Phylogeny of Asian Bufonids inferred from mitochondrial DNA sequences (Anura: Amphibia): implication for the speciation of East Asian Bufonids

Peng, Zhaojie; Wan, Yaqiong; Qian, Lifu; Wu, Jun; Zhang, Baowei

doi:10.3109/19401736.2015.1122778

Cited by 5 publications

(2 citation statements)

References 14 publications

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“…At the time this manuscript was written, GenBank (https://www.ncbi.nlm.nih.gov/genbank/) listed partial mitogenomes for 107 species from 71 genera and 35 families and complete mitogenomes for 238 species from 76 genera and 27 families. Increasing the diversity of studied frog mitogenomes would improve our understanding of mitogenome evolution and provide valuable information for studies ranging from phylogenetics and population genetics to genomic evolution (e.g., Bertrand et al., ; Mueller & Boore, ; Peng et al., ). Further, the dearth of published frog mitogenomes hampers assembly and circularity inference (i.e., validation of sequence completeness) of new mitogenomes.…”

Section: Introductionmentioning

confidence: 99%

A new strategy to infer circularity applied to four new complete frog mitogenomes

Machado

Janies

Brouwer

et al. 2018

Ecology and Evolution

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We applied a novel strategy to infer sequence circularity and complete assembly of four mitochondrial genomes (mitogenomes) of the frog families Bufonidae (Melanophryniscus moreirae), Dendrobatidae (Hyloxalus subpunctatus and Phyllobates terribilis), and Scaphiopodidae (Scaphiopus holbrookii). These are the first complete mitogenomes of these four genera and Scaphiopodidae. We assembled mitogenomes from short genomic sequence reads using a baiting and iterative mapping strategy followed by a new ad hoc mapping strategy developed to test for assembly circularization. To assess the quality of the inferred circularization, we used Bowtie2 alignment scores and a new per‐position sequence coverage value (which we named “connectivity”). Permutation tests with 400 iterations per specimen and 1% or 5% chance of mutation at the ends of the putative circular sequences showed that the proposed method is highly sensitive, with a single nucleotide insertion or deletion being sufficient for circularity to be rejected. False positives comprised only 2% of all observations and possessed significantly lower alignment scores. The size, gene content, and gene arrangement of each mitogenome differed among the species but matched the expectations for their clades. We argue that basic studies on circular sequences can benefit from the results and bioinformatics procedures introduced here, especially when closely related references are lacking.

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Section: Introductionmentioning

confidence: 99%

A new strategy to infer circularity applied to four new complete frog mitogenomes

Machado

Janies

Brouwer

et al. 2018

Ecology and Evolution

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“…Our results in conjunction with previously published data allowed us to propose a hypothesis explaining the formation of the current species range. Based on molecular data (Van Bocxlaer et al, 2010;Peng et al, 2015;Portik & Papenfuss, 2015;Liedtke et al, 2016), the origin of the genus Strauchbufo could be estimated as the Early Miocene-Eocene (about 21.0-39.5 Ma). The closest relatives are genera Bufo, Bufotes, Epidalea and Sabahphrynus, which are distributed throughout Eurasia.…”

Section: Discussionmentioning

confidence: 99%

Reconstruction of past distribution for the Mongolian toad, Strauchbufo raddei (Anura: Bufonidae) using environmental modeling

Litvinchuk

Schepina

Borzée

2020

PeerJ

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The use of ecological models enables determining the current distribution of species, but also their past distribution when matching climatic conditions are available. In specific cases, they can also be used to determine the likelihood of fossils to belong to the same species—under the hypothesis that all individuals of a species have the same ecological requirements. Here, using environmental modeling, we reconstructed the distribution of the Mongolian toad, Strauchbufo raddei, since the Last Glacial Maximum and thus covering the time period between the Late Pleistocene and the Holocene. We found the range of the species to have shifted over time, with the LGM population clustered around the current southern range of the species, before expanding east and north during the Pleistocene, and reaching the current range since the mid-Holocene. Finally, we determined that the ecological conditions during the life-time of the mid-Pleistocene fossils attributed to the species in Europe were too different from the one of the extant species or fossils occurring at the same period in Asia to belong to the same species.

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Diversity, distribution and molecular species delimitation in frogs and toads from the Eastern Palaearctic

Dufresnes

Litvinchuk

2021

Zoological Journal of the Linnean Society

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Biodiversity analyses can greatly benefit from coherent species delimitation schemes and up-to-date distribution data. In this article, we have made the daring attempt to delimit and map described and undescribed lineages of anuran amphibians in the Eastern Palaearctic (EP) region in its broad sense. Through a literature review, we have evaluated the species status considering reproductive isolation and genetic divergence, combined with an extensive occurrence dataset (nearly 85k localities). Altogether 274 native species from 46 genera and ten families were retrieved, plus eight additional species introduced from other realms. Independent hotspots of species richness were concentrated in southern Tibet (Medog County), the circum-Sichuan Basin region, Taiwan, the Korean Peninsula and the main Japanese islands. Phylogeographic breaks responsible for recent in situ speciation events were shared around the Sichuan Mountains, across Honshu and between the Ryukyu Island groups, but not across shallow water bodies like the Yellow Sea and the Taiwan Strait. Anuran compositions suggested to restrict the zoogeographical limits of the EP to East Asia. In a rapidly evolving field, our study provides a checkpoint to appreciate patterns of species diversity in the EP under a single, spatially explicit, species delimitation framework that integrates phylogeographic data in taxonomic research.

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Phylogeny of Asian Bufonids inferred from mitochondrial DNA sequences (Anura: Amphibia): implication for the speciation of East Asian Bufonids

Cited by 5 publications

References 14 publications

A new strategy to infer circularity applied to four new complete frog mitogenomes

A new strategy to infer circularity applied to four new complete frog mitogenomes

Reconstruction of past distribution for the Mongolian toad, Strauchbufo raddei (Anura: Bufonidae) using environmental modeling

Diversity, distribution and molecular species delimitation in frogs and toads from the Eastern Palaearctic

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