1
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Brennan IG, Singhal S, Bkhetan ZA. pipesnake: Generalized software for the assembly and analysis of phylogenomic datasets from conserved genomic loci. Bioinformatics 2024:btae195. [PMID: 38597877 DOI: 10.1093/bioinformatics/btae195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 03/18/2024] [Accepted: 04/08/2024] [Indexed: 04/11/2024]
Abstract
MOTIVATION Phylogenetics has moved into the era of genomics, incorporating enormous volumes of data to study questions at both shallow and deep scales. With this increase in information, phylogeneticists need new tools and skills to manipulate and analyze these data. To facilitate these tasks and encourage reproducibility, the community is increasingly moving towards automated workflows. RESULTS Here we present pipesnake, a phylogenomics pipeline written in Nextflow for the processing, assembly, and phylogenetic estimation of genomic data from short-read sequences. pipesnake is an easy to use and efficient software package designed for this next era in phylogenetics. AVAILABILITY pipesnake is publicly available on GitHub at https://github.com/AusARG/pipesnake and accompanied by documentation and a wiki/tutorial. SUPPLEMENTARY INFORMATION Written in Nextflow, the pipeline is containerized and deployable via Docker, Singularity, and Conda making it easy to run on different compute infrastructures.
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Affiliation(s)
- Ian G Brennan
- Division of Ecology & Evolution, The Australian National University, ACT 2601, Australia
- Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
| | - Sonal Singhal
- Department of Biology, California State University, Dominguez Hills, CA 90747, USA
| | - Ziad Al Bkhetan
- Australian BioCommons, The University of Melbourne, VIC 3010, Australia
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2
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Tiatragul S, Brennan IG, Broady ES, Scott Keogh J. Corrigendum to "Australia's hidden radiation: Phylogenomics analysis reveals rapid Miocene radiation of blindsnakes" [Mol. Phylogenet. Evol. 185 (2023) 107812]. Mol Phylogenet Evol 2023; 188:107889. [PMID: 37633786 DOI: 10.1016/j.ympev.2023.107889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2023]
Affiliation(s)
- Sarin Tiatragul
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra 2601, ACT, Australia.
| | - Ian G Brennan
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra 2601, ACT, Australia.
| | - Elizabeth S Broady
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra 2601, ACT, Australia.
| | - J Scott Keogh
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra 2601, ACT, Australia.
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3
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Brennan IG, Lemmon AR, Lemmon EM, Hoskin CJ, Donnellan SC, Keogh JS. Populating a Continent: Phylogenomics Reveal the Timing of Australian Frog Diversification. Syst Biol 2023:syad048. [PMID: 37527840 DOI: 10.1093/sysbio/syad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Indexed: 08/03/2023] Open
Abstract
The Australian continent's size and isolation make it an ideal place for studying the accumulation and evolution of biodiversity. Long separated from the ancient supercontinent Gondwana, most of Australia's plants and animals are unique and endemic, including the continent's frogs. Australian frogs comprise a remarkable ecological and morphological diversity categorized into a small number of distantly related radiations. We present a phylogenomic hypothesis based on an exon-capture dataset that spans the main clades of Australian myobatrachoid, pelodryadid hyloid, and microhylid frogs. Our time-calibrated phylogenomic-scale phylogeny identifies great disparity in the relative ages of these groups which vary from Gondwanan relics to recent immigrants from Asia and include arguably the continent's oldest living vertebrate radiation. This age stratification provides insight into the colonization of, and diversification on, the Australian continent through deep time, during periods of dramatic climatic and community changes. Contemporary Australian frog diversity highlights the adaptive capacity of anurans, particularly in response to heat and aridity, and explains why they are one of the continent's most visible faunas.
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Affiliation(s)
- Ian G Brennan
- Division of Ecology & Evolution, The Australian National University, Canberra, ACT 2601, Australia
- Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee FL 32316, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee FL 32306, USA
| | - Conrad J Hoskin
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - Stephen C Donnellan
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
| | - J Scott Keogh
- Division of Ecology & Evolution, The Australian National University, Canberra, ACT 2601, Australia
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Tiatragul S, Brennan IG, Broady ES, Keogh JS. Australia's hidden radiation: Phylogenomics analysis reveals rapid Miocene radiation of blindsnakes. Mol Phylogenet Evol 2023; 185:107812. [PMID: 37207892 DOI: 10.1016/j.ympev.2023.107812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 03/24/2023] [Accepted: 05/10/2023] [Indexed: 05/21/2023]
Affiliation(s)
- Sarin Tiatragul
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra 2601, ACT, Australia.
| | - Ian G Brennan
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra 2601, ACT, Australia.
| | - Elizabeth S Broady
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra 2601, ACT, Australia.
| | - J Scott Keogh
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra 2601, ACT, Australia.
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Davis HR, Nashriq I, Woytek KS, Wikramanayake SA, Bauer AM, Karin BR, Brennan IG, Iskandar DT, Das I. Genomic analysis of Bornean geckos (Gekkonidae:
Cyrtodactylus
) reveals need for updated taxonomy. ZOOL SCR 2023. [DOI: 10.1111/zsc.12575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Hayden R. Davis
- Department of Biology Burke Museum of Natural History and Culture University of Washington Seattle Washington USA
| | - Izneil Nashriq
- Institute of Biodiversity and Environmental Conservation University of Malaysia Sarawak Kota Samarahan Malaysia
| | - Kyra S. Woytek
- Department of Biology Burke Museum of Natural History and Culture University of Washington Seattle Washington USA
| | | | - Aaron M. Bauer
- Department of Biology Center for Biodiversity and Ecosystem Stewardship Villanova University Villanova Pennsylvania USA
| | - Benjamin R. Karin
- Museum of Vertebrate Zoology and Department of Integrative Biology University of California Berkeley Berkeley California USA
| | - Ian G. Brennan
- Department of Ecology and Evolution Australian National University Canberra Australian Capital Territory Australia
| | - Djoko T. Iskandar
- Life Sciences and Technology Institut Teknologi Bandung Bandung Indonesia
- The Indonesian Academy of Sciences Basic Sciences Commission Jakarta Indonesia
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation University of Malaysia Sarawak Kota Samarahan Malaysia
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Esquerré D, Brennan IG, Donnellan S, Keogh JS. Evolutionary models demonstrate rapid and adaptive diversification of Australo-Papuan pythons. Biol Lett 2022; 18:20220360. [PMID: 36541096 PMCID: PMC9768648 DOI: 10.1098/rsbl.2022.0360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Lineages may diversify when they encounter available ecological niches. Adaptive divergence by ecological opportunity often appears to follow the invasion of a new environment with open ecological space. This evolutionary process is hypothesized to explain the explosive diversification of numerous Australian vertebrate groups following the collision of the Eurasian and Australian plates 25 Mya. One of these groups is the pythons, which demonstrate their greatest phenotypic and ecological diversity in Australo-Papua (Australia and New Guinea). Here, using an updated and near complete time-calibrated phylogenomic hypothesis of the group, we show that following invasion of this region, pythons experienced a sudden burst of speciation rates coupled with multiple instances of accelerated phenotypic evolution in head and body shape and body size. These results are consistent with adaptive radiation theory with an initial rapid niche-filling phase and later slow-down approaching niche saturation. We discuss these findings in the context of other Australo-Papuan adaptive radiations and the importance of incorporating adaptive diversification systems that are not extraordinarily species-rich but ecomorphologically diverse to understand how biodiversity is generated.
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Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University 0200, Canberra, ACT, Australia
| | - Ian G. Brennan
- Division of Ecology and Evolution, Research School of Biology, The Australian National University 0200, Canberra, ACT, Australia
| | - Stephen Donnellan
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
| | - J. Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University 0200, Canberra, ACT, Australia
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Pavón-Vázquez CJ, Brennan IG, Skeels A, Keogh JS. Competition and geography underlie speciation and morphological evolution in Indo-Australasian monitor lizards. Evolution 2022; 76:476-495. [PMID: 34816437 DOI: 10.1111/evo.14403] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 10/06/2021] [Accepted: 10/16/2021] [Indexed: 01/21/2023]
Abstract
How biotic and abiotic factors act together to shape biological diversity is a major question in evolutionary biology. The recent availability of large datasets and development of new methodological approaches provide new tools to evaluate the predicted effects of ecological interactions and geography on lineage diversification and phenotypic evolution. Here, we use a near complete phylogenomic-scale phylogeny and a comprehensive morphological dataset comprising more than a thousand specimens to assess the role of biotic and abiotic processes in the diversification of monitor lizards (Varanidae). This charismatic group of lizards shows striking variation in species richness among its clades and multiple instances of endemic radiation in Indo-Australasia (i.e., the Indo-Australian Archipelago and Australia), one of Earth's most biogeographically complex regions. We found heterogeneity in diversification dynamics across the family. Idiosyncratic biotic and geographic conditions appear to have driven diversification and morphological evolution in three endemic Indo-Australasian radiations. Furthermore, incumbency effects partially explain patterns in the biotic exchange between Australia and New Guinea. Our results offer insight into the dynamic history of Indo-Australasia, the evolutionary significance of competition, and the long-term consequences of incumbency effects.
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Affiliation(s)
- Carlos J Pavón-Vázquez
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia.,Current Address: Department of Biological Sciences, New York City College of Technology, City University of New York, Brooklyn, New York, 11201
| | - Ian G Brennan
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Alexander Skeels
- Landscape Ecology, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zürich, CH-8092, Switzerland.,Swiss Federal Research Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, CH-8903, Switzerland
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
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Melville J, Chapple DG, Keogh JS, Sumner J, Amey A, Bowles P, Brennan IG, Couper P, Donnellan SC, Doughty P, Edwards DL, Ellis RJ, Esquerré D, Fenker J, Gardner MG, Georges A, Haines ML, Hoskin CJ, Hutchinson M, Moritz C, Nankivell J, Oliver P, Pavón-Vázquez CJ, Pepper M, Rabosky DL, Sanders K, Shea G, Singhal S, Worthington Wilmer J, Tingley R. A return-on-investment approach for prioritization of rigorous taxonomic research needed to inform responses to the biodiversity crisis. PLoS Biol 2021; 19:e3001210. [PMID: 34061821 PMCID: PMC8168848 DOI: 10.1371/journal.pbio.3001210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/29/2021] [Indexed: 11/19/2022] Open
Abstract
Global biodiversity loss is a profound consequence of human activity. Disturbingly, biodiversity 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 biodiversity is described. Here, we provide a new quantitative approach for prioritizing rigorous taxonomic research for conservation. We implement this approach in a highly diverse 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.
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Affiliation(s)
- Jane Melville
- Department of Sciences, Museums Victoria, Melbourne, Australia
- Department of Biology, Washington University, St. Louis, MI, United States of America
- School of Biological Sciences, Monash University, Clayton, Australia
| | - David G. Chapple
- School of Biological Sciences, Monash University, Clayton, Australia
| | - J. Scott Keogh
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Joanna Sumner
- Department of Sciences, Museums Victoria, Melbourne, Australia
| | - Andrew Amey
- Biodiversity & Geosciences Program, Queensland Museum, Brisbane, Australia
| | - Phil Bowles
- Snake & Lizard Red List Authority, CI-IUCN Biodiversity Assessment Unit, IUCN North America Office, Washington, DC, United States of America
| | - Ian G. Brennan
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Patrick Couper
- Biodiversity & Geosciences Program, Queensland Museum, Brisbane, Australia
| | | | - Paul Doughty
- Collections & Research, Western Australian Museum, Welshpool, Australia
| | - Danielle L. Edwards
- Department of Life & Environmental Sciences, University of California, Merced, Merced, CA, United States of America
| | - Ryan J. Ellis
- Collections & Research, Western Australian Museum, Welshpool, Australia
- Biologic Environmental Survey, East Perth, Australia
| | - Damien Esquerré
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Jéssica Fenker
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Michael G. Gardner
- South Australian Museum, North Terrace, Adelaide, Australia
- College of Science & Engineering, Flinders University, Adelaide, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | | | - Conrad J. Hoskin
- College of Science & Engineering, James Cook University, Townsville, Australia
| | | | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - James Nankivell
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Paul Oliver
- Biodiversity & Geosciences Program, Queensland Museum, Brisbane, Australia
- Environmental Futures Research Institute, Griffith University, Australia
| | - Carlos J. Pavón-Vázquez
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Mitzy Pepper
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Daniel L. Rabosky
- Museum of Zoology & Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Kate Sanders
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Glenn Shea
- School of Veterinary Science, University of Sydney, Sydney, Australia
- Australian Museum Research Institute, The Australian Museum, Sydney, Australia
| | - Sonal Singhal
- Department of Biology, California State University, Dominguez Hills, Carson, CA, United States of America
| | | | - Reid Tingley
- School of Biological Sciences, Monash University, Clayton, Australia
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Gurgis GP, Daza JD, Brennan IG, Hutchinson M, Bauer AM, Stocker MR, Olori JC. Ecomorphometric Analysis of Diversity in Cranial Shape of Pygopodid Geckos. Integr Org Biol 2021; 3:obab013. [PMID: 34377940 PMCID: PMC8341893 DOI: 10.1093/iob/obab013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Pygopodids are elongate, functionally limbless geckos found throughout Australia. The clade presents low taxonomic diversity (∼45 spp.), but a variety of cranial morphologies, habitat use, and locomotor abilities that vary between and within genera. In order to assess potential relationships between cranial morphology and ecology, computed tomography scans of 29 species were used for 3D geometric morphometric analysis. A combination of 24 static landmarks and 20 sliding semi-landmarks were subjected to Generalized Procrustes Alignment. Disparity in cranial shape was visualized through Principal Component Analysis, and a multivariate analysis of variance (MANOVA) was used to test for an association between shape, habitat, and diet. A subset of 27 species with well-resolved phylogenetic relationships was used to generate a phylomorphospace and conduct phylogeny-corrected MANOVA. Similar analyses were done solely on Aprasia taxa to explore species-level variation. Most of the variation across pygopodids was described by principal component (PC) 1(54%: cranial roof width, parabasisphenoid, and occipital length), PC2 (12%: snout elongation and braincase width), and PC3 (6%: elongation and shape of the palate and rostrum). Without phylogenetic correction, both habitat and diet were significant influencers of variation in cranial morphology. However, in the phylogeny-corrected MANOVA, habitat remained weakly significant, but not diet, which can be explained by generic-level differences in ecology rather than among species. Our results demonstrate that at higher levels, phylogeny has a strong effect on morphology, but that influence may be due to small sample size when comparing genera. However, because some closely related taxa occupy distant regions of morphospace, diverging diets, and use of fossorial habitats may contribute to variation seen in these geckos.
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Affiliation(s)
- George P Gurgis
- Department of Biological Sciences, State University of New York at Oswego, Oswego, NY, USA
| | - Juan D Daza
- Deparment of Biological Sciences, Sam Houston State University, Huntsville, TX, USA
| | - Ian G Brennan
- Division of Ecology & Evolution, Australian National University, Canberra, Australia
| | - Mark Hutchinson
- Biological and Earth Sciences, South Australian Museum, Adelaide, Australia
| | - Aaron M Bauer
- Department of Biology and Center for Biodiversity and Ecosystem Stewardship, Villanova University, Villanova, PA, USA
| | | | - Jennifer C Olori
- Department of Biological Sciences, State University of New York at Oswego, Oswego, NY, USA
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Davis HR, Das I, Leaché AD, Karin BR, Brennan IG, Jackman TR, Nashriq I, Onn Chan K, Bauer AM. Genetically diverse yet morphologically conserved: Hidden diversity revealed among Bornean geckos (Gekkonidae:
Cyrtodactylus
). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hayden R. Davis
- Department of Biology Burke Museum of Natural History and Culture University of Washington Seattle WA USA
- Department of Biology Center for Biodiversity and Ecosystem Stewardship Villanova University Villanova PA USA
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation Universiti Malaysia Sarawak Kota Samarahan Malaysia
| | - Adam D. Leaché
- Department of Biology Burke Museum of Natural History and Culture University of Washington Seattle WA USA
| | - Benjamin R. Karin
- Department of Integrative Biology Museum of Vertebrate Zoology University of California Berkeley CA USA
| | - Ian G. Brennan
- Division of Ecology and Evolution Research School of Biology The Australian National University Canberra ACT Australia
| | - Todd R. Jackman
- Department of Biology Center for Biodiversity and Ecosystem Stewardship Villanova University Villanova PA USA
| | - Izneil Nashriq
- Institute of Biodiversity and Environmental Conservation Universiti Malaysia Sarawak Kota Samarahan Malaysia
| | - Kin Onn Chan
- Lee Kong Chian Natural History Museum National University of Singapore Singapore
| | - Aaron M. Bauer
- Department of Biology Center for Biodiversity and Ecosystem Stewardship Villanova University Villanova PA USA
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Pavón-Vázquez CJ, Brennan IG, Keogh JS. A Comprehensive Approach to Detect Hybridization Sheds Light on the Evolution of Earth's Largest Lizards. Syst Biol 2021; 70:877-890. [PMID: 33512509 DOI: 10.1093/sysbio/syaa102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 11/14/2022] Open
Abstract
Hybridization between species occurs more frequently in vertebrates than traditionally thought but distinguishing ancient hybridization from other phenomena that generate similar evolutionary patterns remains challenging. Here, we used a comprehensive workflow to discover evidence of ancient hybridization between the Komodo dragon (Varanus komodoensis) from Indonesia and a common ancestor of an Australian group of monitor lizards known colloquially as sand monitors. Our data comprises >300 nuclear loci, mitochondrial genomes, phenotypic data, fossil and contemporary records, and past/present climatic data. We show that the four sand monitor species share more nuclear alleles with V. komodoensis than expected given a bifurcating phylogeny, likely as a result of hybridization between the latter species and a common ancestor of sand monitors. Sand monitors display phenotypes that are intermediate between their closest relatives and V. komodoensis. Biogeographic analyses suggest that V. komodoensis and ancestral sand monitors co-occurred in northern Australia. In agreement with the fossil record, this provides further evidence that the Komodo dragon once inhabited the Australian continent. Our study shows how different sources of evidence can be used to thoroughly characterize evolutionary histories that deviate from a treelike pattern, that hybridization can have long-lasting effects on phenotypes and that detecting hybridization can improve our understanding of evolutionary and biogeographic patterns.
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Affiliation(s)
- Carlos J Pavón-Vázquez
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Ian G Brennan
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
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Abstract
Abstract
Subspecies designations for herpetofauna in Western Australia were largely coined in the 20th century where rigorous evolutionary concepts to species were not consistently applied. Rather, subspecies tended to designate geographic populations of similar-looking taxa to nominate forms, usually differing in size, pattern or colour and, at best, a few scalation differences. Here we re-evaluate two pygopodoid taxa from Western Australia using a combination of published and original genetic data coupled with a reassessment of morphology. We review these differences in light of an integrative taxonomic approach that looks to find multiple independent lines of evidence to establish the evolutionary independence of populations. For the pygopod species Pletholax gracilis, we found consistent diagnostic characters (e.g. body size, visibility of ear opening, scalation) and a deep genetic divergence between the two subspecies. We therefore raise each subspecies to full species: P. gracilis and P. edelensis. The two subspecies of the carphodactylid gecko Nephrurus wheeleri were also assessed, and we found strong genetic and morphological evidence (e.g. body size, scalation, pattern) to raise these to full species: N. wheeleri and N. cinctus. By revisiting Storr’s morphological insights and newly acquired genetic evidence, in addition to a thorough re-examination of morphological traits, our study provides a robust foundation to raise Storr’s morphological subspecies into full species based upon multiple lines of evidence. Such an approach applied to other subspecies in the Australian herpetofauna also may result in revised taxonomies.
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Affiliation(s)
- Luke Kealley
- a Department of Terrestrial Zoology, Western Australian Museum, 49 Kew Street, Welshpool 6106, Australia
| | - Paul Doughty
- a Department of Terrestrial Zoology, Western Australian Museum, 49 Kew Street, Welshpool 6106, Australia
| | - Danielle Edwards
- b School of Natural Sciences, University of California, Merced, CA 95343, U.S.A
| | - Ian G. Brennan
- c Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
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13
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Brennan IG, Lemmon AR, Lemmon EM, Portik DM, Weijola V, Welton L, Donnellan SC, Keogh JS. Phylogenomics of Monitor Lizards and the Role of Competition in Dictating Body Size Disparity. Syst Biol 2020; 70:120-132. [PMID: 32521014 DOI: 10.1093/sysbio/syaa046] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/22/2020] [Accepted: 05/27/2020] [Indexed: 12/13/2022] Open
Abstract
Organismal interactions drive the accumulation of diversity by influencing species ranges, morphology, and behavior. Interactions vary from agonistic to cooperative and should result in predictable patterns in trait and range evolution. However, despite a conceptual understanding of these processes, they have been difficult to model, particularly on macroevolutionary timescales and across broad geographic spaces. Here, we investigate the influence of biotic interactions on trait evolution and community assembly in monitor lizards (Varanus). Monitors are an iconic radiation with a cosmopolitan distribution and the greatest size disparity of any living terrestrial vertebrate genus. Between the colossal Komodo dragon Varanus komodoensis and the smallest Australian dwarf goannas, Varanus length and mass vary by multiple orders of magnitude. To test the hypothesis that size variation in this genus was driven by character displacement, we extended existing phylogenetic comparative methods which consider lineage interactions to account for dynamic biogeographic history and apply these methods to Australian monitors and marsupial predators. Incorporating both exon-capture molecular and morphological data sets we use a combined evidence approach to estimate the relationships among living and extinct varaniform lizards. Our results suggest that communities of Australian Varanus show high functional diversity as a result of continent-wide interspecific competition among monitors but not with faunivorous marsupials. We demonstrate that patterns of trait evolution resulting from character displacement on continental scales are recoverable from comparative data and highlight that these macroevolutionary patterns may develop in parallel across widely distributed sympatric groups.[Character displacement; comparative methods; phylogenetics; trait evolution; Varanus.].
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Affiliation(s)
- Ian G Brennan
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Alan R Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Daniel M Portik
- Department of Ecology and Evolution, University of Arizona, Biosciences West Rm 310, 1041 E. Lowell St, Tucson, AZ 85745 USA
| | - Valter Weijola
- Zoological Museum, Biodiversity Unit, FI-20014 University of Turku, Finland
| | - Luke Welton
- Univeristy of Kansas Biodiversity Institute & Natural History Museum, 1345 Jayhawk Blvd, Lawrence, KS 66045, USA
| | - Stephen C Donnellan
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia.,South Australian Museum, North Terrace, Adelaide SA 5000 Australia
| | - J Scott Keogh
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
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14
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Esquerré D, Donnellan S, Brennan IG, Lemmon AR, Moriarty Lemmon E, Zaher H, Grazziotin FG, Keogh JS. Phylogenomics, Biogeography, and Morphometrics Reveal Rapid Phenotypic Evolution in Pythons After Crossing Wallace’s Line. Syst Biol 2020; 69:1039-1051. [DOI: 10.1093/sysbio/syaa024] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/02/2020] [Accepted: 03/17/2020] [Indexed: 11/13/2022] Open
Abstract
Abstract
Ecological opportunities can be provided to organisms that cross stringent biogeographic barriers towards environments with new ecological niches. Wallace’s and Lyddeker’s lines are arguably the most famous biogeographic barriers, separating the Asian and Australo-Papuan biotas. One of the most ecomorphologically diverse groups of reptiles, the pythons, is distributed across these lines, and are remarkably more diverse in phenotype and ecology east of Lydekker’s line in Australo-Papua. We used an anchored hybrid enrichment approach, with near complete taxon sampling, to extract mitochondrial genomes and 376 nuclear loci to resolve and date their phylogenetic history. Biogeographic reconstruction demonstrates that they originated in Asia around 38-45 Ma and then invaded Australo-Papua around 23 Ma. Australo-Papuan pythons display a sizeable expansion in morphological space, with shifts towards numerous new adaptive optima in head and body shape, coupled with the evolution of new micro-habitat preferences. We provide an updated taxonomy of pythons and our study also demonstrates how ecological opportunity following colonization of novel environments can promote morphological diversification in a formerly ecomorphologically conservative group. [Adaptive radiation; anchored hybrid enrichment; biogeography; morphometrics; snakes.]
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Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Stephen Donnellan
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- South Australian Museum, North Terrace, Adelaide SA 5000 Australia
| | - Ian G Brennan
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, 400 Dirac Science Library Tallahassee, FL 32306-4120, United States
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, United States
| | - Hussam Zaher
- Museu de Zoologia, Universidade de São Paulo, Avenida Nazaré 481, CEP 04263-000, São Paulo, SP, Brazil
- CR2P – Centre de Recherche em Paléontologie – MNHN – Sorbonne Université – CNRS, 8 rue Buffon, CP 38, 75005 Paris, France
| | - Felipe G Grazziotin
- Laboratório de Coleções Zoológicas, Instituto Butantan, São Paulo, SP, Brazil
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
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15
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Maryan B, Brennan IG, Hutchinson MN, Geidans LS. What's under the hood? Phylogeny and taxonomy of the snake genera Parasuta Worrell and Suta Worrell (Squamata: Elapidae), with a description of a new species from the Pilbara, Western Australia. Zootaxa 2020; 4778:zootaxa.4778.1.1. [PMID: 33055830 DOI: 10.11646/zootaxa.4778.1.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Indexed: 11/04/2022]
Abstract
Despite decades of phylogenetic studies, the generic and species-level relationships of some Australian elapid snakes remain problematic. The morphologically conservative genus Parasuta comprises small nocturnal snakes with a particularly obfuscated taxonomic history. Here we provide a molecular phylogenetic analysis of all currently recognised species including members of the sister genus Suta and provide new morphological data that lead to a taxonomic revision of generic and species boundaries. We failed to find support for monophyly of Parasuta or Suta, instead supporting previous evidence that these two genera should be combined. Our species-level investigations revise the boundaries between P. gouldii (Gray) and P. spectabilis (Krefft) resulting in recognition that both P. spectabilis bushi (Storr) and P. spectabilis nullarbor (Storr) are conspecific with P. gouldii. We also find the Pilbara population of P. monachus (Storr) to be specifically distinct. As a consequence of this information, we synonymise Parasuta with its senior synonym Suta, redescribe S. gouldii, S. monachus and S. spectabilis to clarify morphological and geographical boundaries and describe S. gaikhorstorum sp. nov., which differs from all other described Suta species, including the geographically proximate and similar-looking S. monachus, by a combination of molecular genetic markers, morphometric attributes, details of colouration and scalation. The recognition of S. gaikhorstorum sp. nov. adds to the growing list of the many endemic reptiles from this exceptionally diverse biotic region. We also designate a lectotype for S. spectabilis from the original syntype series, highlight a distinctive population from the Great Victoria Desert in Western Australia and comment on further unresolved issues regarding the relationships between S. dwyeri (Worrell) and S. nigriceps (Gȕnther).
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Affiliation(s)
- Brad Maryan
- Research Associate, Department of Terrestrial Zoology, Western Australian Museum, 49 Kew Street, Welshpool, Western Australia 6106, AUSTRALIA..
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16
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Novikova PY, Brennan IG, Booker W, Mahony M, Doughty P, Lemmon AR, Moriarty Lemmon E, Roberts JD, Yant L, Van de Peer Y, Keogh JS, Donnellan SC. Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus. PLoS Genet 2020; 16:e1008769. [PMID: 32392206 PMCID: PMC7259803 DOI: 10.1371/journal.pgen.1008769] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 05/29/2020] [Accepted: 04/08/2020] [Indexed: 01/13/2023] Open
Abstract
Polyploidy has played an important role in evolution across the tree of life but it is still unclear how polyploid lineages may persist after their initial formation. While both common and well-studied in plants, polyploidy is rare in animals and generally less understood. The Australian burrowing frog genus Neobatrachus is comprised of six diploid and three polyploid species and offers a powerful animal polyploid model system. We generated exome-capture sequence data from 87 individuals representing all nine species of Neobatrachus to investigate species-level relationships, the origin and inheritance mode of polyploid species, and the population genomic effects of polyploidy on genus-wide demography. We describe rapid speciation of diploid Neobatrachus species and show that the three independently originated polyploid species have tetrasomic or mixed inheritance. We document higher genetic diversity in tetraploids, resulting from widespread gene flow between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate on differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which correspond to population genomic estimates of demographic histories. We propose that Neobatrachus diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on the evolution of adaptation in animals.
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Affiliation(s)
- Polina Yu. Novikova
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Ian G. Brennan
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, Australia
| | - William Booker
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Michael Mahony
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, Australia
| | - Paul Doughty
- Western Australian Museum, Welshpool, Perth, Australia
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, Florida, United States of America
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - J. Dale Roberts
- School of Biological Sciences, and, Centre for Evolutionary Biology, University of Western Australia, Albany, Western Australia, Australia
| | - Levi Yant
- School of Life Sciences and Future Food Beacon, University of Nottingham, Nottingham, United Kingdom
| | - Yves Van de Peer
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - J. Scott Keogh
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, Australia
| | - Stephen C. Donnellan
- South Australian Museum, North Terrace, Adelaide, Australia
- School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, Australia
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17
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Esquerré D, Brennan IG, Catullo RA, Torres‐Pérez F, Keogh JS. How mountains shape biodiversity: The role of the Andes in biogeography, diversification, and reproductive biology in South America's most species‐rich lizard radiation (Squamata: Liolaemidae). Evolution 2018; 73:214-230. [DOI: 10.1111/evo.13657] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 11/04/2018] [Accepted: 11/19/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of BiologyThe Australian National University 0200 Canberra Australian Capital Territory Australia
| | - Ian G. Brennan
- Division of Ecology and Evolution, Research School of BiologyThe Australian National University 0200 Canberra Australian Capital Territory Australia
| | - Renee A. Catullo
- Division of Ecology and Evolution, Research School of BiologyThe Australian National University 0200 Canberra Australian Capital Territory Australia
- School of Science & Health and Hawkesbury Institute for the EnvironmentWestern Sydney University 2751 Perth New South Wales Australia
| | - Fernando Torres‐Pérez
- Instituto de BiologíaPontificia Universidad Católica de Valparaíso 2950 Valparaíso Chile
| | - J. Scott Keogh
- Division of Ecology and Evolution, Research School of BiologyThe Australian National University 0200 Canberra Australian Capital Territory Australia
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18
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Brennan IG, Keogh JS. Miocene biome turnover drove conservative body size evolution across Australian vertebrates. Proc Biol Sci 2018; 285:rspb.2018.1474. [PMID: 30333208 DOI: 10.1098/rspb.2018.1474] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 09/26/2018] [Indexed: 11/12/2022] Open
Abstract
On deep time scales, changing climatic trends can have a predictable influence on macroevolution. From evidence of mass extinctions, we know that rapid climatic oscillations can indirectly open niche space and precipitate adaptive radiation, changing the course of ecological diversification. These dramatic shifts in the global climate, however, are rare events relative to extended periods of protracted climate change and biome turnover. It remains unclear whether during gradually changing periods, shifting habitats may instead promote non-adaptive speciation by facilitating allopatry and phenotypic conservatism. Using fossil-calibrated, species-level phylogenies for five Australian radiations comprising more than 800 species, we investigated temporal trends in biogeography and body size evolution. Here, we demonstrate that gradual Miocene cooling and aridification correlates with the restricted phenotypic diversification of multiple ecologically diverse vertebrate groups. This probably occurred as species ranges became fractured and isolated during continental biome restructuring, encouraging a shift towards conservatism in body size evolution. Our results provide further evidence that abiotic changes, not only biotic interactions, may act as selective forces influencing phenotypic macroevolution.
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Affiliation(s)
- Ian G Brennan
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
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19
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Brennan IG, Oliver PM. Mass turnover and recovery dynamics of a diverse Australian continental radiation. Evolution 2017; 71:1352-1365. [PMID: 28213971 DOI: 10.1111/evo.13207] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 02/03/2017] [Accepted: 02/06/2017] [Indexed: 11/29/2022]
Abstract
Trends in global and local climate history have been linked to observed macroevolutionary patterns across a variety of organisms. These climatic pressures may unilaterally or asymmetrically influence the evolutionary trajectory of clades. To test and compare signatures of changing global (Eocene-Oligocene boundary cooling) and continental (Miocene aridification) environments on a continental fauna, we investigated the macroevolutionary dynamics of one of Australia's most diverse endemic radiations, pygopodoid geckos. We generated a time-calibrated phylogeny (>90% taxon coverage) to test whether (i) asymmetrical pygopodoid tree shape may be the result of mass turnover deep in the group's history, and (ii) how Miocene aridification shaped trends in biome assemblages. We find evidence of mass turnover in pygopodoids following the isolation of the Australian continental plate ∼30 million years ago, and in contrast, gradual aridification is linked to elevated speciation rates in the young arid zone. Surprisingly, our results suggest that invasion of arid habitats was not an evolutionary end point. Instead, arid Australia has acted as a source for diversity, with repeated outward dispersals having facilitated diversification of this group. This pattern contrasts trends in richness and distribution of other Australian vertebrates, illustrating the profound effects historical biome changes have on macroevolutionary patterns.
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Affiliation(s)
- Ian G Brennan
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Paul M Oliver
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
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20
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Ziegler T, Botov A, Nguyen TT, Bauer AM, Brennan IG, Ngo HT, Nguyen TQ. First molecular verification of Dixonius vietnamensis Das, 2004 (Squamata: Gekkonidae) with the description of a new species from Vinh Cuu Nature Reserve, Dong Nai Province, Vietnam. Zootaxa 2016; 4136:553-66. [PMID: 27395733 DOI: 10.11646/zootaxa.4136.3.7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Indexed: 11/04/2022]
Abstract
Based on near-topotypic specimens of Dixonius vietnamensis from Khanh Hoa Province in southern Vietnam genetic analyses showed that the recently described D. taoi is sister to D. vietnamensis and several separate forms exist which previously have been misidentified as D. vietnamensis and D. siamensis. The Dixonius population from Vinh Cuu Nature Reserve, Dong Nai Province, Vietnam, represents an undescribed species. Dixonius minhlei sp. nov. can be distinguished from its congeners based on the following diagnostic characters: small size (up to 47.5 mm SVL); 7-9 supralabials; 14-15 rows of keeled tubercles on dorsum; 20-23 ventral scale rows; 7 or 8 precloacal pores in males; a canthal stripe running from rostrum through the eye and terminating at back of head; lateral second pair of postmentals maximum one quarter the size of first pair; dorsum olive gray with more or less discernible brownish olive blotches. This is the sixth species of Dixonius known to occur in Vietnam.
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Affiliation(s)
- Thomas Ziegler
- AG Zoologischer Garten Köln, Riehler Straße 173, D-50735 Köln, Germany Zoological Institute, University of Cologne, Zülpicher Strasse 47b, D-50674 Cologne, Germany Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, Vietnam;
| | - Andreas Botov
- AG Zoologischer Garten Köln, Riehler Straße 173, D-50735 Köln, Germany.; unknown
| | - Tao Thien Nguyen
- Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, Vietnam; unknown
| | - Aaron M Bauer
- Department of Biology, Villanova University, 800 Lancaster Avenue, Villanova, Pennsylvania 19085, USA; unknown
| | - Ian G Brennan
- Department of Biology, Villanova University, 800 Lancaster Avenue, Villanova, Pennsylvania 19085, USA Evolution, Ecology, and Genetics, Research School of Biology, The Australian National University, Canberra, ACT, Australia; unknown
| | - Hanh Thi Ngo
- Faculty of Biology, Hanoi University of Science, Vietnam National University, 334 Nguyen Trai Road, Hanoi, Vietnam; unknown
| | - Truong Quang Nguyen
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, Vietnam.; unknown
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21
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Brennan IG, Bauer AM, Jackman TR. Mitochondrial introgression via ancient hybridization, and systematics of the Australian endemic pygopodid gecko genus Delma. Mol Phylogenet Evol 2015; 94:577-590. [PMID: 26505536 DOI: 10.1016/j.ympev.2015.10.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 09/21/2015] [Accepted: 10/06/2015] [Indexed: 11/28/2022]
Abstract
Of the more than 1500 species of geckos found across six continents, few remain as unfamiliar as the pygopodids - Family Pygopodidae (Gray, 1845). These gekkotans are limited to Australia (44 species) and New Guinea (2 species), but have diverged extensively into the most ecologically diverse limbless radiation save Serpentes. Current phylogenetic understanding of the family has relied almost exclusively on two works, which have produced and synthesized an immense amount of morphological, geographical, and molecular data. However, current interspecific relationships within the largest genus Delma Gray 1831 are based chiefly upon data from two mitochondrial loci (16s, ND2). Here, we reevaluate the interspecific relationships within the genus Delma using two mitochondrial and four nuclear loci (RAG1, MXRA5, MOS, DYNLL1), and identify points of strong conflict between nuclear and mitochondrial genomic data. We address mito-nuclear discordance, and remedy this conflict by recognizing several points of mitochondrial introgression as the result of ancient hybridization events. Owing to the legacy value and intraspecific informativeness, we suggest the continued use of ND2 as a phylogenetic marker. Results identify strong support for species groups, but relationships among these clades, and the placement of several enigmatic taxa remain uncertain. We suggest a more careful review of Delma australis and the 'northwest Australia' clade. Accurately assessing and addressing species richness and relationships within this endemic Australian Gekkotan genus is relevant for understanding patterns of squamate speciation across the region.
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Affiliation(s)
- Ian G Brennan
- Department of Biology, Villanova University, 800 Lancaster Avenue, Villanova, PA 19085, USA.
| | - Aaron M Bauer
- Department of Biology, Villanova University, 800 Lancaster Avenue, Villanova, PA 19085, USA
| | - Todd R Jackman
- Department of Biology, Villanova University, 800 Lancaster Avenue, Villanova, PA 19085, USA
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22
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Maryan B, Brennan IG, Adams M, Aplin KP. Molecular and morphological assessment of Delma australis Kluge (Squamata: Pygopodidae), with a description of a new species from the biodiversity 'hotspot' of southwestern Western Australia. Zootaxa 2015; 3946:301-30. [PMID: 25947694 DOI: 10.11646/zootaxa.3946.3.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Indexed: 11/04/2022]
Abstract
The Australian pygopodid lizard genus Delma is characterised by morphologically conservative but genetically divergent lineages and species. An initial assessment of molecular and morphological variation in Delma australis Kluge, 1974 throughout its main distribution in Western and South Australia reveals at least two undescribed species that are presently included under this epithet. Here we describe the most distinctive and easily diagnosed taxon of these, D. hebesa sp. nov., from the proteaceous scrub and mallee heath on the south coast sandplains of southwestern Western Australia. We also foreshadow the need for an expanded genetic framework to assist in unequivocally diagnosing additional candidate species in D. australis, which is redescribed herein and shown to be monophyletic for those specimens sampled, albeit displaying geographic variation in a range of molecular and morphological characters. Delma hebesa sp. nov. differs from all other described Delma species, including regional populations of D. australis, by a combination of molecular genetic markers, colouration and scalation. Based on phylogenetic affinities and shared morphologies, a D. australis species-group is proposed to accommodate D. australis, D. torquata and the new species described herein. The addition of another new vertebrate species from southwestern Western Australia, recognised globally as a biodiversity 'hotspot', underlines our lack of understanding of genetic diversity and evolutionary histories in this biodiverse region.
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Affiliation(s)
- Brad Maryan
- Biologic Environmental Survey, 50B Angove Street, North Perth, Western Australia 6006, AUSTRALIA. Research Associate, Department of Terrestrial Zoology, Western Australian Museum, 49 Kew Street, Welshpool, Western Australia 6106, AUSTRALIA.;
| | - Ian G Brennan
- Department of Biology, Villanova University, 800 Lancaster Avenue, Villanova, Pennsylvania 19085, USA Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT 0200, AUSTRALIA 5Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, AUSTRALIA; unknown
| | - Mark Adams
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, AUSTRALIA Australian Centre for Evolutionary Biology and Biodiversity, University of Adelaide, Adelaide, South Australia 5000, AUSTRALIA; unknown
| | - Ken P Aplin
- Research Associate, Department of Terrestrial Zoology, Western Australian Museum, 49 Kew Street, Welshpool, Western Australia 6106, AUSTRALIA.; unknown
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