Multilocus approaches reveal underestimated species diversity and inter-specific gene flow in pikas (Ochotona) from southwestern China

Koju, Narayan Prasad; He, Kai; Chalise, Mukesh Kumar; Ray, Chris; Chen, Zhongzheng; Zhang, Bin; Wan, Tao; Chen, Shunde; Jiang, Xue‐Long

doi:10.1016/j.ympev.2016.11.005

Cited by 37 publications

(40 citation statements)

References 55 publications

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“…The majority of the species have overlapping morphological variation (Figure ), which can contribute to the taxonomic study after the application of sophisticated methods only (Figure ). Our results as well as those of another published study (Koju et al, ) show that mtDNA introgression is not a rare case in the group in question. Earlier taxonomic studies based solely on mtDNA have lead to errors (Chang et al, ; Liu et al, ; Yu et al, ).…”

Section: Discussionsupporting

confidence: 91%

“…Craniometric or nuclear DNA variation has not yet been described. Mitochondrial introgression involving Plateau pika is known in both directions: from O. curzoniae to O. nubrica (this study) and from O. cansus to O. curzoniae (Koju et al, 2017).…”

Section: Ochotona Curzoniaementioning

confidence: 72%

“…A subsequent study revealed that the species O. syrinx occupies an isolated position on mitochondrial-based trees (Yu et al, 2000) and was considered as a member of the separated subgenus Alienauroa Liu et al, 2017. This result was supported by nuclear gene analysis (Koju et al, 2017). Thus, it appears that many papers on Ochotona taxonomy combined representatives of two remote subgenera into one species-O.…”

Section: Introductionmentioning

confidence: 71%

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Multilocus phylogeny and taxonomy of pikas of the subgenus Ochotona (Lagomorpha, Ochotonidae)

2018

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A complete set of pika taxa, belonging to the subgenus Ochotona, was studied using craniometric and multilocus genetic analyses. We examined 1,007 skulls, covering the entire distribution range of the subgenus, as well as the mitochondrial COI gene and three nuclear introns in 31 specimens, representing nearly all taxa in question. An additional set of 167 COI gene sequences and 357 cytb gene sequences was analysed to enlarge the geographical extent of genetic data and to compare the results with previous publications. We found that the subgenus consists of eight species. One of them, Ochotona morosa, is elevated to the full species rank for the first time. The name of this species is given preliminarily and should be studied additionally. Several cases of interspecies hybridisation were found, which indicates that mitochondrial DNA cannot be used for species identification in this subgenus. Taxon Ochotona qionglaiensis, which was recently described as a separate species, represents a relic mitochondrial lineage of Ochotona thibetana. Another recently described species, Ochotona yarlungensis, is a Nubra pika with its native mitochondrial DNA, firstly found for this species. Intraspecies variation was analysed for several species for the first time. Thus, new subspecies (Ochotona thibetana fengii ssp. n.) was found within O. thibetana.

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Section: Discussionsupporting

confidence: 91%

Section: Ochotona Curzoniaementioning

confidence: 72%

Section: Introductionmentioning

confidence: 71%

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Multilocus phylogeny and taxonomy of pikas of the subgenus Ochotona (Lagomorpha, Ochotonidae)

2018

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“…The cryptic diversity we observed in S. fusicaudus has also been demonstrated in other mammals we examined (e.g., Koju et al, ; Zhang et al, ), indicating the existence of taxonomically undescribed species (Fan et al, ), and could be the result of highly stable environments in the mountain ranges inhabited by these moles. Such stability could have buffered dramatic global cooling periods since the late Miocene as well as periodical climatic changes during the Pliocene and Pleistocene.…”

Section: Discussionsupporting

confidence: 82%

Cryptic phylogeographic history sheds light on the generation of species diversity in sky‐island mountains

Gutiérrez

Heming

et al. 2019

Journal of Biogeography

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Aim The aim of this study was to conduct comprehensive phylogeographic and demographic analyses to examine the degree to which topographic and climatic conditions have affected the patterns of diversification and migration in a strictly montane inhabitant, the montane long‐tailed mole (Scaptonyx fusicaudus). Location The mountains of south‐western China and adjacent mountains including Mts. Bashan, Dalou and Qinling also known as the sky islands in south‐western China. Taxon The long‐tailed mole (S. fusicaudus), a semi‐fossorial mammal distributed in the sky islands of south‐western China, is a relict species and the sole representative of the tribe Scaptonychini. Methods We sequenced one mitochondrial and six nuclear genes from 113 samples across the species’ range. We estimated phylogenetic relationships and divergence times, conducted genetic structuring and species delimitation using multiple approaches and used Approximate Bayesian Computation to test potential gene flow. We conducted ecological niche modelling to predict the species’ potential distribution in the present, the last glacial maximum and the last interglacial (LIG). Results The species comprises a minimum of 17 operational taxonomic units which are isolated in different mountain ranges. The lowlands and large rivers act as barriers to dispersal, and have isolated evolutionary lineages for up to 11 million years. Long‐distance dispersal is evident among a few discrete montane archipelagos. Suitable climatic conditions during the LIG are limited to only a few sites, thus geographically restricting climatic stable areas across geological periods (from the LIG to the present). Main conclusions For low‐vagility species, the complex topography of the sky islands has promoted exceptional diversification through a combination of eco‐environmental stability as well as geographic fragmentation. The mountains have acted as a buffer against climate change, and have provided continuously suitable habitats for S. fusicaudus since the early Late Miocene, supporting the hypothesis that the sky islands constitute “museums” of ancient lineages. Lowlands and river valleys have acted as barriers preventing gene flow, while the montane archipelagos could have provided stepping stones to facilitate dispersal.

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“…sector was lower because mostly the birds were inbred but the genetic diversity of private sector was higher. The same findings were reported by Koju et al, (2017) when t h ey r epor t ed t he phylogeny of living pikas (Ochotonidae, Ochotona) from China by using two mitochondrial (CYT B and COI) and five nuclear gene segments (RAG1,RAG2,TTN,OXAIL and IL1RAPL1). Mitochondrial DNA in animals causes the five to ten times greater rate of evolution than in nuclear genome, that is why it is hypothesized to be ideal marker to study divergence between domestic and wild animals (Saikia et al, 2015).…”

Section: Phylogenetic Analysissupporting

confidence: 75%

Phylogenetic analysis based studies on genetic variation of Cytochrome b gene of Indian peafowl (Pavo cristatus) in Pakistan

Ng’ambi

Ramuthaga

Brown

2017

IJAR

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This study was designed to analyze genetic variation between Indian peafowl available at different locations by targeting the Cytochrome b gene. A total of ten birds (n=10) were selected randomly for sample collection. Five birds were selected from Government sector and five from private breeding farms. DNA was extracted, purified and measured by using Nano drop. Extracted DNA was amplified using universal primers targeting Cytochrome b gene on polymerase chain reaction (PCR). PCR product was run on a gel for the desired DNA bands. DNA from gel was eluted and sent for sequencing. The sequences were compared with a reference reported sequence of cyt b gene of Indian peafowl with Accession No. L08379.1to find out the genetic diversity. Indian peafowl of government sector showed more similarity 95% rather than bird of private sector with 90% homology with reference Accession No. More genetic variation, which is the guarantee of resistance to disease and environmental fitness among the Indian peafowl at private sector, might be due to random reproductive behavior.

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Multilocus approaches reveal underestimated species diversity and inter-specific gene flow in pikas (Ochotona) from southwestern China

Cited by 37 publications

References 55 publications

Multilocus phylogeny and taxonomy of pikas of the subgenus Ochotona (Lagomorpha, Ochotonidae)

Multilocus phylogeny and taxonomy of pikas of the subgenus Ochotona (Lagomorpha, Ochotonidae)

Cryptic phylogeographic history sheds light on the generation of species diversity in sky‐island mountains

Phylogenetic analysis based studies on genetic variation of Cytochrome b gene of Indian peafowl (Pavo cristatus) in Pakistan

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