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Liang X, Duan Q, Li B, Wang Y, Bu Y, Zhang Y, Kuang Z, Mao L, An X, Wang H, Yang X, Wan N, Feng Z, Shen W, Miao W, Chen J, Liu S, Storz JF, Liu J, Nevo E, Li K. Genomic structural variation contributes to evolved changes in gene expression in high-altitude Tibetan sheep. Proc Natl Acad Sci U S A 2024; 121:e2322291121. [PMID: 38913905 PMCID: PMC11228492 DOI: 10.1073/pnas.2322291121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/06/2024] [Indexed: 06/26/2024] Open
Abstract
Tibetan sheep were introduced to the Qinghai Tibet plateau roughly 3,000 B.P., making this species a good model for investigating genetic mechanisms of high-altitude adaptation over a relatively short timescale. Here, we characterize genomic structural variants (SVs) that distinguish Tibetan sheep from closely related, low-altitude Hu sheep, and we examine associated changes in tissue-specific gene expression. We document differentiation between the two sheep breeds in frequencies of SVs associated with genes involved in cardiac function and circulation. In Tibetan sheep, we identified high-frequency SVs in a total of 462 genes, including EPAS1, PAPSS2, and PTPRD. Single-cell RNA-Seq data and luciferase reporter assays revealed that the SVs had cis-acting effects on the expression levels of these three genes in specific tissues and cell types. In Tibetan sheep, we identified a high-frequency chromosomal inversion that exhibited modified chromatin architectures relative to the noninverted allele that predominates in Hu sheep. The inversion harbors several genes with altered expression patterns related to heart protection, brown adipocyte proliferation, angiogenesis, and DNA repair. These findings indicate that SVs represent an important source of genetic variation in gene expression and may have contributed to high-altitude adaptation in Tibetan sheep.
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Affiliation(s)
- Xiaolong Liang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Qijiao Duan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Bowen Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Yinjia Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Yueting Bu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Yonglu Zhang
- Fengjia Town Health Center, Rushan City, Weihai City264200, China
| | - Zhuoran Kuang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Leyan Mao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Xuan An
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Huihua Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing100193, China
| | - Xiaojie Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Na Wan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Zhilong Feng
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Wei Shen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Weilan Miao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Jiaqi Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Sanyuan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Jay F. Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE68588
| | - Jianquan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa3498838, Israel
| | - Kexin Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
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Fox JA, Hunt DAGA, Hendry AP, Chapman LJ, Barrett RDH. Counter-gradient variation in gene expression between fish populations facilitates colonization of low-dissolved oxygen environments. Mol Ecol 2024; 33:e17419. [PMID: 38808559 DOI: 10.1111/mec.17419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 05/10/2024] [Accepted: 05/16/2024] [Indexed: 05/30/2024]
Abstract
The role of phenotypic plasticity during colonization remains unclear due to the shifting importance of plasticity across timescales. In the early stages of colonization, plasticity can facilitate persistence in a novel environment; but over evolutionary time, processes such as genetic assimilation may reduce variation in plastic traits such that species with a longer evolutionary history in an environment can show lower levels of plasticity than recent invaders. Therefore, comparing species in the early stages of colonization to long-established species provides a powerful approach for uncovering the role of phenotypic plasticity during different stages of colonization. We compared gene expression between low-dissolved oxygen (DO) and high-DO populations of two cyprinid fish: Enteromius apleurogramma, a species that has undergone a recent range expansion, and E. neumayeri, a long-established native species in the same region. We sampled tissue either immediately after capture from the field or after a 2-week acclimation under high-DO conditions, allowing us to test for both evolved and plastic differences in low-DO vs high-DO populations of each species. We found that most genes showing candidate-evolved differences in gene expression did not overlap with those showing plastic differences in gene expression. However, in the genes that did overlap, there was counter-gradient variation such that plastic and evolved gene expression responses were in opposite directions in both species. Additionally, E. apleurogramma had higher levels of plasticity and evolved divergence in gene expression between field populations. We suggest that the higher level of plasticity and counter-gradient variation may have allowed rapid genetic adaptation in E. apleurogramma and facilitated colonization. This study shows how counter-gradient variation may impact the colonization of divergent oxygen environments.
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Affiliation(s)
- Janay A Fox
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - David A G A Hunt
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Andrew P Hendry
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Lauren J Chapman
- Department of Biology, McGill University, Montreal, Quebec, Canada
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3
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Bautista NM, Herrera ND, Shadowitz E, Wearing OH, Cheviron ZA, Scott GR, Storz JF. Local adaptation, plasticity, and evolved resistance to hypoxic cold stress in high-altitude deer mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600120. [PMID: 38979138 PMCID: PMC11230211 DOI: 10.1101/2024.06.21.600120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
A fundamental question in evolutionary biology concerns the relative contributions of phenotypic plasticity vs. local adaptation (genotypic specialization) in enabling wide-ranging species to inhabit diverse environmental conditions. Here we conduct a long-term hypoxia acclimation experiment to assess the relative roles of local adaptation and plasticity in enabling highland and lowland deer mice (Peromyscus maniculatus) to sustain aerobic thermogenesis at progressively increasing elevations. We assessed the relative physiological performance capacities of highland and lowland natives as they were exposed to progressive, stepwise increases in hypoxia, simulating the gradual ascent from sea level to an elevation of 6000 m. The final elevation of 6000 m far exceeds the highest attainable elevations within the species' range, and therefore tests the animals' ability to tolerate levels of hypoxia that surpass the prevailing conditions within their current distributional limits. Our results demonstrate that highland natives exhibit superior thermogenic capacities at the most severe levels of hypoxia, suggesting that the species' broad fundamental niche and its ability to inhabit such a broad range of elevational zones is attributable to a combination of genetically based local adaptation and plasticity. Transcriptomic and physiological measurements identify evolved changes in the acclimation response to hypoxia that contribute to the enhanced thermogenic capacity of highland natives.
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Affiliation(s)
- Naim M Bautista
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588, USA
| | | | - Ellen Shadowitz
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Oliver H Wearing
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Zachary A Cheviron
- Division of Biological Sciences, University of Montana, Missoula, MT 59812
| | - Graham R Scott
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588, USA
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4
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Cadena CD. Endurance athletes hiding in plain sight in the high Andes. Proc Natl Acad Sci U S A 2024; 121:e2407414121. [PMID: 38781224 PMCID: PMC11161742 DOI: 10.1073/pnas.2407414121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024] Open
Affiliation(s)
- Carlos Daniel Cadena
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá111711, Colombia
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Storz JF, Quiroga-Carmona M, Liphardt S, Herrera ND, Bautista NM, Opazo JC, Rico-Cernohorska A, Salazar-Bravo J, Good JM, D'Elía G. Extreme High-Elevation Mammal Surveys Reveal Unexpectedly High Upper Range Limits of Andean Mice. Am Nat 2024; 203:726-735. [PMID: 38781524 DOI: 10.1086/729513] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
AbstractIn the world's highest mountain ranges, uncertainty about the upper elevational range limits of alpine animals represents a critical knowledge gap regarding the environmental limits of life and presents a problem for detecting range shifts in response to climate change. Here we report results of mountaineering mammal surveys in the Central Andes, which led to the discovery of multiple species of mice living at extreme elevations that far surpass previously assumed range limits for mammals. We livetrapped small mammals from ecologically diverse sites spanning >6,700 m of vertical relief, from the desert coast of northern Chile to the summits of the highest volcanoes in the Andes. We used molecular sequence data and whole-genome sequence data to confirm the identities of species that represent new elevational records and to test hypotheses regarding species limits. These discoveries contribute to a new appreciation of the environmental limits of vertebrate life.
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Jiang Q, Zhu L, Zeng H, Basang Z, Suolang Q, Huang J, Cai Y. Evolutionary adaptations generally reverse phenotypic plasticity to restore ancestral phenotypes during new environment adaptation in cattle. Ecol Evol 2024; 14:e11489. [PMID: 38840586 PMCID: PMC11150418 DOI: 10.1002/ece3.11489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/11/2024] [Accepted: 05/15/2024] [Indexed: 06/07/2024] Open
Abstract
Phenotype plasticity and evolution adaptations are the two main ways in which allow populations to deal with environmental changes, but the potential relationship between them remains controversial. Using a reciprocal transplant approach with cattle adapted to the Tibetan Plateau and adjacent lowlands, we aim to investigate the relative contributions of evolutionary processes and phenotypic plasticity in driving both phenotypic and transcriptomic changes under natural conditions. We observed that while numerous genetic transcriptomic changes were evident during the forward adaptation to highland environments, plastic changes predominantly facilitate the transformation of transcriptomes into a preferred state when Tibetan cattle are reintroduced to lowland habitats. Genes with ancestral plasticity are generally reversed by evolutionary adaptations and show a closer expression level to the ancestral stage in evolved Tibetan cattle. A similar trend was also observed at the phenotypes level, with a majority of biochemical and hemorheology phenotypes showing a tendency to revert to their ancestral patterns, suggesting the restoration of ancestral expression levels is a widespread evolutionary trend during adaptation. The findings of our study contribute to the debate regarding the relative contributions of plasticity and genetic changes in mammal environment adaptation. Furthermore, we highlight that the restoration of ancestral phenotypes represents a general pattern in cattle new environment adaptation.
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Affiliation(s)
- Qiang Jiang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and TechnologyNanjing Agricultural UniversityNanjingChina
- Institute of Animal Science and Veterinary MedicineShandong Academy of Agricultural SciencesJinanChina
| | - Li Zhu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and TechnologyYunnan Agricultural UniversityKunmingChina
| | - Hao Zeng
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and TechnologyYunnan Agricultural UniversityKunmingChina
| | - Zhuzha Basang
- Institute of Animal Science and Veterinary MedicineTibet Academy of Agricultural and Animal Husbandry SciencesLhasaChina
| | - Quji Suolang
- Institute of Animal Science and Veterinary MedicineTibet Academy of Agricultural and Animal Husbandry SciencesLhasaChina
| | - Jinming Huang
- Institute of Animal Science and Veterinary MedicineShandong Academy of Agricultural SciencesJinanChina
| | - Yafei Cai
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and TechnologyNanjing Agricultural UniversityNanjingChina
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7
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Yan Z, Yang J, Wei WT, Zhou ML, Mo DX, Wan X, Ma R, Wu MM, Huang JH, Liu YJ, Lv FH, Li MH. A time-resolved multi-omics atlas of transcriptional regulation in response to high-altitude hypoxia across whole-body tissues. Nat Commun 2024; 15:3970. [PMID: 38730227 PMCID: PMC11087590 DOI: 10.1038/s41467-024-48261-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
High-altitude hypoxia acclimatization requires whole-body physiological regulation in highland immigrants, but the underlying genetic mechanism has not been clarified. Here we use sheep as an animal model for low-to-high altitude translocation. We generate multi-omics data including whole-genome sequences, time-resolved bulk RNA-Seq, ATAC-Seq and single-cell RNA-Seq from multiple tissues as well as phenotypic data from 20 bio-indicators. We characterize transcriptional changes of all genes in each tissue, and examine multi-tissue temporal dynamics and transcriptional interactions among genes. Particularly, we identify critical functional genes regulating the short response to hypoxia in each tissue (e.g., PARG in the cerebellum and HMOX1 in the colon). We further identify TAD-constrained cis-regulatory elements, which suppress the transcriptional activity of most genes under hypoxia. Phenotypic and transcriptional evidence indicate that antenatal hypoxia could improve hypoxia tolerance in offspring. Furthermore, we provide time-series expression data of candidate genes associated with human mountain sickness (e.g., BMPR2) and high-altitude adaptation (e.g., HIF1A). Our study provides valuable resources and insights for future hypoxia-related studies in mammals.
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Affiliation(s)
- Ze Yan
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ji Yang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Wen-Tian Wei
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ming-Liang Zhou
- Sichuan Academy of Grassland Science, Chengdu, 611743, China
| | - Dong-Xin Mo
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xing Wan
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Rui Ma
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Mei-Ming Wu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jia-Hui Huang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ya-Jing Liu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Feng-Hua Lv
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Meng-Hua Li
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Jin X, Zhang Y, Wang D, Zhang X, Li Y, Wang D, Liang Y, Wang J, Zheng L, Song H, Zhu X, Liang J, Ma J, Gao J, Tong J, Shi L. Metabolite and protein shifts in mature erythrocyte under hypoxia. iScience 2024; 27:109315. [PMID: 38487547 PMCID: PMC10937114 DOI: 10.1016/j.isci.2024.109315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024] Open
Abstract
As the only cell type responsible for oxygen delivery, erythrocytes play a crucial role in supplying oxygen to hypoxic tissues, ensuring their normal functions. Hypoxia commonly occurs under physiological or pathological conditions, and understanding how erythrocytes adapt to hypoxia is fundamental for exploring the mechanisms of hypoxic diseases. Additionally, investigating acute and chronic mountain sickness caused by plateaus, which are naturally hypoxic environments, will aid in the study of hypoxic diseases. In recent years, increasingly developed proteomics and metabolomics technologies have become powerful tools for studying mature enucleated erythrocytes, which has significantly contributed to clarifying how hypoxia affects erythrocytes. The aim of this article is to summarize the composition of the cytoskeleton and cytoplasmic proteins of hypoxia-altered erythrocytes and explore the impact of hypoxia on their essential functions. Furthermore, we discuss the role of microRNAs in the adaptation of erythrocytes to hypoxia, providing new perspectives on hypoxia-related diseases.
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Affiliation(s)
- Xu Jin
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Yingnan Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Ding Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Xiaoru Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Yue Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Di Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Yipeng Liang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Jingwei Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Lingyue Zheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Haoze Song
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Xu Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Jing Liang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Jinfa Ma
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Jie Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Jingyuan Tong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Lihong Shi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
- CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
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Yan F, Wang Y, Wei M, Zhang J, Ye Y, Duan M, Chamba Y, Shang P. Exploring the role of the CapG gene in hypoxia adaptation in Tibetan pigs. Front Genet 2024; 15:1339683. [PMID: 38680426 PMCID: PMC11045884 DOI: 10.3389/fgene.2024.1339683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/28/2024] [Indexed: 05/01/2024] Open
Abstract
Introduction: The CapG gene, which is an actin-binding protein, is prevalent in eukaryotic cells and is abundantly present in various pathways associated with plateau hypoxia adaptation. Tibetan pigs, which have inhabited high altitudes for extended periods, provide an excellent research population for investigating plateau hypoxia adaptation. Results: This study focused on Tibetan pigs and Yorkshire pigs residing in Nyingchi, Tibet. The blood physiological data of Tibetan pigs were found to be significantly higher than those of Yorkshire pigs, including RBC, HGB, HCT, MCH, and MCHC. The SNP analysis of the CapG gene identified six sites with mutations only present in Tibetan pigs. Notably, the transcription factors at sites C-489T, C-274T, and A-212G were found to be altered, and these sites are known to be associated with hypoxia adaptation and blood oxygen transportation. The mRNA expression of the CapG gene exhibited highly significant differences in several tissues, with the target proteins predominantly higher in the Yorkshire pig compared to the Tibetan pig. Specifically, a notable difference was observed in the lung tissues. Immunohistochemistry analysis revealed high expression levels of CapG proteins in the lung tissues of both Tibetan and Yorkshire pigs, primarily localized in the cytoplasm and cell membrane. Conclusion: The CapG gene plays a significant role in regulating hypoxia adaptation in Tibetan pigs. This study provides a theoretical basis for the conservation and utilization of Tibetan pig resources, the breeding of highland breeds, epidemic prevention and control, and holds great importance for the development of the highland livestock economy.
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Affiliation(s)
- Feifei Yan
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, Tibet, China
- Key Laboratory for the Genetic Improvement and Reproduction Technology of the Tibetan Swine, Linzhi, Tibet, China
| | - Yu Wang
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, Tibet, China
- Key Laboratory for the Genetic Improvement and Reproduction Technology of the Tibetan Swine, Linzhi, Tibet, China
| | - Mingbang Wei
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, Tibet, China
- Key Laboratory for the Genetic Improvement and Reproduction Technology of the Tibetan Swine, Linzhi, Tibet, China
| | - Jian Zhang
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, Tibet, China
- Key Laboratory for the Genetic Improvement and Reproduction Technology of the Tibetan Swine, Linzhi, Tibet, China
| | - Yourong Ye
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, Tibet, China
- Key Laboratory for the Genetic Improvement and Reproduction Technology of the Tibetan Swine, Linzhi, Tibet, China
| | - Mengqi Duan
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, Tibet, China
- Key Laboratory for the Genetic Improvement and Reproduction Technology of the Tibetan Swine, Linzhi, Tibet, China
| | - Yangzom Chamba
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, Tibet, China
- Key Laboratory for the Genetic Improvement and Reproduction Technology of the Tibetan Swine, Linzhi, Tibet, China
| | - Peng Shang
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi, Tibet, China
- Key Laboratory for the Genetic Improvement and Reproduction Technology of the Tibetan Swine, Linzhi, Tibet, China
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10
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Comte L, Bertrand R, Diamond S, Lancaster LT, Pinsky ML, Scheffers BR, Baecher JA, Bandara RMWJ, Chen IC, Lawlor JA, Moore NA, Oliveira BF, Murienne J, Rolland J, Rubenstein MA, Sunday J, Thompson LM, Villalobos F, Weiskopf SR, Lenoir J. Bringing traits back into the equation: A roadmap to understand species redistribution. GLOBAL CHANGE BIOLOGY 2024; 30:e17271. [PMID: 38613240 DOI: 10.1111/gcb.17271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 03/06/2024] [Accepted: 03/11/2024] [Indexed: 04/14/2024]
Abstract
Ecological and evolutionary theories have proposed that species traits should be important in mediating species responses to contemporary climate change; yet, empirical evidence has so far provided mixed evidence for the role of behavioral, life history, or ecological characteristics in facilitating or hindering species range shifts. As such, the utility of trait-based approaches to predict species redistribution under climate change has been called into question. We develop the perspective, supported by evidence, that trait variation, if used carefully can have high potential utility, but that past analyses have in many cases failed to identify an explanatory value for traits by not fully embracing the complexity of species range shifts. First, we discuss the relevant theory linking species traits to range shift processes at the leading (expansion) and trailing (contraction) edges of species distributions and highlight the need to clarify the mechanistic basis of trait-based approaches. Second, we provide a brief overview of range shift-trait studies and identify new opportunities for trait integration that consider range-specific processes and intraspecific variability. Third, we explore the circumstances under which environmental and biotic context dependencies are likely to affect our ability to identify the contribution of species traits to range shift processes. Finally, we propose that revealing the role of traits in shaping species redistribution may likely require accounting for methodological variation arising from the range shift estimation process as well as addressing existing functional, geographical, and phylogenetic biases. We provide a series of considerations for more effectively integrating traits as well as extrinsic and methodological factors into species redistribution research. Together, these analytical approaches promise stronger mechanistic and predictive understanding that can help society mitigate and adapt to the effects of climate change on biodiversity.
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Affiliation(s)
- Lise Comte
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
- Conservation Science Partners, Inc., Truckee, California, USA
| | - Romain Bertrand
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE UMR5300), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 Paul Sabatier (UT3), Toulouse, France
| | - Sarah Diamond
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, USA
| | | | - Malin L Pinsky
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, New Jersey, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, USA
| | - Brett R Scheffers
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, USA
| | - J Alex Baecher
- School of Natural Resources and Environment, University of Florida, Gainesville, Florida, USA
| | - R M W J Bandara
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, New Jersey, USA
| | - I-Ching Chen
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Jake A Lawlor
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Nikki A Moore
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Brunno F Oliveira
- Fondation pour la Recherche sur la Biodiversité (FRB), Centre de Synthèse et d'Analyse sur la Biodiversité (CESAB), Montpellier, France
| | - Jerome Murienne
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE UMR5300), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 Paul Sabatier (UT3), Toulouse, France
| | - Jonathan Rolland
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE UMR5300), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 Paul Sabatier (UT3), Toulouse, France
| | - Madeleine A Rubenstein
- U.S. Geological Survey National Climate Adaptation Science Center, Reston, Virginia, USA
| | - Jennifer Sunday
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Laura M Thompson
- U.S. Geological Survey National Climate Adaptation Science Center, Reston, Virginia, USA
- School of Natural Resources, University of Tennessee, Knoxville, Tennessee, USA
| | - Fabricio Villalobos
- Red de Biología Evolutiva, Instituto de Ecología A.C. - INECOL, Veracruz, Mexico
| | - Sarah R Weiskopf
- U.S. Geological Survey National Climate Adaptation Science Center, Reston, Virginia, USA
| | - Jonathan Lenoir
- UMR CNRS 7058, Ecologie et Dynamique Des Systèmes Anthropisés (EDYSAN), Université de Picardie Jules Verne, Amiens, France
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11
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She H, Hao Y, Song G, Luo X, Lei F, Zhai W, Qu Y. Gene expression plasticity followed by genetic change during colonization in a high-elevation environment. eLife 2024; 12:RP86687. [PMID: 38470231 DOI: 10.7554/elife.86687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024] Open
Abstract
Phenotypic plasticity facilitates organismal invasion of novel environments, and the resultant phenotypic change may later be modified by genetic change, so called 'plasticity first.' Herein, we quantify gene expression plasticity and regulatory adaptation in a wild bird (Eurasian Tree Sparrow) from its original lowland (ancestral stage), experimentally implemented hypoxia acclimation (plastic stage), and colonized highland (colonized stage). Using a group of co-expressed genes from the cardiac and flight muscles, respectively, we demonstrate that gene expression plasticity to hypoxia tolerance is more often reversed than reinforced at the colonized stage. By correlating gene expression change with muscle phenotypes, we show that colonized tree sparrows reduce maladaptive plasticity that largely associated with decreased hypoxia tolerance. Conversely, adaptive plasticity that is congruent with increased hypoxia tolerance is often reinforced in the colonized tree sparrows. Genes displaying large levels of reinforcement or reversion plasticity (i.e. 200% of original level) show greater genetic divergence between ancestral and colonized populations. Overall, our work demonstrates that gene expression plasticity at the initial stage of high-elevation colonization can be reversed or reinforced through selection-driven adaptive modification.
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Affiliation(s)
- Huishang She
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xu Luo
- Faculty of Biodiversity and Conservation, Southwest Forestry University, Kunming, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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12
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Wang YL, Li L, Paudel BR, Zhao JL. Genomic Insights into High-Altitude Adaptation: A Comparative Analysis of Roscoea alpina and R. purpurea in the Himalayas. Int J Mol Sci 2024; 25:2265. [PMID: 38396942 PMCID: PMC10889555 DOI: 10.3390/ijms25042265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Environmental stress at high altitudes drives the development of distinct adaptive mechanisms in plants. However, studies exploring the genetic adaptive mechanisms of high-altitude plant species are scarce. In the present study, we explored the high-altitude adaptive mechanisms of plants in the Himalayas through whole-genome resequencing. We studied two widespread members of the Himalayan endemic alpine genus Roscoea (Zingiberaceae): R. alpina (a selfing species) and R. purpurea (an outcrossing species). These species are distributed widely in the Himalayas with distinct non-overlapping altitude distributions; R. alpina is distributed at higher elevations, and R. purpurea occurs at lower elevations. Compared to R. purpurea, R. alpina exhibited higher levels of linkage disequilibrium, Tajima's D, and inbreeding coefficient, as well as lower recombination rates and genetic diversity. Approximately 96.3% of the genes in the reference genome underwent significant genetic divergence (FST ≥ 0.25). We reported 58 completely divergent genes (FST = 1), of which only 17 genes were annotated with specific functions. The functions of these genes were primarily related to adapting to the specific characteristics of high-altitude environments. Our findings provide novel insights into how evolutionary innovations promote the adaptation of mountain alpine species to high altitudes and harsh habitats.
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Affiliation(s)
- Ya-Li Wang
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China; (Y.-L.W.); (L.L.)
| | - Li Li
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China; (Y.-L.W.); (L.L.)
| | - Babu Ram Paudel
- Research Centre for Applied Science and Technology, Tribhuvan University, Kirtipur 44613, Nepal
| | - Jian-Li Zhao
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China; (Y.-L.W.); (L.L.)
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13
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Taylor PJ, Nengovhela A, Denys C, Scott GR, Ivy CM. Adaptation in brain structure and respiratory and olfactory structures across environmental gradients in African and North American muroid rodents. Integr Zool 2024; 19:165-181. [PMID: 38044327 DOI: 10.1111/1749-4877.12788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Morphometric studies of 3D micro CT-scanned images can provide insights into the evolution of the brain and sensory structures but such data are still scarce for the most diverse mammalian order of rodents. From reviewed and new data, we tested for convergence to extreme aridity and high elevation in the sensory and brain morphology of rodents, from morphometric data from micro-CT X-ray scans of 174 crania of 16 species of three distantly related African murid (soft-furred mice, Praomyini, laminate-toothed rats, Otomyini, and gerbils, Gerbillinae) clades and one North American cricetid (deer mice and white-footed mice, Peromyscus) clade. Recent studies demonstrated convergent evolution acting on the oval window area of the cochlea (enlarged in extremely arid-adapted species of Otomyini and Gerbillinae) and on endocranial volume (reduced in high elevation taxa of Otomyini and Peromyscus). However, contrary to our predictions, we did not find evidence of convergence in brain structure to aridity, or in the olfactory/respiratory system (turbinate bones) to high elevation. Brain structure differed, particularly in the petrosal lobules of the cerebellum and the olfactory bulbs, between Otomyini and Gerbillinae, with extreme arid-adapted species in each clade being highly divergent (not convergent) from other species in the same clade. We observed greater "packing" of the maxillary turbinate bones, which have important respiratory functions, in Peromyscus mice from high and low elevations compared to the high-elevation African Praomyini, but more complex patterns within Peromyscus, probably related to trade-offs in respiratory physiology and heat exchange in the nasal epithelium associated with high-elevation adaptation.
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Affiliation(s)
- Peter J Taylor
- Department of Zoology, School of Natural and Mathematical Sciences, University of Venda, Thohoyandou, South Africa
- Afromontane Unit, Department of Zoology and Entomology, University of the Free State, Phuthaditjhaba, South Africa
| | | | - Christiane Denys
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université Des Antilles, Paris, France
| | - Graham R Scott
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Catherine M Ivy
- Guglielmo and Shoemaker Labs, Advanced Facility for Avian Research, University of Western Ontario, London, Ontario, Canada
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14
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Souchet J, Josserand A, Darnet E, Le Chevalier H, Trochet A, Bertrand R, Calvez O, Martinez-Silvestre A, Guillaume O, Mossoll-Torres M, Pottier G, Philippe H, Aubret F, Gangloff EJ. Embryonic and juvenile snakes (Natrix maura, Linnaeus 1758) compensate for high elevation hypoxia via shifts in cardiovascular physiology and metabolism. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2023; 339:1102-1115. [PMID: 37723946 DOI: 10.1002/jez.2756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/30/2023] [Accepted: 08/30/2023] [Indexed: 09/20/2023]
Abstract
The colonization of novel environments requires a favorable response to conditions never, or rarely, encountered in recent evolutionary history. For example, populations colonizing upslope habitats must cope with lower atmospheric pressure at elevation, and thus reduced oxygen availability. The embryo stage in oviparous organisms is particularly susceptible, given its lack of mobility and limited gas exchange via diffusion through the eggshell and membranes. Especially little is known about responses of Lepidosaurian reptiles to reduced oxygen availability. To test the role of physiological plasticity during early development in response to high elevation hypoxia, we performed a transplant experiment with the viperine snake (Natrix maura, Linnaeus 1758). We maintained gravid females originating from low elevation populations (432 m above sea level [ASL]-normoxia) at both the elevation of origin and high elevation (2877 m ASL-extreme high elevation hypoxia; approximately 72% oxygen availability relative to sea level), then incubated egg clutches at both low and high elevation. Regardless of maternal exposure to hypoxia during gestation, embryos incubated at extreme high elevation exhibited altered developmental trajectories of cardiovascular function and metabolism across the incubation period, including a reduction in late-development egg mass. This physiological response may have contributed to the maintenance of similar incubation duration, hatching success, and hatchling body size compared to embryos incubated at low elevation. Nevertheless, after being maintained in hypoxia, juveniles exhibit reduced carbon dioxide production relative to oxygen consumption, suggesting altered energy pathways compared to juveniles maintained in normoxia. These findings highlight the role of physiological plasticity in maintaining rates of survival and fitness-relevant phenotypes in novel environments.
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Affiliation(s)
- Jérémie Souchet
- Station d'Ecologie Théorique et Expérimentale (UAR CNRS 2029), Moulis, France
| | - Alicia Josserand
- Station d'Ecologie Théorique et Expérimentale (UAR CNRS 2029), Moulis, France
| | - Elodie Darnet
- Station d'Ecologie Théorique et Expérimentale (UAR CNRS 2029), Moulis, France
| | - Hugo Le Chevalier
- Station d'Ecologie Théorique et Expérimentale (UAR CNRS 2029), Moulis, France
| | - Audrey Trochet
- Société Herpétologique de France, Muséum National d'Histoire Naturelle, Paris, France
| | - Romain Bertrand
- Laboratoire Évolution et Diversité Biologique (UMR CNRS 5174), Université de Toulouse III Paul Sabatier, IRD, Toulouse, France
| | - Olivier Calvez
- Station d'Ecologie Théorique et Expérimentale (UAR CNRS 2029), Moulis, France
| | | | - Olivier Guillaume
- Station d'Ecologie Théorique et Expérimentale (UAR CNRS 2029), Moulis, France
| | | | | | - Hervé Philippe
- Station d'Ecologie Théorique et Expérimentale (UAR CNRS 2029), Moulis, France
| | - Fabien Aubret
- Station d'Ecologie Théorique et Expérimentale (UAR CNRS 2029), Moulis, France
- School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Eric J Gangloff
- Station d'Ecologie Théorique et Expérimentale (UAR CNRS 2029), Moulis, France
- Department of Biological Sciences, Ohio Wesleyan University, Delaware, Ohio, USA
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15
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Zhang X, Men S, Jia L, Tang X, Storey KB, Niu Y, Chen Q. Comparative metabolomics analysis reveals high-altitude adaptations in a toad-headed viviparous lizard, Phrynocephalus vlangalii. Front Zool 2023; 20:35. [PMID: 37919723 PMCID: PMC10621141 DOI: 10.1186/s12983-023-00513-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 10/27/2023] [Indexed: 11/04/2023] Open
Abstract
Extreme environmental conditions at high altitude, such as hypobaric hypoxia, low temperature, and strong UV radiation, pose a great challenge to the survival of animals. Although the mechanisms of adaptation to high-altitude environments have attracted much attention for native plateau species, the underlying metabolic regulation remains unclear. Here, we used a multi-platform metabolomic analysis to compare metabolic profiles of liver between high- and low-altitude populations of toad-headed lizards, Phrynocephalus vlangalii, from the Qinghai-Tibet Plateau. A total of 191 differential metabolites were identified, consisting of 108 up-regulated and 83 down-regulated metabolites in high-altitude lizards as compared with values for low-altitude lizards. Pathway analysis revealed that the significantly different metabolites were associated with carbohydrate metabolism, amino acid metabolism, purine metabolism, and glycerolipid metabolism. Most intermediary metabolites of glycolysis and the tricarboxylic acid cycle were not significantly altered between the two altitudes, but most free fatty acids as well as β-hydroxybutyric acid were significantly lower in the high-altitude population. This may suggest that high-altitude lizards rely more on carbohydrates as their main energy fuel rather than lipids. Higher levels of phospholipids occurred in the liver of high-altitude populations, suggesting that membrane lipids may undergo adaptive remodeling in response to low-temperature stress at high altitude. In summary, this study demonstrates that metabolic profiles differ substantially between high- and low-altitude lizard populations, and that these differential metabolites and metabolic pathways can provide new insights to reveal mechanisms of adaptation to extreme environments at high altitude.
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Affiliation(s)
- Xuejing Zhang
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Shengkang Men
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Lun Jia
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Xiaolong Tang
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Kenneth B Storey
- Department of Biology, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Yonggang Niu
- Department of Life Sciences, Dezhou University, Dezhou, 253023, Shandong, China.
| | - Qiang Chen
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China.
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16
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Storz JF, Scott GR. To what extent do physiological tolerances determine elevational range limits of mammals? J Physiol 2023:10.1113/JP284586. [PMID: 37889163 PMCID: PMC11052920 DOI: 10.1113/jp284586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
A key question in biology concerns the extent to which distributional range limits of species are determined by intrinsic limits of physiological tolerance. Here, we use common-garden data for wild rodents to assess whether species with higher elevational range limits typically have higher thermogenic capacities in comparison to closely related lowland species. Among South American leaf-eared mice (genus Phyllotis), mean thermogenic performance is higher in species with higher elevational range limits, but there is little among-species variation in the magnitude of plasticity in this trait. In the North American rodent genus Peromyscus, highland deer mice (Peromyscus maniculatus) have greater thermogenic maximal oxygen uptake (V ̇ O 2 max ${\dot V_{{{\mathrm{O}}_{\mathrm{2}}}{\mathrm{max}}}}$ ) than lowland white-footed mice (Peromyscus leucopus) at a level of hypoxia that matches the upper elevational range limit of the former species. In highland deer mice, the enhanced thermogenicV ̇ O 2 max ${\dot V_{{{\mathrm{O}}_{\mathrm{2}}}{\mathrm{max}}}}$ in hypoxia is attributable to a combination of evolved and plastic changes in physiological pathways that govern the transport and utilization of O2 and metabolic substrates. Experiments with Peromyscus mice also demonstrate that exposure to hypoxia during different stages of development elicits plastic changes in cardiorespiratory traits that improve thermogenicV ̇ O 2 max ${\dot V_{{{\mathrm{O}}_{\mathrm{2}}}{\mathrm{max}}}}$ via distinct physiological mechanisms. Evolved differences in thermogenic capacity provide clues about why some species are able to persist in higher-elevation habitats that lie slightly beyond the tolerable limits of other species. Such differences in environmental tolerance also suggest why some species might be more vulnerable to climate change than others.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Graham R Scott
- Department of Biology, McMaster University, Hamilton, ON, Canada
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17
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Claramunt S, Haddrath O. No Signs of Adaptations for High Flight Intensity in the Mitochondrial Genome of Birds. Genome Biol Evol 2023; 15:evad173. [PMID: 37758449 PMCID: PMC10563790 DOI: 10.1093/gbe/evad173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 08/14/2023] [Accepted: 09/20/2023] [Indexed: 10/03/2023] Open
Abstract
Mitochondrial genomes are expected to show adaptations for optimizing aerobic respiration in birds that make intense use of flight. However, there is limited empirical evidence of such a relationship. We here examine correlates of several mitochondrial genome characteristics and flight use across a diverse sample of 597 bird species. We developed an index of flight use intensity that ranged from 0 in flightless species to 9 in migratory hummingbirds and examined its association with nucleobase composition, amino acid class composition, and amino acid site allelic variation using phylogenetic comparative methods. We found no evidence of mitochondrial genome adaptations to flight intensity. Neither nucleotide composition nor amino acid properties showed consistent patterns related to flight use. While specific sites in mitochondrial genes exhibited variation associated with flight intensity, there was limited association between specific amino acid residues and flight intensity levels. Our findings suggest a complex genetic architecture for aerobic performance traits, where multiple genes in both mitochondria and the nucleus may contribute to overall performance. Other factors, such as gene expression regulation and anatomical adaptations, may play a more significant role in influencing flight performance than changes in mitochondrial genes. These findings highlight the need for comprehensive genomic analyses to unravel the intricate relationship between genetic variants and aerobic performance in birds.
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Affiliation(s)
- Santiago Claramunt
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Oliver Haddrath
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
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18
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Palacios C, Wang P, Wang N, Brown MA, Capatosto L, Du J, Jiang J, Zhang Q, Dahal N, Lamichhaney S. Genomic Variation, Population History, and Long-Term Genetic Adaptation to High Altitudes in Tibetan Partridge (Perdix hodgsoniae). Mol Biol Evol 2023; 40:msad214. [PMID: 37768198 PMCID: PMC10583571 DOI: 10.1093/molbev/msad214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 09/09/2023] [Accepted: 09/25/2023] [Indexed: 09/29/2023] Open
Abstract
Species residing across elevational gradients display adaptations in response to environmental changes such as oxygen availability, ultraviolet radiation, and temperature. Here, we study genomic variation, gene expression, and long-term adaptation in Tibetan Partridge (Perdix hodgsoniae) populations residing across the elevational gradient of the Tibetan Plateau. We generated a high-quality draft genome and used it to carry out downstream population genomic and transcriptomic analysis. The P. hodgsoniae populations residing across various elevations were genetically distinct, and their phylogenetic clustering was consistent with their geographic distribution. We identified possible evidence of gene flow between populations residing in <3,000 and >4,200 m elevation that is consistent with known habitat expansion of high-altitude populations of P. hodgsoniae to a lower elevation. We identified a 60 kb haplotype encompassing the Estrogen Receptor 1 (ESR1) gene, showing strong genetic divergence between populations of P. hodgsoniae. We identified six single nucleotide polymorphisms within the ESR1 gene fixed for derived alleles in high-altitude populations that are strongly conserved across vertebrates. We also compared blood transcriptome profiles and identified differentially expressed genes (such as GAPDH, LDHA, and ALDOC) that correlated with differences in altitude among populations of P. hodgsoniae. These candidate genes from population genomics and transcriptomics analysis were enriched for neutrophil degranulation and glycolysis pathways, which are known to respond to hypoxia and hence may contribute to long-term adaptation to high altitudes in P. hodgsoniae. Our results highlight Tibetan Partridges as a useful model to study molecular mechanisms underlying long-term adaptation to high altitudes.
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Affiliation(s)
- Catalina Palacios
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Pengcheng Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Nan Wang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, P. R. China
| | - Megan A Brown
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Lukas Capatosto
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Juan Du
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Jiahu Jiang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, P. R. China
| | - Qingze Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, P. R. China
| | - Nishma Dahal
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, HP 176061, India
| | - Sangeet Lamichhaney
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
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19
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Webb KL, Joyner MJ, Wiggins CC, Secomb TW, Roy TK. The dependence of maximum oxygen uptake and utilization (V̇O 2 max) on hemoglobin-oxygen affinity and altitude. Physiol Rep 2023; 11:e15806. [PMID: 37653565 PMCID: PMC10471793 DOI: 10.14814/phy2.15806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 09/02/2023] Open
Abstract
Oxygen transport from the lungs to peripheral tissue is dependent on the affinity of hemoglobin for oxygen. Recent experimental data have suggested that the maximum human capacity for oxygen uptake and utilization (V̇O2 max) at sea level and altitude (~3000 m) is sensitive to alterations in hemoglobin-oxygen affinity. However, the effect of such alterations on V̇O2 max at extreme altitudes remains largely unknown due to the rarity of mutations affecting hemoglobin-oxygen affinity. This work uses a mathematical model that couples pulmonary oxygen uptake with systemic oxygen utilization under conditions of high metabolic demand to investigate the effect of hemoglobin-oxygen affinity on V̇O2 max as a function of altitude. The model includes the effects of both diffusive and convective limitations on oxygen transport. Pulmonary oxygen uptake is calculated using a spatially-distributed model that accounts for the effects of hematocrit and hemoglobin-oxygen affinity. Systemic oxygen utilization is calculated assuming Michaelis-Menten kinetics. The pulmonary and systemic model components are solved iteratively to compute predicted arterial and venous oxygen levels. Values of V̇O2 max are predicted for several values of hemoglobin-oxygen affinity and hemoglobin concentration based on data from humans with hemoglobin mutations. The model predicts that increased hemoglobin-oxygen affinity leads to increased V̇O2 max at altitudes above ~4500 m.
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Affiliation(s)
- Kevin L. Webb
- Department of Anesthesiology and Perioperative MedicineMayo ClinicRochesterMinnesotaUSA
- Department of Physiology and Biomedical EngineeringMayo ClinicRochesterMinnesotaUSA
| | - Michael J. Joyner
- Department of Anesthesiology and Perioperative MedicineMayo ClinicRochesterMinnesotaUSA
| | - Chad C. Wiggins
- Department of Anesthesiology and Perioperative MedicineMayo ClinicRochesterMinnesotaUSA
| | | | - Tuhin K. Roy
- Department of Anesthesiology and Perioperative MedicineMayo ClinicRochesterMinnesotaUSA
- Department of Physiology and Biomedical EngineeringMayo ClinicRochesterMinnesotaUSA
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20
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Feng J, Zhu W, Shi H, Peng D, Zang L, Wang Y, ZhaXi L, BaiMa J, Amevor FK, Wang X, Ma X, Zhao X. Analysis of the Selection Signal of the Tibetan Black Chicken Genome Based on Whole-Genome Sequencing. Genes (Basel) 2023; 14:1672. [PMID: 37761812 PMCID: PMC10531317 DOI: 10.3390/genes14091672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/18/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND The Tibetan chicken has adapted well to high altitudes genetically after its long-term habitation in the plateau. In this study, we analyzed the selection signal of Tibetan black chickens (TBCs) and discovered genes associated with the characteristics of germplasm. METHODS Whole-genome sequencing (WGS) was used to identify the single-nucleotide polymorphism (SNP) markers and genetic structures in the genome of Tibetan black chickens. Further, we performed a comparative population genomics analysis between the genomic data obtained in this present study and the genomic data for five wild red jungle fowls (RJFs) accessed from the NCBI database (GenBank accession number PRJNA241474). Thereafter, the Fst and Pi selections were used to identify genes under positive selection in the Tibetan black chicken genome. RESULTS A total of 9,490,690 SNPs were identified in the Tibetan black chickens. In addition, the results from the gene ontology (GO) analysis showed that 732 genes of TBCs were enriched in a total of 210 GO terms with specific molecular functions such as regulation of cellular catabolic process, the MAPK signaling pathway, regulation of ion transport, growth, morphogenesis and lung alveolus development which may provide a better mechanism to facilitate oxygen transport and utilization in TBCs. Moreover, the results from the KEGG analysis showed that 732 genes of the TBCs were significantly enriched in the calcium signaling pathway, circadian entrainment (ADCY1, GNG7 and PER3), oxytocin signaling pathway and pathways of multiple neurodegeneration diseases. In addition, the CD86 antigen (CD86) was identified as a gene associated with the immune response in chickens. It was also revealed that genes such as TRIT1, HPCAL4, NT5C1A and HEYL were discovered under selection in Tibetan black chickens on chromosome 23. These genes may be related to the local adaptive characteristics of Tibetan black chickens, for instance, NT5C1A and HEYL may be involved in the high-altitude adaption of oxygen delivery in Tibetan black chickens. CONCLUSIONS In summary, we found that selection mainly affects the disease resistance and cold acclimatization of Tibetan black chickens. Hence, these results may provide important genetic information for the evolution and breeding of Tibetan black chickens.
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Affiliation(s)
- Jing Feng
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China; (H.S.); (D.P.); (Y.W.); (X.M.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lhasa 850009, China
| | - Wei Zhu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (W.Z.); (F.K.A.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Hairen Shi
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China; (H.S.); (D.P.); (Y.W.); (X.M.)
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Da Peng
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China; (H.S.); (D.P.); (Y.W.); (X.M.)
| | - Lei Zang
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China; (H.S.); (D.P.); (Y.W.); (X.M.)
| | - Yan Wang
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China; (H.S.); (D.P.); (Y.W.); (X.M.)
| | - Luobu ZhaXi
- Shannan Longzi County Agriculture and Animal Husbandry Comprehensive Service Center, Shannan 856600, China (J.B.)
| | - Jiancai BaiMa
- Shannan Longzi County Agriculture and Animal Husbandry Comprehensive Service Center, Shannan 856600, China (J.B.)
| | - Felix Kwame Amevor
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (W.Z.); (F.K.A.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoqi Wang
- Agriculture and Animal Husbandry Comprehensive Service Center of Lazi County, Shigatse 858100, China;
| | - Xueying Ma
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China; (H.S.); (D.P.); (Y.W.); (X.M.)
| | - Xiaoling Zhao
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (W.Z.); (F.K.A.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
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21
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Zhang Z, Guo Y, Zhuang M, Liu F, Xia Z, Zhang Z, Yang F, Zeng H, Wu Y, Huang J, Li J. Potential role of the gut microbiota of bumblebee Bombus pyrosoma in adaptation to high-altitude habitats. Front Microbiol 2023; 14:1218560. [PMID: 37601385 PMCID: PMC10433375 DOI: 10.3389/fmicb.2023.1218560] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 07/11/2023] [Indexed: 08/22/2023] Open
Abstract
The gut microbiota affects the health and overall fitness of bumblebees. It can enhance the host's ecological range by leveraging their metabolic capacities. However, the diversity of the gut microbiota and adaptive functional evolution in high-altitude regions remain unclear. To explore how the gut microbiota helps the host adapt to high-altitude environments, we analyzed the differences in diversity and function of the gut microbiota between high- and low-altitude regions through full-length 16S rRNA sequencing. Our results show that high-altitude regions have a lower abundance of Fructobacillus and Saccharibacter compared to low-altitude regions. Additionally, some individuals in low-altitude regions were invaded by opportunistic pathogens. The gut microbiota in high-altitude regions has a greater number of pathways involved in "Protein digestion and absorption" and "Biosynthesis of amino acids," while fewer carbohydrate pathways are involved in "digestion and absorption" and "Salmonella infection." Our finding suggests that plateau hosts typically reduce energy metabolism and enhance immunity in response to adverse environments. Correspondingly, the gut microbiota also makes changes, such as reducing carbohydrate degradation and increasing protein utilization in response to the host. Additionally, the gut microbiota regulates their abundance and function to help the host adapt to adverse high-altitude environments.
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Affiliation(s)
- Zhengyi Zhang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China
| | - Yulong Guo
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China
| | - Mingsheng Zhuang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China
- Shanghai Suosheng Biotechnology Co., Ltd., Shanghai, China
| | - Fugang Liu
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China
| | - Zhongyan Xia
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China
| | - Zhihao Zhang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China
| | - Fan Yang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China
| | - Huayan Zeng
- Luoping Yunling Bee Industry and Trade Co., Ltd., Qujing, Yunnan, China
| | - Yueguo Wu
- Luoping Yunling Bee Industry and Trade Co., Ltd., Qujing, Yunnan, China
| | - Jiaxing Huang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China
| | - Jilian Li
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China
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22
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Jorgensen K, Song D, Weinstein J, Garcia OA, Pearson LN, Inclán M, Rivera-Chira M, León-Velarde F, Kiyamu M, Brutsaert TD, Bigham AW, Lee FS. High-Altitude Andean H194R HIF2A Allele Is a Hypomorphic Allele. Mol Biol Evol 2023; 40:msad162. [PMID: 37463421 PMCID: PMC10370452 DOI: 10.1093/molbev/msad162] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/15/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
For over 10,000 years, Andeans have resided at high altitude where the partial pressure of oxygen challenges human survival. Recent studies have provided evidence for positive selection acting in Andeans on the HIF2A (also known as EPAS1) locus, which encodes for a central transcription factor of the hypoxia-inducible factor pathway. However, the precise mechanism by which this allele might lead to altitude-adaptive phenotypes, if any, is unknown. By analyzing whole genome sequencing data from 46 high-coverage Peruvian Andean genomes, we confirm evidence for positive selection acting on HIF2A and a unique pattern of variation surrounding the Andean-specific single nucleotide variant (SNV), rs570553380, which encodes for an H194R amino acid substitution in HIF-2α. Genotyping the Andean-associated SNV rs570553380 in a group of 299 Peruvian Andeans from Cerro de Pasco, Peru (4,338 m), reveals a positive association with increased fraction of exhaled nitric oxide, a marker of nitric oxide biosynthesis. In vitro assays show that the H194R mutation impairs binding of HIF-2α to its heterodimeric partner, aryl hydrocarbon receptor nuclear translocator. A knockin mouse model bearing the H194R mutation in the Hif2a gene displays decreased levels of hypoxia-induced pulmonary Endothelin-1 transcripts and protection against hypoxia-induced pulmonary hypertension. We conclude the Andean H194R HIF2A allele is a hypomorphic (partial loss of function) allele.
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Affiliation(s)
- Kelsey Jorgensen
- Department of Anthropology, University of California, Los Angeles, CA, USA
| | - Daisheng Song
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Julien Weinstein
- Department of Anthropology, The University of Michigan, Ann Arbor, MI, USA
| | - Obed A Garcia
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Laurel N Pearson
- Department of Anthropology, The Pennsylvania State University, State College, PA, USA
| | - María Inclán
- División de. Estudios Políticos, Centro de Investigación y Docencia Económicas, Mexico City, CDMX, Mexico
| | - Maria Rivera-Chira
- Departamento de Ciencias Biológicas y Fisiológicas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Lima, Peru
| | - Fabiola León-Velarde
- Departamento de Ciencias Biológicas y Fisiológicas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Lima, Peru
| | - Melisa Kiyamu
- Departamento de Ciencias Biológicas y Fisiológicas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Lima, Peru
| | - Tom D Brutsaert
- Department of Exercise Science, Syracuse University, Syracuse, NY, USA
| | - Abigail W Bigham
- Department of Anthropology, University of California, Los Angeles, CA, USA
| | - Frank S Lee
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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23
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Schweizer RM, Ivy CM, Natarajan C, Scott GR, Storz JF, Cheviron ZA. Gene regulatory changes underlie developmental plasticity in respiration and aerobic performance in highland deer mice. Mol Ecol 2023; 32:3483-3496. [PMID: 37073620 PMCID: PMC10330314 DOI: 10.1111/mec.16953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 03/27/2023] [Accepted: 04/03/2023] [Indexed: 04/20/2023]
Abstract
Phenotypic plasticity can play an important role in the ability of animals to tolerate environmental stress, but the nature and magnitude of plastic responses are often specific to the developmental timing of exposure. Here, we examine changes in gene expression in the diaphragm of highland deer mice (Peromyscus maniculatus) in response to hypoxia exposure at different stages of development. In highland deer mice, developmental plasticity in diaphragm function may mediate changes in several respiratory traits that influence aerobic metabolism and performance under hypoxia. We generated RNAseq data from diaphragm tissue of adult deer mice exposed to (1) life-long hypoxia (before conception to adulthood), (2) post-natal hypoxia (birth to adulthood), (3) adult hypoxia (6-8 weeks only during adulthood) or (4) normoxia. We found five suites of co-regulated genes that are differentially expressed in response to hypoxia, but the patterns of differential expression depend on the developmental timing of exposure. We also identified four transcriptional modules that are associated with important respiratory traits. Many of the genes in these transcriptional modules bear signatures of altitude-related selection, providing an indirect line of evidence that observed changes in gene expression may be adaptive in hypoxic environments. Our results demonstrate the importance of developmental stage in determining the phenotypic response to environmental stressors.
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Affiliation(s)
- Rena M. Schweizer
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Catherine M. Ivy
- Department of Biology, McMaster University, Hamilton, ON, Canada, L8S 4K1
| | | | - Graham R. Scott
- Department of Biology, McMaster University, Hamilton, ON, Canada, L8S 4K1
| | - Jay F. Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
| | - Zachary A. Cheviron
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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24
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Joyner MJ, Wiggins CC, Baker SE, Klassen SA, Senefeld JW. Exercise and Experiments of Nature. Compr Physiol 2023; 13:4879-4907. [PMID: 37358508 PMCID: PMC10853940 DOI: 10.1002/cphy.c220027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
Abstract
In this article, we highlight the contributions of passive experiments that address important exercise-related questions in integrative physiology and medicine. Passive experiments differ from active experiments in that passive experiments involve limited or no active intervention to generate observations and test hypotheses. Experiments of nature and natural experiments are two types of passive experiments. Experiments of nature include research participants with rare genetic or acquired conditions that facilitate exploration of specific physiological mechanisms. In this way, experiments of nature are parallel to classical "knockout" animal models among human research participants. Natural experiments are gleaned from data sets that allow population-based questions to be addressed. An advantage of both types of passive experiments is that more extreme and/or prolonged exposures to physiological and behavioral stimuli are possible in humans. In this article, we discuss a number of key passive experiments that have generated foundational medical knowledge or mechanistic physiological insights related to exercise. Both natural experiments and experiments of nature will be essential to generate and test hypotheses about the limits of human adaptability to stressors like exercise. © 2023 American Physiological Society. Compr Physiol 13:4879-4907, 2023.
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Affiliation(s)
- Michael J Joyner
- Department of Anesthesiology & Perioperative Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
| | - Chad C Wiggins
- Department of Anesthesiology & Perioperative Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Sarah E Baker
- Department of Anesthesiology & Perioperative Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
| | - Stephen A Klassen
- Department of Kinesiology, Brock University, St. Catharines, Ontario, Canada
| | - Jonathon W Senefeld
- Department of Anesthesiology & Perioperative Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
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25
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Williamson JL, Linck EB, Bautista E, Smiley A, McGuire JA, Dudley R, Witt CC. Hummingbird blood traits track oxygen availability across space and time. Ecol Lett 2023. [PMID: 37178017 DOI: 10.1111/ele.14235] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/20/2023] [Accepted: 04/13/2023] [Indexed: 05/15/2023]
Abstract
Predictable trait variation across environments suggests shared adaptive responses via repeated genetic evolution, phenotypic plasticity or both. Matching of trait-environment associations at phylogenetic and individual scales implies consistency between these processes. Alternatively, mismatch implies that evolutionary divergence has changed the rules of trait-environment covariation. Here we tested whether species adaptation alters elevational variation in blood traits. We measured blood for 1217 Andean hummingbirds of 77 species across a 4600-m elevational gradient. Unexpectedly, elevational variation in haemoglobin concentration ([Hb]) was scale independent, suggesting that physics of gas exchange, rather than species differences, determines responses to changing oxygen pressure. However, mechanisms of [Hb] adjustment did show signals of species adaptation: Species at either low or high elevations adjusted cell size, whereas species at mid-elevations adjusted cell number. This elevational variation in red blood cell number versus size suggests that genetic adaptation to high altitude has changed how these traits respond to shifts in oxygen availability.
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Affiliation(s)
- Jessie L Williamson
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA
- Cornell Lab of Ornithology, Cornell University, Ithaca, New York, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
- Cornell University Museum of Vertebrates, Cornell University, Ithaca, New York, USA
| | - Ethan B Linck
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Emil Bautista
- Centro de Ornitología y Biodiversidad (CORBIDI), Lima, Peru
| | - Ashley Smiley
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Robert Dudley
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Christopher C Witt
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA
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26
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Linck EB, Williamson JL, Bautista E, Beckman EJ, Benham PM, DuBay SG, Flores LM, Gadek CR, Johnson AB, Jones MR, Núñez-Zapata J, Quiñonez A, Schmitt CJ, Susanibar D, Tiravanti C J, Verde-Guerra K, Wright NA, Valqui T, Storz JF, Witt CC. Blood Variation Implicates Respiratory Limits on Elevational Ranges of Andean Birds. Am Nat 2023; 201:741-754. [PMID: 37130238 DOI: 10.1086/723222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
AbstractThe extent to which species ranges reflect intrinsic physiological tolerances is a major question in evolutionary ecology. To date, consensus has been hindered by the limited tractability of experimental approaches across most of the tree of life. Here, we apply a macrophysiological approach to understand how hematological traits related to oxygen transport shape elevational ranges in a tropical biodiversity hot spot. Along Andean elevational gradients, we measured traits that affect blood oxygen-carrying capacity-total and cellular hemoglobin concentration and hematocrit, the volume percentage of red blood cells-for 2,355 individuals of 136 bird species. We used these data to evaluate the influence of hematological traits on elevational ranges. First, we asked whether the sensitivity of hematological traits to changes in elevation is predictive of elevational range breadth. Second, we asked whether variance in hematological traits changed as a function of distance to the nearest elevational range limit. We found that birds showing greater hematological sensitivity had broader elevational ranges, consistent with the idea that a greater acclimatization capacity facilitates elevational range expansion. We further found reduced variation in hematological traits in birds sampled near their elevational range limits and at high absolute elevations, patterns consistent with intensified natural selection, reduced effective population size, or compensatory changes in other cardiorespiratory traits. Our findings suggest that constraints on hematological sensitivity and local genetic adaptation to oxygen availability promote the evolution of the narrow elevational ranges that underpin tropical montane biodiversity.
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27
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Yuan C, Zhang Q. Risk factors for microalbuminuria in adult Tibetan patients with high-altitude pulmonary hypertension: a cross-sectional study. Cardiovasc Diagn Ther 2023; 13:336-344. [PMID: 37583683 PMCID: PMC10423733 DOI: 10.21037/cdt-22-385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 02/10/2023] [Indexed: 08/17/2023]
Abstract
Background It has been suggested that chronic hypoxia underlies the higher prevalence of microalbuminuria in high-altitude residents than in sea-level dwellers. This study explored the risk factors for microalbuminuria in Tibetans with high-altitude pulmonary hypertension (HAPH). Methods This retrospective cross-sectional study included adult patients with HAPH admitted to the People's Hospital of Tibet Autonomous Region between November 2018 and August 2019. Results One hundred and twenty patients with HAPH were included in this study, and 69 patients (57.5%) had microalbuminuria. Compared with the patients without microalbuminuria, the microalbuminuria group had significantly higher values for age, pulmonary arterial systolic pressure (PASP), systolic blood pressure, diastolic blood pressure, blood hemoglobin concentration, glycated hemoglobin, serum creatinine, and serum uric acid, significantly lower values for heart rate, peripheral oxygen saturation (SpO2), estimated glomerular filtration rate, and 6-min walking distance, and poorer New York Heart Association functional class (P<0.05 for all variables). PASP [odds ratio (OR): 1.55; 95% CI: 1.19-2.00; P=0.001] and SpO2 (OR = 0.78; 95% CI: 0.63-0.97; P=0.02) were independently associated with microalbuminuria. Conclusions Higher PASP and lower SpO2 were independently associated with microalbuminuria in adult Tibetan patients with HAPH.
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Macotela L, Naya DE, González-Morales JC, Anaya M, Fajardo V, Manjarrez J. Altitudinal variation in organ mass from three mountain systems: The case of mesquite lizard Sceloporus grammicus. Comp Biochem Physiol A Mol Integr Physiol 2023; 281:111426. [PMID: 37059292 DOI: 10.1016/j.cbpa.2023.111426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 04/10/2023] [Accepted: 04/10/2023] [Indexed: 04/16/2023]
Abstract
High altitude environments provide a fertile ground for investigating the benefits of phenotypic adjustments at several levels of biological organization. Low oxygen partial pressure and low environmental temperature are the main limiting factors that promote phenotypic variation in different organs, such as the lung and heart. Although high-altitude environments act like natural laboratories, most morphological studies conducted to date lack replication. Here, we evaluated organ mass variation in nine populations of Sceloporus grammicus, throughout three altitudinal gradients (mountains) from the Trans-Mexican volcanic belt. A total of 84 individuals from three different altitudes at three different mountains were collected. Then, we used generalized linear models to analyze the pattern of variation in internal organs mass as a function of altitude and temperature. We observed a striking pattern of altitudinal variation in the size of cardiorespiratory organs: while heart mass increased with altitude and decreased with temperature, the lung showed a significant statistical interaction between mountain transect and temperature. Overall, our results support the hypothesis that cardiorespiratory organs should be bigger in populations occurring at higher altitudes. Moreover, the study of different mountain systems allowed us to observe some differences in one mountain in relation to the other two.
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Affiliation(s)
- Luis Macotela
- Doctorado en Ciencias Agropecuarias y Recursos Naturales, Universidad Autónoma del Estado de México, Instituto Literario No. 100, Col. Centro, C. P. 5000 Toluca, Estado de Mexico, Mexico; Instituto para la Conservación de la Cordillera Neovolcánica ante el Cambio Climático, A.C. Calle Lago de Atitlán No. 502, C. P. 50100 Toluca, Estado de México, Mexico
| | - Daniel E Naya
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Juan C González-Morales
- Centro Universitario Amecameca, Universidad Autónoma del Estado de México, Instituto Literario 100, Col. Centro, CP 50000 Toluca, Estado de México, Mexico
| | - Mariluz Anaya
- Instituto para la Conservación de la Cordillera Neovolcánica ante el Cambio Climático, A.C. Calle Lago de Atitlán No. 502, C. P. 50100 Toluca, Estado de México, Mexico; Maestría en Ciencias Biológicas, Facultad de Ciencias, Universidad Autónoma del Estado de Mexico, Mexico
| | - Víctor Fajardo
- Instituto para la Conservación de la Cordillera Neovolcánica ante el Cambio Climático, A.C. Calle Lago de Atitlán No. 502, C. P. 50100 Toluca, Estado de México, Mexico
| | - Javier Manjarrez
- Facultad de Ciencias, Universidad Autónoma del Estado de México, Campus El Cerrillo, Carretera Toluca - Ixtlahuaca Km 15.5, Piedras Blancas, 50200 Toluca de Lerdo, Mexico.
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Nengovhela A, Ivy CM, Scott GR, Denys C, Taylor PJ. Counter-gradient variation and the expensive tissue hypothesis explain parallel brain size reductions at high elevation in cricetid and murid rodents. Sci Rep 2023; 13:5617. [PMID: 37024565 PMCID: PMC10079977 DOI: 10.1038/s41598-023-32498-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 03/28/2023] [Indexed: 04/08/2023] Open
Abstract
To better understand functional morphological adaptations to high elevation (> 3000 m above sea level) life in both North American and African mountain-associated rodents, we used microCT scanning to acquire 3D images and a 3D morphometric approach to calculate endocranial volumes and skull lengths. This was done on 113 crania of low-elevation and high-elevation populations in species of North American cricetid mice (two Peromyscus species, n = 53), and African murid rodents of two tribes, Otomyini (five species, n = 49) and Praomyini (four species, n = 11). We tested two distinct hypotheses for how endocranial volume might vary in high-elevation populations: the expensive tissue hypothesis, which predicts that brain and endocranial volumes will be reduced to lessen the costs of growing and maintaining a large brain; and the brain-swelling hypothesis, which predicts that endocranial volumes will be increased either as a direct phenotypic effect or as an adaptation to accommodate brain swelling and thus minimize pathological symptoms of altitude sickness. After correcting for general allometric variation in cranial size, we found that in both North American Peromyscus mice and African laminate-toothed (Otomys) rats, highland rodents had smaller endocranial volumes than lower-elevation rodents, consistent with the expensive tissue hypothesis. In the former group, Peromyscus mice, crania were obtained not just from wild-caught mice from high and low elevations but also from those bred in common-garden laboratory conditions from parents caught from either high or low elevations. Our results in these mice showed that brain size responses to elevation might have a strong genetic basis, which counters an opposite but weaker environmental effect on brain volume. These results potentially suggest that selection may act to reduce brain volume across small mammals at high elevations but further experiments are needed to assess the generality of this conclusion and the nature of underlying mechanisms.
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Affiliation(s)
- Aluwani Nengovhela
- Department of Mammalogy, National Museum, Bloemfontein, 9300, South Africa.
- Department of Zoology, School of Natural and Mathematical Sciences, University of Venda, Thohoyandou, South Africa.
| | - Catherine M Ivy
- Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Graham R Scott
- Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Christiane Denys
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 57 Rue Cuvier, 75005, Paris, France
| | - Peter J Taylor
- Department of Zoology, School of Natural and Mathematical Sciences, University of Venda, Thohoyandou, South Africa
- Afromontane Unit, Department of Zoology and Entomology, University of the Free State, Phuthaditjhaba, South Africa
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30
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Kuo HC, Yao CT, Liao BY, Weng MP, Dong F, Hsu YC, Hung CM. Weak gene-gene interaction facilitates the evolution of gene expression plasticity. BMC Biol 2023; 21:57. [PMID: 36941675 PMCID: PMC10029303 DOI: 10.1186/s12915-023-01558-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/10/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Individual organisms may exhibit phenotypic plasticity when they acclimate to different conditions. Such plastic responses may facilitate or constrain the adaptation of their descendant populations to new environments, complicating their evolutionary trajectories beyond the genetic blueprint. Intriguingly, phenotypic plasticity itself can evolve in terms of its direction and magnitude during adaptation. However, we know little about what determines the evolution of phenotypic plasticity, including gene expression plasticity. Recent laboratory-based studies suggest dominance of reversing gene expression plasticity-plastic responses that move the levels of gene expression away from the new optima. Nevertheless, evidence from natural populations is still limited. RESULTS Here, we studied gene expression plasticity and its evolution in the montane and lowland populations of an elevationally widespread songbird-the Rufous-capped Babbler (Cyanoderma ruficeps)-with reciprocal transplant experiments and transcriptomic analyses; we set common gardens at altitudes close to these populations' native ranges. We confirmed the prevalence of reversing plasticity in genes associated with altitudinal adaptation. Interestingly, we found a positive relationship between magnitude and degree of evolution in gene expression plasticity, which was pertinent to not only adaptation-associated genes but also the whole transcriptomes from multiple tissues. Furthermore, we revealed that genes with weaker expressional interactions with other genes tended to exhibit stronger plasticity and higher degree of plasticity evolution, which explains the positive magnitude-evolution relationship. CONCLUSIONS Our experimental evidence demonstrates that species may initiate their adaptation to new habitats with genes exhibiting strong expression plasticity. We also highlight the role of expression interdependence among genes in regulating the magnitude and evolution of expression plasticity. This study illuminates how the evolution of phenotypic plasticity in gene expression facilitates the adaptation of species to challenging environments in nature.
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Affiliation(s)
- Hao-Chih Kuo
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Cheng-Te Yao
- Division of Zoology, Endemic Species Research Institute, Nantou, 55244, Taiwan
| | - Ben-Yang Liao
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, 35053, Taiwan
| | - Meng-Pin Weng
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, 35053, Taiwan
| | - Feng Dong
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Yu-Cheng Hsu
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien, 97401, Taiwan
| | - Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
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Function of left ventricle mitochondria in highland deer mice and lowland mice. J Comp Physiol B 2023; 193:207-217. [PMID: 36795175 DOI: 10.1007/s00360-023-01476-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/26/2023] [Accepted: 02/03/2023] [Indexed: 02/17/2023]
Abstract
To gain insight into the mitochondrial mechanisms of hypoxia tolerance in high-altitude natives, we examined left ventricle mitochondrial function of highland deer mice compared with lowland native deer mice and white-footed mice. Highland and lowland native deer mice (Peromyscus maniculatus) and lowland white-footed mice (P. leucopus) were first-generation born and raised in common lab conditions. Adult mice were acclimated to either normoxia or hypoxia (60 kPa) equivalent to ~ 4300 m for at least 6 weeks. Left ventricle mitochondrial physiology was assessed by determining respiration in permeabilized muscle fibers with carbohydrates, lipids, and lactate as substrates. We also measured the activities of several left ventricle metabolic enzymes. Permeabilized left ventricle muscle fibers of highland deer mice showed greater rates of respiration with lactate than either lowland deer mice or white-footed mice. This was associated with higher activities of lactate dehydrogenase in tissue and isolated mitochondria in highlanders. Normoxia-acclimated highlanders also showed higher respiratory rates with palmitoyl-carnitine than lowland mice. Maximal respiratory capacity through complexes I and II was also greater in highland deer mice but only compared with lowland deer mice. Acclimation to hypoxia had little effect on respiration rates with these substrates. In contrast, left ventricle activities of hexokinase increased in both lowland and highland deer mice after hypoxia acclimation. These data suggest that highland deer mice support an elevated cardiac function in hypoxia, in part, with high ventricle cardiomyocyte respiratory capacities supported by carbohydrates, fatty acids, and lactate.
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32
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Elevation and blood traits in the mesquite lizard: Are patterns repeatable between mountains? Comp Biochem Physiol A Mol Integr Physiol 2023; 276:111338. [PMID: 36336309 DOI: 10.1016/j.cbpa.2022.111338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/29/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
Ecogeographical patterns describe predictable variation in phenotypic traits between ecological communities. For example, high-altitude animals are expected to show elevated hematological values as an adaptation to the lower oxygen pressure. Mountains act like ecological islands and therefore are considered natural laboratories. However, the majority of ecophysiological studies on blood traits lack replication that would allow us to infer if the pattern reported is a local event or whether it is a widespread pattern resulting from larger-scale ecological processes. In lizards, in fact, the increase of hematological values at high altitudes has received mixed support. Here, for the first time, we compare blood traits in lizards along elevational gradients with replication. We tested the repeatability of blood traits in mesquite lizards between different elevations in three different mountains from the Trans-Mexican Volcanic Belt. We measured hematocrit, hemoglobin concentration, mean corpuscular hemoglobin concentration, and erythrocyte size in blood samples of low, medium, and high-elevation lizards. We obtained similar elevational patterns between mountains, but the blood traits differed among mountains. Middle-altitude populations had greater oxygen-carrying capacity than lizards from low and high altitudes. The differences found between mountain systems could be the result of phenotypic plasticity or genetic differentiation as a consequence of abiotic factors not considered.
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33
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Liu S, Zhou C, Meng G, Wan T, Tang M, Yang C, Murphy RW, Fan Z, Liu Y, Zeng T, Zhao Y, Liu S. Evolution and diversification of Mountain voles (Rodentia: Cricetidae). Commun Biol 2022; 5:1417. [PMID: 36572770 PMCID: PMC9792541 DOI: 10.1038/s42003-022-04371-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 12/13/2022] [Indexed: 12/27/2022] Open
Abstract
The systematics of the Cricetid genus Neodon have long been fraught with uncertainty due to sampling issues and a lack of comprehensive datasets. To gain better insights into the phylogeny and evolution of Neodon, we systematically sampled Neodon across the Hengduan and Himalayan Mountains, which cover most of its range in China. Analyses of skulls, teeth, and bacular structures revealed 15 distinct patterns corresponding to 15 species of Neodon. In addition to morphological analyses, we generated a high-quality reference genome for the mountain vole and generated whole-genome sequencing data for 47 samples. Phylogenomic analyses supported the recognition of six new species, revealing a long-term underestimation of Neodon diversity. We further identified positively selected genes potentially related to high-elevation adaptation. Together, our results illuminate how climate change caused the plateau to become the centre of Neodon origin and diversification and how mountain voles have adapted to the hypoxic high-altitude plateau environment.
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Affiliation(s)
- Shaoying Liu
- Sichuan Academy of Forestry, No.18, Xinhui xilu, Chengdu, 610081, China.
| | - Chengran Zhou
- BGI-Shenzhen, Shenzhen, 518083, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Guanliang Meng
- Zoological Research Museum Alexander Koenig, D-53113, Bonn, Germany
| | - Tao Wan
- Sichuan Academy of Forestry, No.18, Xinhui xilu, Chengdu, 610081, China
| | - Mingkun Tang
- Sichuan Academy of Forestry, No.18, Xinhui xilu, Chengdu, 610081, China
| | | | - Robert W Murphy
- Reptilia Sanctuary and Education Centre, Concord, ON, L4K 2N6, Canada
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, M5S 2C6, Canada
| | - Zhenxin Fan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yang Liu
- Sichuan Academy of Forestry, No.18, Xinhui xilu, Chengdu, 610081, China
| | - Tao Zeng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yun Zhao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Shanlin Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, China.
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Terefe E, Belay G, Han J, Hanotte O, Tijjani A. Genomic adaptation of Ethiopian indigenous cattle to high altitude. Front Genet 2022; 13:960234. [PMID: 36568400 PMCID: PMC9780680 DOI: 10.3389/fgene.2022.960234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
The mountainous areas of Ethiopia represent one of the most extreme environmental challenges in Africa faced by humans and other inhabitants. Selection for high-altitude adaptation is expected to have imprinted the genomes of livestock living in these areas. Here we assess the genomic signatures of positive selection for high altitude adaptation in three cattle populations from the Ethiopian mountainous areas (Semien, Choke, and Bale mountains) compared to three Ethiopian lowland cattle populations (Afar, Ogaden, and Boran), using whole-genome resequencing and three genome scan approaches for signature of selection (iHS, XP-CLR, and PBS). We identified several candidate selection signature regions and several high-altitude adaptation genes. These include genes such as ITPR2, MB, and ARNT previously reported in the human population inhabiting the Ethiopian highlands. Furthermore, we present evidence of strong selection and high divergence between Ethiopian high- and low-altitude cattle populations at three new candidate genes (CLCA2, SLC26A2, and CBFA2T3), putatively linked to high-altitude adaptation in cattle. Our findings provide possible examples of convergent selection between cattle and humans as well as unique African cattle signature to the challenges of living in the Ethiopian mountainous regions.
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Affiliation(s)
- Endashaw Terefe
- Department of Microbial Cellular and Molecular Biology (MCMB), College of Natural and Computational Science, Addis Ababa University, Addis Ababa, Ethiopia,International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia,Department of Animal Science, College of Agriculture and Environmental Science, Arsi University, Asella, Ethiopia,*Correspondence: Endashaw Terefe, Abdulfatai Tijjani,
| | - Gurja Belay
- Department of Microbial Cellular and Molecular Biology (MCMB), College of Natural and Computational Science, Addis Ababa University, Addis Ababa, Ethiopia
| | - Jianlin Han
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia,Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Midlothian, United Kingdom,School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Abdulfatai Tijjani
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia,Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Midlothian, United Kingdom,*Correspondence: Endashaw Terefe, Abdulfatai Tijjani,
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35
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Gray OA, Yoo J, Sobreira DR, Jousma J, Witonsky D, Sakabe NJ, Peng YJ, Prabhakar NR, Fang Y, Nobréga MA, Di Rienzo A. A pleiotropic hypoxia-sensitive EPAS1 enhancer is disrupted by adaptive alleles in Tibetans. SCIENCE ADVANCES 2022; 8:eade1942. [PMID: 36417539 PMCID: PMC9683707 DOI: 10.1126/sciadv.ade1942] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
In Tibetans, noncoding alleles in EPAS1-whose protein product hypoxia-inducible factor 2α (HIF-2α) drives the response to hypoxia-carry strong signatures of positive selection; however, their functional mechanism has not been systematically examined. Here, we report that high-altitude alleles disrupt the activity of four EPAS1 enhancers in one or more cell types. We further characterize one enhancer (ENH5) whose activity is both allele specific and hypoxia dependent. Deletion of ENH5 results in down-regulation of EPAS1 and HIF-2α targets in acute hypoxia and in a blunting of the transcriptional response to sustained hypoxia. Deletion of ENH5 in mice results in dysregulation of gene expression across multiple tissues. We propose that pleiotropic adaptive effects of the Tibetan alleles in EPAS1 underlie the strong selective signal at this gene.
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Affiliation(s)
- Olivia A. Gray
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Jennifer Yoo
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
- Institute for Integrative Physiology and Center for Systems Biology of O2 Sensing, The University of Chicago, Chicago, IL 60637, USA
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Débora R. Sobreira
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Jordan Jousma
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - David Witonsky
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Noboru J. Sakabe
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Ying-Jie Peng
- Institute for Integrative Physiology and Center for Systems Biology of O2 Sensing, The University of Chicago, Chicago, IL 60637, USA
| | - Nanduri R. Prabhakar
- Institute for Integrative Physiology and Center for Systems Biology of O2 Sensing, The University of Chicago, Chicago, IL 60637, USA
| | - Yun Fang
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Marcelo A. Nobréga
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Anna Di Rienzo
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
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36
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Perry I, Hernadi SB, Cunha L, Short S, Marchbank A, Spurgeon DJ, Orozco-terWengel P, Kille P. Molecular insights into high-altitude adaption and acclimatisation of Aporrectodea caliginosa. Life Sci Alliance 2022; 5:5/11/e202201513. [PMID: 35977843 PMCID: PMC9386962 DOI: 10.26508/lsa.202201513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 12/02/2022] Open
Abstract
A megabase genome assembly for Aporrectodea caliginosa is presented with transcriptomic and SNP-based evidence for acclimatisation and adaption to extreme weather conditions found at high altitude. Here, we explore the high-altitude adaptions and acclimatisation of Aporrectodea caliginosa. Population diversity is assessed through mitochondrial barcoding, identifying closely related populations across the island of Pico (Azores). We present the first megabase N50 assembly size (1.2 Mbp) genome for A. caliginosa. High- and low-altitude populations were exposed experimentally to a range of oxygen and temperature conditions, simulating altitudinal conditions, and the transcriptomic responses explored. SNP densities are assessed to identify signatures of selective pressure and their link to differentially expressed genes. The high-altitude A. caliginosa population had lower differential expression and fewer co-expressed genes between conditions, indicating a more condition-refined epigenetic response. Genes identified as under adaptive pressure through Fst and nucleotide diversity in the high-altitude population clustered around the differentially expressed an upstream environmental response control gene, HMGB1. The high-altitude population of A. caliginosa indicated adaption and acclimatisation to high-altitude conditions and suggested resilience to extreme weather events. This mechanistic understanding could help offer a strategy in further identifying other species capable of maintaining soil fertility in extreme environments.
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Affiliation(s)
- Iain Perry
- Organisms and Environment, Cardiff University, Wales, UK .,Wales Gene Park, Cardiff University, Wales, UK
| | | | - Luis Cunha
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal.,School of Applied Sciences, University of South Wales, Wales, UK
| | - Stephen Short
- Organisms and Environment, Cardiff University, Wales, UK.,UK Centre for Ecology and Hydrology, Maclean Building, Wallingford, UK
| | | | - David J Spurgeon
- UK Centre for Ecology and Hydrology, Maclean Building, Wallingford, UK
| | | | - Peter Kille
- Organisms and Environment, Cardiff University, Wales, UK
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37
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Beckman EJ, Vargas Campos W, Benham PM, Schmitt CJ, Cheviron ZA, Witt CC. Selection on embryonic haemoglobin in an elevational generalist songbird. Biol Lett 2022; 18:20220105. [PMCID: PMC9554719 DOI: 10.1098/rsbl.2022.0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Animals developing at high elevation experience a suite of environmental challenges, most notably the low partial pressure of oxygen (PO2) in ambient air. In low PO2, bird species with high-elevation ancestry consistently demonstrate higher hatching success than lowland counterparts, suggesting highland birds are adapted to restricted O2 (hypoxia) in early development. Haemoglobin (Hb), the critical oxygen-transport protein, is a likely target of PO2-related selection across ontogeny since Hb isoforms expressed at distinct developmental stages demonstrate different O2 affinities. To test if Hb function is under PO2-related selection at different ontogenetic stages, we sampled a songbird, the hooded siskin (Spinus magellanicus), across two approximately 4000 m elevational transects. We sequenced all of the loci that encode avian Hb isoforms, and tested for signatures of spatially varying selection by comparing divergence patterns in Hb loci to other loci sampled across the genome. We found strong signatures of diversifying selection at non-synonymous sites in loci that contribute to embryonic (απ, βH) and definitive (βA) Hb isoforms. This is the first evidence for selection on embryonic haemoglobin in high-elevation Neoaves. We conclude that selection on Hb function at brief, but critical stages of ontogeny may be a vital component to high elevation adaptation in birds.
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Affiliation(s)
- Elizabeth J. Beckman
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA,Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Walter Vargas Campos
- Centro de Ornitología y Biodiversidad, Calle Sta. Rita 105, Oficina 202, Santiago de Surco, Lima, Perú
| | - Phred M. Benham
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA,Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - C. Jonathan Schmitt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA,Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | | | - Christopher C. Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
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Fu Y, Song Y, Yang C, Liu X, Liu Y, Huang Y. Relationship between brain size and digestive tract length support the expensive-tissue hypothesis in Feirana quadranus. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.982590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The brain is among the most energetically costly organs in the vertebrate body, while the size of the brain varies within species. The expensive-tissue hypothesis (ETH) predicts that increasing the size of another costly organ, such as the gut, should compensate for the cost of a small brain. Here, the ETH was tested by analyzing the relationship between brain size variation and digestive tract length in a Swelled-vented frog (Feirana quadranus). A total of 125 individuals across 10 populations ranging from 586 to 1,702 m a.s.l. from the Qinling-Daba Mountains were sampled. With the increase in altitude, the brain size decreases and the digestive tract length increases. Different brain regions do not change their relative size in a consistent manner. The sizes of telencephalon and cerebellum decrease with the increase in altitude, while the olfactory nerve increases its size at high altitudes. However, the olfactory bulb and optic tectum have no significant relationship with altitude. After controlling for snout-vent length (SVL), a significant negative correlation could be found between brain size and digestive tract length in F. quadranus. Therefore, the intraspecific variation of brain size follows the general patterns of ETH in this species. The results suggest that annual mean temperature and annual precipitation are environmental factors influencing the adaptive evolution of brain size and digestive tract length. This study also suggests that food composition, activity times, and habitat complexity are the potential reasons driving the adaptive evolution of brain size and digestive tract length.
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39
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Wearing OH, Scott GR. Evolved reductions in body temperature and the metabolic costs of thermoregulation in deer mice native to high altitude. Proc Biol Sci 2022; 289:20221553. [PMID: 36168757 PMCID: PMC9515628 DOI: 10.1098/rspb.2022.1553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 08/30/2022] [Indexed: 11/12/2022] Open
Abstract
The evolution of endothermy was instrumental to the diversification of birds and mammals, but the energetic demands of maintaining high body temperature could offset the advantages of endothermy in some environments. We hypothesized that reductions in body temperature help high-altitude natives overcome the metabolic challenges of cold and hypoxia in their native environment. Deer mice (Peromyscus maniculatus) from high-altitude and low-altitude populations were bred in captivity to the second generation and were acclimated as adults to warm normoxia or cold hypoxia. Subcutaneous temperature (Tsub, used as a proxy for body temperature) and cardiovascular function were then measured throughout the diel cycle using biotelemetry. Cold hypoxia increased metabolic demands, as reflected by increased food consumption and heart rate (associated with reduced vagal tone). These increased metabolic demands were offset by plastic reductions in Tsub (approx. 2°C) in response to cold hypoxia, and highlanders had lower Tsub (approx. 1°C) than lowlanders in both environmental treatments. Empirical and theoretical evidence suggested that these reductions could together reduce metabolic demands by approximately 10-30%. Therefore, plastic and evolved reductions in body temperature can help mammals overcome the metabolic challenges at high altitude and may be a valuable energy-saving strategy in some non-hibernating endotherms in extreme environments.
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Affiliation(s)
- Oliver H. Wearing
- Department of Biology, McMaster University, Life Sciences Building, 1280 Main Street W, Hamilton, ON, Canada L8S 4K1
| | - Graham R. Scott
- Department of Biology, McMaster University, Life Sciences Building, 1280 Main Street W, Hamilton, ON, Canada L8S 4K1
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40
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Chen Y, Tan S, Fu J. Modified Metabolism and Response to UV Radiation: Gene Expression Variations Along an Elevational Gradient in the Asiatic Toad (Bufo gargarizans). J Mol Evol 2022; 90:389-399. [PMID: 36029325 DOI: 10.1007/s00239-022-10070-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 08/09/2022] [Indexed: 12/01/2022]
Abstract
High-elevation adaptation provides an excellent system for examining adaptive evolution, and adaptive variations may manifest at gene expression or any other phenotypic levels. We examined gene expression profiles of Asiatic toads (Bufo gargarizans) along an elevational gradient from both wild and common-garden acclimated populations. Asiatic toads originated from high altitudes have distinctive gene expression patterns. We identified 18 fixed differentially expressed genes (DEGs), which are different in both wild and acclimated samples, and 1217 plastic DEGs, which are different among wild samples. The expression levels of most genes were linearly correlated with altitude gradient and down-regulated in high-altitude populations. Expression variations of several genes associated with metabolic process are fixed, and we also identified a co-expression module that is significantly different between acclimated populations and has functions related to DNA repair. The differential expression of the vast majority genes, however, are due to phenotypic plasticity, revealing the highly plastic nature of gene expression variations. Expression modification of some specific genes related to metabolism and response to UV radiation play crucial role in adaptation to high altitude for Asiatic toads. Common-garden experiments are essential for evaluating adaptive evolution of natural populations.
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Affiliation(s)
- Ying Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.
- The University of Chinese Academy of Science, Beijing, China.
| | - Song Tan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- The University of Chinese Academy of Science, Beijing, China
| | - Jinzhong Fu
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada.
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41
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Avoiding the effects of translocation on the estimates of the metabolic rates across an elevational gradient. J Comp Physiol B 2022; 192:659-668. [DOI: 10.1007/s00360-022-01448-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 05/30/2022] [Accepted: 06/24/2022] [Indexed: 10/17/2022]
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42
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Melcore I, Bertolino S, Boratyński Z. Variation of rodents’ body temperature across elevation in Alps. Physiol Biochem Zool 2022; 95:517-524. [DOI: 10.1086/721477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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43
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Spence AR, LeWinter H, Tingley MW. Anna's hummingbird (Calypte anna) physiological response to novel thermal and hypoxic conditions at high elevations. J Exp Biol 2022; 225:275376. [PMID: 35617822 DOI: 10.1242/jeb.243294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 03/09/2022] [Indexed: 12/19/2022]
Abstract
Many species have not tracked their thermal niches upslope as predicted by climate change, potentially because higher elevations are associated with abiotic challenges beyond temperature. To better predict whether organisms can continue to move upslope with rising temperatures, we need to understand their physiological performance when subjected to novel high-elevation conditions. Here, we captured Anna's hummingbirds - a species expanding their elevational distribution in concordance with rising temperatures - from across their current elevational distribution and tested their physiological response to novel abiotic conditions. First, at a central aviary within their current elevational range, we measured hovering metabolic rate to assess their response to oxygen conditions and torpor use to assess their response to thermal conditions. Second, we transported the hummingbirds to a location 1200 m above their current elevational range limit to test for an acute response to novel oxygen and thermal conditions. Hummingbirds exhibited lower hovering metabolic rates above their current elevational range limit, suggesting lower oxygen availability may reduce performance after an acute exposure. Alternatively, hummingbirds showed a facultative response to thermal conditions by using torpor more frequently and for longer. Finally, post-experimental dissection found that hummingbirds originating from higher elevations within their range had larger hearts, a potential plastic response to hypoxic environments. Overall, our results suggest lower oxygen availability and low air pressure may be difficult challenges to overcome for hummingbirds shifting upslope as a consequence of rising temperatures, especially if there is little to no long-term acclimatization. Future studies should investigate how chronic exposure and acclimatization to novel conditions, as opposed to acute experiments, may result in alternative outcomes that help organisms better respond to abiotic challenges associated with climate-induced range shifts.
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Affiliation(s)
- Austin R Spence
- Ecology & Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269, USA
| | - Hannah LeWinter
- Wildlife Conservation & Management, Humboldt State University, 1 Harpst St. Arcata, CA 95521, USA
| | - Morgan W Tingley
- Ecology & Evolutionary Biology, University of California - Los Angeles, 621 Charles E. Young Dr. S. #951606, Los Angeles, CA 90095, USA
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44
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Genomic signatures of high-altitude adaptation and chromosomal polymorphism in geladas. Nat Ecol Evol 2022; 6:630-643. [PMID: 35332281 PMCID: PMC9090980 DOI: 10.1038/s41559-022-01703-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/15/2022] [Indexed: 01/31/2023]
Abstract
Primates have adapted to numerous environments and lifestyles, but very few species are native to high elevations. Here, we investigated high-altitude adaptations in the gelada (Theropithecus gelada), a monkey endemic to the Ethiopian Plateau. We examined genome-wide variation in conjunction with measurements of hematological and morphological traits. Our new gelada reference genome is highly intact and assembled at chromosome-length levels. Unexpectedly, we identified a chromosomal polymorphism in geladas that could potentially contribute to reproductive barriers between populations. Compared to baboons at low altitude, we found that high-altitude geladas exhibit significantly expanded chest circumferences, potentially allowing for greater lung surface area for increased oxygen diffusion. We identified gelada-specific amino acid substitutions in the alpha-chain subunit of adult hemoglobin but found that gelada hemoglobin does not exhibit markedly altered oxygenation properties compared to lowland primates. We also found that geladas at high altitude do not exhibit elevated blood hemoglobin concentrations, in contrast to the normal acclimatization response to hypoxia in lowland primates. The absence of altitude-related polycythemia suggests that geladas are able to sustain adequate tissue-oxygen delivery despite environmental hypoxia. Finally, we identified numerous genes and genomic regions exhibiting accelerated rates of evolution, as well as gene families exhibiting expansions in the gelada lineage, potentially reflecting altitude-related selection. Our findings lend insight into putative mechanisms of high-altitude adaptation while suggesting promising avenues for functional hypoxia research.
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45
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Cai C, Yang Y, Ga Q, Xu G, Ge R, Tang F. Comparative genomic analysis of high-altitude adaptation for Mongolia Mastiff, Tibetan Mastiff, and Canis Lupus. Genomics 2022; 114:110359. [PMID: 35364265 DOI: 10.1016/j.ygeno.2022.110359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 03/03/2022] [Accepted: 03/27/2022] [Indexed: 01/14/2023]
Abstract
Tibetan Mastiff has adapted to the extreme environment of the Qinghai-Tibetan Plateau. Yet, the underlying mechanisms of its high-altitude-adaptation and origin remains elusive. Here, we generated the draft genomes of Mongolia Mastiff, Tibetan Mastiff, and Canis Lupus. The phylogenetic tree uncovered that Tibetan Mastiff and Mongolia Mastiff were derived from Canis Lupus species. The comparative genomic analyses identified that the expansion of gene families related to DNA repair and damage response, and contraction related to ATPase activity revealed the genetic adaptations of Tibetan Mastiff and Canis Lupus to high altitude. In addition, the Tibetan Mastiff and Canis Lupus had signals of positive selection for genes involved in fatty-acid α/β- oxidation for highland adaptation. Notably, the positively selected TERT of Tibetan Mastiff should be an adaptive trait for correcting DNA damage. These findings suggested that the Tibetan Mastiff and Canis Lupus evolves basic strategies for adaptation to high altitude.
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Affiliation(s)
- Chunmei Cai
- Research Center for High Altitude Medicine, School of Medical, Qinghai University, Xining 810016, PR China; Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinghai Province, Xining 810016, PR China
| | - Yingzhong Yang
- Research Center for High Altitude Medicine, School of Medical, Qinghai University, Xining 810016, PR China; Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinghai Province, Xining 810016, PR China
| | - Qin Ga
- Research Center for High Altitude Medicine, School of Medical, Qinghai University, Xining 810016, PR China; Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinghai Province, Xining 810016, PR China
| | - Guocai Xu
- Research Center for High Altitude Medicine, School of Medical, Qinghai University, Xining 810016, PR China; Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinghai Province, Xining 810016, PR China
| | - Rili Ge
- Research Center for High Altitude Medicine, School of Medical, Qinghai University, Xining 810016, PR China; Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinghai Province, Xining 810016, PR China.
| | - Feng Tang
- Research Center for High Altitude Medicine, School of Medical, Qinghai University, Xining 810016, PR China; Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinghai Province, Xining 810016, PR China.
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46
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Yang Y, Yuan H, Yang Q, Cai Y, Ren Y, Li Y, Gao C, Zhao S. Post-transcriptional regulation through alternative splicing in the lungs of Tibetan pigs under hypoxia. Gene 2022; 819:146268. [PMID: 35124151 DOI: 10.1016/j.gene.2022.146268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/22/2022] [Accepted: 01/28/2022] [Indexed: 11/15/2022]
Abstract
In multicellular organisms, alternative splicing (AS) is central to the regulation of multiple biological processes. To further elucidate the adaptive strategy of AS in the lungs of Tibetan pigs in response to hypoxia, we identified and analyzed five basic AS types and 59,930 AS events in 18,179 genes. We found that approximately 65.10% of the total expressed genes underwent AS in the lungs of Tibetan pigs at a high altitude (TH). The frequencies of AS events were similar among the different groups (5.06-5.30 events in each gene on average). Skipped exons (SEs) were the predominant type of AS event, followed by mutually exclusive exons (MXEs), alternative 3' splice sites (A3SSs) and alternative 5' splice sites (A5SSs). Retained introns (RIs), the remaining type of AS event, showed lower frequencies. Further comparison analysis of differentially expressed genes (DEGs) and differentially spliced genes (DSGs) identified 2,209 differential splicing events in the above 18,000 expressed genes, including 918 increased and 1,291 decreased splicing events between the TH and Tibetan pigs at a low altitude (TL) groups. We identified 227 hypoxia-related genes involved in lung development that were differentially regulated through AS. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis clearly identified many DEGs and DSGs at high or low altitude. Seven pathways in the top 20 enriched KEGG terms overlapped for the DEGs and DSGs, including the chemokine signaling pathway, B cell receptor signaling pathway, and cytokine-cytokine receptor interaction, which exert many immunoregulatory and inflammatory actions critical to the lung under hypoxia. Twelve pathways overlapped in hypoxic DEGs and DSGs and included antigen processing, presentation and biosynthesis. GO analysis of the DEGs and DSGs among the four groups showed that numerous GO terms were enriched in the biological category, and the proportion of genes with downregulated expression was greater among 227 hypoxic genes than that of all genes. The results suggest that AS plays an essential role in the regulation of gene expression during hypoxia and that numerous genes involved in lung development are differentially regulated through AS.
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Affiliation(s)
- Yanan Yang
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Haonan Yuan
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Qiaoli Yang
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yuan Cai
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yue Ren
- Academy of Agriculture and Animal Husbandry Sciences, Institute of Animal Husbandry and Veterinary Medicine, Lhasa, Xizang, China
| | - Yongqing Li
- Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, China
| | - Caixia Gao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Shengguo Zhao
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, China.
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47
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Steppan SJ, Bowen T, Bangs MR, Farson M, Storz JF, Quiroga-Carmona M, D’Elía G, Vimercati L, Dorador Ortiz C, Zimmerman G, Schmidt SK. Evidence of a population of leaf-eared mice Phyllotis vaccarum above 6,000 m in the Andes and a survey of high-elevation mammals. J Mammal 2022; 103:776-785. [PMID: 36118797 PMCID: PMC9469927 DOI: 10.1093/jmammal/gyac028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 02/10/2022] [Indexed: 01/01/2023] Open
Abstract
Biologists have long pondered the extreme limits of life on Earth, including the maximum elevation at which species can live and reproduce. Here we review evidence of a self-sustaining population of mice at an elevation that exceeds that of all previously reported for mammals. Five expeditions over 10 years to Volcán Llullaillaco on the Argentina/Chile border observed and collected mice at elevations ranging from 5,070 m at the mountain's base to the summit at 6,739 m (22,110 feet). Previously unreported evidence includes observations and photographs of live animals and mummified remains, environmental DNA, and a soil microbial community reflecting animal activity that are evaluated in combination with previously reported video recordings and capture of live mice. All of the evidence identifies the mouse as the leaf-eared mouse Phyllotis vaccarum, and it robustly places the population within a haplotype group containing individuals from the Chilean Atacama Desert and nearby regions of Argentina. A critical review of the literature affirms that this population is not only an elevational record for mammals but for all terrestrial vertebrates to date, and we further find that many extreme elevations previously reported for mammals are based on scant or dubious evidence.
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Affiliation(s)
| | | | - Max R Bangs
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Matthew Farson
- Emergency Services, Modoc Medical Center, Alturas, California 96101, USA
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588, USA
| | - Marcial Quiroga-Carmona
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile and Colección de Mamíferos de la Universidad de Austral de Chile, Valdivia 5090000, Chile
| | - Guillermo D’Elía
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile and Colección de Mamíferos de la Universidad de Austral de Chile, Valdivia 5090000, Chile
| | - Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Cristina Dorador Ortiz
- Departamento de Biotecnología and Center for Biotechnology and Bioengineering, Universidad de Antofagasta, Antofagasta 1270300, Chile
| | | | - Steve K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
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48
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Storz JF, Bautista NM. Altitude acclimatization, hemoglobin-oxygen affinity, and circulatory oxygen transport in hypoxia. Mol Aspects Med 2022; 84:101052. [PMID: 34879970 PMCID: PMC8821351 DOI: 10.1016/j.mam.2021.101052] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 01/01/2023]
Abstract
In mammals and other air-breathing vertebrates that live at high altitude, adjustments in convective O2 transport via changes in blood hemoglobin (Hb) content and/or Hb-O2 affinity can potentially mitigate the effects of arterial hypoxemia. However, there are conflicting views about the optimal values of such traits in hypoxia, partly due to the intriguing observation that hypoxia-induced acclimatization responses in humans and other predominantly lowland mammals are frequently not aligned in the same direction as evolved phenotypic changes in high-altitude natives. Here we review relevant theoretical and empirical results and we highlight experimental studies of rodents and humans that provide insights into the combination of hematological changes that help attenuate the decline in aerobic performance in hypoxia. For a given severity of hypoxia, experimental results suggest that optimal values for hematological traits are conditional on the states of other interrelated phenotypes that govern different steps in the O2-transport pathway.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA.
| | - Naim M Bautista
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
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49
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Qi Y, Zhang T, Wu Y, Yao Z, Qiu X, Pu P, Tang X, Fu J, Yang W. A Multilevel Assessment of Plasticity in Response to High-Altitude Environment for Agama Lizards. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.845072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Upslope range shifting has been documented in diverse species in response to global warming. Plasticity, which refers to the ability of organisms to alter their phenotypes in changing environments, is crucial for the survival of those that newly migrated to a high-altitude environment. The scope and mechanisms of plasticity across biological levels, however, have rarely been examined. We used two agama lizards (genus Phrynocephalus) as model systems and a transplant experiment to comprehensively assess their plasticity on multiple organization levels. Two low-altitude (934 m) agama species, Phrynocephalus axillaris (oviparous) and P. forsythii (viviparous), were transplanted to a high-altitude site (3,400 m). After acclimation for 6 weeks in seminatural enclosures, plasticity was measured from bite force, tail display behavior, gene expression, and metabolome. Both lizards were capable of acclimating to the high-altitude environment without sacrificing their performance in bite force, but they also showed high plasticity in tail display behavior by either decreasing the intensity of a specific display component (P. forsythii) or by the trade-off between display components (P. axillaris). Genes and metabolites associated with lipids, especially fatty acid metabolism, exhibited significant differentiation in expression, compared to individuals from their native habitats. Improved fatty acid storage and metabolism appeared to be a common response among animals at high altitudes. Despite distinct reproductive modes that may differ in response to physiological pressure, the two lizards demonstrated high concordance in plasticity when they faced a novel environment at high altitudes. Taken together, lizards likely acclimate to high-altitude environments by reducing behavioral activity and increasing energy efficiency after range shifting. Our results provide new insights into our understanding of phenotypic plasticity and its importance in today’s changing climate.
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50
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Yao Z, Huang K, Qi Y. Post-exercise Hypothermia Varies Between High- and Low-Altitude Populations in the Asiatic Toad (Bufo gargarizans). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.846663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Whether and how poikilothermic animals change their thermal performance to cope with global warming are crucial questions to predict the future of biodiversity. Intraspecific comparison among populations that occur in different climatic zones can provide insight into how poikilotherms may alter their thermal performance under a particular climatic event. We compared populations of the Asiatic toad (Bufo gargarizans) from two altitudinal zones (3239 and 926 m above sea level) to explore variations of post-exercise hypothermia, which can lead to lower temperature preference than normal conditions. Common garden experiment was also employed to test plasticity of hypothermic performance in adult toads. As results, exhaustive exercise induced measurable reduction in body temperature for both populations. Furthermore, high-altitude population experienced larger reduction in body temperature than low-altitude conspecifics in both original habitat and common garden conditions. Therefore, low-altitude toads may to enhance their hypothermic reaction if they shift their ranges to higher altitudes to survive warming climate; However, the relatively limited plasticity of hypothermic performance may constraint their adaptative process.
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