1
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Potter S, Moritz C, Piggott MP, Bragg JG, Afonso Silva AC, Bi K, McDonald-Spicer C, Turakulov R, Eldridge MDB. Museum skins enable identification of introgression associated with cytonuclear discordance. Syst Biol 2024:syae016. [PMID: 38577768 DOI: 10.1093/sysbio/syae016] [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: 03/10/2022] [Indexed: 04/06/2024] Open
Abstract
Increased sampling of genomes and populations across closely related species has revealed that levels of genetic exchange during and after speciation are higher than previously thought. One obvious manifestation of such exchange is strong cytonuclear discordance, where the divergence in mitochondrial DNA (mtDNA) differs from that for nuclear genes more (or less) than expected from differences between mtDNA and nuclear DNA (nDNA) in population size and mutation rate. Given genome-scale datasets and coalescent modelling, we can now confidently identify cases of strong discordance and test specifically for historical or recent introgression as the cause. Using population sampling, combining exon capture data from historical museum specimens and recently collected tissues we showcase how genomic tools can resolve complex evolutionary histories in the brachyotis group of rock-wallabies (Petrogale). In particular, applying population and phylogenomic approaches we can assess the role of demographic processes in driving complex evolutionary patterns and assess a role of ancient introgression and hybridisation. We find that described species are well supported as monophyletic taxa for nDNA genes, but not for mtDNA, with cytonuclear discordance involving at least four operational taxonomic units (OTUs) across four species which diverged 183-278 kya. ABC modelling of nDNA gene trees supports introgression during or after speciation for some taxon pairs with cytonuclear discordance. Given substantial differences in body size between the species involved, this evidence for gene flow is surprising. Heterogenous patterns of introgression were identified but do not appear to be associated with chromosome differences between species. These and previous results suggest that dynamic past climates across the monsoonal tropics could have promoted reticulation among related species.
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Affiliation(s)
- Sally Potter
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Maxine P Piggott
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
| | - Jason G Bragg
- National Herbarium of New South Wales, The Royal Botanical Gardens and Domain Trust, Sydney, NSW, Australia
| | | | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Christiana McDonald-Spicer
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | | | - Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
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2
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Roycroft E, Ford F, Ramm T, Schembri R, Breed WG, Burns PA, Rowe KC, Moritz C. Speciation across biomes: Rapid diversification with reproductive isolation in the Australian delicate mice. Mol Ecol 2024; 33:e17301. [PMID: 38385302 DOI: 10.1111/mec.17301] [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: 10/17/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/23/2024]
Abstract
Phylogeographic studies of continental clades, especially when combined with palaeoclimate modelling, provide powerful insight into how environment drives speciation across climatic contexts. Australia, a continent characterized by disparate modern biomes and dynamic climate change, provides diverse opportunity to reconstruct the impact of past and present environments on diversification. Here, we use genomic-scale data (1310 exons and whole mitogenomes from 111 samples) to investigate Pleistocene diversification, cryptic diversity, and secondary contact in the Australian delicate mice (Hydromyini: Pseudomys), a recent radiation spanning almost all Australian environments. Across northern Australia, we find no evidence for introgression between cryptic lineages within Pseudomys delicatulus sensu lato, with palaeoclimate models supporting contraction and expansion of suitable habitat since the last glacial maximum. Despite multiple contact zones, we also find little evidence of introgression at a continental scale, with the exception of a potential hybrid zone in the mesic biome. In the arid zone, combined insights from genetic data and palaeomodels support a recent expansion in the arid specialist P. hermannsburgensis and contraction in the semi-arid P. bolami. In the face of repeated secondary contact, differences in sperm morphology and chromosomal rearrangements are potential mechanisms that maintain species boundaries in these recently diverged species. Additionally, we describe the western delicate mouse as a new species and recommend taxonomic reinstatement of the eastern delicate mouse. Overall, we show that speciation in an evolutionarily young and widespread clade has been driven by environmental change, and potentially maintained by divergence in reproductive morphology and chromosome rearrangements.
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Affiliation(s)
- Emily Roycroft
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Australian Capital Territory, Australia
| | - Fred Ford
- Biodiversity Conservation and Science, New South Wales Department of Planning and Environment, Queanbeyan, New South Wales, Australia
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Till Ramm
- Zoo Leipzig, Leipzig, Germany
- Museum für Naturkunde Berlin, Berlin, Germany
| | - Rhiannon Schembri
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Australian Capital Territory, Australia
- School of Natural Sciences, Macquarie University, Macquarie Park, New South Wales, Australia
| | - William G Breed
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Phoebe A Burns
- Wildlife Conservation and Science, Zoos Victoria, Parkville, Victoria, Australia
| | - Kevin C Rowe
- Sciences Department, Museums Victoria, Melbourne, Victoria, Australia
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Australian Capital Territory, Australia
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3
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Title PO, Singhal S, Grundler MC, Costa GC, Pyron RA, Colston TJ, Grundler MR, Prates I, Stepanova N, Jones MEH, Cavalcanti LBQ, Colli GR, Di-Poï N, Donnellan SC, Moritz C, Mesquita DO, Pianka ER, Smith SA, Vitt LJ, Rabosky DL. The macroevolutionary singularity of snakes. Science 2024; 383:918-923. [PMID: 38386744 DOI: 10.1126/science.adh2449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 01/02/2024] [Indexed: 02/24/2024]
Abstract
Snakes and lizards (Squamata) represent a third of terrestrial vertebrates and exhibit spectacular innovations in locomotion, feeding, and sensory processing. However, the evolutionary drivers of this radiation remain poorly known. We infer potential causes and ultimate consequences of squamate macroevolution by combining individual-based natural history observations (>60,000 animals) with a comprehensive time-calibrated phylogeny that we anchored with genomic data (5400 loci) from 1018 species. Due to shifts in the dynamics of speciation and phenotypic evolution, snakes have transformed the trophic structure of animal communities through the recurrent origin and diversification of specialized predatory strategies. Squamate biodiversity reflects a legacy of singular events that occurred during the early history of snakes and reveals the impact of historical contingency on vertebrate biodiversity.
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Affiliation(s)
- Pascal O Title
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
- Environmental Resilience Institute, Indiana University, Bloomington, IN 47408, USA
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sonal Singhal
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biology, California State University, Dominguez Hills, Carson, CA 90747, USA
| | - Michael C Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gabriel C Costa
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biology and Environmental Sciences, Auburn University at Montgomery, Montgomery, AL 36117, USA
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
| | - Timothy J Colston
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00680, Puerto Rico
| | - Maggie R Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ivan Prates
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Natasha Stepanova
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marc E H Jones
- Science Group: Fossil Reptiles, Amphibians and Birds Section, Natural History Museum, London SW7 5BD, UK
- Research Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
- Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Lucas B Q Cavalcanti
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, Paraíba 58051-900, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Distrito Federal 70910-900, Brazil
| | - Nicolas Di-Poï
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | | | - Craig Moritz
- Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
| | - Daniel O Mesquita
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, Paraíba 58051-900, Brazil
| | - Eric R Pianka
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laurie J Vitt
- Sam Noble Museum and Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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4
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Rick K, Byrne M, Cameron S, Cooper SJB, Dunlop J, Hill B, Lohr C, Mitchell NJ, Moritz C, Travouillon KJ, von Takach B, Ottewell K. Population genomic diversity and structure in the golden bandicoot: a history of isolation, extirpation, and conservation. Heredity (Edinb) 2023; 131:374-386. [PMID: 37806995 PMCID: PMC10673901 DOI: 10.1038/s41437-023-00653-2] [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: 05/30/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/10/2023] Open
Abstract
Using genetic information to develop and implement conservation programs is vital for maintaining biodiversity and ecosystem resilience. Evaluation of the genetic variability within and among remnant populations can inform management of both natural and translocated populations to maximise species' adaptive potential, mitigate negative impacts of inbreeding, and subsequently minimise risk of extinction. Here we use reduced representation sequencing to undertake a genetic assessment of the golden bandicoot (Isoodon auratus), a threatened marsupial endemic to Australia. The currently recognised taxon consists of three subspecies distributed among multiple natural and translocated populations. After confirming the genetic distinctiveness of I. auratus from two closely related taxa, I. fusciventer and I. macrourus, we identified four genetic clusters within I. auratus. These clusters exhibited substantial genetic differentiation (pairwise FST values ranging from 0.18 to 0.65, pairwise DXY ranging from 0.1 to 0.168), reflecting long-term isolation of some populations on offshore islands and the influence of genetic drift. Mainland natural populations in the Kimberley region had the highest genetic diversity and the largest contribution to overall allelic and gene diversity compared to both natural and translocated island populations. A population translocated to Guluwuru Island in the Northern Territory had the lowest genetic diversity. Our data suggest that island populations can appear genetically unique due to genetic drift and this needs to be taken into account when considering genetic diversity in conservation efforts to maintain overall genetic diversity of the species. We effectively demonstrate how genomic information can guide practical conservation planning, especially when declining species are represented by multiple isolated populations.
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Affiliation(s)
- Kate Rick
- School of Biological Sciences, The University of Western Australia, Crawley, WA, 6009, Australia.
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, WA, 6152, Australia
| | - Skye Cameron
- Australian Wildlife Conservancy, Level 2 322 Hay Street, Subiaco, WA, 6008, Australia
| | - Steve J B Cooper
- South Australian Museum, North Terrace, Adelaide, SA, 5000, Australia
- Department of Ecology and Evolutionary Biology, Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Judy Dunlop
- School of Agriculture and Environment, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Brydie Hill
- Flora and Fauna Division, Department of Environment, Parks and Water Security, Northern Territory Government, Darwin, NT, Australia
| | - Cheryl Lohr
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, WA, 6152, Australia
| | - Nicola J Mitchell
- School of Biological Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Kenny J Travouillon
- Collections and Research, Western Australian Museum, Welshpool, WA, 6106, Australia
| | - Brenton von Takach
- School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia
| | - Kym Ottewell
- School of Biological Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, WA, 6152, Australia
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5
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Nistelberger HM, Roycroft E, Macdonald AJ, McArthur S, White LC, Grady PGS, Pierson J, Sims C, Cowen S, Moseby K, Tuft K, Moritz C, Eldridge MDB, Byrne M, Ottewell K. Genetic mixing in conservation translocations increases diversity of a keystone threatened species, Bettongia lesueur. Mol Ecol 2023. [PMID: 37715549 DOI: 10.1111/mec.17119] [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: 04/10/2023] [Revised: 07/11/2023] [Accepted: 08/17/2023] [Indexed: 09/17/2023]
Abstract
Translocation programmes are increasingly being informed by genetic data to monitor and enhance conservation outcomes for both natural and established populations. These data provide a window into contemporary patterns of genetic diversity, structure and relatedness that can guide managers in how to best source animals for their translocation programmes. The inclusion of historical samples, where possible, strengthens monitoring by allowing assessment of changes in genetic diversity over time and by providing a benchmark for future improvements in diversity via management practices. Here, we used reduced representation sequencing (ddRADseq) data to report on the current genetic health of three remnant and seven translocated boodie (Bettongia lesueur) populations, now extinct on the Australian mainland. In addition, we used exon capture data from seven historical mainland specimens and a subset of contemporary samples to compare pre-decline and current diversity. Both data sets showed the significant impact of population founder source (whether multiple or single) on the genetic diversity of translocated populations. Populations founded by animals from multiple sources showed significantly higher genetic diversity than the natural remnant and single-source translocation populations, and we show that by mixing the most divergent populations, exon capture heterozygosity was restored to levels close to that observed in pre-decline mainland samples. Relatedness estimates were surprisingly low across all contemporary populations and there was limited evidence of inbreeding. Our results show that a strategy of genetic mixing has led to successful conservation outcomes for the species in terms of increasing genetic diversity and provides strong rationale for mixing as a management strategy.
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Affiliation(s)
- Heidi M Nistelberger
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Emily Roycroft
- Division of Ecology & Evolution, Research School of Biology, ANU College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Anna J Macdonald
- Division of Ecology & Evolution, Research School of Biology, ANU College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Shelley McArthur
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Lauren C White
- Department of Environment, Land, Water and Planning, Arthur Rylah Institute for Environmental Research, Heidelberg, Victoria, Australia
| | - Patrick G S Grady
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Jennifer Pierson
- Australian Wildlife Conservancy, Subiaco, Western Australia, Australia
| | - Colleen Sims
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Saul Cowen
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Katherine Moseby
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology, ANU College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Mark D B Eldridge
- Terrestrial Vertebrates, Australian Museum Research Institute, Sydney, New South Wales, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Kym Ottewell
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
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6
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Zozaya SM, Teasdale LC, Tedeschi LG, Higgie M, Hoskin CJ, Moritz C. Initiation of speciation across multiple dimensions in a rock-restricted, tropical lizard. Mol Ecol 2023; 32:680-695. [PMID: 36394360 PMCID: PMC10099344 DOI: 10.1111/mec.16787] [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: 09/02/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022]
Abstract
Population isolation and concomitant genetic divergence, resulting in strong phylogeographical structure, is a core aspect of speciation initiation. If and how speciation then proceeds and ultimately completes depends on multiple factors that mediate reproductive isolation, including divergence in genomes, ecology and mating traits. Here we explored these multiple dimensions in two young (Plio-Pleistocene) species complexes of gekkonid lizards (Heteronotia) from the Kimberley-Victoria River regions of tropical Australia. Using mitochondrial DNA screening and exon capture phylogenomics, we show that the rock-restricted Heteronotia planiceps exhibits exceptional fine-scale phylogeographical structure compared to the codistributed habitat generalist Heteronotia binoei. This indicates pervasive population isolation and persistence in the rock-specialist, and thus a high rate of speciation initiation across this geographically complex region, with levels of genomic divergence spanning the "grey zone" of speciation. Proximal lineages of H. planiceps were often separated by different rock substrates, suggesting a potential role for ecological isolation; however, phylogenetic incongruence and historical introgression were inferred between one such pair. Ecomorphological divergence among lineages within both H. planiceps and H. binoei was limited, except that limestone-restricted lineages of H. planiceps tended to be larger than rock-generalists. By contrast, among-lineage divergence in the chemical composition of epidermal pore secretions (putative mating trait) exceeded ecomorphology in both complexes, but with less trait overlap among lineages in H. planiceps. This system-particularly the rock-specialist H. planiceps-highlights the role of multidimensional divergence during incipient speciation, with divergence in genomes, ecomorphology and chemical signals all at play at very fine spatial scales.
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Affiliation(s)
- Stephen M Zozaya
- Research School of Biology, Australian National University, Australian Capital Territory, Canberra, Australia
| | - Luisa C Teasdale
- Research School of Biology, Australian National University, Australian Capital Territory, Canberra, Australia.,Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Leonardo G Tedeschi
- Research School of Biology, Australian National University, Australian Capital Territory, Canberra, Australia
| | - Megan Higgie
- College of Science and Engineering, James Cook University, Queensland, Townsville, Australia
| | - Conrad J Hoskin
- College of Science and Engineering, James Cook University, Queensland, Townsville, Australia
| | - Craig Moritz
- Research School of Biology, Australian National University, Australian Capital Territory, Canberra, Australia
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7
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Shaw RE, Spencer PB, Gibson LA, Dunlop JA, Kinloch JE, Mokany K, Byrne M, Moritz C, Davie H, Travouillon KJ, Ottewell KM. Linking life history to landscape for threatened species conservation in a multiuse region. Conserv Biol 2023; 37:e13989. [PMID: 35979681 PMCID: PMC10100189 DOI: 10.1111/cobi.13989] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/24/2022] [Accepted: 08/01/2022] [Indexed: 05/24/2023]
Abstract
Landscape-scale conservation that considers metapopulation dynamics will be essential for preventing declines of species facing multiple threats to their survival. Toward this end, we developed a novel approach that combines occurrence records, spatial-environmental data, and genetic information to model habitat, connectivity, and patterns of genetic structure and link spatial attributes to underlying ecological mechanisms. Using the threatened northern quoll (Dasyurus hallucatus) as a case study, we applied this approach to address the need for conservation decision-making tools that promote resilient metapopulations of this threatened species in the Pilbara, Western Australia, a multiuse landscape that is a hotspot for biodiversity and mining. Habitat and connectivity were predicted by different landscape characteristics. Whereas habitat suitability was overwhelmingly driven by terrain ruggedness, dispersal was facilitated by proximity to watercourses. Although there is limited evidence for major physical barriers in the Pilbara, areas with high silt and clay content (i.e., alluvial and hardpan plains) showed high resistance to dispersal. Climate subtlety shaped distributions and patterns of genetic turnover, suggesting the potential for local adaptation. By understanding these spatial-environmental associations and linking them to life-history and metapopulation dynamics, we highlight opportunities to provide targeted species management. To support this, we have created habitat, connectivity, and genetic uniqueness maps for conservation decision-making in the region. These tools have the potential to provide a more holistic approach to conservation in multiuse landscapes globally.
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Affiliation(s)
- Robyn E. Shaw
- Environmental & Conservation SciencesMurdoch UniversityPerthWestern AustraliaAustralia
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia
- Division of Ecology and Evolution, Research School of BiologyThe Australian National University, Australian Capital TerritoryCanberraAustralia
| | - Peter B. Spencer
- Environmental & Conservation SciencesMurdoch UniversityPerthWestern AustraliaAustralia
| | - Lesley A. Gibson
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia
| | - Judy A. Dunlop
- WA Feral Cat Working GroupPerthWestern AustraliaAustralia
| | - Janine E. Kinloch
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia
| | - Karel Mokany
- CSIROCanberraAustralian Capital TerritoryAustralia
| | - Margaret Byrne
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of BiologyThe Australian National University, Australian Capital TerritoryCanberraAustralia
| | - Harriet Davie
- Roy Hill Iron Ore Pty LtdPerthWestern AustraliaAustralia
| | | | - Kym M. Ottewell
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia
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8
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Roycroft E, Fabre PH, MacDonald AJ, Moritz C, Moussalli A, Rowe KC. New Guinea uplift opens ecological opportunity across a continent. Curr Biol 2022; 32:4215-4224.e3. [PMID: 36057260 DOI: 10.1016/j.cub.2022.08.021] [Citation(s) in RCA: 1] [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: 06/21/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 12/14/2022]
Abstract
Sahul unites the world's largest and highest tropical island and the oldest and most arid continent on the backdrop of dynamic environmental conditions. Massive geological uplift in New Guinea is predicted to have acted as a species pump from the late Miocene onward, but the impact of this process on biogeography and diversification remains untested across Sahul as a whole. To address this, we reconstruct the assembly of a recent and diverse radiation of rodents (Murinae: Hydromyini) spanning New Guinea, Australia, and oceanic islands. Using phylogenomic data from 270 specimens, including many recently extinct and highly elusive species, we find that the orogeny and expansion of New Guinea opened ecological opportunity and triggered diversification across a continent. After a single over-water colonization from Asia ca. 8.5 Ma, ancestral Hydromyini were restricted to the tropical rainforest of proto-New Guinea for 3.5 million years. Following a shift in diversification coincident with the orogeny of New Guinea ca. 5 Ma and subsequent colonization of Australia, transitions between geographic regions (n = 24) and biomes (n = 34) become frequent. Recurrent over-water colonization between mainland and islands demonstrate how islands can play a substantial role in the assembly of continental fauna. Our results are consistent with a model of increased ecological opportunity across Sahul following major geological uplift in New Guinea ca. 5 Ma, with sustained diversification facilitated by over-water colonization from the Pleistocene to present. We show how geological processes, biome transitions, and over-water colonization collectively drove the diversification of an expansive continental radiation.
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Affiliation(s)
- Emily Roycroft
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia; Sciences Department, Museums Victoria, GPO Box 666, Melbourne, VIC 3001, Australia; Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia.
| | - Pierre-Henri Fabre
- Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS-IRD-UM), Université de Montpellier, Place E. Bataillon, CC 064, 34095 Montpellier Cedex 5, France; Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Anna J MacDonald
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia; The John Curtin School of Medical Research, The Australian National University, Acton, ACT 2601, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
| | - Adnan Moussalli
- Sciences Department, Museums Victoria, GPO Box 666, Melbourne, VIC 3001, Australia
| | - Kevin C Rowe
- Sciences Department, Museums Victoria, GPO Box 666, Melbourne, VIC 3001, Australia
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9
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Roycroft E, Moritz C, Rowe KC, Moussalli A, Eldridge MDB, Portela Miguez R, Piggott MP, Potter S. Sequence Capture From Historical Museum Specimens: Maximizing Value for Population and Phylogenomic Studies. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.931644] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The application of high-throughput, short-read sequencing to degraded DNA has greatly increased the feasibility of generating genomic data from historical museum specimens. While many published studies report successful sequencing results from historical specimens; in reality, success and quality of sequence data can be highly variable. To examine predictors of sequencing quality, and methodological approaches to improving data accuracy, we generated and analyzed genomic sequence data from 115 historically collected museum specimens up to 180 years old. Data span both population genomic and phylogenomic scales, including historically collected specimens from 34 specimens of four species of Australian rock-wallabies (genus Petrogale) and 92 samples from 79 specimens of Australo-Papuan murine rodents (subfamily Murinae). For historical rodent specimens, where the focus was sampling for phylogenomics, we found that regardless of specimen age, DNA sequence libraries prepared from toe pad or bone subsamples performed significantly better than those taken from the skin (in terms of proportion of reads on target, number of loci captured, and data accuracy). In total, 93% of DNA libraries from toe pad or bone subsamples resulted in reliable data for phylogenetic inference, compared to 63% of skin subsamples. For skin subsamples, proportion of reads on target weakly correlated with collection year. Then using population genomic data from rock-wallaby skins as a test case, we found substantial improvement in final data quality by mapping to a high-quality “closest sister” de novo assembly from fresh tissues, compared to mapping to a sample-specific historical de novo assembly. Choice of mapping approach also affected final estimates of the number of segregating sites and Watterson's θ, both important parameters for population genomic inference. The incorporation of accurate and reliable sequence data from historical specimens has important outcomes for evolutionary studies at both population and phylogenomic scales. By assessing the outcomes of different approaches to specimen subsampling, library preparation and bioinformatic processing, our results provide a framework for increasing sequencing success for irreplaceable historical specimens.
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10
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Zozaya SM, Teasdale LC, Moritz C, Higgie M, Hoskin CJ. Composition of a chemical signalling trait varies with phylogeny and precipitation across an Australian lizard radiation. J Evol Biol 2022; 35:919-933. [PMID: 35665557 DOI: 10.1111/jeb.14031] [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: 03/13/2022] [Revised: 04/18/2022] [Accepted: 05/06/2022] [Indexed: 12/01/2022]
Abstract
The environment presents challenges to the transmission and detection of animal signalling systems, resulting in selective pressures that can drive signal divergence amongst populations in disparate environments. For chemical signals, climate is a potentially important selective force because factors such as temperature and moisture influence the persistence and detection of chemicals. We investigated an Australian lizard radiation (Heteronotia) to explore relationships between a sexually dimorphic chemical signalling trait (epidermal pore secretions) and two key climate variables: temperature and precipitation. We reconstructed the phylogeny of Heteronotia with exon capture phylogenomics, estimated phylogenetic signal in amongst-lineage chemical variation and assessed how chemical composition relates to temperature and precipitation using multivariate phylogenetic regressions. High estimates of phylogenetic signal indicate that the composition of epidermal pore secretions varies amongst lineages in a manner consistent with Brownian motion, although there are deviations to this, with stark divergences coinciding with two phylogenetic splits. Accounting for phylogenetic non-independence, we found that amongst-lineage chemical variation is associated with geographic variation in precipitation but not temperature. This contrasts somewhat with previous lizard studies, which have generally found an association between temperature and chemical composition. Our results suggest that geographic variation in precipitation can affect the evolution of chemical signalling traits, possibly influencing patterns of divergence amongst lineages and species.
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Affiliation(s)
- Stephen M Zozaya
- Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia.,College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Luisa C Teasdale
- Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia.,Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Craig Moritz
- Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia
| | - Megan Higgie
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Conrad J Hoskin
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
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11
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Ivan J, Moritz C, Potter S, Bragg J, Turakulov R, Hua X. Temperature predicts the rate of molecular evolution in Australian Eugongylinae skinks. Evolution 2022; 76:252-261. [PMID: 34486736 DOI: 10.1111/evo.14342] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 03/15/2021] [Revised: 07/12/2021] [Accepted: 08/15/2021] [Indexed: 01/21/2023]
Abstract
Temperature differences over time and space have been hypothesized to cause variation in the rate of molecular evolution of species, but empirical evidence is mixed. To further test this hypothesis, we utilized a large exon-capture sequence data of Australian Eugongylinae skinks, exemplifying a radiation of temperature-sensitive ectotherms spanning a large latitudinal gradient. The association between temperature (and other species traits) and long-term substitution rate was assessed based on 1268 sequenced exons of 44 species pairs from the Eugongylinae subfamily using regression analyses. Temperature is the strongest, positively correlated predictor of variation in substitution rate across the Australian Eugongylinae. It explains 45% of variation in synonymous substitution rate, and 11% after controlling for all the other factors. Synonymous substitution rate is also negatively associated with body size, with a 6% variation explained by body size after controlling for the effects of temperature. Other factors are not associated with synonymous substitution rate after controlling for temperature. Overall, this study points to temperature as a strong predictor of the molecular evolution rate in the Eugongylinae subfamily, and demonstrates the power of large-scale exonic data to identify correlates of the rate of molecular evolution.
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Affiliation(s)
- Jeremias Ivan
- Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Sally Potter
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jason Bragg
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, New South Wales, Australia
| | - Rust Turakulov
- Laboratory of Pathology, National Cancer Institute, Bethesda, Maryland, United States
| | - Xia Hua
- Mathematical Sciences Institute, Australian National University, Canberra, Australian Capital Territory, Australia
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12
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Marques AJD, Hanson JO, Camacho-Sanchez M, Martínez-Solano I, Moritz C, Tarroso P, Velo-Antón G, Veríssimo A, Carvalho SB. Range-wide genomic scans and tests for selection identify non-neutral spatial patterns of genetic variation in a non-model amphibian species (Pelobates cultripes). CONSERV GENET 2022. [DOI: 10.1007/s10592-021-01425-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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13
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Prates I, Singhal S, Marchán-Rivadeneira MR, Grundler MR, Moritz C, Donnellan SC, Rabosky DL. Genetic and Ecogeographic Controls on Species Cohesion in Australia’s Most Diverse Lizard Radiation. Am Nat 2022; 199:E57-E75. [DOI: 10.1086/717411] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Ivan Prates
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, Michigan 48109
| | - Sonal Singhal
- Department of Biology, California State University–Dominguez Hills, Carson, California 90747
| | | | - Maggie R. Grundler
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720; and Museum of Vertebrate Zoology, University of California, Berkeley, California 94720
| | - Craig Moritz
- Division of Ecology and Evolution and Centre for Biodiversity Analysis, Australian National University, Camberra, Australian Capital Territory, Australia
| | | | - Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, Michigan 48109
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14
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Fukuda Y, Moritz C, Jang N, Webb G, Campbell H, Christian K, Lindner G, Banks S. Environmental resistance and habitat quality influence dispersal of the saltwater crocodile. Mol Ecol 2021; 31:1076-1092. [PMID: 34865283 PMCID: PMC9299799 DOI: 10.1111/mec.16310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 11/15/2021] [Accepted: 11/22/2021] [Indexed: 11/29/2022]
Abstract
Landscape genetics commonly focuses on the effects of environmental resistance on animal dispersal patterns, but there is an emerging focus on testing environmental effects on emigration and settlement choices. In this study, we used landscape genetics approaches to quantify dispersal patterns in the world's largest crocodilian, the saltwater crocodile (Crocodylus porosus), and demonstrated environmental influences on three processes that comprise dispersal: emigration, movement and settlement. We found that both environmental resistance and properties of the source and destination catchments (proportion of breeding habitat) were important factors influencing observed dispersal events. Our habitat quality variables related to hypotheses about resource competition and represented the ratio of breeding habitat (which limits carrying capacity), suggesting that competition for habitat influences emigration and settlement choices, together with the strong effect of environmental resistance to movement (where high-quality habitat was associated with greatest environmental permeability). Approximately 42% of crocodiles were migrants from populations other than their sampling locations and some outstandingly productive populations had a much higher proportion of emigration rather than immigration. The distance most commonly travelled between source and destination was 150-200 km although a few travelled much longer distances, up to 600-700 km. Given the extensive dispersal range, individual catchments or hydrographic regions that combine two or three adjacent catchments are an appropriate scale for population management.
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Affiliation(s)
- Yusuke Fukuda
- Research School of Biology and Center for Biodiversity Analysis, The Australian National University, Canberra, ACT, Australia.,Department of Environment, Parks and Water Security, Northern Territory Government, Darwin, Northern Territory, Australia
| | - Craig Moritz
- Research School of Biology and Center for Biodiversity Analysis, The Australian National University, Canberra, ACT, Australia
| | - Namchul Jang
- Namchul Photography, Palmerston, Northern Territory, Australia
| | - Grahame Webb
- Wildlife Management International Pty Ltd, Darwin, Northern Territory, Australia
| | - Hamish Campbell
- Research Institute for the Environment and Livelihoods, College of Engineering, IT and the Environment, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Keith Christian
- Research Institute for the Environment and Livelihoods, College of Engineering, IT and the Environment, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Garry Lindner
- Parks Australia, Australian Government, Jabiru, Northern Territory, Australia
| | - Sam Banks
- Research Institute for the Environment and Livelihoods, College of Engineering, IT and the Environment, Charles Darwin University, Darwin, Northern Territory, Australia
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15
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Potter S, Bragg JG, Turakulov R, Eldridge MDB, Deakin J, Kirkpatrick M, Edwards RJ, Moritz C. Limited introgression between rock-wallabies with extensive chromosomal rearrangements. Mol Biol Evol 2021; 39:6448774. [PMID: 34865126 PMCID: PMC8788226 DOI: 10.1093/molbev/msab333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chromosome rearrangements can result in the rapid evolution of hybrid incompatibilities. Robertsonian fusions, particularly those with monobrachial homology, can drive reproductive isolation amongst recently diverged taxa. The recent radiation of rock-wallabies (genus Petrogale) is an important model to explore the role of Robertsonian fusions in speciation. Here, we pursue that goal using an extensive sampling of populations and genomes of Petrogale from north-eastern Australia. In contrast to previous assessments using mitochondrial DNA or nuclear microsatellite loci, genomic data are able to separate the most closely related species and to resolve their divergence histories. Both phylogenetic and population genetic analyses indicate introgression between two species that differ by a single Robertsonian fusion. Based on the available data, there is also evidence for introgression between two species which share complex chromosomal rearrangements. However, the remaining results show no consistent signature of introgression amongst species pairs and where evident, indicate generally low introgression overall. X-linked loci have elevated divergence compared with autosomal loci indicating a potential role for genic evolution to produce reproductive isolation in concert with chromosome change. Our results highlight the value of genome scale data in evaluating the role of Robertsonian fusions and structural variation in divergence, speciation, and patterns of molecular evolution.
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Affiliation(s)
- Sally Potter
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia.,Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Jason G Bragg
- National Herbarium of New South Wales, The Royal Botanical Gardens and Domain Trust, Sydney, NSW, Australia
| | - Rustamzhon Turakulov
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Janine Deakin
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin, TX, United States of America
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
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16
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Abstract
Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics-genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations-has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.
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Affiliation(s)
- Daren C Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, California 95064, USA
| | - Gonzalo Giribet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Craig Moritz
- Centre for Biodiversity Analysis and Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
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17
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Edwards SV, Robin V, Ferrand N, Moritz C. The evolution of comparative phylogeography: putting the geography (and more) into comparative population genomics. Genome Biol Evol 2021; 14:6339579. [PMID: 34347070 PMCID: PMC8743039 DOI: 10.1093/gbe/evab176] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
Comparative population genomics is an ascendant field using genomic comparisons between species to draw inferences about forces regulating genetic variation. Comparative phylogeography, by contrast, focuses on the shared lineage histories of species codistributed geographically and is decidedly organismal in perspective. Comparative phylogeography is approximately 35 years old, and, by some metrics, is showing signs of reduced growth. Here, we contrast the goals and methods of comparative population genomics and comparative phylogeography and argue that comparative phylogeography offers an important perspective on evolutionary history that succeeds in integrating genomics with landscape evolution in ways that complement the suprageographic perspective of comparative population genomics. Focusing primarily on terrestrial vertebrates, we review the history of comparative phylogeography, its milestones and ongoing conceptual innovations, its increasingly global focus, and its status as a bridge between landscape genomics and the process of speciation. We also argue that, as a science with a strong “sense of place,” comparative phylogeography offers abundant “place-based” educational opportunities with its focus on geography and natural history, as well as opportunities for collaboration with local communities and indigenous peoples. Although comparative phylogeography does not yet require whole-genome sequencing for many of its goals, we conclude that it nonetheless plays an important role in grounding our interpretation of genetic variation in the fundamentals of geography and Earth history.
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Affiliation(s)
- Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Vv Robin
- Indian Institute of Science Education and Research (IISER) Tirupati, Karakambadi Road, Tirupati, Andhra Pradesh, 517507, India
| | - Nuno Ferrand
- CIBIO/InBIO, Laboratório Associado, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Portugal
| | - Craig Moritz
- Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
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18
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Fenker J, Tedeschi LG, Melville J, Moritz C. Predictors of phylogeographic structure among codistributed taxa across the complex Australian monsoonal tropics. Mol Ecol 2021; 30:4276-4291. [PMID: 34216506 DOI: 10.1111/mec.16057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 06/16/2021] [Accepted: 06/28/2021] [Indexed: 11/28/2022]
Abstract
Differences in the geographic scale and depth of phylogeographic structure across codistributed taxa can reveal how microevolutionary processes such as population isolation and persistence drive diversification. In turn, environmental heterogeneity, species' traits, and historical biogeographic barriers may influence the potential for isolation and persistence. Using extensive SNP data and a combination of population genetic summary statistics and landscape genomic analyses, we explored predictors of the scale and depth of phylogeographic structure in codistributed lizard taxa from the topographically and climatically complex monsoonal tropics (AMT) of Australia. We first resolved intraspecific lineages and then tested whether genetic divergence across space within lineages is related to isolation by distance, resistance and/or environment and whether these factors differ across genera or between rock-related versus habitat generalist taxa. We then tested whether microevolutionary processes within lineages explain differences in the geographic scale and depth of intraspecific phylogeographic lineages. The results indicated that landscape predictors of phylogeographic structure differ between taxa. Within lineages, there was prevalent isolation by distance, but the strength of isolation by distance is independent of the taxonomic family, habitat specialization, and climate. Isolation by environment is the strongest predictor of landscape-scale genetic divergence for all taxa, with both temperature and precipitation acting as limiting factors. The strength of isolation by distance does not predict the geographic scale of the phylogeographic structure. However, more localized lineages had higher mean individual heterozygosity and less negative Tajima's D. This result implies that finer-scale phylogeographic structuring within species is associated with larger and more stable populations and, hence, persistence.
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Affiliation(s)
- Jessica Fenker
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Leonardo G Tedeschi
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Jane Melville
- Department of Sciences, Museums Victoria, Melbourne, VIC, Australia.,School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
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19
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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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20
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Lambert M, Awan S, Imtiaz A, Alpy F, Tomasetto C, Schaeffer C, Moritz C, Julien-David D, Matz R, Terrand J, Boucher P. WNT5A promotes endosomal cholesterol trafficking to the er and protects against atherosclerosis. Atherosclerosis 2020. [DOI: 10.1016/j.atherosclerosis.2020.10.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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21
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Coman A, Potter S, Moritz C, Campbell CD, Joseph L. Biotic and abiotic drivers of evolution in some Australian thornbills (Passeriformes:
Acanthiza
) in allopatry, sympatry, and parapatry including a case of character displacement. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12355] [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: 11/28/2022]
Affiliation(s)
- Amelia Coman
- Division of Ecology and Evolution Research School of Biology, and Centre for Biodiversity Analysis The Australian National University Acton ACT Australia
- Australian National Wildlife Collection CSIRO National Research Collections Australia Canberra ACT Australia
| | - Sally Potter
- Division of Ecology and Evolution Research School of Biology, and Centre for Biodiversity Analysis The Australian National University Acton ACT Australia
| | - Craig Moritz
- Division of Ecology and Evolution Research School of Biology, and Centre for Biodiversity Analysis The Australian National University Acton ACT Australia
| | - Catriona D. Campbell
- Australian National Wildlife Collection CSIRO National Research Collections Australia Canberra ACT Australia
| | - Leo Joseph
- Australian National Wildlife Collection CSIRO National Research Collections Australia Canberra ACT Australia
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22
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Damasceno RP, Carnaval AC, Sass C, Sousa Recoder R, Moritz C, Trefaut Rodrigues M. Geographic restriction, genetic divergence, and morphological disparity in the Brazilian Atlantic Forests: Insights from Leposoma lizards (Gymnophthalmidae, Squamata). Mol Phylogenet Evol 2020; 154:106993. [PMID: 33148523 DOI: 10.1016/j.ympev.2020.106993] [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] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 09/01/2020] [Accepted: 09/28/2020] [Indexed: 10/23/2022]
Abstract
Lineage differentiation, long-term persistence, and range limitation promote high levels of phylogenetic and phylogeographic endemisms and likely underlie the abundant morphologically cryptic diversity observed in the Brazilian Atlantic Forests (AF). We explore lineage differentiation and range restriction in the AF and ask if genetic divergence and morphological disparity are correlated by integrating coalescent-based species delimitation, molecular phylogenetic, and morphological analyses in the lizard genus Leposoma. We present the first species tree for Leposoma and of their tribe, the Ecpleopodini. The analyses are based on the largest dataset ever assembled for Leposoma in terms of number of species (all represented), genetic markers (12 loci), and geographic coverage (~2,500 km). The exercise allows us to robustly delimit species within the genus and phylogeographic lineages within all species. We find support for the monophyly of the genus and for the recognition of a yet undescribed species around the Baía de Todos-os-Santos, in the state of Bahia; this form is distinct from all other congeners, both genetically and morphologically. We find that L. baturitensis, from the northeastern state of Ceará, is basal to the genus - and sister to a clade of six species restricted to the AF across the eastern coast of Brazil. Relationships within this coastal clade are ((((L. annectans, Leposoma sp.), L. scincoides), L. puk) (L. nanodactylus, L. sinepollex)). Phylogenetic and phylogeographic analyses, together with precise distribution data, allowed us to update the ranges of species and phylogeographic lineages. We reveal pervasive geographic restriction of divergent lineages in Leposoma at and below species level and discuss how forest refuges and rivers might have contributed to it. We find that morphological disparity lags behind genetic divergence in the genus because although they are correlated, the first accumulates at a much slower rate than the latter. We hope to encourage new studies in the area of AF north of the Doce river; phylogeographic sampling in that region has been much less common relative to southern sites, yet it may hold the key to several important processes defining biodiversity patterns in eastern Brazil. This appears to specially apply to processes underlying geographic restriction of morphologically cryptic, yet genetic divergent lineages, as the case of Leposoma.
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Affiliation(s)
- Roberta P Damasceno
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão, trav. 14, n. 321, Cidade Universitária, São Paulo, SP 05508-090, Brazil; Museum of Vertebrate Zoology, University of California, Berkeley, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA.
| | - Ana Carolina Carnaval
- Department of Biology, City College of New York and the Biology Program at the Graduate Center of CUNY, 160 Convent Avenue, Marshak Life Science Building J-526, New York, NY 10031, USA.
| | - Chodon Sass
- Museum of Vertebrate Zoology, University of California, Berkeley, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA; University and Jepson Herbaria, University of California, Berkeley, 1001 Valley Life Sciences Building, Berkeley, CA 94720, USA.
| | - Renato Sousa Recoder
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão, trav. 14, n. 321, Cidade Universitária, São Paulo, SP 05508-090, Brazil
| | - Craig Moritz
- Museum of Vertebrate Zoology, University of California, Berkeley, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA; Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, The Australian National University, 46 Sullivans Creek Road, Acton, ACT 2601, Australia.
| | - Miguel Trefaut Rodrigues
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão, trav. 14, n. 321, Cidade Universitária, São Paulo, SP 05508-090, Brazil.
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Camacho-Sanchez M, Velo-Antón G, Hanson JO, Veríssimo A, Martínez-Solano Í, Marques A, Moritz C, Carvalho SB. Comparative assessment of range-wide patterns of genetic diversity and structure with SNPs and microsatellites: A case study with Iberian amphibians. Ecol Evol 2020; 10:10353-10363. [PMID: 33072264 PMCID: PMC7548196 DOI: 10.1002/ece3.6670] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 11/11/2022] Open
Abstract
Reduced representation genome sequencing has popularized the application of single nucleotide polymorphisms (SNPs) to address evolutionary and conservation questions in nonmodel organisms. Patterns of genetic structure and diversity based on SNPs often diverge from those obtained with microsatellites to different degrees, but few studies have explicitly compared their performance under similar sampling regimes in a shared analytical framework. We compared range‐wide patterns of genetic structure and diversity in two amphibians endemic to the Iberian Peninsula: Hyla molleri and Pelobates cultripes, based on microsatellite (18 and 14 loci) and SNP (15,412 and 33,140 loci) datasets of comparable sample size and spatial extent. Model‐based clustering analyses with STRUCTURE revealed minor differences in genetic structure between marker types, but inconsistent values of the optimal number of populations (K) inferred. SNPs yielded more repeatable and less admixed ancestries with increasing K compared to microsatellites. Genetic diversity was weakly correlated between marker types, with SNPs providing a better representation of southern refugia and of gradients of genetic diversity congruent with the demographic history of both species. Our results suggest that the larger number of loci in a SNP dataset can provide more reliable inferences of patterns of genetic structure and diversity than a typical microsatellite dataset, at least at the spatial and temporal scales investigated.
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Affiliation(s)
- Miguel Camacho-Sanchez
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
| | - Guillermo Velo-Antón
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
| | - Jeffrey O Hanson
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
| | - Ana Veríssimo
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
| | | | - Adam Marques
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
| | - Craig Moritz
- Centre for Biodiversity Analysis and Research School of Biology The Australian National University Canberra ACT Australia
| | - Sílvia B Carvalho
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
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Singhal S, Colston TJ, Grundler MR, Smith SA, Costa GC, Colli GR, Moritz C, Pyron RA, Rabosky DL. Congruence and Conflict in the Higher-Level Phylogenetics of Squamate Reptiles: An Expanded Phylogenomic Perspective. Syst Biol 2020; 70:542-557. [PMID: 32681800 DOI: 10.1093/sysbio/syaa054] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 05/05/2020] [Accepted: 07/05/2020] [Indexed: 12/16/2022] Open
Abstract
Genome-scale data have the potential to clarify phylogenetic relationships across the tree of life but have also revealed extensive gene tree conflict. This seeming paradox, whereby larger data sets both increase statistical confidence and uncover significant discordance, suggests that understanding sources of conflict is important for accurate reconstruction of evolutionary history. We explore this paradox in squamate reptiles, the vertebrate clade comprising lizards, snakes, and amphisbaenians. We collected an average of 5103 loci for 91 species of squamates that span higher-level diversity within the clade, which we augmented with publicly available sequences for an additional 17 taxa. Using a locus-by-locus approach, we evaluated support for alternative topologies at 17 contentious nodes in the phylogeny. We identified shared properties of conflicting loci, finding that rate and compositional heterogeneity drives discordance between gene trees and species tree and that conflicting loci rarely overlap across contentious nodes. Finally, by comparing our tests of nodal conflict to previous phylogenomic studies, we confidently resolve 9 of the 17 problematic nodes. We suggest this locus-by-locus and node-by-node approach can build consensus on which topological resolutions remain uncertain in phylogenomic studies of other contentious groups. [Anchored hybrid enrichment (AHE); gene tree conflict; molecular evolution; phylogenomic concordance; target capture; ultraconserved elements (UCE).].
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Affiliation(s)
- Sonal Singhal
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.,Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Biology, CSU Dominguez Hills, Carson, CA 90747, USA
| | - Timothy J Colston
- Department of Biological Sciences, The George Washington University, Washington D.C. 20052, USA.,Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Maggie R Grundler
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.,Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Environmental Science, Policy, & Management, University of California Berkeley, Berkeley, CA 94720, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gabriel C Costa
- Department of Biology and Environmental Sciences, Auburn University at Montgomery, Montgomery, AL, USA
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, DF, Brazil
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, The Australian National University, 46 Sullivans Creek Road, Acton, ACT 2601, Australia
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington D.C. 20052, USA
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.,Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
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25
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Porter AF, Pettersson JHO, Chang WS, Harvey E, Rose K, Shi M, Eden JS, Buchmann J, Moritz C, Holmes EC. Novel hepaci- and pegi-like viruses in native Australian wildlife and non-human primates. Virus Evol 2020; 6:veaa064. [PMID: 33240526 PMCID: PMC7673076 DOI: 10.1093/ve/veaa064] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Flaviviridae family of positive-sense RNA viruses contains important pathogens of humans and other animals, including Zika virus, dengue virus, and hepatitis C virus. The Flaviviridae are currently divided into four genera-Hepacivirus, Pegivirus, Pestivirus, and Flavivirus-each with a diverse host range. Members of the genus Hepacivirus are associated with an array of animal species, including humans, non-human primates, other mammalian species, as well as birds and fish, while the closely related pegiviruses have been identified in a variety of mammalian taxa, also including humans. Using a combination of total RNA and whole-genome sequencing we identified four novel hepaci-like viruses and one novel variant of a known hepacivirus in five species of Australian wildlife. The hosts infected comprised native Australian marsupials and birds, as well as a native gecko (Gehyra lauta). From these data we identified a distinct marsupial clade of hepaci-like viruses that also included an engorged Ixodes holocyclus tick collected while feeding on Australian long-nosed bandicoots (Perameles nasuta). Distinct lineages of hepaci-like viruses associated with geckos and birds were also identified. By mining the SRA database we similarly identified three new hepaci-like viruses from avian and primate hosts, as well as two novel pegi-like viruses associated with primates. The phylogenetic history of the hepaci- and pegi-like viruses as a whole, combined with co-phylogenetic analysis, provided support for virus-host co-divergence over the course of vertebrate evolution, although with frequent cross-species virus transmission. Overall, our work highlights the diversity of the Hepacivirus and Pegivirus genera as well as the uncertain phylogenetic distinction between.
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Affiliation(s)
- Ashleigh F Porter
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
| | - John H-O Pettersson
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
| | - Wei-Shan Chang
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
| | - Erin Harvey
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
| | - Karrie Rose
- Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Mosman 2088, Australia
| | - Mang Shi
- School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - John-Sebastian Eden
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
| | - Jan Buchmann
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
| | - Craig Moritz
- Research School of Biology, Centre for Biodiversity Analysis, Australian National University, Acton, ACT, Australia
| | - Edward C Holmes
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
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26
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Elith J, Graham C, Valavi R, Abegg M, Bruce C, Ford A, Guisan A, Hijmans RJ, Huettmann F, Lohmann L, Loiselle B, Moritz C, Overton J, Peterson AT, Phillips S, Richardson K, Williams S, Wiser SK, Wohlgemuth T, Zimmermann NE. Presence-only and Presence-absence Data for Comparing Species Distribution Modeling Methods. Biodiv Inf 2020. [DOI: 10.17161/bi.v15i2.13384] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Species distribution models (SDMs) are widely used to predict and study distributions of species. Many different modeling methods and associated algorithms are used and continue to emerge. It is important to understand how different approaches perform, particularly when applied to species occurrence records that were not gathered in structured surveys (e.g. opportunistic records). This need motivated a large-scale, collaborative effort, published in 2006, that aimed to create objective comparisons of algorithm performance. As a benchmark, and to facilitate future comparisons of approaches, here we publish that dataset: point location records for 226 anonymized species from six regions of the world, with accompanying predictor variables in raster (grid) and point formats. A particularly interesting characteristic of this dataset is that independent presence-absence survey data are available for evaluation alongside the presence-only species occurrence data intended for modeling. The dataset is available on Open Science Framework and as an R package and can be used as a benchmark for modeling approaches and for testing new ways to evaluate the accuracy of SDMs.
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27
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Ortiz-Baez AS, Eden JS, Moritz C, Holmes EC. A Divergent Articulavirus in an Australian Gecko Identified Using Meta-Transcriptomics and Protein Structure Comparisons. Viruses 2020; 12:v12060613. [PMID: 32512909 PMCID: PMC7354609 DOI: 10.3390/v12060613] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/01/2020] [Accepted: 06/03/2020] [Indexed: 02/02/2023] Open
Abstract
The discovery of highly divergent RNA viruses is compromised by their limited sequence similarity to known viruses. Evolutionary information obtained from protein structural modelling offers a powerful approach to detect distantly related viruses based on the conservation of tertiary structures in key proteins such as the RNA-dependent RNA polymerase (RdRp). We utilised a template-based approach for protein structure prediction from amino acid sequences to identify distant evolutionary relationships among viruses detected in meta-transcriptomic sequencing data from Australian wildlife. The best predicted protein structural model was compared with the results of similarity searches against protein databases. Using this combination of meta-transcriptomics and protein structure prediction we identified the RdRp (PB1) gene segment of a divergent negative-sense RNA virus, denoted Lauta virus (LTAV), in a native Australian gecko (Gehyra lauta). The presence of this virus was confirmed by PCR and Sanger sequencing. Phylogenetic analysis revealed that Lauta virus likely represents a newly described genus within the family Amnoonviridae, order Articulavirales, that is most closely related to the fish virus Tilapia tilapinevirus (TiLV). These findings provide important insights into the evolution of negative-sense RNA viruses and structural conservation of the viral replicase among members of the order Articulavirales.
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Affiliation(s)
- Ayda Susana Ortiz-Baez
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney NSW 2006, Australia; (A.S.O.-B.); (J-S.E.)
| | - John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney NSW 2006, Australia; (A.S.O.-B.); (J-S.E.)
- Centre for Virus Research, Westmead Institute for Medical Research, Westmead NSW 2145, Australia
| | - Craig Moritz
- Research School of Biology & Centre for Biodiversity Analysis, The Australian National University, Acton ACT 6201, Australia;
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney NSW 2006, Australia; (A.S.O.-B.); (J-S.E.)
- Correspondence:
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Moritz C, Scheiwe C, Malgras B. Colonic volvulus after laparoscopic left colectomy. J Visc Surg 2020; 157:493-494. [PMID: 32389393 DOI: 10.1016/j.jviscsurg.2020.04.012] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Volvulus of the mobilized colon after laparoscopic left colectomy is rare. Contributing factors seem to be excessive length of the mobilized colon, absence of peritonization and absence of adhesions due to laparoscopy. Onset of colonic volvulus after laparoscopic left colectomy should lead to routine computerized tomography (CT), searching for an image suggestive of small intestinal incarceration under the neo-mesocolon, which might be an additional risk factor. Treatment consists of disincarceration of the small intestines while closing the mesocolic defect remains a subject of controversy.
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Affiliation(s)
- C Moritz
- Department of digestive and endocrine surgery, Bégin Army training hospital, 69, avenue de Paris, 94160 Saint-Mandé, France
| | - C Scheiwe
- Department of digestive and endocrine surgery, Bégin Army training hospital, 69, avenue de Paris, 94160 Saint-Mandé, France
| | - B Malgras
- Department of digestive and endocrine surgery, Bégin Army training hospital, 69, avenue de Paris, 94160 Saint-Mandé, France; École du Val-de-Grâce, 1, place Alphonse-Laveran, 75230 Paris cedex 05, France.
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29
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Oliver PM, Prasetya AM, Tedeschi LG, Fenker J, Ellis RJ, Doughty P, Moritz C. Crypsis and convergence: integrative taxonomic revision of the Gehyra australis group (Squamata: Gekkonidae) from northern Australia. PeerJ 2020; 8:e7971. [PMID: 32025362 PMCID: PMC6991128 DOI: 10.7717/peerj.7971] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 10/01/2019] [Indexed: 11/20/2022] Open
Abstract
For over two decades, assessments of geographic variation in mtDNA and small numbers of nuclear loci have revealed morphologically similar, but genetically divergent, intraspecific lineages in lizards from around the world. Subsequent morphological analyses often find subtle corresponding diagnostic characters to support the distinctiveness of lineages, but occasionally do not. In recent years it has become increasingly possible to survey geographic variation by sequencing thousands of loci, enabling more rigorous assessment of species boundaries across morphologically similar lineages. Here we take this approach, adding new, geographically extensive SNP data to existing mtDNA and exon capture datasets for the Gehyra australis and G. koira species complexes of gecko from northern Australia. The combination of exon-based phylogenetics with dense spatial sampling of mitochondrial DNA sequencing, SNP-based tests for introgression at lineage boundaries and newly-collected morphological evidence supports the recognition of nine species, six of which are newly described here. Detection of discrete genetic clusters using new SNP data was especially convincing where candidate taxa were continuously sampled across their distributions up to and across geographic boundaries with analyses revealing no admixture. Some species defined herein appear to be truly cryptic, showing little, if any, diagnostic morphological variation. As these SNP-based approaches are progressively applied, and with all due conservatism, we can expect to see a substantial improvement in our ability to delineate and name cryptic species, especially in taxa for which previous approaches have struggled to resolve taxonomic boundaries.
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Affiliation(s)
- Paul M Oliver
- Environmental Futures Research Institute and School of Environment and Science, Griffith University, South Brisbane, QLD, Australia.,Biodiversity and Geosciences Programme, Queensland Museum, Brisbane, QLD, Australia
| | - Audrey Miranda Prasetya
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, Australian National University, Acton, ACT, Australia
| | - Leonardo G Tedeschi
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, Australian National University, Acton, ACT, Australia
| | - Jessica Fenker
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, Australian National University, Acton, ACT, Australia
| | - Ryan J Ellis
- Terrestrial Zoology, Western Australian Museum, Welshpool, WA, Australia.,Biologic Environmental Survey, East Perth, WA, Australia
| | - Paul Doughty
- Terrestrial Zoology, Western Australian Museum, Welshpool, WA, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, Australian National University, Acton, ACT, Australia
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30
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Peñalba JV, Deng Y, Fang Q, Joseph L, Moritz C, Cockburn A. Genome of an iconic Australian bird: High-quality assembly and linkage map of the superb fairy-wren (Malurus cyaneus). Mol Ecol Resour 2020; 20:560-578. [PMID: 31821695 DOI: 10.1111/1755-0998.13124] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/09/2019] [Accepted: 12/02/2019] [Indexed: 12/13/2022]
Abstract
The superb fairy-wren, Malurus cyaneus, is one of the most iconic Australian passerine species. This species belongs to an endemic Australasian clade, Meliphagides, which diversified early in the evolution of the oscine passerines. Today, the oscine passerines comprise almost half of all avian species diversity. Despite the rapid increase of available bird genome assemblies, this part of the avian tree has not yet been represented by a high-quality reference. To rectify that, we present the first high-quality genome assembly of a Meliphagides representative: the superb fairy-wren. We combined Illumina shotgun and mate-pair sequences, PacBio long-reads, and a genetic linkage map from an intensively sampled pedigree of a wild population to generate this genome assembly. Of the final assembled 1.07-Gb genome, 975 Mb (90.4%) was anchored onto 25 pseudochromosomes resulting in a final superscaffold N50 of 68.11 Mb. This high-quality bird genome assembly is one of only a handful which is also accompanied by a genetic map and recombination landscape. In comparison to other pedigree-based bird genetic maps, we find that the fairy-wren genetic map more closely resembles those of Taeniopygia guttata and Parus major maps, unlike the Ficedula albicollis map which more closely resembles that of Gallus gallus. Lastly, we also provide a predictive gene and repeat annotation of the genome assembly. This new high-quality, annotated genome assembly will be an invaluable resource not only regarding the superb fairy-wren species and relatives but also broadly across the avian tree by providing a novel reference point for comparative genomic analyses.
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Affiliation(s)
- Joshua V Peñalba
- Division of Evolutionary Biology, Ludwig Maximilian University of Munich, Munich, Germany
| | | | - Qi Fang
- BGI-Shenzhen, Shenzhen, China
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections, Australia, Canberra, ACT, Australia
| | - Craig Moritz
- Centre for Biodiversity Analysis, Acton, ACT, Australia.,Division of Ecology and Evolution, Australian National University, Acton, ACT, Australia
| | - Andrew Cockburn
- Division of Ecology and Evolution, Australian National University, Acton, ACT, Australia
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von May R, Catenazzi A, Santa-Cruz R, Gutierrez AS, Moritz C, Rabosky DL. Thermal physiological traits in tropical lowland amphibians: Vulnerability to climate warming and cooling. PLoS One 2019; 14:e0219759. [PMID: 31369565 PMCID: PMC6675106 DOI: 10.1371/journal.pone.0219759] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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: 01/09/2019] [Accepted: 07/02/2019] [Indexed: 11/22/2022] Open
Abstract
Climate change is affecting biodiversity and ecosystem function worldwide, and the lowland tropics are of special concern because organisms living in this region experience temperatures that are close to their upper thermal limits. However, it remains unclear how and whether tropical lowland species will be able to cope with the predicted pace of climate warming. Additionally, there is growing interest in examining how quickly thermal physiological traits have evolved across taxa, and whether thermal physiological traits are evolutionarily conserved or labile. We measured critical thermal maximum (CTmax) and minimum (CTmin) in 56 species of lowland Amazonian frogs to determine the extent of phylogenetic conservatism in tolerance to heat and cold, and to predict species' vulnerability to climate change. The species we studied live in sympatry and represent ~65% of the known alpha diversity at our study site. Given that critical thermal limits may have evolved differently in response to different temperature constraints, we tested whether CTmax and CTmin exhibit different rates of evolutionary change. Measuring both critical thermal traits allowed us to estimate species' thermal breadth and infer their potential to respond to abrupt changes in temperature (warming and cooling). Additionally, we assessed the contribution of life history traits and found that both critical thermal traits were correlated with species' body size and microhabitat use. Specifically, small direct-developing frogs in the Strabomantidae family appear to be at highest risk of thermal stress while tree frogs (Hylidae) and narrow mouthed frogs (Microhylidae) tolerate higher temperatures. While CTmax and CTmin had considerable variation within and among families, both critical thermal traits exhibited similar rates of evolutionary change. Our results suggest that 4% of lowland rainforest frogs assessed will experience temperatures exceeding their CTmax, 25% might be moderately affected and 70% are unlikely to experience pronounced heat stress under a hypothetical 3°C temperature increase.
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Affiliation(s)
- Rudolf von May
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI, United States of America
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States of America
| | - Alessandro Catenazzi
- Department of Biological Sciences, Florida International University, Miami, FL, United States of America
| | - Roy Santa-Cruz
- Área de Herpetología, Museo de Historia Natural de la Universidad Nacional de San Agustín (MUSA), Arequipa, Perú
| | - Andrea S. Gutierrez
- Facultad de Ciencias Biológicas, Universidad Nacional Agraria La Molina, Lima, Perú
| | - Craig Moritz
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States of America
- Centre for Biodiversity Analysis and Research School of Biology, The Australian National University, Canberra, Australia
| | - Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI, United States of America
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33
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Llewelyn J, Macdonald SL, Moritz C, Martins F, Hatcher A, Phillips BL. Adjusting to climate: Acclimation, adaptation and developmental plasticity in physiological traits of a tropical rainforest lizard. Integr Zool 2019; 13:411-427. [PMID: 29316349 DOI: 10.1111/1749-4877.12309] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The impact of climate change may be felt most keenly by tropical ectotherms. In these taxa, it is argued, thermal specialization means a given shift in temperature will have a larger effect on fitness. For species with limited dispersal ability, the impact of climate change depends on the capacity for their climate-relevant traits to shift. Such shifts can occur through genetic adaptation, various forms of plasticity, or a combination of these processes. Here we assess the extent and causes of shifts in 7 physiological traits in a tropical lizard, the rainforest sunskink (Lampropholis coggeri). Two populations were sampled that differ from each other in both climate and physiological traits. We compared trait values in each animal soon after field collection versus following acclimation to laboratory conditions. We also compared trait values between populations in: (i) recently field-collected animals; (ii) the same animals following laboratory acclimation; and (iii) the laboratory-reared offspring of these animals. Our results reveal high trait lability, driven primarily by acclimation and local adaptation. By contrast, developmental plasticity, resulting from incubation temperature, had little to no effect on most traits. These results suggest that, while specialized, tropical ectotherms may be capable of rapid shifts in climate-relevant traits.
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Affiliation(s)
- John Llewelyn
- Centre for Tropical Biodiversity and Climate Change, James Cook University, Townsville, Queensland, Australia.,CSIRO Land and Water, Townsville, Queensland, Australia
| | - Stewart L Macdonald
- Centre for Tropical Biodiversity and Climate Change, James Cook University, Townsville, Queensland, Australia.,CSIRO Land and Water, Townsville, Queensland, Australia
| | - Craig Moritz
- Centre for Biodiversity Analysis, Australian National University, Canberra, Australia
| | - Felipe Martins
- Centre for Biodiversity Analysis, Australian National University, Canberra, Australia
| | - Amberlee Hatcher
- Centre for Tropical Biodiversity and Climate Change, James Cook University, Townsville, Queensland, Australia
| | - Ben L Phillips
- Centre for Tropical Biodiversity and Climate Change, James Cook University, Townsville, Queensland, Australia.,School of BioSciences, University of Melbourne, Melbourne, Australia
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34
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Blom MPK, Matzke NJ, Bragg JG, Arida E, Austin CC, Backlin AR, Carretero MA, Fisher RN, Glaw F, Hathaway SA, Iskandar DT, McGuire JA, Karin BR, Reilly SB, Rittmeyer EN, Rocha S, Sanchez M, Stubbs AL, Vences M, Moritz C. Habitat preference modulates trans-oceanic dispersal in a terrestrial vertebrate. Proc Biol Sci 2019; 286:20182575. [PMID: 31161911 DOI: 10.1098/rspb.2018.2575] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The importance of long-distance dispersal (LDD) in shaping geographical distributions has been debated since the nineteenth century. In terrestrial vertebrates, LDD events across large water bodies are considered highly improbable, but organismal traits affecting dispersal capacity are generally not taken into account. Here, we focus on a recent lizard radiation and combine a summary-coalescent species tree based on 1225 exons with a probabilistic model that links dispersal capacity to an evolving trait, to investigate whether ecological specialization has influenced the probability of trans-oceanic dispersal. Cryptoblepharus species that occur in coastal habitats have on average dispersed 13 to 14 times more frequently than non-coastal species and coastal specialization has, therefore, led to an extraordinarily widespread distribution that includes multiple continents and distant island archipelagoes. Furthermore, their presence across the Pacific substantially predates the age of human colonization and we can explicitly reject the possibility that these patterns are solely shaped by human-mediated dispersal. Overall, by combining new analytical methods with a comprehensive phylogenomic dataset, we use a quantitative framework to show how coastal specialization can influence dispersal capacity and eventually shape geographical distributions at a macroevolutionary scale.
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Affiliation(s)
- Mozes P K Blom
- 1 Research School of Biology, The Australian National University , Canberra , Australia.,2 Museum für Naturkunde, Leibniz Institut für Evolutions- und Biodiversitätsforschung , Berlin , Germany
| | - Nicholas J Matzke
- 1 Research School of Biology, The Australian National University , Canberra , Australia.,3 School of Biological Sciences, University of Auckland , Auckland , New Zealand
| | - Jason G Bragg
- 1 Research School of Biology, The Australian National University , Canberra , Australia
| | - Evy Arida
- 4 Research Center for Biology, The Indonesian Institute of Sciences , Cibinong , Indonesia
| | | | - Adam R Backlin
- 6 U.S. Geological Survey, Western Ecological Research Center , Santa Ana, CA , USA
| | | | - Robert N Fisher
- 8 U.S. Geological Survey, Western Ecological Research Center , San Diego, CA , USA
| | - Frank Glaw
- 9 Department of Herpetology, Zoologische Staatssamlung Münich , Munich , Germany
| | - Stacie A Hathaway
- 8 U.S. Geological Survey, Western Ecological Research Center , San Diego, CA , USA
| | - Djoko T Iskandar
- 10 School of Life Sciences and Technology, Institut Teknologi , Bandung , Indonesia
| | - Jimmy A McGuire
- 11 Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley , Berkeley, CA , USA
| | - Benjamin R Karin
- 11 Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley , Berkeley, CA , USA
| | - Sean B Reilly
- 11 Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley , Berkeley, CA , USA
| | - Eric N Rittmeyer
- 1 Research School of Biology, The Australian National University , Canberra , Australia.,5 Museum of Natural Science, Louisiana State University , Baton Rouge, LA , USA
| | - Sara Rocha
- 12 Department of Biochemistry, Genetics and Immunology & Biomedical Research Center (CINBIO), University of Vigo , Vigo , Spain
| | | | - Alexander L Stubbs
- 11 Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley , Berkeley, CA , USA
| | - Miguel Vences
- 14 Zoological Institute, Technische Universität Braunschweig , Braunschweig , Germany
| | - Craig Moritz
- 1 Research School of Biology, The Australian National University , Canberra , Australia
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35
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Bi K, Linderoth T, Singhal S, Vanderpool D, Patton JL, Nielsen R, Moritz C, Good JM. Temporal genomic contrasts reveal rapid evolutionary responses in an alpine mammal during recent climate change. PLoS Genet 2019; 15:e1008119. [PMID: 31050681 PMCID: PMC6519841 DOI: 10.1371/journal.pgen.1008119] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [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: 12/29/2018] [Revised: 05/15/2019] [Accepted: 04/01/2019] [Indexed: 12/12/2022] Open
Abstract
Many species have experienced dramatic changes in their abundance and distribution during recent climate change, but it is often unclear whether such ecological responses are accompanied by evolutionary change. We used targeted exon sequencing of 294 museum specimens (160 historic, 134 modern) to generate independent temporal genomic contrasts spanning a century of climate change (1911-2012) for two co-distributed chipmunk species: an endemic alpine specialist (Tamias alpinus) undergoing severe range contraction and a stable mid-elevation species (T. speciosus). Using a novel analytical approach, we reconstructed the demographic histories of these populations and tested for evidence of recent positive directional selection. Only the retracting species showed substantial population genetic fragmentation through time and this was coupled with positive selection and substantial shifts in allele frequencies at a gene, Alox15, involved in regulation of inflammation and response to hypoxia. However, these rapid population and gene-level responses were not detected in an analogous temporal contrast from another area where T. alpinus has also undergone severe range contraction. Collectively, these results highlight that evolutionary responses may be variable and context dependent across populations, even when they show seemingly synchronous ecological shifts. Our results demonstrate that temporal genomic contrasts can be used to detect very recent evolutionary responses within and among contemporary populations, even in the face of complex demographic changes. Given the wealth of specimens archived in natural history museums, comparative analyses of temporal population genomic data have the potential to improve our understanding of recent and ongoing evolutionary responses to rapidly changing environments.
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Affiliation(s)
- Ke Bi
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
- Computational Genomics Resource Laboratory (CGRL), California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California, United States of America
| | - Tyler Linderoth
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
| | - Sonal Singhal
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
| | - Dan Vanderpool
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - James L. Patton
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
| | - Craig Moritz
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, ACT, Australia
| | - Jeffrey M. Good
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
- Wildlife Biology Program, University of Montana, Missoula, MT, United States of America
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36
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Peñalba JV, Joseph L, Moritz C. Current geography masks dynamic history of gene flow during speciation in northern Australian birds. Mol Ecol 2019; 28:630-643. [PMID: 30561150 DOI: 10.1111/mec.14978] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [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: 09/05/2017] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 12/25/2022]
Abstract
Genome divergence is greatly influenced by gene flow during early stages of speciation. As populations differentiate, geographic barriers can constrain gene flow and so affect the dynamics of divergence and speciation. Current geography, specifically disjunction and continuity of ranges, is often used to predict the historical gene flow during the divergence process. We test this prediction in eight meliphagoid bird species complexes codistributed in four regions. These regions are separated by known biogeographical barriers across northern Australia and Papua New Guinea. We find that bird populations currently separated by terrestrial habitat barriers within Australia and marine barriers between Australia and Papua New Guinea have a range of divergence levels and probability of gene flow not associated with current range connectivity. Instead, geographic distance and historical range connectivity better predict divergence and probability of gene flow. In this dynamic environmental context, we also find support for a nonlinear decrease of the probability of gene flow during the divergence process. The probability of gene flow initially decreases gradually after a certain level of divergence is reached. Its decrease then accelerates until the probability is close to zero. This implies that although geographic connectivity may have more of an effect early in speciation, other factors associated with higher divergence may play a more important role in influencing gene flow midway through and later in speciation. Current geographic connectivity may then mislead inferences regarding potential for gene flow during speciation under a complex and dynamic history of geographic and reproductive isolation.
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Affiliation(s)
- Joshua V Peñalba
- Ecology and Evolution, Australian National University, Acton, ACT, Australia.,Centre for Biodiversity Analysis, Acton, ACT, Australia.,Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, Canberra, ACT, Australia.,Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, Germany
| | - Leo Joseph
- Centre for Biodiversity Analysis, Acton, ACT, Australia.,Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, Canberra, ACT, Australia
| | - Craig Moritz
- Ecology and Evolution, Australian National University, Acton, ACT, Australia.,Centre for Biodiversity Analysis, Acton, ACT, Australia
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37
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Coates DJ, Byrne M, Moritz C. Genetic Diversity and Conservation Units: Dealing With the Species-Population Continuum in the Age of Genomics. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00165] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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38
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Ashman LG, Bragg JG, Doughty P, Hutchinson MN, Bank S, Matzke NJ, Oliver P, Moritz C. Diversification across biomes in a continental lizard radiation. Evolution 2018; 72:1553-1569. [PMID: 29972238 DOI: 10.1111/evo.13541] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 12/14/2017] [Revised: 06/15/2018] [Accepted: 06/15/2018] [Indexed: 12/23/2022]
Abstract
Ecological opportunity is a powerful driver of evolutionary diversification, and predicts rapid lineage and phenotypic diversification following colonization of competitor-free habitats. Alternatively, topographic or environmental heterogeneity could be key to generating and sustaining diversity. We explore these hypotheses in a widespread lineage of Australian lizards: the Gehyra variegata group. This clade occurs across two biomes: the Australian monsoonal tropics (AMT), where it overlaps a separate, larger bodied clade of Gehyra and is largely restricted to rocks; and in the larger Australian arid zone (AAZ) where it has no congeners and occupies trees and rocks. New phylogenomic data and coalescent analyses of AAZ taxa resolve lineages and their relationships and reveal high diversity in the western AAZ (Pilbara region). The AMT and AAZ radiations represent separate radiations with no difference in speciation rates. Most taxa occur on rocks, with small geographic ranges relative to widespread generalist taxa across the vast central AAZ. Rock-dwelling and generalist taxa differ morphologically, but only the lineage-poor central AAZ taxa have accelerated evolution. This accords with increasing evidence that lineage and morphological diversity are poorly correlated, and suggests environmental heterogeneity and refugial dynamics have been more important than ecological release in elevating lineage diversity.
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Affiliation(s)
- L G Ashman
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
| | - J G Bragg
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
- Royal Botanic Garden, Sydney, NSW 2000, Australia
| | - P Doughty
- Department of Terrestrial Zoology, Western Australian Museum, Perth, WA 6016, Australia
| | - M N Hutchinson
- South Australian Museum, Adelaide, SA 5000, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- School of Biological Sciences, Flinders University, Adelaide, SA 5042, Australia
| | - S Bank
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
- Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, University of Göttingen, Göttingen 37073, Germany
| | - N J Matzke
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - P Oliver
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
- Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia
- Biodiversity and Geosciences Program, Queensland Museum, Brisbane, QLD 4101, Australia
| | - C Moritz
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
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39
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Martins F, Kruuk L, Llewelyn J, Moritz C, Phillips B. Heritability of climate-relevant traits in a rainforest skink. Heredity (Edinb) 2018; 122:41-52. [PMID: 29789644 DOI: 10.1038/s41437-018-0085-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/19/2018] [Accepted: 04/15/2018] [Indexed: 11/09/2022] Open
Abstract
There is justified concern about the impact of global warming on the persistence of tropical ectotherms. There is also growing evidence for strong selection on climate-relevant physiological traits. Understanding the evolutionary potential of populations is especially important for low dispersal organisms in isolated populations, because these populations have little choice but to adapt. Despite this, direct estimates of heritability and genetic correlations for physiological traits in ectotherms-which will determine their evolutionary responses to selection-are sparse, especially for reptiles. Here we examine the heritabilities and genetic correlations for a set of four morphological and six climate-relevant physiological traits in an isolated population of an Australian rainforest lizard, Lampropholis coggeri. These traits show considerable variation across populations in this species, suggesting local adaptation. From laboratory crosses, we estimated very low to moderate heritability of temperature-related physiological traits (h2 < 0.31), but significant and higher heritability of desiccation resistance (h2~0.42). These values contrasted with uniformly higher heritabilities (h2 > 0.51) for morphological traits. At the phenotypic level, there were positive associations among the morphological traits and between thermal limits. Growth rate was positively correlated with thermal limits, but there was no indication that morphology and physiology were linked in any other way. We found some support for a specialist-generalist trade-off in the thermal performance curve, but otherwise there was no evidence for evolutionary constraints, suggesting broadly labile multivariate trait structure. Our results indicate little potential to respond to selection on thermal traits in this population and provide new insights into the capacity of tropical ectotherms to adapt in situ to rapid climate change.
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Affiliation(s)
- Felipe Martins
- Research School of Biology, Dept. of Ecology and Evolution, The Australian National University Acton, Canberra, ACT, 2601, Australia.
| | - Loeske Kruuk
- Research School of Biology, Dept. of Ecology and Evolution, The Australian National University Acton, Canberra, ACT, 2601, Australia
| | - John Llewelyn
- Centre for Tropical Biodiversity and Climate, James Cook University, Townsville, QLD, 4811, Australia
| | - Craig Moritz
- Research School of Biology, Dept. of Ecology and Evolution, The Australian National University Acton, Canberra, ACT, 2601, Australia
| | - Ben Phillips
- School of Biosciences, University of Melbourne, Parkville, VIC, 3010, Australia
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40
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Martin HC, Batty EM, Hussin J, Westall P, Daish T, Kolomyjec S, Piazza P, Bowden R, Hawkins M, Grant T, Moritz C, Grutzner F, Gongora J, Donnelly P. Insights into Platypus Population Structure and History from Whole-Genome Sequencing. Mol Biol Evol 2018; 35:1238-1252. [PMID: 29688544 PMCID: PMC5913675 DOI: 10.1093/molbev/msy041] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The platypus is an egg-laying mammal which, alongside the echidna, occupies a unique place in the mammalian phylogenetic tree. Despite widespread interest in its unusual biology, little is known about its population structure or recent evolutionary history. To provide new insights into the dispersal and demographic history of this iconic species, we sequenced the genomes of 57 platypuses from across the whole species range in eastern mainland Australia and Tasmania. Using a highly improved reference genome, we called over 6.7 M SNPs, providing an informative genetic data set for population analyses. Our results show very strong population structure in the platypus, with our sampling locations corresponding to discrete groupings between which there is no evidence for recent gene flow. Genome-wide data allowed us to establish that 28 of the 57 sampled individuals had at least a third-degree relative among other samples from the same river, often taken at different times. Taking advantage of a sampled family quartet, we estimated the de novo mutation rate in the platypus at 7.0 × 10-9/bp/generation (95% CI 4.1 × 10-9-1.2 × 10-8/bp/generation). We estimated effective population sizes of ancestral populations and haplotype sharing between current groupings, and found evidence for bottlenecks and long-term population decline in multiple regions, and early divergence between populations in different regions. This study demonstrates the power of whole-genome sequencing for studying natural populations of an evolutionarily important species.
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Affiliation(s)
- Hilary C Martin
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Elizabeth M Batty
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Julie Hussin
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Portia Westall
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
| | - Tasman Daish
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Stephen Kolomyjec
- School of Biological Sciences, Lake Superior State University, Sault Sainte Marie, MI
| | - Paolo Piazza
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Department of Medicine, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Rory Bowden
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Tom Grant
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Craig Moritz
- Research School of Biology and Centre for Biodiversity Analysis, The Australian National University, Acton, ACT, Australia
| | - Frank Grutzner
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Jaime Gongora
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
| | - Peter Donnelly
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Department of Statistics, University of Oxford, Oxford, United Kingdom
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41
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Singhal S, Hoskin CJ, Couper P, Potter S, Moritz C. A Framework for Resolving Cryptic Species: A Case Study from the Lizards of the Australian Wet Tropics. Syst Biol 2018; 67:1061-1075. [DOI: 10.1093/sysbio/syy026] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/27/2018] [Indexed: 12/19/2022] Open
Affiliation(s)
- Sonal Singhal
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biology, California State University—Dominguez Hills, Carson, CA 90747, USA
| | - Conrad J Hoskin
- College of Science & Engineering, James Cook University, Townsville, Queensland 4811, Australia
| | - Patrick Couper
- Biodiversity Program, Queensland Museum, South Brisbane, Queensland 4101, Australia
| | - Sally Potter
- Division of Ecology and Evolution, Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Acton, ACT 2601, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Acton, ACT 2601, Australia
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42
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Rosauer DF, Byrne M, Blom MPK, Coates DJ, Donnellan S, Doughty P, Keogh JS, Kinloch J, Laver RJ, Myers C, Oliver PM, Potter S, Rabosky DL, Afonso Silva AC, Smith J, Moritz C. Real‐world conservation planning for evolutionary diversity in the Kimberley, Australia, sidesteps uncertain taxonomy. Conserv Lett 2018. [DOI: 10.1111/conl.12438] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Dan F. Rosauer
- Division of Ecology & Evolution, Research School of Biology Australian National University Acton ACT Australia
- Centre for Biodiversity Analysis Canberra, ACT Australia
| | - Margaret Byrne
- Science and Conservation Department of Biodiversity Conservation and Attractions Kensington WA Australia
| | - Mozes P. K. Blom
- Division of Ecology & Evolution, Research School of Biology Australian National University Acton ACT Australia
- Centre for Biodiversity Analysis Canberra, ACT Australia
| | - David J. Coates
- Science and Conservation Department of Biodiversity Conservation and Attractions Kensington WA Australia
| | - Stephen Donnellan
- South Australian Museum North Terrace Adelaide SA Australia
- School of Biological Sciences University of Adelaide Adelaide SA Australia
| | - Paul Doughty
- Department of Terrestrial Zoology Western Australian Museum Welshpool WA Australia
| | - J. Scott Keogh
- Division of Ecology & Evolution, Research School of Biology Australian National University Acton ACT Australia
| | - Janine Kinloch
- Science and Conservation Department of Biodiversity Conservation and Attractions Kensington WA Australia
| | - Rebecca J. Laver
- Division of Ecology & Evolution, Research School of Biology Australian National University Acton ACT Australia
- Centre for Biodiversity Analysis Canberra, ACT Australia
- Department of Biosciences University of Melbourne Parkville VIC Australia
| | - Cecilia Myers
- Dunkeld Pastoral Company Pty Ltd. Dunkeld VIC Australia
| | - Paul M. Oliver
- Division of Ecology & Evolution, Research School of Biology Australian National University Acton ACT Australia
- Centre for Biodiversity Analysis Canberra, ACT Australia
| | - Sally Potter
- Division of Ecology & Evolution, Research School of Biology Australian National University Acton ACT Australia
- Centre for Biodiversity Analysis Canberra, ACT Australia
- Australian Museum Research Institute Australian Museum Sydney NSW Australia
| | - Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Ann Arbor MI USA
| | - Ana Catarina Afonso Silva
- Division of Ecology & Evolution, Research School of Biology Australian National University Acton ACT Australia
- Centre for Biodiversity Analysis Canberra, ACT Australia
- Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências Universidade de Lisboa Lisboa Portugal
| | - James Smith
- Australian Wildlife Conservancy Mornington Sanctuary Derby WA Australia
- Research Institute for the Environment and Livelihoods Charles Darwin University Darwin NT Australia
| | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology Australian National University Acton ACT Australia
- Centre for Biodiversity Analysis Canberra, ACT Australia
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43
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Bragg JG, Potter S, Afonso Silva AC, Hoskin CJ, Bai BYH, Moritz C. Phylogenomics of a rapid radiation: the Australian rainbow skinks. BMC Evol Biol 2018; 18:15. [PMID: 29402211 PMCID: PMC5800007 DOI: 10.1186/s12862-018-1130-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 01/25/2018] [Indexed: 12/13/2022] Open
Abstract
Background The application of target capture with next-generation sequencing now enables phylogenomic analyses of rapidly radiating clades of species. But such analyses are complicated by extensive incomplete lineage sorting, demanding the use of methods that consider this process explicitly, such as the multispecies coalescent (MSC) model. However, the MSC makes strong assumptions about divergence history and population structure, and when using the full Bayesian implementation, current computational limits mean that relatively few loci and samples can be analysed for even modest sized radiations. We explore these issues through analyses of an extensive (> 1000 loci) dataset for the Australian rainbow skinks. This group consists of 3 genera and 41 described species, which likely diversified rapidly in Australia during the mid-late Miocene to occupy rainforest, woodland, and rocky habitats with corresponding diversity of morphology and breeding colouration. Previous phylogenetic analyses of this group have revealed short inter-nodes and high discordance among loci, limiting the resolution of inferred trees. A further complication is that many species have deep phylogeographic structure – this poses the question of how to sample individuals within species for analyses using the MSC. Results Phylogenies obtained using concatenation and summary coalescent species tree approaches to the full dataset are well resolved with generally consistent topology, including for previously intractable relationships near the base of the clade. As expected, branch lengths at the tips are substantially overestimated using concatenation. Comparisons of different strategies for sampling haplotypes for full Bayesian MSC analyses (for one clade and using smaller sets of loci) revealed, unexpectedly, that combining haplotypes across divergent phylogeographic lineages yielded consistent species trees. Conclusions This study of more than 1000 loci provides a strongly-supported estimate of the phylogeny of the Australian rainbow skinks, which will inform future research on the evolution and taxonomy of this group. Our analyses suggest that species tree estimation with the MSC can be quite robust to violation of the assumption that the individuals representing a taxon are sampled from a panmictic population. Electronic supplementary material The online version of this article (10.1186/s12862-018-1130-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jason G Bragg
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, Australia. .,Herbarium of NSW, Royal Botanic Gardens & Domain Trust, Sydney, Australia.
| | - Sally Potter
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, Australia
| | - Ana C Afonso Silva
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, Australia.,cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Conrad J Hoskin
- College of Science & Engineering, James Cook University, Qld, Townsville, 4811, Australia
| | - Benjamin Y H Bai
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, Australia.,Present address: Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Craig Moritz
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, Australia
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Blom MPK, Bragg JG, Potter S, Moritz C. Accounting for Uncertainty in Gene Tree Estimation: Summary-Coalescent Species Tree Inference in a Challenging Radiation of Australian Lizards. Syst Biol 2018; 66:352-366. [PMID: 28039387 DOI: 10.1093/sysbio/syw089] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 09/27/2016] [Indexed: 11/12/2022] Open
Abstract
Accurate gene tree inference is an important aspect of species tree estimation in a summary-coalescent framework. Yet, in empirical studies, inferred gene trees differ in accuracy due to stochastic variation in phylogenetic signal between targeted loci. Empiricists should, therefore, examine the consistency of species tree inference, while accounting for the observed heterogeneity in gene tree resolution of phylogenomic data sets. Here, we assess the impact of gene tree estimation error on summary-coalescent species tree inference by screening ${\sim}2000$ exonic loci based on gene tree resolution prior to phylogenetic inference. We focus on a phylogenetically challenging radiation of Australian lizards (genus Cryptoblepharus, Scincidae) and explore effects on topology and support. We identify a well-supported topology based on all loci and find that a relatively small number of high-resolution gene trees can be sufficient to converge on the same topology. Adding gene trees with decreasing resolution produced a generally consistent topology, and increased confidence for specific bipartitions that were poorly supported when using a small number of informative loci. This corroborates coalescent-based simulation studies that have highlighted the need for a large number of loci to confidently resolve challenging relationships and refutes the notion that low-resolution gene trees introduce phylogenetic noise. Further, our study also highlights the value of quantifying changes in nodal support across locus subsets of increasing size (but decreasing gene tree resolution). Such detailed analyses can reveal anomalous fluctuations in support at some nodes, suggesting the possibility of model violation. By characterizing the heterogeneity in phylogenetic signal among loci, we can account for uncertainty in gene tree estimation and assess its effect on the consistency of the species tree estimate. We suggest that the evaluation of gene tree resolution should be incorporated in the analysis of empirical phylogenomic data sets. This will ultimately increase our confidence in species tree estimation using summary-coalescent methods and enable us to exploit genomic data for phylogenetic inference. [Coalescence; concatenation; Cryptoblepharus; exon capture; gene tree; phylogenomics; species tree.].
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Affiliation(s)
- Mozes P K Blom
- Research School of Biology, Australian National University, Canberra ACT 0200, Australia
| | - Jason G Bragg
- Research School of Biology, Australian National University, Canberra ACT 0200, Australia
| | - Sally Potter
- Research School of Biology, Australian National University, Canberra ACT 0200, Australia
| | - Craig Moritz
- Research School of Biology, Australian National University, Canberra ACT 0200, Australia
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Morelli TL, Maher SP, Lim MCW, Kastely C, Eastman LM, Flint LE, Flint AL, Beissinger SR, Moritz C. Climate change refugia and habitat connectivity promote species persistence. ACTA ACUST UNITED AC 2017. [DOI: 10.1186/s40665-017-0036-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Potter S, Xue AT, Bragg JG, Rosauer DF, Roycroft EJ, Moritz C. Pleistocene climatic changes drive diversification across a tropical savanna. Mol Ecol 2017; 27:520-532. [DOI: 10.1111/mec.14441] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/20/2017] [Accepted: 10/31/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Sally Potter
- Research School of Biology The Australian National University Acton ACT Australia
- Centre for Biodiversity Analysis Acton ACT Australia
| | - Alexander T. Xue
- Department of Biology City University of New York New York NY USA
- Department of Genetics Rutgers University Piscataway NJ USA
| | - Jason G. Bragg
- Research School of Biology The Australian National University Acton ACT Australia
- Centre for Biodiversity Analysis Acton ACT Australia
| | - Dan F. Rosauer
- Research School of Biology The Australian National University Acton ACT Australia
- Centre for Biodiversity Analysis Acton ACT Australia
| | - Emily J. Roycroft
- School of Biosciences The University of Melbourne Parkville Vic. Australia
- Sciences Department Museums Victoria Melbourne Vic. Australia
| | - Craig Moritz
- Research School of Biology The Australian National University Acton ACT Australia
- Centre for Biodiversity Analysis Acton ACT Australia
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Blom MPK, Horner P, Moritz C. Convergence across a continent: adaptive diversification in a recent radiation of Australian lizards. Proc Biol Sci 2017; 283:rspb.2016.0181. [PMID: 27306048 DOI: 10.1098/rspb.2016.0181] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [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: 01/27/2016] [Accepted: 05/19/2016] [Indexed: 12/11/2022] Open
Abstract
Recent radiations are important to evolutionary biologists, because they provide an opportunity to study the mechanisms that link micro- and macroevolution. The role of ecological speciation during adaptive radiation has been intensively studied, but radiations can arise from a diversity of evolutionary processes; in particular, on large continental landmasses where allopatric speciation might frequently precede ecological differentiation. It is therefore important to establish a phylogenetic and ecological framework for recent continental-scale radiations that are species-rich and ecologically diverse. Here, we use a genomic (approx. 1 200 loci, exon capture) approach to fit branch lengths on a summary-coalescent species tree and generate a time-calibrated phylogeny for a recent and ecologically diverse radiation of Australian scincid lizards; the genus Cryptoblepharus We then combine the phylogeny with a comprehensive phenotypic dataset for over 800 individuals across the 26 species, and use comparative methods to test whether habitat specialization can explain current patterns of phenotypic variation in ecologically relevant traits. We find significant differences in morphology between species that occur in distinct environments and convergence in ecomorphology with repeated habitat shifts across the continent. These results suggest that isolated analogous habitats have provided parallel ecological opportunity and have repeatedly promoted adaptive diversification. By contrast, speciation processes within the same habitat have resulted in distinct lineages with relatively limited morphological variation. Overall, our study illustrates how alternative diversification processes might have jointly stimulated species proliferation across the continent and generated a remarkably diverse group of Australian lizards.
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Affiliation(s)
- Mozes P K Blom
- Research School of Biology, The Australian National University, Canberra ACT 0200, Australia
| | - Paul Horner
- Museum and Art Gallery of the Northern Territory, GPO Box 4646, Darwin NT 0801, Australia
| | - Craig Moritz
- Research School of Biology, The Australian National University, Canberra ACT 0200, Australia
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Abstract
This paper explores what the virtual biodiversity e-infrastructure will look like as it takes advantage of advances in ‘Big Data’ biodiversity informatics and e-research infrastructure, which allow integration of various taxon-level data types (genome, morphology, distribution and species interactions) within a phylogenetic and environmental framework. By overcoming the data scaling problem in ecology, this integrative framework will provide richer information and fast learning to enable a deeper understanding of biodiversity evolution and dynamics in a rapidly changing world. The Atlas of Living Australia is used as one example of the advantages of progressing towards this future. Living in this future will require the adoption of new ways of integrating scientific knowledge into societal decision making. This article is part of the themed issue ‘From DNA barcodes to biomes’.
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Affiliation(s)
- John La Salle
- Atlas of Living Australia, CSIRO National Research Collections Australia, GPO Box 1700, Canberra ACT 2601, Australia
| | - Kristen J Williams
- Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), GPO Box 1600, Canberra ACT 2601, Australia
| | - Craig Moritz
- Centre for Biodiversity Analysis and Research School of Biology, The Australian National University, Acton ACT 2601, Australia
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Santos MJ, Smith AB, Thorne JH, Moritz C. The relative influence of change in habitat and climate on elevation range limits in small mammals in Yosemite National Park, California, U.S.A. ACTA ACUST UNITED AC 2017. [DOI: 10.1186/s40665-017-0035-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Duchêne DA, Bragg JG, Duchêne S, Neaves LE, Potter S, Moritz C, Johnson RN, Ho SYW, Eldridge MDB. Analysis of Phylogenomic Tree Space Resolves Relationships Among Marsupial Families. Syst Biol 2017; 67:400-412. [DOI: 10.1093/sysbio/syx076] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 09/08/2017] [Indexed: 02/02/2023] Open
Affiliation(s)
- David A Duchêne
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Jason G Bragg
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
- National Herbarium of NSW, The Royal Botanic Gardens and Domain Trust, Sydney, NSW 2000, Australia
| | - Sebastián Duchêne
- Centre for Systems Genomics, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Linda E Neaves
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2000, Australia
| | - Sally Potter
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2000, Australia
| | - Craig Moritz
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Rebecca N Johnson
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2000, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2000, Australia
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