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Nuñez LP, Gray LN, Weisrock DW, Burbrink FT. The Phylogenomic and Biogeographic History of the Gartersnakes, Watersnakes, and Allies (Natricidae: Thamnophiini). Mol Phylogenet Evol 2023:107844. [PMID: 37301486 DOI: 10.1016/j.ympev.2023.107844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/01/2023] [Accepted: 06/03/2023] [Indexed: 06/12/2023]
Abstract
North American Thamnophiini (gartersnakes, watersnakes, brownsnakes, and swampsnakes) are an ecologically and phenotypically diverse temperate clade of snakes representing 61 species across 10 genera. In this study, we estimate phylogenetic trees using ∼3,700 ultraconserved elements (UCEs) for 76 specimens representing 75% of all Thamnophiini species. We infer phylogenies using multispecies coalescent methods and time calibrate them using the fossil record. We also conducted ancestral area estimation to identify how major biogeographic boundaries in North America affect broadscale diversification in the group. While most nodes exhibited strong statistical support, analysis of concordant data across gene trees reveals substantial heterogeneity. Ancestral area estimation demonstrated that the genus Thamnophis was the only taxon in this subfamily to cross the Western Continental Divide, even as other taxa dispersed southward toward the tropics. Additionally, levels of gene tree discordance are overall higher in transition zones between bioregions, including the Rocky Mountains. Therefore, the Western Continental Divide may be a significant transition zone structuring the diversification of Thamnophiini during the Neogene and Pleistocene. Here we show that despite high levels of discordance across gene trees, we were able to infer a highly resolved and well-supported phylogeny for Thamnophiini, which allows us to understand broadscale patterns of diversity and biogeography.
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Affiliation(s)
- Leroy P Nuñez
- Department of Herpetology, American Museum of Natural History, New York, NY, USA; Richard Gilder Graduate School, American Museum of Natural History, New York, NY, USA.
| | - Levi N Gray
- Fort Collins Science Center, United States Geological Survey, Guam, USA
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, New York, NY, USA
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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] [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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Camurugi F, Oliveira EF, Lima GS, Marques R, Magalhães FM, Colli GR, Mesquita DO, Garda AA. Isolation by distance and past climate resistance shaped the distribution of genealogical lineages of a neotropical lizard. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2084470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Felipe Camurugi
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Cidade Universitária, Campo Grande, Brazil
| | - Eliana F. Oliveira
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Cidade Universitária, Campo Grande, Brazil
| | - Guilherme S. Lima
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - Ricardo Marques
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - Felipe M. Magalhães
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
- Earth and Environmental Sciences, Ecology and Evolution, Rutgers University-Newark, Newark, New Jersey, USA
| | - Guarino R. Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Daniel O. Mesquita
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - Adrian A. Garda
- Departamento Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, Natal, Rio Grande do Norte, Brazil
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Derkarabetian S, Starrett J, Hedin M. Using natural history to guide supervised machine learning for cryptic species delimitation with genetic data. Front Zool 2022; 19:8. [PMID: 35193622 PMCID: PMC8862334 DOI: 10.1186/s12983-022-00453-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/27/2022] [Indexed: 12/28/2022] Open
Abstract
The diversity of biological and ecological characteristics of organisms, and the underlying genetic patterns and processes of speciation, makes the development of universally applicable genetic species delimitation methods challenging. Many approaches, like those incorporating the multispecies coalescent, sometimes delimit populations and overestimate species numbers. This issue is exacerbated in taxa with inherently high population structure due to low dispersal ability, and in cryptic species resulting from nonecological speciation. These taxa present a conundrum when delimiting species: analyses rely heavily, if not entirely, on genetic data which over split species, while other lines of evidence lump. We showcase this conundrum in the harvester Theromaster brunneus, a low dispersal taxon with a wide geographic distribution and high potential for cryptic species. Integrating morphology, mitochondrial, and sub-genomic (double-digest RADSeq and ultraconserved elements) data, we find high discordance across analyses and data types in the number of inferred species, with further evidence that multispecies coalescent approaches over split. We demonstrate the power of a supervised machine learning approach in effectively delimiting cryptic species by creating a "custom" training data set derived from a well-studied lineage with similar biological characteristics as Theromaster. This novel approach uses known taxa with particular biological characteristics to inform unknown taxa with similar characteristics, using modern computational tools ideally suited for species delimitation. The approach also considers the natural history of organisms to make more biologically informed species delimitation decisions, and in principle is broadly applicable for taxa across the tree of life.
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Affiliation(s)
- Shahan Derkarabetian
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford St., Cambridge, MA, 02138, USA.
| | - James Starrett
- Department of Entomology and Nematology, University of California, Davis, Briggs Hall, Davis, CA, 95616-5270, USA
| | - Marshal Hedin
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182-4614, USA
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