Phylogenetic relationships of the Chinese torrent frogs (Ranidae: Amolops) revealed by phylogenomic analyses of AFLP-Capture data

Zeng, Zhao-Chi; Liang, Dan; Li, Jiaxuan; Lyu, Zhi-Tong; Wang, Ying-Yong; Zhang, Peng

doi:10.1016/j.ympev.2020.106753

Cited by 14 publications

(14 citation statements)

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“…Bayesian analyses were conducted using MrBayes 3.2.7 with the Marko chain Monte Carlo (MCMC) for 20,000,000 generations and 1000 sampled generations (Ronquist et al 2012). The phylogenetic tree indicated that the mitogenome of A. jinjiangensis and A. loloensis clustered together, which supported the phylogenetic inferences estimated by Lyu et al (2019) and Zeng et al (2020) with samples also from Deqin County in Yunnan Province, but conflicted with those from Zhongdian County in Yunnan Province (Lu et al 2014). Furthermore, our analyses recovered a sister taxa relationship between A. jinjiangensis þ A. loloensis and A. mantzorum þ A. tuberodepressus.…”

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confidence: 76%

“…( 2019 ) and Zeng et al. ( 2020 ) with samples also from Deqin County in Yunnan Province, but conflicted with those from Zhongdian County in Yunnan Province (Lu et al. 2014 ).…”

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confidence: 95%

“… 2019 ; Zeng et al. 2020 ). In this study, we identified complete mitochondrial genomes of the A. jinjiangensis by using restriction site-associated DNA sequencing (RAD-seq) to gain additional molecular information and contribute to better understanding of the evolutionary aspects of this frog taxon.…”

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confidence: 99%

“…The previous studies had phylogenetic inferences based on the partial mitochondrial sequences, i.e. COI and Cyt-b, but the phylogenetic relationship and position of A. jinjiangensis were remaining controversial (Lu et al 2014;Lyu et al 2019;Zeng et al 2020). In this study, we identified complete mitochondrial genomes of the A. jinjiangensis by using restriction siteassociated DNA sequencing (RAD-seq) to gain additional molecular information and contribute to better understanding of the evolutionary aspects of this frog taxon.…”

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confidence: 99%

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The complete mitogenome of the Amolops jinjiangensis (Anura: Ranidae)

Wang

Ping

Xia

et al. 2021

Mitochondrial DNA Part B

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We describe the mitochondrial genome sequence of a torrent frog, Amolops jinjiangensis . The mitogenome was extracted and assembled for the first time by restriction site-associated DNA sequencing (RAD-seq). The total length is 17,780 bp, containing 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes, and one control region. The gene rearrangement was detected as the W-O L -ANCY gene cluster which consisted with several published Amolops mitogenomes. The phylogenetic tree was constructed based on 13 protein-coding genes of A. jinjiangensis and 11 closely related species by Bayesian analyses.

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confidence: 76%

“…( 2019 ) and Zeng et al. ( 2020 ) with samples also from Deqin County in Yunnan Province, but conflicted with those from Zhongdian County in Yunnan Province (Lu et al. 2014 ).…”

mentioning

confidence: 95%

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confidence: 99%

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confidence: 99%

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The complete mitogenome of the Amolops jinjiangensis (Anura: Ranidae)

Wang

Ping

Xia

et al. 2021

Mitochondrial DNA Part B

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“…The south-eastern China clade comprising A. spinapectoralis Inger, Orlov & Darevsky, 1999, and the hainanensis, daiyunensis and ricketti species groups, has been demonstrated to be the sister taxon to the clade containing all remaining Amolops species in phylogenetic studies that utilised high-throughput sequencing techniques (i.e. 330 loci in Wu et al [2020]; 242 nuclear loci + mitogenomes in Zeng et al [2020]). Therefore, we rooted the tree ("user selected" option in FigTree) with the south-eastern China clade.…”

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confidence: 99%

A review of torrent frogs ([i]Amolops[/i]: Ranidae) from Bhutan, the description of a new species, and reassessment of the taxonomic validity of some [i]A. viridimaculatus[/i] group species aided by archival DNA sequences of century-old type specimens

Mahony¹

2022

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Seven species of the Asian torrent frogs (genus Amolops) have previously been reported from the eastern Himalayan country of Bhutan. Species identifications from the region have been largely based on photographed animals with few voucher specimens available and no molecular sampling. Understanding the taxonomic status of Bhutan’s torrent frogs has also been hampered by the poorly understood distributional limits of species from surrounding regions. Herein we utilised molecular phylogenetic and morphological data for vouchered specimens from Bhutan and provide a complete literature review of all Amolops populations reported from the country. Phylogenetic relationships were estimated by combining available sequence data (from GenBank) with newly generated sequences from recently collected Bhutanese Amolops populations. We also obtained archival DNA sequences from the type specimens of Amolops formosus, A. himalayanus, and A. kaulbacki, collected between 82 and 151 years ago. Our comparative analyses revealed a large, new (to science) species of the Amolops viridimaculatus group from eastern Bhutan. Morphological examinations of related taxa revealed that A. senchalensis from India is not a synonym of A. marmoratus. Molecular phylogenetic results supplemented by morphological data unambiguously demonstrate i) that A. himalayanus is present in eastern Nepal, ii) the presence of a previously undocumented population of A. nepalicus in eastern Nepal, iii) a 200 km range extention for A. kaulbacki into Yunnan, China, iv) that A. gyirongensis should be considered a junior subjective synonym of A. formosus, and v) that A. splendissimus from Vietnam should be considered a junior subjective synonym of A. viridimaculatus. Based on our results, we expand the Amolops viridimaculatus group to include nine species, including A. formosus, A. himalayanus, A. kaulbacki, and the new species described herein. We provisionally include a further three species in the viridimaculatus group based on morphology, A. longimanus, A. nidorbellus, and A. senchalensis. Combining our data with the literature review allowed us to identify several unidentified Amolops species from recent phylogenetic studies and remove nine frog species (including Hyla, Sylvirana, and seven Amolops species) from Bhutan’s amphibian checklist. We recognise four species of Amolops in Bhutan, three of which cannot be confidently identified to the species level based on currently available data. Keywords: Anura, taxonomy, Himalayas, conservation, vouchered-specimens

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Unrecognized diversity, genetic structuring, and phylogeography of the genus Triplophysa (Cypriniformes: Nemacheilidae) sheds light on two opposite colonization routes during Quaternary glaciation that occurred in the Qilian Mountains

Du¹,

Zhang²,

Lou³

et al. 2023

Ecology and Evolution

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In recent years, the influence of historical geological and climatic events on the evolution of flora and fauna in the Tibetan Plateau has been a hot research topic. The Qilian Mountain region is one of the most important sources of biodiversity on the Qinghai-Tibet Plateau. Many species existed in the region during the Pleistocene glacial oscillation, and the complex geographical environment provided suitable conditions for the survival of local species. The shrinkage, expansion, and transfer of the distribution range and population size of species have significant effects on genetic diversity and intraspecific differentiation. To reveal the effects of geological uplift and climate oscillation on the evolution of fish populations in the Qilian Mountains, we investigated the genetic structure, phylogenetic relationship, and phylogeographical characteristics of genus Triplophysa species in the Qilian Mountains using the mitochondrial DNA gene (COI), three nuclear genes (RAG1, sRH, and Myh6) and 11 pairs of nuclear microsatellite markers. We collected 11 species of genus Triplophysa living in the Qilian Mountains, among which Triplophysa hsutschouensis and Triplophysa papillosolabiata are widely distributed in the rivers on the northern slope of the Qilian Mountains.There was a high degree of lineage differentiation among species, and the genetic diversity of endemic species was low. The different geographical groups of T. papillosolabiata presented some allogeneic adaptation and differentiation, which was closely related to the changes in the river system. Except for the population expansion event of T. hsutschouensis during the last glacial period of the Qinghai-Tibet Plateau (0.025 MYA), the population sizes of other plateau loach species remained stable without significant population expansion. Starting from the east and west sides of the Qilian Mountains, T. hsutschouensis, and T. papillosolabiata showed two species colonization routes in opposite directions. The geological events of the uplift of the Qinghai-Tibet Plateau and the climatic oscillation of the Quaternary glaciation had a great influence 2of24 | DU et al.

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Phylogenetic relationships of the Chinese torrent frogs (Ranidae: Amolops) revealed by phylogenomic analyses of AFLP-Capture data

Cited by 14 publications

References 42 publications

The complete mitogenome of the Amolops jinjiangensis (Anura: Ranidae)

The complete mitogenome of the Amolops jinjiangensis (Anura: Ranidae)

A review of torrent frogs ([i]Amolops[/i]: Ranidae) from Bhutan, the description of a new species, and reassessment of the taxonomic validity of some [i]A. viridimaculatus[/i] group species aided by archival DNA sequences of century-old type specimens

Unrecognized diversity, genetic structuring, and phylogeography of the genus Triplophysa (Cypriniformes: Nemacheilidae) sheds light on two opposite colonization routes during Quaternary glaciation that occurred in the Qilian Mountains

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