Out of the Hengduan Mountains: Molecular phylogeny and historical biogeography of the Asian water snake genus Trimerodytes (Squamata: Colubridae)

Guo, Peng; Zhu, Fei; Liu, Qin; Wang, Ping; Che, Jing; Nguyen, Truong Q.

doi:10.1016/j.ympev.2020.106927

Cited by 12 publications

(18 citation statements)

References 54 publications

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“…Asian water snake genus Trimerodytes from Guo et al . 2020). Considering that the uplift of the Qinghai–Tibetan Plateau at different times has had different degrees of influence on the differentiation and migration of terrestrial species and the formation of zoogeographical regions in the surrounding area (Favre et al .…”

Section: Discussionmentioning

confidence: 99%

“…3) and is closely related to the second uplift of the Qinghai-Tibetan Plateau and the lateral extrusion of the Indochina at the Oligocene/Miocene boundary (ca. 22-25 Ma;Wang et al 2006;Yin et al 2010;Zheng 2015), as many plants (Xiang et al 2016;Deng et al 2018;Xiang et al 2021), frogs and snakes (Che et al 2010;Guo et al 2020;Wu et al 2020) are also closely related with this geological event. On the one hand, geological uplift has exacerbated the environmental heterogeneity of the karst area of southwest China.…”

Section: Historical Biogeography Of Sinocyclocheilusmentioning

confidence: 99%

“…Biogeographic studies in southwestern China have made important progress in the past decade. For example the diversification of frogs and mountain salamanders (Che et al 2010;Yuan et al 2016;Wang et al 2018;Xu et al 2021), snakes (Guo et al 2019(Guo et al , 2020, mammals (Deng et al 2020), spiders (Zhao et al 2017), and plants (Deng et al 2018;Xiang et al 2021) is associated with environmental changes along the Oligocene/ Miocene boundary Asian margin, particularly the uplift of the Qinghai−Tibet Plateau triggered by strong tectonic movements. Few biologists have focused on cave biology in subsurface ecosystems.…”

Section: Historical Biogeography Of Sinocyclocheilusmentioning

confidence: 99%

“…the torrent frog genus Amolops from Wu et al 2020; the Asian leaf litter toads genus Leptobrachella from Chen et al 2018) and snakes (e.g. Asian water snake genus Trimerodytes from Guo et al 2020). Considering that the uplift of the Qinghai-Tibetan Plateau at different times has had different degrees of influence on the differentiation and migration of terrestrial species and the formation of zoogeographical regions in the surrounding area (Favre et al 2015;Deng et al 2020;He et al 2020;Xu et al 2021).…”

Section: Historical Biogeography Of Sinocyclocheilusmentioning

confidence: 99%

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Molecular phylogeny and historical biogeography of the cave fish genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in southwest China

et al. 2022

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Modern accumulations of genetic data offer unprecedented opportunities for understanding the systematic classification and origins of specific groups of organisms. The genus Sinocyclocheilus is among the most cave abundant genera in Cyprinidae, with 76 recognized species, belonging to 4 species groups. Recent phylogenetic studies have shown that the classification of species groups within the genus Sinocyclocheilus remains controversial. In this study, we constructed a sequence supermatrix of 26 species from 4 species groups of the genus Sinocyclocheilus using the mitochondrial genome to reveal phylogenetic relationships, historical biogeography and patterns of species diversification in the genus Sinocyclocheilus. Phylogenetic analysis strongly supports the monophyletic groups of the 3 species groups (S. jii, S. cyphotergous, and S. tingi groups) except the S. angularis group. Phylogenetic analysis showed that S. anshuiensis and S. microphthalmus, which were recognized as numbers of S. angularis group, formed a strongly supported independent clade. Therefore, we propose a new species group, the S. microphthalmus group, which contains S. anshuiensis and S. microphthalmus. Biogeographic reconstruction suggests that the living Sinocyclocheilus may have originated in north‐central Guangxi at the late Eocene and dispersed outward after a vicariance at 32.31 Million years ago (Ma). Early diversification is focused on the late Oligocene (ca. 25 Ma), which is related to the second uplift of the Qinghai−Tibetan Plateau and the lateral extrusion of the Indochina at the Oligocene/Miocene boundary. Our results suggest that 2 uplifts of the Qinghai−Tibetan Plateau and climate change in the Miocene may have influenced the diversification of the Sinocyclocheilus lineage.

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Section: Discussionmentioning

confidence: 99%

Section: Historical Biogeography Of Sinocyclocheilusmentioning

confidence: 99%

Section: Historical Biogeography Of Sinocyclocheilusmentioning

confidence: 99%

Section: Historical Biogeography Of Sinocyclocheilusmentioning

confidence: 99%

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Molecular phylogeny and historical biogeography of the cave fish genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in southwest China

et al. 2022

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“…The divergence dates of H. periops and Trimerodytes occur at interesting points in Indochina's geological record. Specifically, the rise of the Hengduan Mountains of the eastern Tibetan Plateau (Western China) are considered to have been a diversification driver of Trimerodytes ∼23.9 mya (Guo et al, 2020). While greater taxonomic sampling of Hydrablabes and other Borneo-endemics, as well as increased molecular sampling, will help to elucidate the evolutionary history of Hydrablabes amongst natricids, these initial results provide evolutionary and phylogeographic hypotheses for future testing.…”

Section: Museum Genomics Confirms Hydrablabes Is An Asian Natricidmentioning

confidence: 99%

Maximizing Molecular Data From Low-Quality Fluid-Preserved Specimens in Natural History Collections

Bernstein

Ruane

2022

Front. Ecol. Evol.

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Over the past decade, museum genomics studies have focused on obtaining DNA of sufficient quality and quantity for sequencing from fluid-preserved natural history specimens, primarily to be used in systematic studies. While these studies have opened windows to evolutionary and biodiversity knowledge of many species worldwide, published works often focus on the success of these DNA sequencing efforts, which is undoubtedly less common than obtaining minimal or sometimes no DNA or unusable sequence data from specimens in natural history collections. Here, we attempt to obtain and sequence DNA extracts from 115 fresh and 41 degraded samples of homalopsid snakes, as well as from two degraded samples of a poorly known snake, Hydrablabes periops. Hydrablabes has been suggested to belong to at least two different families (Natricidae and Homalopsidae) and with no fresh tissues known to be available, intractable museum specimens currently provide the only opportunity to determine this snake’s taxonomic affinity. Although our aim was to generate a target-capture dataset for these samples, to be included in a broader phylogenetic study, results were less than ideal due to large amounts of missing data, especially using the same downstream methods as with standard, high-quality samples. However, rather than discount results entirely, we used mapping methods with references and pseudoreferences, along with phylogenetic analyses, to maximize any usable molecular data from our sequencing efforts, identify the taxonomic affinity of H. periops, and compare sequencing success between fresh and degraded tissue samples. This resulted in largely complete mitochondrial genomes for five specimens and hundreds to thousands of nuclear loci (ultra-conserved loci, anchored-hybrid enrichment loci, and a variety of loci frequently used in squamate phylogenetic studies) from fluid-preserved snakes, including a specimen of H. periops from the Field Museum of Natural History collection. We combined our H. periops data with previously published genomic and Sanger-sequenced datasets to confirm the familial designation of this taxon, reject previous taxonomic hypotheses, and make biogeographic inferences for Hydrablabes. A second H. periops specimen, despite being seemingly similar for initial raw sequencing results and after being put through the same protocols, resulted in little usable molecular data. We discuss the successes and failures of using different pipelines and methods to maximize the products from these data and provide expectations for others who are looking to use DNA sequencing efforts on specimens that likely have degraded DNA.Life Science Identifier (Hydrablabes periops)urn:lsid:zoobank.org:pub:F2AA44 E2-D2EF-4747-972A-652C34C2C09D.

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Molecular phylogeny reveals cryptic diversity in Sibynophis from China (Serpentes: Sibynophiidae)

Guo

Wang

Lyu

et al. 2023

Ecology and Evolution

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The elucidation of species diversity and distribution is critical within the fields of evolution, genetics, and conservation. The genus Sibynophis contains rare snakes that have historically received little attention. In this study, we conducted comprehensive sampling and use both mitochondrial and nuclear genetic markers to explore Sibynophis species diversity within China. Our findings revealed that S. c. miyiensis should be considered synonymous with S. c. grahami, and S. c. grahami should be gave a specific rank as S. grahami. In addition, we discovered S. triangularis was new to China and Myanmar. Based on the specimens and molecular phylogeny results, we redefined the species distribution boundaries of each Chinese species.

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Out of the Hengduan Mountains: Molecular phylogeny and historical biogeography of the Asian water snake genus Trimerodytes (Squamata: Colubridae)

Cited by 12 publications

References 54 publications

Molecular phylogeny and historical biogeography of the cave fish genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in southwest China

Molecular phylogeny and historical biogeography of the cave fish genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in southwest China

Maximizing Molecular Data From Low-Quality Fluid-Preserved Specimens in Natural History Collections

Molecular phylogeny reveals cryptic diversity in Sibynophis from China (Serpentes: Sibynophiidae)

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