Complete mitochondrial genomes of <i>Scincella vandenburghi</i> and <i>S. huanrenensis</i> (Squamata: Scincidae)

Park, Jaejin; Koo, Kyo-Soung; Kim, Il-Hun; Park, Daesik

doi:10.1080/23802359.2016.1156490

Cited by 11 publications

(7 citation statements)

References 5 publications

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“…Following the recommendation of Renner (2016) , we visually identified diagnostic SNPs within the ND4 mtDNA gene using all Afonso Silva et al (2017) sequences with Genbank accessions codes MF083173 – MF083508 in Geneious v.7.1.9 ( http://www.geneious.com , Kearse et al, 2012 ). Using as a reference an available skink mitogenome from Scincella vandenburghi ( Park et al, 2016 ), we selected the available diagnostic SNPs per lineage within each species, where the nucleotide difference would correspond to an amino acid substitution.…”

Section: Methodsmentioning

confidence: 99%

Validation and description of two new north-western Australian Rainbow skinks with multispecies coalescent methods and morphology

Silva

Santos

Ogilvie

et al. 2017

PeerJ

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While methods for genetic species delimitation have noticeably improved in the last decade, this remains a work in progress. Ideally, model based approaches should be applied and considered jointly with other lines of evidence, primarily morphology and geography, in an integrative taxonomy framework. Deep phylogeographic divergences have been reported for several species of Carlia skinks, but only for some eastern taxa have species boundaries been formally tested. The present study does this and revises the taxonomy for two species from northern Australia, Carlia johnstonei and C. triacantha. We introduce an approach that is based on the recently published method StarBEAST2, which uses multilocus data to explore the support for alternative species delimitation hypotheses using Bayes Factors (BFD). We apply this method, jointly with two other multispecies coalescent methods, using an extensive (from 2,163 exons) data set along with measures of 11 morphological characters. We use this integrated approach to evaluate two new candidate species previously revealed in phylogeographic analyses of rainbow skinks (genus Carlia) in Western Australia. The results based on BFD StarBEAST2, BFD* SNAPP and BPP genetic delimitation, together with morphology, support each of the four recently identified Carlia lineages as separate species. The BFD StarBEAST2 approach yielded results highly congruent with those from BFD* SNAPP and BPP. This supports use of the robust multilocus multispecies coalescent StarBEAST2 method for species delimitation, which does not require a priori resolved species or gene trees. Compared to the situation in C. triacantha, morphological divergence was greater between the two lineages within Kimberley endemic C. johnstonei, which also had deeper divergent histories. This congruence supports recognition of two species within C. johnstonei. Nevertheless, the combined evidence also supports recognition of two taxa within the more widespread C. triacantha. With this work, we describe two new species, Carlia insularis sp. nov and Carlia isostriacantha sp. nov. in the northwest of Australia. This contributes to increasing recognition that this region of tropical Australia has a rich and unique fauna.

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Section: Methodsmentioning

confidence: 99%

Validation and description of two new north-western Australian Rainbow skinks with multispecies coalescent methods and morphology

Silva

Santos

Ogilvie

et al. 2017

PeerJ

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“…However, we were able to confidently identify this name to be S. huanrenensis based on the combination of morphological characteristics and ovoviviparity of these skinks, as reported by both authors. The latter characteristic is especially conclusive in identifying S. huanrenensis because the sympatric species S. vandenburghi is oviparous [15,24]. As the reported localities largely overlapped between the two studies, we extracted five unique datapoints from both Won [20] and Kim and Han [21].…”

Section: Data Collectionmentioning

confidence: 99%

How Threatened Is Scincella huanrenensis? An Update on Threats and Trends

et al. 2021

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It is important to understand the dynamics of population size to accurately assess threats and implement conservation activities when required. However, inaccurate estimates are harming both the threat estimation process, and the resulting conservation actions. Here, we address the extinction threats to Scincella huanrenensis, a species described in the People’s Republic of China, but also occurring on the Korean peninsula. Estimating the threats to the species is not an easy task due to its unknown population status in the Democratic People’s Republic of Korea. Here we analysed the literature to acquire the known presence point for the species, along with datapoints originating from opportunistic field surveys, and employed habitat suitability models to estimate the range of the species. We then followed the categories and criteria of the IUCN Red List of Threatened Species to assess the extinction risk of the species. We found the species not to be fitting the threatened category at the global scale based on the range size, the only category for which enough data was available. We recommend the status of the species on the IUCN Red List of Threatened Species to be updated as it is now listed as critically endangered (CR), a listing fitting a national assessment for the People’s Republic (PR) of China. While this species is possibly less threatened than currently listed, this is not a genuine improvement, and specific conservation aspects should not be neglected due to its specialisation to medium to high elevation habitat.

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“…KU641018) was employed as the reference sequence (Park et al. 2016 ). We used the NOVO Plasty 3.7 (Dierckxsens et al.…”

mentioning

confidence: 99%

Complete mitochondrial genome of Takydromus kuehnei (Squamata: Takydromus) and its phylogenetic analysis

Luo

Ding

2022

Mitochondrial DNA Part B

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We sequenced and annotated the complete mitochondrial genome (mitogenome) of Takydromus kuehnei Van Denburgh, 1909 (Squamata: Takydromus ). This mitogenome was 17,224 bp long and encoded 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, one non-coding regions of an L-strand replication origin and a displacement loop region. The overall nucleotide composition was 32.8% of A, 13.8% of G, 24.8% of T, and 30.5% of C. Phylogenetic analysis using maximum likelihood method validated the taxonomic status of T. kuehnei , exhibiting the close relationship with the species from the genus Takydromus .

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Complete mitochondrial genomes of Scincella vandenburghi and S. huanrenensis (Squamata: Scincidae)

Cited by 11 publications

References 5 publications

Validation and description of two new north-western Australian Rainbow skinks with multispecies coalescent methods and morphology

Validation and description of two new north-western Australian Rainbow skinks with multispecies coalescent methods and morphology

How Threatened Is Scincella huanrenensis? An Update on Threats and Trends

Complete mitochondrial genome of Takydromus kuehnei (Squamata: Takydromus) and its phylogenetic analysis

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