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Karin BR, Lough-Stevens M, Lin TE, Reilly SB, Barley AJ, Das I, Iskandar DT, Arida E, Jackman TR, McGuire JA, Bauer AM. The natural and human-mediated expansion of a human-commensal lizard into the fringes of Southeast Asia. BMC Ecol Evol 2024; 24:25. [PMID: 38378475 PMCID: PMC10880348 DOI: 10.1186/s12862-024-02212-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 02/09/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Human-commensal species often display deep ancestral genetic structure within their native range and founder-effects and/or evidence of multiple introductions and admixture in newly established areas. We investigated the phylogeography of Eutropis multifasciata, an abundant human-commensal scincid lizard that occurs across Southeast Asia, to determine the extent of its native range and to assess the sources and signatures of human introduction outside of the native range. We sequenced over 350 samples of E. multifasciata for the mitochondrial ND2 gene and reanalyzed a previous RADseq population genetic dataset in a phylogenetic framework. RESULTS Nuclear and mitochondrial trees are concordant and show that E. multifasciata has retained high levels of genetic structure across Southeast Asia despite being frequently moved by humans. Lineage boundaries in the native range roughly correspond to several major biogeographic barriers, including Wallace's Line and the Isthmus of Kra. Islands at the outer fringe of the range show evidence of founder-effects and multiple introductions. CONCLUSIONS Most of enormous range of E. multifasciata across Southeast Asia is native and it only displays signs of human-introduction or recent expansion along the eastern and northern fringe of its range. There were at least three events of human-introductions to Taiwan and offshore islands, and several oceanic islands in eastern Indonesia show a similar pattern. In Myanmar and Hainan, there is a founder-effect consistent with post-warming expansion after the last glacial maxima or human introduction.
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Affiliation(s)
- Benjamin R Karin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA.
- Department of Biology, Villanova University, Villanova, PA, 19085, USA.
| | - Michael Lough-Stevens
- Department of Biology, Villanova University, Villanova, PA, 19085, USA
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Te-En Lin
- Endemic Species Research Institute, 1, Minsheng E Rd., Jiji Township, Nantou County, 55244, Taiwan
| | - Sean B Reilly
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, 95060, USA
| | - Anthony J Barley
- Department of Evolution and Ecology, University of California, 2320 Storer Hall, Davis, CA, 95616, USA
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Djoko T Iskandar
- School of Life Sciences and Technology, Bandung Institute of Technology, 10 Jalan Ganesa, Bandung, 40132, Indonesia
- Basic Sciences Commission, Indonesian Academy of Sciences, 11 Jalan Medan Merdeka Selatan, Jakarta, 10110, Indonesia
| | - Evy Arida
- Research Center for Ecology and Ethnobiology, Badan Riset dan Inovasi Nasional (BRIN), Cibinong Science Center, Jalan Raya Jakarta-Bogor km 46, Cibinong, 16911, Indonesia
| | - Todd R Jackman
- Department of Biology, Villanova University, Villanova, PA, 19085, USA
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Aaron M Bauer
- Department of Biology, Villanova University, Villanova, PA, 19085, USA
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2
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Shea GM. Nomenclature of supra-generic units within the Family Scincidae (Squamata). Zootaxa 2021; 5067:301-351. [PMID: 34810739 DOI: 10.11646/zootaxa.5067.3.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Indexed: 11/04/2022]
Abstract
The modern classification of skinks is based on a nomenclature that dates to the 1970s. However, there are a number of earlier names in the family group that have been overlooked by recent workers. These names are identified and their validity with respect to the International Code of Zoological Nomenclature investigated, along with their type genera. In most cases, use of these names to supplant junior synonyms in modern day use is avoidable by use of the Reversal of Precedence articles of the Code, but the names remain available in case of future divisions at the tribe and subtribe level. Other names are unavailable due to homonymy, either of their type genera or the stems from similar but non-homonymous type genera. However, the name Egerniini is replaced by Tiliquini, due to a limited timespan of use of Egerniini. A new classification of the Family Scincidae is proposed, providing a more extensive use of Code-regulated levels of classification, including tribes and subtribes, and a detailed synonymy provided for each taxonomic unit.
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Affiliation(s)
- Glenn M Shea
- Sydney School of Veterinary Science B01, University of Sydney, NSW 2006, Australia Australian Museum Research Institute, Australian Museum, 1 William St, Sydney, NSW 2010, Australia .
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3
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Chen L, Lin Y, Xiao Q, Lin Y, Du Y, Lin C, Ward-Fear G, Hu C, Qu Y, Li H. Characterization of the complete mitochondrial genome of the many-lined sun skink (Eutropis multifasciata) and comparison with other Scincomorpha species. Genomics 2021; 113:2526-2536. [PMID: 34051326 DOI: 10.1016/j.ygeno.2021.05.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 02/04/2021] [Accepted: 05/25/2021] [Indexed: 11/28/2022]
Abstract
Characterizating the complete mitochondrial genome (mitogenome) of an organism allows detailed genomic studies in systematics and evolution. The present study decodes the mitogenome (17,062 bp) of the many-lined sun skink, Eutropis multifasciata, using next-generation sequencing. To compare the diversity of mitogenomic structure and investigate intraspecific evolutionary relationships among the Asian Scincomorpha, the mitogenomes of 46 other species were examined concurrently. Within the group, the size of mitogenomes varied predominantly in the length at their control regions. The Ka/Ks ratios of 12 protein codon genes (PCGs) were lower than 1.00, demonstrating that they were under relaxed or moderate purifying selection. However, the ND5 had a Ka/Ks ratio >1, and was considered to be under positive selection. Currently there are two superfamilies in Scincomorpha (i.e. Scincoidea and Lacertoidea), but phylogenetic analysis using Bayesian Inference and Maximum-Likelihood Estimations produced phylogenetic trees with three clades in Scincomorpha ((Scincoidea + Lacertoidea (part)) + Gymnophthalmidae)).
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Affiliation(s)
- Lian Chen
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Youfu Lin
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Qi Xiao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Ying Lin
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yu Du
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; Hainan Key Laboratory for Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya 572022, China
| | - Chixian Lin
- Hainan Key Laboratory for Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya 572022, China
| | - Georgia Ward-Fear
- School of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Chaochao Hu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yanfu Qu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Hong Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
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4
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Stewart JR, Blackburn DG. A developmental synapomorphy of squamate reptiles. Evol Dev 2019; 21:342-353. [DOI: 10.1111/ede.12317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James R. Stewart
- Department of Biological SciencesEast Tennessee State UniversityJohnson City Tennessee 37614
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5
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Weinell JL, Branch WR, Colston TJ, Jackman TR, Kuhn A, Conradie W, Bauer AM. A species-level phylogeny of Trachylepis (Scincidae: Mabuyinae) provides insight into their reproductive mode evolution. Mol Phylogenet Evol 2019; 136:183-195. [DOI: 10.1016/j.ympev.2019.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/24/2019] [Accepted: 04/01/2019] [Indexed: 10/27/2022]
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6
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Romeiras MM, Pena AR, Menezes T, Vasconcelos R, Monteiro F, Paulo OS, Moura M. Shortcomings of Phylogenetic Studies on Recent Radiated Insular Groups: A Meta-Analysis Using Cabo Verde Biodiversity. Int J Mol Sci 2019; 20:E2782. [PMID: 31174340 PMCID: PMC6600550 DOI: 10.3390/ijms20112782] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/16/2019] [Accepted: 06/04/2019] [Indexed: 12/22/2022] Open
Abstract
Over the previous decades, numerous studies focused on how oceanic islands have contributed to determine the phylogenetic relationships and times of origin and diversification of different endemic lineages. The Macaronesian Islands (i.e., Azores, Madeira, Selvagens, Canaries, and Cabo Verde), harbour biotas with exceptionally high levels of endemism. Within the region, the vascular plants and reptiles constitute two of the most important radiations. In this study we compare relevant published phylogenetic data and diversification rates retrieved within Cabo Verde endemic lineages and discuss the importance of choosing appropriate phylogeny-based methods to investigate diversification dynamics on islands. From this selective literature-based review, we summarize the software packages used in Macaronesian studies and discuss their adequacy considering the published data to obtain well-supported phylogenies in the target groups. We further debate the importance of Next Generation Sequencing (NGS), to investigate the evolutionary processes of diversification in the Macaronesian Islands. Analysis of genomic data provides phylogenetic resolution for rapidly evolving species radiations, suggesting a great potential to improve the phylogenetic signal and divergence time estimates in insular lineages. The most important Macaronesian reptile radiations provide good case-studies to compare classical phylogenetic methods with new tools, such as phylogenomics, revealing a high value for research on this hotspot area.
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Affiliation(s)
- Maria M Romeiras
- LEAF, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal.
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal.
| | - Ana Rita Pena
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal.
| | - Tiago Menezes
- CIBIO, Research Centre in Biodiversity and Genetic Resources, Azores Group, InBIO Associate Laboratory, Universidade dos Açores, 9501-855 Ponta Delgada, Azores, Portugal.
| | - Raquel Vasconcelos
- CIBIO, Research Centre in Biodiversity and Genetic Resources, InBIO Associate Laboratory, Universidade do Porto, 4485-661 Vairão, Portugal.
| | - Filipa Monteiro
- LEAF, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal.
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal.
| | - Octávio S Paulo
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal.
| | - Mónica Moura
- CIBIO, Research Centre in Biodiversity and Genetic Resources, Azores Group, InBIO Associate Laboratory, Universidade dos Açores, 9501-855 Ponta Delgada, Azores, Portugal.
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Systematics and phylogeography of the widely distributed African skink Trachylepis varia species complex. Mol Phylogenet Evol 2018; 120:103-117. [DOI: 10.1016/j.ympev.2017.11.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 10/23/2017] [Accepted: 11/27/2017] [Indexed: 11/23/2022]
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8
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An endogenous retroviral envelope syncytin and its cognate receptor identified in the viviparous placental Mabuya lizard. Proc Natl Acad Sci U S A 2017; 114:E10991-E11000. [PMID: 29162694 DOI: 10.1073/pnas.1714590114] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Syncytins are envelope genes from endogenous retroviruses that have been captured during evolution for a function in placentation. They have been found in all placental mammals in which they have been searched, including marsupials. Placental structures are not restricted to mammals but also emerged in some other vertebrates, most frequently in lizards, such as the viviparous Mabuya Scincidae. Here, we performed high-throughput RNA sequencing of a Mabuya placenta transcriptome and screened for the presence of retroviral env genes with a full-length ORF. We identified one such gene, which we named "syncytin-Mab1," that has all the characteristics expected for a syncytin gene. It encodes a membrane-bound envelope protein with fusogenic activity ex vivo, is expressed at the placental level as revealed by in situ hybridization and immunohistochemistry, and is conserved in all Mabuya species tested, spanning over 25 My of evolution. Its cognate receptor, required for its fusogenic activity, was searched for by a screening assay using the GeneBridge4 human/Chinese hamster radiation hybrid panel and found to be the MPZL1 gene, previously identified in mammals as a signal-transducing transmembrane protein involved in cell migration. Together, these results show that syncytin capture is not restricted to placental mammals, but can also take place in the rare nonmammalian vertebrates in which a viviparous placentotrophic mode of reproduction emerged. It suggests that similar molecular tools have been used for the convergent evolution of placentation in independently evolved and highly distant vertebrates.
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9
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Pereira AG, Schrago CG. Arrival and diversification of mabuyine skinks (Squamata: Scincidae) in the Neotropics based on a fossil-calibrated timetree. PeerJ 2017; 5:e3194. [PMID: 28439466 PMCID: PMC5398276 DOI: 10.7717/peerj.3194] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/16/2017] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The evolution of South American Mabuyinae skinks holds significant biogeographic interest because its sister lineage is distributed across the African continent and adjacent islands. Moreover, at least one insular species, Trachylepis atlantica, has independently reached the New World through transoceanic dispersal. To clarify the evolutionary history of both Neotropical lineages, this study aimed to infer an updated timescale using the largest species and gene sampling dataset ever assembled for this group. By extending the analysis to the Scincidae family, we could employ fossil information to estimate mabuyinae divergence times and carried out a formal statistical biogeography analysis. To unveil macroevolutionary patterns, we also inferred diversification rates for this lineage and evaluated whether the colonization of South American continent significantly altered the mode of Mabuyinae evolution. METHODS A time-calibrated phylogeny was inferred under the Bayesian framework employing fossil information. This timetree was used to (i) evaluate the historical biogeography of mabuiyines using the statistical approach implemented in BioGeoBEARS; (ii) estimate macroevolutionary diversification rates of the South American Mabuyinae lineages and the patterns of evolution of selected traits, namely, the mode of reproduction, body mass and snout-vent length; (iii) test the hypothesis of differential macroevolutionary patterns in South American lineages in BAMM and GeoSSE; and (iv) re-evaluate the ancestral state of the mode of reproduction of mabuyines. RESULTS Our results corroborated the hypothesis that the occupation of the South American continent by Mabuyinae consisted of two independent dispersion events that occurred between the Oligocene and the Miocene. We found significant differences in speciation rates between the New World and the remaining Mabuyinae clades only in GeoSSE. The influence of phenotypic traits on diversification rates was not supported by any method. Ancestral state reconstruction suggested that the ancestor of South American mabuyine was likely viviparous. DISCUSSION Our analyses further corroborated the existence of a transoceanic connection between Africa and South America in the Eocene/Oligocene period (Atlantogea). Following colonization of the isolated South America and subsequent dispersal through the continent by the ancestral mabuyine stock, we detected no difference in macroevolutionary regimes of New World clades. This finding argued against the ecological opportunity model as an explanation for the diversity of living mabuyines.
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Affiliation(s)
- Anieli Guirro Pereira
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Carlos G. Schrago
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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10
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Stanley SG, Liniewski RM, Senter PJ. Appendicular skeleton of the vestigial-limbed African skinkEumecia anchietae. AFR J HERPETOL 2016. [DOI: 10.1080/21564574.2016.1258012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Shane G. Stanley
- Department of Biology, Fayetteville Technical Community College, PO Box 35236, 2201 Hull Road, Fayetteville, North Carolina 28303, USA
| | - Rachel M. Liniewski
- Department of Biological Sciences, Fayetteville State University, 1200 Murchison Road, Fayetteville, North Carolina 28301, USA
| | - Philip J. Senter
- Department of Biological Sciences, Fayetteville State University, 1200 Murchison Road, Fayetteville, North Carolina 28301, USA
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11
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Griffith OW, Brandley MC, Belov K, Thompson MB. Reptile Pregnancy Is Underpinned by Complex Changes in Uterine Gene Expression: A Comparative Analysis of the Uterine Transcriptome in Viviparous and Oviparous Lizards. Genome Biol Evol 2016; 8:3226-3239. [PMID: 27635053 PMCID: PMC5174741 DOI: 10.1093/gbe/evw229] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The evolution of new organs is difficult to study because most vertebrate organs evolved only once, more than 500 million years ago. An ideal model for understanding complex organ evolution is the placenta, a structure that is present in live bearing reptiles and mammals (amniotes), which has evolved independently more than 115 times. Using transcriptomics, we characterized the uterine gene expression patterns through the reproductive cycle of a viviparous skink lizard, Pseudemoia entrecasteauxii. Then we compare these patterns with the patterns of gene expression from two oviparous skinks Lampropholis guichenoti and Lerista bougainvillii. While thousands of genes are differentially expressed between pregnant and non-pregnant uterine tissue in the viviparous skink, few differentially expressed genes were identified between gravid and non-gravid oviparous skinks. This finding suggests that in P. entrecasteauxii, a pregnant-specific gene expression profile has evolved, allowing for the evolution of pregnancy-specific innovations in the uterus. We find substantial gene expression differences between the uterus of the chorioallantoic and the yolk sac placenta in P. entrecasteauxii, suggesting these placental regions are specialized for different placental functions. In particular, the chorioallantoic placenta is likely a major site of nutrient transport by membrane-bound transport proteins, while the yolk sac placenta also likely transports nutrients but via apocrine secretions. We discuss how the evolution of transcription factor networks is likely to underpin the evolution of the new transcriptional states in the uterine tissue of viviparous reptiles.
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Affiliation(s)
- Oliver W Griffith
- School of Life and Environmental Science, University of Sydney, Camperdown, NSW, Australia .,Department of Ecology and Evolutionary Biology, Yale University
| | - Matthew C Brandley
- School of Life and Environmental Science, University of Sydney, Camperdown, NSW, Australia.,New York University-Sydney, The Rocks, NSW, Australia
| | - Katherine Belov
- School of Life and Environmental Science, University of Sydney, Camperdown, NSW, Australia
| | - Michael B Thompson
- School of Life and Environmental Science, University of Sydney, Camperdown, NSW, Australia
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