Genetics, morphology and ecology reveal a cryptic pika lineage in the Sikkim Himalaya

Dahal, Nishma; Lissovsky, Andrey A.; Lin, Zhenzhen; Solari, Katherine A.; Hadly, Elizabeth A.; Zhan, Xiangjiang; Ramakrishnan, Uma

doi:10.1016/j.ympev.2016.09.015

Cited by 19 publications

(29 citation statements)

References 23 publications

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“…We had no genetic material on this species; however, Dahal et al () showed that it is closer to O. cansus and O. curzoniae than to O. thibetana . The species has a notable intraspecies differentiation (Dahal et al, ; Liu et al, ; Supporting Information Figure ).…”

Section: Discussionmentioning

confidence: 92%

“…The taxonomic composition of O. thibetana was changed recently, with the remote part of distribution in Sikkim, India, being moved to another species, O. sikimaria (Dahal et al, ). Thus, the distribution range of the proper O. thibetana is quite compact and covers the eastern slope of the Tibetan Plateau or, more exactly, the proximal parts of the Hengduan Mts in the provinces Yunnan and Sichuan in China.…”

Section: Discussionmentioning

confidence: 99%

“…The distribution of the species covers the Sikkim Himalayas (Dahal et al, ) and penetrates China in the bordering county Rikaze, Xizang (Liu et al, ).…”

Section: Discussionmentioning

confidence: 99%

“…Pikas, belonging to the subgenus Ochotona , are burrowing mammals of small or medium size. The distribution range of six (Hoffmann & Smith, ) or seven (Dahal et al, ) species covers the Tibetan Plateau and its various benches: high‐altitude steppes to the north, deserts adjoining the Himalayas to the south, high‐altitude and forest habitats of the Hengduan Mountain to the east. One species, Ochotona dauurica (Pallas, 1776), has extended its distribution further north—through the Mongolian dry steppes to the Russian Tuva and Transbaikalian regions.…”

Section: Introductionmentioning

confidence: 99%

“…The modern integration of species in the subgenus Ochotona is a result of recent genetic studies (Yu, Zheng, Zhang, & Li, ; Lissovsky ; Dahal et al, ; Liu et al, ). Never before, this set of species was recognised as a separate taxon.…”

Section: Introductionmentioning

confidence: 99%

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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: Discussionmentioning

confidence: 92%

Section: Discussionmentioning

confidence: 99%

“…The distribution of the species covers the Sikkim Himalayas (Dahal et al, ) and penetrates China in the bordering county Rikaze, Xizang (Liu et al, ).…”

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

2018

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Gene flow drives genomic diversity in Asian Pikas distributed along the core and range‐edge habitats in the Himalayas

Dahal

Romine

Khatiwara

et al. 2023

Ecology and Evolution

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Studying the genetic variation among different species distributed across their core and range‐edge habitats can provide valuable insights into how genetic variation changes across the species' distribution range. This information can be important for understanding local adaptation, as well as for conservation and management efforts. In this study, we have carried out genomic characterization of six species of Asian Pikas distributed along their core and range‐edge habitats in the Himalayas. We utilized a population genomics approach using ~28,000 genome‐wide SNP markers obtained from restriction‐site associated DNA sequencing. We identified low nucleotide diversity and high inbreeding coefficients in all six species across their core and range‐edge habitats. We also identified evidence of gene flow among genetically diverse species. Our results provide evidence of reduced genetic diversity in Asian pikas distributed across the Himalayas and the neighboring regions and indicate that recurrent gene flow is possibly a key mechanism for maintaining genetic diversity and adaptive potential in these pikas. However, full‐scale genomics studies that utilize whole‐genome sequencing approaches will be needed to quantify the direction and timing of gene flow and functional changes associated with introgressed regions in the genome. Our results represent an important step toward understanding the patterns and consequences of gene flow in species, sampled at the least studied, yet climatically vulnerable part of their habitat that can be further used to inform conservation strategies that promote connectivity and gene flow between populations.

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The role of geography, environment, and genetic divergence on the distribution of pikas in the Himalaya

Dahal

Kumar

Noon

et al. 2020

Ecology and Evolution

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Pikas (Ochotona Link, 1795) are high‐altitude specialist species making them a useful bioindicator species to warming in high‐altitude ecosystem. The Himalayan Mountains are an important part of their range, supporting approximately 23%–25% of total pika species worldwide, yet we lack basic information on the distribution patterns. We combine field‐based surveys with genetics‐based identification and phylogeny to identify differences in species‐environment relationships. Further, we suggest putative evolutionary causes for the observed niche patterns. Location Himalayan high‐altitude region. Methods We sampled 11 altitudinal transects (ranging from ~2,000 to 5,000 m) in the Himalaya to establish occurrence records. We collected 223 species records using genetic analyses to confirm species' identity (based on some invasive and mostly noninvasive biological samples). Niche and geographic overlap were estimated using kernel density estimates. Results Most pikas in the Himalaya span wide elevation ranges and exhibit extensive spatial overlap with other species. However, even in areas of high species diversity, we found species to have a distinct environmental niche. Despite apparent overlapping distributions at broad spatial scales, in our field surveys, we encountered few cases of co‐occurrence of species in the sampled transects. Deeply diverged sister‐species pair had the least environmental niche overlap despite having the highest geographic range overlap. In contrast, sister‐species pair with shallow genetic divergence had a higher environmental niche overlap but was geographically isolated. We hypothesize that the extent of environmental niche divergence in pikas is a function of divergence time within the species complex. We assessed vulnerability of species to future climate change using environmental niche and geographic breadth sizes as a proxies. Our findings suggest that O. sikimaria may be the most vulnerable species. Ochotona roylii appears to have the most unique environmental niche space, with least niche overlap with other pika species from the study area.

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Genetics, morphology and ecology reveal a cryptic pika lineage in the Sikkim Himalaya

Cited by 19 publications

References 23 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)

Gene flow drives genomic diversity in Asian Pikas distributed along the core and range‐edge habitats in the Himalayas

The role of geography, environment, and genetic divergence on the distribution of pikas in the Himalaya

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