1
|
Dahal N, Romine MG, Khatiwara S, Ramakrishnan U, Lamichhaney S. Gene flow drives genomic diversity in Asian Pikas distributed along the core and range-edge habitats in the Himalayas. Ecol Evol 2023; 13:e10129. [PMID: 37250448 PMCID: PMC10208896 DOI: 10.1002/ece3.10129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/31/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- Nishma Dahal
- Biotechnology DivisionCSIR‐Institute of Himalayan Bioresource TechnologyPalampurHimachal PradeshIndia
- National Centre for Biological Sciences, TIFRBangaloreIndia
| | - Melia G. Romine
- School of Biomedical SciencesKent State UniversityKentOhioUSA
| | - Sunita Khatiwara
- Forest and Environment Department, Government of SikkimGangtokIndia
| | | | - Sangeet Lamichhaney
- School of Biomedical SciencesKent State UniversityKentOhioUSA
- Department of Biological SciencesKent State UniversityKentUSA
| |
Collapse
|
2
|
Mu D, Wu X, Feijó A, Wu W, Wen Z, Cheng J, Xia L, Yang Q, Shan W, Ge D. Transcriptome analysis of pika heart tissue reveals mechanisms underlying the adaptation of a keystone species on the roof of the world. Front Genet 2022; 13:1020789. [PMID: 36506315 PMCID: PMC9728954 DOI: 10.3389/fgene.2022.1020789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/10/2022] [Indexed: 11/25/2022] Open
Abstract
High-altitude environments impose intense stresses on living organisms and drive striking phenotypic and genetic adaptations, such as hypoxia resistance, cold tolerance, and increases in metabolic capacity and body mass. As one of the most successful and dominant mammals on the Qinghai-Tibetan Plateau (QHTP), the plateau pika (Ochotona curzoniae) has adapted to the extreme environments of the highest altitudes of this region and exhibits tolerance to cold and hypoxia, in contrast to closely related species that inhabit the peripheral alpine bush or forests. To explore the potential genetic mechanisms underlying the adaptation of O. curzoniae to a high-altitude environment, we sequenced the heart tissue transcriptomes of adult plateau pikas (comparing specimens from sites at two different altitudes) and Gansu pikas (O. cansus). Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were used to identify differentially expressed genes (DEGs) and their primary functions. Key genes and pathways related to high-altitude adaptation were identified. In addition to the biological processes of signal transduction, energy metabolism and material transport, the identified plateau pika genes were mainly enriched in biological pathways such as the negative regulation of smooth muscle cell proliferation, the apoptosis signalling pathway, the cellular response to DNA damage stimulus, and ossification involved in bone maturation and heart development. Our results showed that the plateau pika has adapted to the extreme environments of the QHTP via protection against cardiomyopathy, tissue structure alterations and improvements in the blood circulation system and energy metabolism. These adaptations shed light on how pikas thrive on the roof of the world.
Collapse
Affiliation(s)
- Danping Mu
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xinlai Wu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China,Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China
| | - Anderson Feijó
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wei Wu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wenjuan Shan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China,*Correspondence: Wenjuan Shan, ; Deyan Ge,
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China,*Correspondence: Wenjuan Shan, ; Deyan Ge,
| |
Collapse
|
3
|
Dahal N, Kumar S, Noon BR, Nayak R, Lama RP, Ramakrishnan U. The role of geography, environment, and genetic divergence on the distribution of pikas in the Himalaya. Ecol Evol 2020; 10:1539-1551. [PMID: 32076532 PMCID: PMC7029102 DOI: 10.1002/ece3.6007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 12/12/2019] [Accepted: 12/19/2019] [Indexed: 12/04/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Nishma Dahal
- National Centre for Biological SciencesTIFR, GKVK campusBangaloreIndia
- Nature Conservation FoundationMysoreIndia
- Manipal Academy of Higher EducationManipalIndia
| | - Sunil Kumar
- Natural Resource Ecology LaboratoryColorado State UniversityFort CollinsCOUSA
| | - Barry R. Noon
- Natural Resource Ecology LaboratoryColorado State UniversityFort CollinsCOUSA
| | - Rajat Nayak
- Foundation for Ecological Research, Advocacy and LearningMorattandiTamil NaduIndia
| | | | - Uma Ramakrishnan
- National Centre for Biological SciencesTIFR, GKVK campusBangaloreIndia
| |
Collapse
|
4
|
Hall LE, Chalfoun AD. Behavioural plasticity modulates temperature-related constraints on foraging time for a montane mammal. J Anim Ecol 2018; 88:363-375. [PMID: 30449046 DOI: 10.1111/1365-2656.12925] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 09/10/2018] [Indexed: 11/29/2022]
Abstract
Contemporary climate change is altering temperature profiles across the globe. Increasing temperatures can reduce the amount of time during which conditions are suitable for animals to engage in essential activities, such as securing food. Behavioural plasticity, the ability to alter behaviour in response to the environment, may provide animals with a tool to adjust to changes in the availability of suitable thermal conditions. The extent to which individuals can alter fitness-enhancing behaviours, such as food collection, to proximately buffer variation in temperature, however, remains unclear. Even less well understood are the potential performance advantages of flexible strategies among endotherms. We examined the degree to which individuals altered rates of food collection in response to temperature, and two potential benefits, using the American pika (Ochotona princeps), a temperature-sensitive, food-hoarding mammal, as a model. From July-September 2013-2015, we used motion-activated cameras and in situ temperature loggers to examine pika food-caching activity for 72 individuals across 10 sites in the central Rocky Mountains, USA. We quantified % nitrogen by cache volume as a metric of cache quality, and the number of events during which pikas were active in temperatures ≥25°C as a measure of potential thermoregulatory stress. We found a strong negative effect of temperature on the rate at which pikas cached food. Individual responses to temperature varied substantially in both the level of food-collecting activity and in the degree to which individuals shifted activity with warming temperature. After accounting for available foraging time, individuals that exhibited greater plasticity collected a comparable amount of nitrogen, while simultaneously experiencing fewer occasions in which temperatures eclipsed estimated thermal tolerances. By varying food-collection norms of reaction, individuals were able to plastically respond to temperature-driven reductions in foraging time. Through this increased flexibility, individuals amassed food caches of comparable quality, while minimizing exposure to potentially stressful thermal conditions. Our results suggest that, given sufficient resource quality and availability, plasticity in foraging activity may help temperature-limited endotherms adjust to climate-related constraints on foraging time.
Collapse
Affiliation(s)
- L Embere Hall
- Wyoming Cooperative Fish and Wildlife Research Unit, Department of Zoology and Physiology and Program in Ecology, University of Wyoming, Laramie, Wyoming
| | - Anna D Chalfoun
- U.S. Geological Survey, Wyoming Cooperative Fish and Wildlife Research Unit, Department of Zoology and Physiology and Program in Ecology, University of Wyoming, Laramie, Wyoming
| |
Collapse
|
5
|
Solari KA, Hadly EA. Evolution for extreme living: variation in mitochondrial cytochrome c oxidase genes correlated with elevation in pikas (genus Ochotona). Integr Zool 2018; 13:517-535. [PMID: 29851233 DOI: 10.1111/1749-4877.12332] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The genus Ochotona (pikas) is a clade of cold-tolerant lagomorphs that includes many high-elevation species. Pikas offer a unique opportunity to study adaptations and potential limitations of an ecologically important mammal to high-elevation hypoxia. We analyzed the evolution of 3 mitochondrial genes encoding the catalytic core of cytochrome c oxidase (COX) in 10 pika species occupying elevations from sea level to 5000 m. COX is an enzyme highly reliant on oxygen and essential for cell function. One amino acid property, the equilibrium constant (ionization of COOH), was found to be under selection in the overall protein complex. We observed a strong relationship between the net value change in this property and the elevation each species occupies, with higher-elevation species having potentially more efficient proteins. We also found evidence of selection in low-elevation species for potentially less efficient COX, perhaps trading efficiency for heat production in the absence of hypoxia. Our results suggest that different pika species may have evolved elevation-specific COX proteins, specialization that may indicate limitations in their ability to shift their elevational ranges in response to future climate change.
Collapse
Affiliation(s)
| | - Elizabeth A Hadly
- Department of Biology, Stanford University, Stanford, California, USA.,Woods Institute for the Environment, Stanford University, Stanford, California, USA.,Program for Conservation Genomics, Stanford University, Stanford, California, USA
| |
Collapse
|
6
|
Vakurin AA, Korablev VP, Xue-Long J, Grigor'eva TV. The chromosomes of Tsing-Ling pika, Ochotona huangensis Matschie, 1908 (Lagomorpha, Ochotonidae). Comp Cytogenet 2012; 6:347-58. [PMID: 24260675 PMCID: PMC3834567 DOI: 10.3897/compcytogen.v6i4.3183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 09/18/2012] [Indexed: 06/02/2023]
Abstract
The karyotype of the Tsing-Ling (Huanghe) pika, Ochotona huangensis Matschie, 1908 from the forest habitats of the Qinling Mountains (Shaanxi Province, China) was described for the first time. The chromosome set contains 42 chromosomes (NFa=80). The autosomes are 15 meta-submetacentric pairs and 5 subtelocentric pairs. The X chromosome is a medium sized submetacentric; the Y chromosome is a small sized acrocentric. C-banding revealed a localization of heterochromatin in the pericentromeric regions of all autosomes.
Collapse
Affiliation(s)
- Alexey A. Vakurin
- Institute of Biology and Soil Science, Far Eastern Branch of the Russian Academy of Sciences; pr. Stoletiya 159, Vladivostok, 690022, Russia
| | - Vladimir P. Korablev
- Institute of Biology and Soil Science, Far Eastern Branch of the Russian Academy of Sciences; pr. Stoletiya 159, Vladivostok, 690022, Russia
| | - Jiang Xue-Long
- Kunming Institute of Zoology, the Chinese Academy of Sciences; Kunming, Yunnan, 650223, China
| | - Tat'iana V. Grigor'eva
- Faculty of Biology, M. V. Lomonosov Moscow State University; Vorob’evy Gory 1, p. 12, Moscow, 119991, Russia
| |
Collapse
|