding of historical biogeographic processes in both space and time. Faunistic studies, by contrast, have played little or no role in defining hotspot concepts, despite several decades of accumulating quantitative research on the phylogeny and phylogeography of multiple lineages. In this review we critically analyse datasets with explicit supporting phylogenetic data and estimates of the time since ergence for all available elements of the terrestrial fauna, and compare these datasets to those available for plants. In situ speciation has played more of a role in shaping the south-western Australian fauna than has long been supposed, and has occurred in numerous endemic lineages of freshwater fish, frogs, reptiles, snails and less-vagile arthropods. By contrast, relatively low levels of endemism are found in birds, mammals and highly dispersive insects, and in situ speciation has played a negligible role in generating local endemism in birds and mammals. Quantitative studies provide evidence for at least four mechanisms driving patterns of endemism in south-western Australian animals, including: (i) relictualism of ancient Gondwanan or Pangaean taxa in the High Rainfall Province (ii) vicariant isolation of lineages west of the Nullarbor ide (iii) in situ speciation and (iv) recent population sub ision. From dated quantitative studies we derive four testable models of historical biogeography for animal taxa in SWWA, each explicit in providing a spatial, temporal and topological perspective on patterns of speciation or ergence. For each model we also propose candidate lineages that may be worthy of further study, given what we know of their taxonomy, distributions or relationships. These models formalise four of the strongest patterns seen in many animal taxa from SWWA, although other models are clearly required to explain particular, idiosyncratic patterns. Generating numerous new datasets for suites of co-occurring lineages in SWWA will help refine our understanding of the historical biogeography of the region, highlight gaps in our knowledge, and allow us to derive general postulates from quantitative (rather than qualitative) results. For animals, this process has now begun in earnest, as has the process of taxonomically documenting many of the more erse invertebrate lineages. The latter remains central to any attempt to appreciate holistically biogeographic patterns and processes in SWWA, and molecular phylogenetic studies should - where possible - also lead to tangible taxonomic outcomes.
Publisher: Wiley
Date: 06-2022
DOI: 10.1002/ECE3.9009
Abstract: Evolutionary correlations between phenotypic and environmental traits characterize adaptive radiations. However, the lizard genus Liolaemus , one of the most ecologically erse terrestrial vertebrate radiations on earth, has so far shown limited or mixed evidence of adaptive ersification in phenotype. Restricted use of comprehensive environmental data, incomplete taxonomic representation and not considering phylogenetic uncertainty may have led to contradictory evidence. We compiled a 26‐taxon dataset for the Liolaemus gracilis species group, representing much of the ecological ersity represented within Liolaemus and used environmental data to characterize how environments occupied by species' relate to phenotypic evolution. Our analyses, explicitly accounting for phylogenetic uncertainty, suggest ersification in phenotypic traits toward the present, with body shape evolution rapidly evolving in this group. Body shape evolution correlates with the occupation of different structural habitats indicated by vegetation axes suggesting species have adapted for maximal locomotory performance in these habitats. Our results also imply that the effects of phylogenetic uncertainty and model misspecification may be more extensive on univariate, relative to multivariate analyses of evolutionary correlations, which is an important consideration in analyzing data from rapidly radiating adaptive radiations.
Start Date: 2015
End Date: 2017
Funder: Australian Research Council
View Funded ActivityStart Date: 2023
End Date: 2027
Funder: U.S. Bureau of Land Management
View Funded ActivityStart Date: 2015
End Date: 12-2017
Amount: $385,481.00
Funder: Australian Research Council
View Funded Activity