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Li C, Chen B, Langda S, Pu P, Zhu X, Zhou S, Kalds P, Zhang K, Bhati M, Leonard A, Huang S, Li R, Cuoji A, Wang X, Zhu H, Wu Y, Cuomu R, Gui B, Li M, Wang Y, Li Y, Fang W, Jia T, Pu T, Pan X, Cai Y, He C, Wang L, Jiang Y, Han JL, Chen Y, Zhou P, Pausch H, Wang X. Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae030. [PMID: 39142817 DOI: 10.1093/gpbjnl/qzae030] [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: 09/17/2023] [Revised: 01/09/2024] [Accepted: 02/29/2024] [Indexed: 08/16/2024]
Abstract
Sheep were domesticated in the Fertile Crescent and then spread globally, where they have been encountering various environmental conditions. The Tibetan sheep has adapted to high altitudes on the Qinghai-Tibet Plateau over the past 3000 years. To explore genomic variants associated with high-altitude adaptation in Tibetan sheep, we analyzed Illumina short-reads of 994 whole genomes representing ∼ 60 sheep breeds/populations at varied altitudes, PacBio High fidelity (HiFi) reads of 13 breeds, and 96 transcriptomes from 12 sheep organs. Association testing between the inhabited altitudes and 34,298,967 variants was conducted to investigate the genetic architecture of altitude adaptation. Highly accurate HiFi reads were used to complement the current ovine reference assembly at the most significantly associated β-globin locus and to validate the presence of two haplotypes A and B among 13 sheep breeds. The haplotype A carried two homologous gene clusters: (1) HBE1, HBE2, HBB-like, and HBBC, and (2) HBE1-like, HBE2-like, HBB-like, and HBB; while the haplotype B lacked the first cluster. The high-altitude sheep showed highly frequent or nearly fixed haplotype A, while the low-altitude sheep dominated by haplotype B. We further demonstrated that sheep with haplotype A had an increased hemoglobin-O2 affinity compared with those carrying haplotype B. Another highly associated genomic region contained the EGLN1 gene which showed varied expression between high-altitude and low-altitude sheep. Our results provide evidence that the rapid adaptive evolution of advantageous alleles play an important role in facilitating the environmental adaptation of Tibetan sheep.
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Affiliation(s)
- Chao Li
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- Animal Genomics, ETH Zürich, Zürich 8092, Switzerland
| | - Bingchun Chen
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Suo Langda
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China
| | - Peng Pu
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Xiaojia Zhu
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Shiwei Zhou
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Peter Kalds
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Ke Zhang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Meenu Bhati
- Animal Genomics, ETH Zürich, Zürich 8092, Switzerland
| | | | - Shuhong Huang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Ran Li
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Awang Cuoji
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China
| | - Xiran Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Haolin Zhu
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Yujiang Wu
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China
| | - Renqin Cuomu
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China
| | - Ba Gui
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China
| | - Ming Li
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Yutao Wang
- College of Life and Geographic Sciences, Kashi University, Kashi 844000, China
| | - Yan Li
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Wenwen Fang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Ting Jia
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing 100044, China
| | - Tianchun Pu
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing 100044, China
| | - Xiangyu Pan
- Department of Medical Research, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Yudong Cai
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Chong He
- Key Laboratory of Agricultural Internet of Things, Ministry of Agriculture and Rural Affairs/Shaanxi Key Laboratory of Agricultural Information Perception and Intelligent Service, College of Information Engineering, Northwest A&F University, Yangling 712100, China
| | - Liming Wang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Yu Jiang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Livestock Genetics Program, International Livestock Research Institute, Nairobi 00100, Kenya
| | - Yulin Chen
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Ping Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Hubert Pausch
- Animal Genomics, ETH Zürich, Zürich 8092, Switzerland
| | - Xiaolong Wang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
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2
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Pu P, Niu Z, Ma M, Tang X, Chen Q. Convergent High O 2 Affinity but Distinct ATP-Mediated Allosteric Regulation of Hemoglobins in Oviparous and Viviparous Eremias Lizards from the Qinghai-Tibet Plateau. Animals (Basel) 2024; 14:1440. [PMID: 38791658 PMCID: PMC11117339 DOI: 10.3390/ani14101440] [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: 03/28/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
The functional adaptation and underlying molecular mechanisms of hemoglobins (Hbs) have primarily concentrated on mammals and birds, with few reports on reptiles. This study aimed to investigate the convergent and species-specific high-altitude adaptation mechanisms of Hbs in two Eremias lizards from the Qinghai-Tibet Plateau. The Hbs of high-altitude E. argus and E. multiocellata were characterized by significantly high overall and intrinsic Hb-O2 affinity compared to their low-altitude populations. Despite the similarly low Cl- sensitivities, the Hbs of high-altitude E. argus exhibited higher ATP sensitivity and ATP-dependent Bohr effects than that of E. multiocellata, which could facilitate O2 unloading in respiring tissues. Eremias lizards Hbs exhibited similarly low temperature sensitivities and relatively high Bohr effects at lower temperatures, which could help to stably deliver and release O2 to cold extremities at low temperatures. The oxygenation properties of Hbs in high-altitude populations might be attributed to varying ratios of β2/β1 globin and substitutions on the β2-type globin. Notably, the Asn12Ala in lowland E. argus could cause localized destabilization of the E-helix in the tetrameric Hb by elimination of hydrogen bonds, thereby resulting in its lowest O2 affinity. This study provides a valuable reference for the high-altitude adaptation mechanisms of hemoglobins in reptiles.
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Affiliation(s)
- Peng Pu
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China;
| | - Zhiyi Niu
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, No. 222 Tianshui South Road, Lanzhou 730000, China; (Z.N.); (M.M.); (X.T.)
| | - Ming Ma
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, No. 222 Tianshui South Road, Lanzhou 730000, China; (Z.N.); (M.M.); (X.T.)
| | - Xiaolong Tang
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, No. 222 Tianshui South Road, Lanzhou 730000, China; (Z.N.); (M.M.); (X.T.)
| | - Qiang Chen
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, No. 222 Tianshui South Road, Lanzhou 730000, China; (Z.N.); (M.M.); (X.T.)
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3
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Iverson ENK, Criswell A, Havird JC. Stronger evidence for relaxed selection than adaptive evolution in high-elevation animal mtDNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576402. [PMID: 38328137 PMCID: PMC10849488 DOI: 10.1101/2024.01.20.576402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Mitochondrial (mt) genes are the subject of many adaptive hypotheses due to the key role of mitochondria in energy production and metabolism. One widespread adaptive hypothesis is that selection imposed by life at high elevation leads to the rapid fixation of beneficial alleles in mtDNA, reflected in the increased rates of mtDNA evolution documented in many high-elevation species. However, the assumption that fast mtDNA evolution is caused by positive, rather than relaxed purifying selection has rarely been tested. Here, we calculated the dN/dS ratio, a metric of nonsynonymous substitution bias, and explicitly tested for relaxed selection in the mtDNA of over 700 species of terrestrial vertebrates, freshwater fishes, and arthropods, with information on elevation and latitudinal range limits, range sizes, and body sizes. We confirmed that mitochondrial genomes of high-elevation taxa have slightly higher dN/dS ratios compared to low-elevation relatives. High-elevation species tend to have smaller ranges, which predict higher dN/dS ratios and more relaxed selection across species and clades, while absolute elevation and latitude do not predict higher dN/dS. We also find a positive relationship between body mass and dN/dS, supporting a role for small effective population size leading to relaxed selection. We conclude that higher mt dN/dS among high-elevation species is more likely to reflect relaxed selection due to smaller ranges and reduced effective population size than adaptation to the environment. Our results highlight the importance of rigorously testing adaptive stories against non-adaptive alternative hypotheses, especially in mt genomes.
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Affiliation(s)
- Erik N K Iverson
- Department of Integrative Biology, the University of Texas at Austin, Austin, TX, United States
| | - Abby Criswell
- Department of Integrative Biology, the University of Texas at Austin, Austin, TX, United States
| | - Justin C Havird
- Department of Integrative Biology, the University of Texas at Austin, Austin, TX, United States
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4
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Graham AM, Lavretsky P, Wilson RE, McCracken KG. High-altitude adaptation is accompanied by strong signatures of purifying selection in the mitochondrial genomes of three Andean waterfowl. PLoS One 2024; 19:e0294842. [PMID: 38170710 PMCID: PMC10763953 DOI: 10.1371/journal.pone.0294842] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/09/2023] [Indexed: 01/05/2024] Open
Abstract
Evidence from a variety of organisms points to convergent evolution on the mitochondria associated with a physiological response to oxygen deprivation or temperature stress, including mechanisms for high-altitude adaptation. Here, we examine whether demography and/or selection explains standing mitogenome nucleotide diversity in high-altitude adapted populations of three Andean waterfowl species: yellow-billed pintail (Anas georgica), speckled teal (Anas flavirostris), and cinnamon teal (Spatula cyanoptera). We compared a total of 60 mitogenomes from each of these three duck species (n = 20 per species) across low and high altitudes and tested whether part(s) or all of the mitogenome exhibited expected signatures of purifying selection within the high-altitude populations of these species. Historical effective population sizes (Ne) were inferred to be similar between high- and low-altitude populations of each species, suggesting that selection rather than genetic drift best explains the reduced genetic variation found in mitochondrial genes of high-altitude populations compared to low-altitude populations of the same species. Specifically, we provide evidence that establishment of these three Andean waterfowl species in the high-altitude environment, coincided at least in part with a persistent pattern of negative purifying selection acting on oxidative phosphorylation (OXPHOS) function of the mitochondria. Our results further reveal that the extent of gene-specific purifying selection has been greatest in the speckled teal, the species with the longest history of high-altitude occupancy.
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Affiliation(s)
- Allie M. Graham
- Eccles Institute for Human Genetics, University of Utah, Salt Lake City, UT, United States of America
| | - Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, United States of America
| | - Robert E. Wilson
- School of Natural Resources and Nebraska State Museum, University of Nebraska–Lincoln, Lincoln, NE, United States of America
| | - Kevin G. McCracken
- Department of Biology, University of Miami, Coral Gables, FL, United States of America
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States of America
- Human Genetics and Genomics, University of Miami Miller School of Medicine, Miami, FL, United States of America
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, AK, United States of America
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5
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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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Yan Y, Shi T, Bao X, Gai Y, Liang X, Jiang Y, Li Q. Combined network analysis and interpretable machine learning reveals the environmental adaptations of more than 10,000 ruminant microbial genomes. Front Microbiol 2023; 14:1147007. [PMID: 37799596 PMCID: PMC10548237 DOI: 10.3389/fmicb.2023.1147007] [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: 01/18/2023] [Accepted: 08/28/2023] [Indexed: 10/07/2023] Open
Abstract
Background The ruminant gastrointestinal contains numerous microbiomes that serve a crucial role in sustaining the host's productivity and health. In recent times, numerous studies have revealed that variations in influencing factors, including the environment, diet, and host, contribute to the shaping of gastrointestinal microbial adaptation to specific states. Therefore, understanding how host and environmental factors affect gastrointestinal microbes will help to improve the sustainability of ruminant production systems. Results Based on a graphical analysis perspective, this study elucidates the microbial topology and robustness of the gastrointestinal of different ruminant species, showing that the microbial network is more resistant to random attacks. The risk of transmission of high-risk metagenome-assembled genome (MAG) was also demonstrated based on a large-scale survey of the distribution of antibiotic resistance genes (ARG) in the microbiota of most types of ecosystems. In addition, an interpretable machine learning framework was developed to study the complex, high-dimensional data of the gastrointestinal microbial genome. The evolution of gastrointestinal microbial adaptations to the environment in ruminants were analyzed and the adaptability changes of microorganisms to different altitudes were identified, including microbial transcriptional repair. Conclusion Our findings indicate that the environment has an impact on the functional features of microbiomes in ruminant. The findings provide a new insight for the future development of microbial resources for the sustainable development in agriculture.
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Affiliation(s)
- Yueyang Yan
- Key Laboratory for Zoonoses Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Tao Shi
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xin Bao
- Department of Stomatology, Taian Central Hospital, Tai'an, Shandong, China
| | - Yunpeng Gai
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Xingxing Liang
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qiushi Li
- Key Laboratory for Zoonoses Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
- Department of Stomatology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China
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7
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Li S, Zhang X, Dong X, Guo R, Nan J, Yuan J, Schlebusch CM, Sheng Z. Genetic structure and characteristics of Tibetan chickens. Poult Sci 2023; 102:102767. [PMID: 37321029 PMCID: PMC10404676 DOI: 10.1016/j.psj.2023.102767] [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: 12/06/2022] [Revised: 04/21/2023] [Accepted: 04/28/2023] [Indexed: 06/17/2023] Open
Abstract
Tibetan chicken is one of the most common and widely distributed highland breeds, and is often used as a model organism for understanding genetic adaptation to extreme environments in Tibet. Despite its apparent geographical diversity and large variations in plumage patterns, the genetic differences within breed were not accounted for in most studies and have not been systematically investigated. In order to reveal and genetically differentiate the current existing TBC sub-populations that might have major implications for genomic research in TBCs, we systematically evaluated the population structure and demography of current TBC populations. Based on 344 whole-genome sequenced birds including 115 Tibetan chickens that were mostly sampled from family-farms across Tibet, we revealed a clear separation of Tibetan chickens into 4 sub-populations that broadly aligns with their geographical distribution. Moreover, population structure, population size dynamics, and the extent of admixture jointly suggest complex demographic histories of these sub-populations, including possible multiple origins, inbreeding, and introgressions. While most of the candidate selected regions found between the TBC sub-populations and Red Jungle fowls were nonoverlapping, 2 genes RYR2 and CAMK2D were revealed as strong selection candidates in all 4 sub-populations. These 2 previously identified high altitude associated genes indicated that the sub-populations responded to similar selection pressures in an independent but functionally similar fashion. Our results demonstrate robust population structure in Tibetan chickens that will help inform future genetic analyses on chickens and other domestic animals alike in Tibet, recommending thoughtful experimental design.
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Affiliation(s)
- Shijun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaojian Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinyu Dong
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruiyang Guo
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiuhong Nan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingwei Yuan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Carina M Schlebusch
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Zheya Sheng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
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8
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Cano AV, Gitschlag BL, Rozhoňová H, Stoltzfus A, McCandlish DM, Payne JL. Mutation bias and the predictability of evolution. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220055. [PMID: 37004719 PMCID: PMC10067271 DOI: 10.1098/rstb.2022.0055] [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: 11/01/2022] [Accepted: 02/16/2023] [Indexed: 04/04/2023] Open
Abstract
Predicting evolutionary outcomes is an important research goal in a diversity of contexts. The focus of evolutionary forecasting is usually on adaptive processes, and efforts to improve prediction typically focus on selection. However, adaptive processes often rely on new mutations, which can be strongly influenced by predictable biases in mutation. Here, we provide an overview of existing theory and evidence for such mutation-biased adaptation and consider the implications of these results for the problem of prediction, in regard to topics such as the evolution of infectious diseases, resistance to biochemical agents, as well as cancer and other kinds of somatic evolution. We argue that empirical knowledge of mutational biases is likely to improve in the near future, and that this knowledge is readily applicable to the challenges of short-term prediction. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.
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Affiliation(s)
- Alejandro V. Cano
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Bryan L. Gitschlag
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Hana Rozhoňová
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Arlin Stoltzfus
- Office of Data and Informatics, Material Measurement Laboratory, National Institute of Standards and Technology, Rockville, MD 20899, USA
- Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - David M. McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Joshua L. Payne
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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9
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Yan C, Song MH, Jiang D, Ren JL, Lv Y, Chang J, Huang S, Zaher H, Li JT. Genomic evidence reveals intraspecific divergence of the hot-spring snake (Thermophis baileyi), an endangered reptile endemic to the Qinghai-Tibet plateau. Mol Ecol 2023; 32:1335-1350. [PMID: 36073004 DOI: 10.1111/mec.16687] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 09/04/2022] [Accepted: 09/06/2022] [Indexed: 11/27/2022]
Abstract
Understanding how and why species evolve requires knowledge on intraspecific divergence. In this study, we examined intraspecific divergence in the endangered hot-spring snake (Thermophis baileyi), an endemic species on the Qinghai-Tibet Plateau (QTP). Whole-genome resequencing of 58 sampled individuals from 15 populations was performed to identify the drivers of intraspecific divergence and explore the potential roles of genes under selection. Our analyses resolved three groups, with major intergroup admixture occurring in regions of group contact. Divergence probably occurred during the Pleistocene as a result of glacial climatic oscillations, Yadong-Gulu rift, and geothermal fields differentiation, while complex gene flow between group pairs reflected a unique intraspecific divergence pattern on the QTP. Intergroup fixed loci involved selected genes functionally related to divergence and local adaptation, especially adaptation to hot spring microenvironments in different geothermal fields. Analysis of structural variants, genetic diversity, inbreeding, and genetic load indicated that the hot-spring snake population has declined to a low level with decreased diversity, which is important for the conservation management of this endangered species. Our study demonstrated that the integration of demographic history, gene flow, genomic divergence genes, and other information is necessary to distinguish the evolutionary processes involved in speciation.
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Affiliation(s)
- Chaochao Yan
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Meng-Huan Song
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Dechun Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jin-Long Ren
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yunyun Lv
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jiang Chang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Song Huang
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Hussam Zaher
- Museu de Zoologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Jia-Tang Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.,Mangkang Biodiversity and Ecological Station, Tibet Ecological Safety Monitor Network, Changdu, China
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10
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Hu Y, Wang X, Xu Y, Yang H, Tong Z, Tian R, Xu S, Yu L, Guo Y, Shi P, Huang S, Yang G, Shi S, Wei F. Molecular mechanisms of adaptive evolution in wild animals and plants. SCIENCE CHINA. LIFE SCIENCES 2023; 66:453-495. [PMID: 36648611 PMCID: PMC9843154 DOI: 10.1007/s11427-022-2233-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 08/30/2022] [Indexed: 01/18/2023]
Abstract
Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning. In this study, we reviewed the latest research advances in wild animals and plants, focusing on adaptive traits, convergent evolution, and coevolution. Firstly, we focused on the adaptive evolution of morphological, behavioral, and physiological traits. Secondly, we reviewed the phenotypic convergences of life history traits and responding to environmental pressures, and the underlying molecular convergence mechanisms. Thirdly, we summarized the advances of coevolution, including the four main types: mutualism, parasitism, predation and competition. Overall, these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction, demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies. Finally, we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.
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Affiliation(s)
- Yibo Hu
- CAS Key Lab of Animal Ecology and Conservation Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xiaoping Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Yongchao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hui Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zeyu Tong
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Ran Tian
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China.
| | - Yalong Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Peng Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Shuangquan Huang
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
| | - Guang Yang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Fuwen Wei
- CAS Key Lab of Animal Ecology and Conservation Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
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11
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Enlarged fins of Tibetan catfish provide new evidence of adaptation to high plateau. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-022-2253-7. [PMID: 36802318 DOI: 10.1007/s11427-022-2253-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/30/2022] [Indexed: 02/23/2023]
Abstract
The uplift of the Tibetan Plateau significantly altered the geomorphology and climate of the Euroasia by creating large mountains and rivers. Fishes are more likely to be affected relative to other organisms, as they are largely restricted to river systems. Faced with the rapidly flowing water in the Tibetan Plateau, a group of catfish has evolved greatly enlarged pectoral fins with more numbers of fin-rays to form an adhesive apparatus. However, the genetic basis of these adaptations in Tibetan catfishes remains elusive. In this study, we performed comparative genomic analyses based on the chromosome-level genome of Glyptosternum maculatum in family Sisoridae and detected some proteins with conspicuously high evolutionary rates in particular in genes involved in skeleton development, energy metabolism, and hypoxia response. We found that the hoxd12a gene evolved faster and a loss-of-function assay of hoxd12a supports a potential role for this gene in shaping the enlarged fins of these Tibetan catfishes. Other genes with amino acid replacements and signatures of positive selection included proteins involved in low temperature (TRMU) and hypoxia (VHL) responses. Functional assays reveal that the G. maculatumTRMU allele generates more mitochondrial ATP than the ancestral allele found in low-altitude fishes. Functional assays of VHL alleles suggest that the G. maculatum allele has lower transactivation activity than the low-altitude forms. These findings provide a window into the genomic underpinnings of physiological adaptations that permit G. maculatum to survive in the harsh environment of the Tibetan Himalayas that mirror those that are convergently found in other vertebrates such as humans.
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12
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Liang C, Liu D, Song P, Zhou Y, Yu H, Sun G, Ma X, Yan J. Transcriptomic Analyses Suggest the Adaptation of Bumblebees to High Altitudes. INSECTS 2022; 13:1173. [PMID: 36555083 PMCID: PMC9783775 DOI: 10.3390/insects13121173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Determining the adaptive mechanisms by which bumblebees adapt to high altitudes can help us to better understand their distribution, providing a basis for the future protection and utilization of bumblebee resources. For this study, the adaptive mechanisms of two dominant bumblebee species in the northeastern Qinghai-Tibet Plateau-Bombus kashmirensis and B. waltoni-were studied through transcriptomics methods. For each species, enrichment analysis of the differentially expressed genes and gene set enrichment analysis were carried out between samples collected at different altitudes (4000 m, 4500 m, and 5000 m). The results indicate that these bumblebees tend to up-regulate energy metabolism-related genes when facing extremely high-altitude environments. Of the enriched pathways up-regulated in higher altitudes, the pentose and glucuronate interconversions pathway presented the most severe up-regulation in multiple comparisons of different altitudes for B. kashmirensis, as well as the AMPK signaling pathway, which was found to be up-regulated in both species. Notably, limited by the extreme hypoxic conditions in this study, oxidative phosphorylation was found to be down-regulated with increasing altitude, which is uncommon in studies on bumblebee adaptation to high altitudes.
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Affiliation(s)
- Chengbo Liang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Daoxin Liu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- Kunlun College, Qinghai University, Xining 810016, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China
| | - Pengfei Song
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China
| | - Yuantao Zhou
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Hongyan Yu
- Qinghai Service Guarantee Center of Qilian Mountain National Park, Xining 810001, China
| | - Guo Sun
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Xiaoxuan Ma
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Jingyan Yan
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
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13
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Hu L, Long J, Lin Y, Gu Z, Su H, Dong X, Lin Z, Xiao Q, Batbayar N, Bold B, Deutschová L, Ganusevich S, Sokolov V, Sokolov A, Patel HR, Waters PD, Graves JAM, Dixon A, Pan S, Zhan X. Arctic introgression and chromatin regulation facilitated rapid Qinghai-Tibet Plateau colonization by an avian predator. Nat Commun 2022; 13:6413. [PMID: 36302769 PMCID: PMC9613686 DOI: 10.1038/s41467-022-34138-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 10/14/2022] [Indexed: 12/25/2022] Open
Abstract
The Qinghai-Tibet Plateau (QTP), possesses a climate as cold as that of the Arctic, and also presents uniquely low oxygen concentrations and intense ultraviolet (UV) radiation. QTP animals have adapted to these extreme conditions, but whether they obtained genetic variations from the Arctic during cold adaptation, and how genomic mutations in non-coding regions regulate gene expression under hypoxia and intense UV environment, remain largely unknown. Here, we assemble a high-quality saker falcon genome and resequence populations across Eurasia. We identify female-biased hybridization with Arctic gyrfalcons in the last glacial maximum, that endowed eastern sakers with alleles conveying larger body size and changes in fat metabolism, predisposing their QTP cold adaptation. We discover that QTP hypoxia and UV adaptations mainly involve independent changes in non-coding genomic variants. Our study highlights key roles of gene flow from Arctic relatives during QTP hypothermia adaptation, and cis-regulatory elements during hypoxic response and UV protection.
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Affiliation(s)
- Li Hu
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Juan Long
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Yi Lin
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Zhongru Gu
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Han Su
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Xuemin Dong
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Zhenzhen Lin
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Qian Xiao
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China ,grid.20513.350000 0004 1789 9964Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, 100875 Beijing, China
| | - Nyambayar Batbayar
- Wildlife Science and Conservation Center, Union Building B-802, Ulaanbaatar, 14210 Mongolia
| | - Batbayar Bold
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China ,Wildlife Science and Conservation Center, Union Building B-802, Ulaanbaatar, 14210 Mongolia
| | - Lucia Deutschová
- grid.455051.0Raptor Protection of Slovakia, Trhová 54, SK-841 01, Bratislava, Slovakia
| | - Sergey Ganusevich
- Wild Animal Rescue Centre, Krasnostudencheskiy pr., 21-45, Moscow, 125422 Russia
| | - Vasiliy Sokolov
- grid.426536.00000 0004 1760 306XInstitute of Plant and Animal Ecology, Ural Division Russian Academy of Sciences, 202-8 Marta Street, Ekaterinburg, 620144 Russia
| | - Aleksandr Sokolov
- Arctic Research Station of the Institute of Plant and Animal Ecology, Ural Division Russian Academy of Sciences, 21 Zelenaya Gorka, Labytnangi, Yamalo-Nenetski District 629400 Russia
| | - Hardip R. Patel
- grid.1001.00000 0001 2180 7477The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601 Australia
| | - Paul D. Waters
- grid.1005.40000 0004 4902 0432School of Biotechnology and Biomolecular Science, Faculty of Science, UNSW Sydney, Sydney, NSW 2052 Australia
| | | | - Andrew Dixon
- Emirates Falconers’ Club, Al Mamoura Building (A), P.O. Box 47716, Muroor Road, Abu Dhabi, UAE ,grid.511767.30000 0004 5895 0922International Wildlife Consultants, P.O. Box 19, Carmarthen, SA33 5YL UK
| | - Shengkai Pan
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Xiangjiang Zhan
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China ,grid.9227.e0000000119573309Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223 China
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14
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Highland adaptation of birds on the Qinghai-Tibet Plateau via gut microbiota. Appl Microbiol Biotechnol 2022; 106:6701-6711. [PMID: 36097173 DOI: 10.1007/s00253-022-12171-y] [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: 06/29/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/02/2022]
Abstract
Highland birds evolve multiple adaptive abilities to cope with the harsh environments; however, how they adapt to the high-altitude habitats via the gut microbiota remains understudied. Here we integrated evidences from comparative analysis of gut microbiota to explore the adaptive mechanism of black-necked crane, a typical highland bird in the Qinghai-Tibet Plateau. Firstly, the gut microbiota diversity and function was compared among seven crane species (one high-altitude species and six low-altitude species), and then among three populations of contrasting altitudes for the black-necked crane. Microbiota community diversity in black-necked crane was significantly lower than its low-altitude relatives, but higher microbiota functional diversity was observed in black-necked crane, suggesting that unique bacteria are developed and acquired due to the selection pressure of high-altitude environments. The functional microbial genes differed significantly between the low- and high-altitude black-necked cranes, indicating that altitude significantly impacted microbial communities' composition and structure. Adaptive changes in microbiota diversity and function are observed in response to high-altitude environments. These findings provide us a new insight into the adaptation mechanism to the high-altitude environment for birds via the gut microbiota. KEY POINTS: • The diversity and function of gut microbiota differed significantly between the low- and high-altitude crane species. • Black-necked crane adapts to the high-altitude environment via specific gut microbiota. • Altitude significantly impacted microbial communities' composition and structure.
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15
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Yu JJ, Non AL, Heinrich EC, Gu W, Alcock J, Moya EA, Lawrence ES, Tift MS, O'Brien KA, Storz JF, Signore AV, Khudyakov JI, Milsom WK, Wilson SM, Beall CM, Villafuerte FC, Stobdan T, Julian CG, Moore LG, Fuster MM, Stokes JA, Milner R, West JB, Zhang J, Shyy JY, Childebayeva A, Vázquez-Medina JP, Pham LV, Mesarwi OA, Hall JE, Cheviron ZA, Sieker J, Blood AB, Yuan JX, Scott GR, Rana BK, Ponganis PJ, Malhotra A, Powell FL, Simonson TS. Time Domains of Hypoxia Responses and -Omics Insights. Front Physiol 2022; 13:885295. [PMID: 36035495 PMCID: PMC9400701 DOI: 10.3389/fphys.2022.885295] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 05/24/2022] [Indexed: 02/04/2023] Open
Abstract
The ability to respond rapidly to changes in oxygen tension is critical for many forms of life. Challenges to oxygen homeostasis, specifically in the contexts of evolutionary biology and biomedicine, provide important insights into mechanisms of hypoxia adaptation and tolerance. Here we synthesize findings across varying time domains of hypoxia in terms of oxygen delivery, ranging from early animal to modern human evolution and examine the potential impacts of environmental and clinical challenges through emerging multi-omics approaches. We discuss how diverse animal species have adapted to hypoxic environments, how humans vary in their responses to hypoxia (i.e., in the context of high-altitude exposure, cardiopulmonary disease, and sleep apnea), and how findings from each of these fields inform the other and lead to promising new directions in basic and clinical hypoxia research.
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Affiliation(s)
- James J. Yu
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Amy L. Non
- Department of Anthropology, Division of Social Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Erica C. Heinrich
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, United States
| | - Wanjun Gu
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
- Herbert Wertheim School of Public Health and Longevity Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Joe Alcock
- Department of Emergency Medicine, University of New Mexico, Albuquerque, MX, United States
| | - Esteban A. Moya
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Elijah S. Lawrence
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Michael S. Tift
- Department of Biology and Marine Biology, College of Arts and Sciences, University of North Carolina Wilmington, Wilmington, NC, United States
| | - Katie A. O'Brien
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
- Department of Physiology, Development and Neuroscience, Faculty of Biology, School of Biological Sciences, University of Cambridge, Cambridge, ENG, United Kingdom
| | - Jay F. Storz
- School of Biological Sciences, College of Arts and Sciences, University of Nebraska-Lincoln, Lincoln, IL, United States
| | - Anthony V. Signore
- School of Biological Sciences, College of Arts and Sciences, University of Nebraska-Lincoln, Lincoln, IL, United States
| | - Jane I. Khudyakov
- Department of Biological Sciences, University of the Pacific, Stockton, CA, United States
| | | | - Sean M. Wilson
- Lawrence D. Longo, MD Center for Perinatal Biology, Loma Linda, CA, United States
| | | | | | | | - Colleen G. Julian
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Lorna G. Moore
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Aurora, CO, United States
| | - Mark M. Fuster
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Jennifer A. Stokes
- Department of Kinesiology, Southwestern University, Georgetown, TX, United States
| | - Richard Milner
- San Diego Biomedical Research Institute, San Diego, CA, United States
| | - John B. West
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Jiao Zhang
- Department of Medicine, UC San Diego School of Medicine, San Diego, CA, United States
| | - John Y. Shyy
- Department of Medicine, UC San Diego School of Medicine, San Diego, CA, United States
| | - Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - José Pablo Vázquez-Medina
- Department of Integrative Biology, College of Letters and Science, University of California, Berkeley, Berkeley, CA, United States
| | - Luu V. Pham
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, School of Medicine, Johns Hopkins Medicine, Baltimore, MD, United States
| | - Omar A. Mesarwi
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - James E. Hall
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Zachary A. Cheviron
- Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT, United States
| | - Jeremy Sieker
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Arlin B. Blood
- Department of Pediatrics Division of Neonatology, School of Medicine, Loma Linda University, Loma Linda, CA, United States
| | - Jason X. Yuan
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Graham R. Scott
- Department of Pediatrics Division of Neonatology, School of Medicine, Loma Linda University, Loma Linda, CA, United States
| | - Brinda K. Rana
- Moores Cancer Center, UC San Diego, La Jolla, CA, United States
- Department of Psychiatry, UC San Diego, La Jolla, CA, United States
| | - Paul J. Ponganis
- Center for Marine Biotechnology and Biomedicine, La Jolla, CA, United States
| | - Atul Malhotra
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Frank L. Powell
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Tatum S. Simonson
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
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16
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Bo T, Song G, Tang S, Zhang M, Ma Z, Lv H, Wu Y, Zhang D, Yang L, Wang D, Lei F. Incomplete Concordance Between Host Phylogeny and Gut Microbial Community in Tibetan Wetland Birds. Front Microbiol 2022; 13:848906. [PMID: 35663854 PMCID: PMC9161150 DOI: 10.3389/fmicb.2022.848906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/08/2022] [Indexed: 01/14/2023] Open
Abstract
Gut microbial communities of animals play key roles in host evolution, while the relationship between gut microbiota and host evolution in Tibetan birds remains unknown. Herein, we sequenced the gut microbiota of 67 wild birds of seven species dwelling in the Tibetan wetlands. We found an obvious species-specific structure of gut microbiota among these plateau birds whose habitats were overlapped. Different from plateau mammals, there was no strict synergy between the hierarchical tree of gut microbial community and species phylogeny. In brown-headed gulls (Larus brunnicephalus) as an example, the structure of gut microbiota differed in different habitats, and the relative abundance of bacteria, such as Lactobacillus, Streptococcus, Paracoccus, Lachnospiraceae, and Vibrio, significantly correlated with altitude. Finally, we found various pathogenic bacteria in the birds of these plateau wetlands, and the interspecific differences were related to their diet and living environments.
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Affiliation(s)
- Tingbei Bo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shiyu Tang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mengru Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhiwei Ma
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- School of Ecology and Environment, Anhui Normal University, Wuhu, China
| | - Hongrui Lv
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yun Wu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Le Yang
- Tibet Plateau Institute of Biology, Lhasa, China
| | - Dehua Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, Shandong University, Qingdao, China
- *Correspondence: Dehua Wang,
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Fumin Lei,
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17
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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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18
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Marcondes RS. Celebrating the great avian evolutionary tradition: Review of how birds evolve, by D. J. Futuyma, Princeton & Oxford: Princeton University Press. Evolution 2022; 76:1366-1369. [PMID: 37139913 DOI: 10.1111/evo.14503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/07/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Rafael S. Marcondes
- Museum of Natural Science and Department of Biological Sciences Louisiana State University Baton Rouge LA 70803 USA
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19
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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: 19] [Impact Index Per Article: 9.5] [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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20
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Comparison between short-term stress and long-term adaptive responses reveal common paths to molecular adaptation. iScience 2022; 25:103899. [PMID: 35243257 PMCID: PMC8873613 DOI: 10.1016/j.isci.2022.103899] [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: 10/11/2021] [Revised: 12/12/2021] [Accepted: 02/07/2022] [Indexed: 11/20/2022] Open
Abstract
The phenotypic plasticity in responses to short-term stress can provide clues for understanding the adaptive fixation mechanism of genetic variation during long-term exposure to extreme environments. However, few studies have compared short-term stress responses with long-term evolutionary patterns; in particular, no interactions between the two processes have been evaluated in high-altitude environment. We performed RNA sequencing in embryo fibroblasts derived from great tits and mice to explore transcriptional responses after exposure to simulated high-altitude environmental stresses. Transcriptional changes of genes associated with metabolic pathways were identified in both bird and mice cells after short-term stress responses. Genomic comparisons among long-term highland tits and mammals and their lowland relatives revealed similar pathways (e.g., metabolic pathways) with that initiated under short-term stress transcriptional responses in vitro. These findings highlight the indicative roles of short-term stress in the long-term adaptation, and adopt common paths to molecular adaptation in mouse and bird cells. Short-term stress and long-term adaptations share the common metabolic pathways Phenotypic plasticity can promote adaptive evolution Adopt common paths to molecular adaptation in mouse and bird cells
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21
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Ivy CM, Wearing OH, Natarajan C, Schweizer RM, Gutiérrez-Pinto N, Velotta JP, Campbell-Staton SC, Petersen EE, Fago A, Cheviron ZA, Storz JF, Scott GR. Genetic variation in haemoglobin is associated with evolved changes in breathing in high-altitude deer mice. J Exp Biol 2022; 225:273749. [PMID: 34913467 PMCID: PMC8917448 DOI: 10.1242/jeb.243595] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/09/2021] [Indexed: 01/21/2023]
Abstract
Physiological systems often have emergent properties but the effects of genetic variation on physiology are often unknown, which presents a major challenge to understanding the mechanisms of phenotypic evolution. We investigated whether genetic variants in haemoglobin (Hb) that contribute to high-altitude adaptation in deer mice (Peromyscus maniculatus) are associated with evolved changes in the control of breathing. We created F2 inter-population hybrids of highland and lowland deer mice to test for phenotypic associations of α- and β-globin variants on a mixed genetic background. Hb genotype had expected effects on Hb-O2 affinity that were associated with differences in arterial O2 saturation in hypoxia. However, high-altitude genotypes were also associated with breathing phenotypes that should contribute to enhancing O2 uptake in hypoxia. Mice with highland α-globin exhibited a more effective breathing pattern, with highland homozygotes breathing deeper but less frequently across a range of inspired O2, and this difference was comparable to the evolved changes in breathing pattern in deer mouse populations native to high altitude. The ventilatory response to hypoxia was augmented in mice that were homozygous for highland β-globin. The association of globin variants with variation in breathing phenotypes could not be recapitulated by acute manipulation of Hb-O2 affinity, because treatment with efaproxiral (a synthetic drug that acutely reduces Hb-O2 affinity) had no effect on breathing in normoxia or hypoxia. Therefore, adaptive variation in Hb may have unexpected effects on physiology in addition to the canonical function of this protein in circulatory O2 transport.
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Affiliation(s)
- Catherine M. Ivy
- Department of Biology, McMaster University, Hamilton, ON, Canada, L8S 4K1,Author for correspondence ()
| | - Oliver H. Wearing
- Department of Biology, McMaster University, Hamilton, ON, Canada, L8S 4K1
| | | | - Rena M. Schweizer
- Divison of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | | | - Jonathan P. Velotta
- Divison of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Shane C. Campbell-Staton
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Elin E. Petersen
- Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Angela Fago
- Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Zachary A. Cheviron
- Divison of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Jay F. Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
| | - Graham R. Scott
- Department of Biology, McMaster University, Hamilton, ON, Canada, L8S 4K1
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22
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Wu L, Jiao X, Zhang D, Cheng Y, Song G, Qu Y, Lei F. Comparative Genomics and Evolution of Avian Specialized Traits. Curr Genomics 2021; 22:496-511. [PMID: 35386431 PMCID: PMC8905638 DOI: 10.2174/1389202923666211227143952] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 11/25/2022] Open
Abstract
Genomic data are important for understanding the origin and evolution of traits. Under the context of rapidly developing of sequencing technologies and more widely available genome sequences, researchers are able to study evolutionary mechanisms of traits via comparative genomic methods. Compared with other vertebrates, bird genomes are relatively small and exhibit conserved synteny with few repetitive elements, which makes them suitable for evolutionary studies. Increasing genomic progress has been reported on the evolution of powered flight, body size variation, beak morphology, plumage colouration, high-elevation colonization, migration, and vocalization. By summarizing previous studies, we demonstrate the genetic bases of trait evolution, highlighting the roles of small-scale sequence variation, genomic structural variation, and changes in gene interaction networks. We suggest that future studies should focus on improving the quality of reference genomes, exploring the evolution of regulatory elements and networks, and combining genomic data with morphological, ecological, behavioural, and developmental biology data.
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Affiliation(s)
- Lei Wu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaolu Jiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
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23
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Cheng Y, Miller MJ, Zhang D, Xiong Y, Hao Y, Jia C, Cai T, Li SH, Johansson US, Liu Y, Chang Y, Song G, Qu Y, Lei F. Parallel genomic responses to historical climate change and high elevation in East Asian songbirds. Proc Natl Acad Sci U S A 2021; 118:e2023918118. [PMID: 34873033 PMCID: PMC8685689 DOI: 10.1073/pnas.2023918118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2021] [Indexed: 12/01/2022] Open
Abstract
Parallel evolution can be expected among closely related taxa exposed to similar selective pressures. However, parallelism is typically stronger at the phenotypic level, while genetic solutions to achieve these phenotypic similarities may differ. For polygenic traits, the availability of standing genetic variation (i.e., heterozygosity) may influence such genetic nonparallelism. Here, we examine the extent to which high-elevation adaptation is parallel-and whether the level of parallelism is affected by heterozygosity-by analyzing genomes of 19 Paridae species distributed across East Asia with a dramatic east-west elevation gradient. We find that western highlands endemic parids have consistently lower levels of heterozygosity-likely the result of late-Pleistocene demographic contraction-than do parids found exclusively in eastern lowlands, which remained unglaciated during the late Pleistocene. Three widespread species (east to west) have high levels of heterozygosity similar to that observed in eastern species, although their western populations are less variable than eastern ones. Comparing genomic responses to extreme environments of the Qinghai-Tibet Plateau, we find that the most differentiated genomic regions between each high-elevation taxon and its low-elevation relative are significantly enriched for genes potentially related to the oxygen transport cascade and/or thermogenesis. Despite no parallelism at particular genes, high similarity in gene function is found among comparisons. Furthermore, parallelism is not higher in more heterozygous widespread parids than in highland endemics. Thus, in East Asian parids, parallel functional response to extreme elevation appears to rely on different genes, with differences in heterozygosity having no effect on the degree of genetic parallelism.
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Affiliation(s)
- Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Matthew J Miller
- Reneco International Wildlife Consultants, LLC, Abu Dhabi, UAE
- University of Alaska Museum, University of Alaska Fairbanks, AK
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Xiong
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tianlong Cai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shou-Hsien Li
- Department of Life Sciences, National Taiwan Normal University, Taipei, 116, Taiwan, China
| | - Ulf S Johansson
- Department of Zoology, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
| | - Yang Liu
- State Key Laboratory of Biocontrol, Department of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yongbin Chang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650201, China
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24
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Galván I, Schwartz TS, Garland T. Evolutionary physiology at 30+: Has the promise been fulfilled?: Advances in Evolutionary Physiology: Advances in Evolutionary Physiology. Bioessays 2021; 44:e2100167. [PMID: 34802161 DOI: 10.1002/bies.202100167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 12/19/2022]
Abstract
Three decades ago, interactions between evolutionary biology and physiology gave rise to evolutionary physiology. This caused comparative physiologists to improve their research methods by incorporating evolutionary thinking. Simultaneously, evolutionary biologists began focusing more on physiological mechanisms that may help to explain constraints on and trade-offs during microevolutionary processes, as well as macroevolutionary patterns in physiological diversity. Here we argue that evolutionary physiology has yet to reach its full potential, and propose new avenues that may lead to unexpected advances. Viewing physiological adaptations in wild animals as potential solutions to human diseases offers enormous possibilities for biomedicine. New evidence of epigenetic modifications as mechanisms of phenotypic plasticity that regulate physiological traits may also arise in coming years, which may also represent an overlooked enhancer of adaptation via natural selection to explain physiological evolution. Synergistic interactions at these intersections and other areas will lead to a novel understanding of organismal biology.
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Affiliation(s)
- Ismael Galván
- Department of Evolutionary Ecology, National Museum of Natural Sciences, CSIC, Madrid, Spain
| | - Tonia S Schwartz
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Theodore Garland
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California, USA
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25
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Pu P, Zhao Y, Niu Z, Cao W, Zhang T, He J, Wang J, Tang X, Chen Q. Comparison of hematological traits and oxygenation properties of hemoglobins from highland and lowland Asiatic toad (Bufo gargarizans). J Comp Physiol B 2021; 191:1019-1029. [PMID: 33876256 DOI: 10.1007/s00360-021-01368-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 03/13/2021] [Accepted: 04/07/2021] [Indexed: 01/09/2023]
Abstract
The Asiatic toad (Bufo gargarizans) belonging to the family of Bufonidae (Anura: Amphibia) is successfully residing on the Qinghai-Tibetan Plateau (QTP). To investigate whether the oxygen delivery undergoes adaptive adjustments to high-altitude environments in Asian toads inhabiting the QTP (Zoige County, 3446 m), choosing low-altitude populations (Chengdu City, 500 m) as control, we measured hematological traits, O2 affinities of whole blood, Hb-O2 affinities of purified Hbs, their sensitivities to temperature, and allosteric effectors (H+, Cl- and ATP). Our results showed that high-altitude Asiatic toads possessed significantly increased hemoglobin concentration, hematocrit, and red blood cell count, but significantly decreased erythrocyte volume compared with low-altitude toads. The whole blood and purified Hbs of high-altitude Asiatic toads both exhibited significantly higher O2 affinities compared with low-altitude toads. Substantially increased intrinsic Hb-O2 affinities of high-altitude Asiatic toads Hbs are likely to be the main reason for its elevated Hb-O2 affinities given the anionic cofactor sensitivities of high- and low-altitude toads were similar. The Hbs of high-altitude toads were also characterized by distinctly strong Bohr effects at the low temperature and low-temperature sensitivities. The adaptive adjustments of hematological traits could enhance the blood-O2 carrying capacity of high-altitude Asiatic toads. The increased Hb-O2 affinities could safeguard the pulmonary O2 uploading under hypoxia. The strong Bohr effects at the low temperature could help the release of O2 in metabolic tissues and cold limbs, while low-temperature sensitivity could minimize the effect of temperature fluctuation on the Hb-O2 affinity.
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Affiliation(s)
- Peng Pu
- Department of Animal and Biomedical Sciences, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Yao Zhao
- Department of Animal and Biomedical Sciences, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Zhiyi Niu
- Department of Animal and Biomedical Sciences, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Wangjie Cao
- Department of Animal and Biomedical Sciences, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Tao Zhang
- Department of Animal and Biomedical Sciences, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Jie He
- Department of Animal and Biomedical Sciences, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Jinzhou Wang
- Department of Animal and Biomedical Sciences, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Xiaolong Tang
- Department of Animal and Biomedical Sciences, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Qiang Chen
- Department of Animal and Biomedical Sciences, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, China.
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26
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Nabi G, Xing D, Sun Y, Zhang Q, Li M, Jiang C, Ahmad IM, Wingfield JC, Wu Y, Li D. Coping with extremes: High-altitude sparrows enhance metabolic and thermogenic capacities in the pectoralis muscle and suppress in the liver relative to their lowland counterparts. Gen Comp Endocrinol 2021; 313:113890. [PMID: 34453929 DOI: 10.1016/j.ygcen.2021.113890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 08/01/2021] [Accepted: 08/18/2021] [Indexed: 11/26/2022]
Abstract
Animals living at high altitudes are challenged by the extreme environmental conditions of cold temperature and hypobaric hypoxia. It is not well understood how high-altitude birds enhance the capacity of metabolic thermogenesis and allocate metabolic capacity in different organs to maximize survival in extreme conditions of a cold winter. The Qinghai-Tibet Plateau (QTP) is the largest and highest plateau globally, offering a natural laboratory for investigating coping mechanisms of organisms inhabiting extreme environments. To understand the adaptive strategies in the morphology and physiology of small songbirds on the QTP, we compared plasma triiodothyronine (T3), pectoralis muscle mitochondrial cytochrome c oxidase (COX) and state IV capacities, the expression of peroxisome proliferator-activated receptor γ coactivator α (PGC-1α), adenine nucleotide translocase (ANT), uncoupling protein (UCP), and adenosine monophosphate-dependent kinase (AMPK) α1 mRNA in the pectoralis and liver of Eurasian tree sparrows (Passer montanus) from high-altitude (3,230 m), medium-altitude (1400 m), and low-altitude (80 m) regions. Our results showed that high-altitude sparrows had greater body masses, longer wings and tarsometatarsi, but comparable bill lengths relative to medium- and low-altitude individuals. High-altitude sparrows had higher plasma T3 levels and pectoralis muscle mitochondrial COX capacities than their lowland counterparts. They also upregulated the pectoralis muscle mRNA expression of UCP, PGC-1α, and ANT proteins relative to low-altitude sparrows. Unlike pectoralis, high-altitude sparrows significantly down-regulated hepatic AMPKα1 and ANT protein expression as compared with their lowland counterparts. Our results contribute to understanding the morphological, biochemical, and molecular adaptations in free-living birds to cope with the cold seasons in the extreme environment of the QTP.
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Affiliation(s)
- Ghulam Nabi
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Danning Xing
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Yanfeng Sun
- Ocean College, Hebei Agricultural University, Qinhuangdao, China
| | - Qian Zhang
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Mo Li
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Chuan Jiang
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Ibrahim M Ahmad
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - John C Wingfield
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, CA, USA
| | - Yuefeng Wu
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Dongming Li
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China.
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27
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Yang L, Wang Y, Sun N, Chen J, He S. Genomic and functional evidence reveals convergent evolution in fishes on the Tibetan Plateau. Mol Ecol 2021; 30:5752-5764. [PMID: 34516715 DOI: 10.1111/mec.16171] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 08/18/2021] [Accepted: 09/02/2021] [Indexed: 12/12/2022]
Abstract
High-altitude environments are strong drivers of adaptive evolution in endemic organisms. However, little is known about the genetic mechanisms of convergent adaptation among different lineages, especially in fishes. There are three independent fish groups on the Tibetan Plateau: Tibetan Loaches, Schizothoracine fishes and Glyptosternoid fishes; all are well adapted to the harsh environmental conditions. They represent an excellent example of convergent evolution but with an unclear genetic basis. We used comparative genomic analyses between Tibetan fishes and fishes from low altitudes and detected genomic signatures of convergent evolution in fishes on the Tibetan Plateau. The Tibetan fishes exhibited genome-wide accelerated evolution in comparison with a control set of fishes from low altitudes. A total of 368 positively selected genes were identified in Tibetan fishes, which were enriched in functional categories related to energy metabolism and hypoxia response. Widespread parallel amino acid substitutions were detected among the Tibetan fishes and a subset of these substitutions occurred in positively selected genes associated with high-altitude adaptation. Functional assays suggested that von Hippel-Lindau (VHL) tumour suppressor genes from Tibetan fishes enhance hypoxia-inducible factor (HIF) activity convergently under hypoxia compared to low-altitude fishes. The results provide genomic and functional evidence supporting convergent genetic mechanisms for high-altitude adaptation in fishes on the Tibetan Plateau.
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Affiliation(s)
- Liandong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, China.,Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ying Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, China
| | - Ning Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Juan Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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28
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Mi X, Feng G, Hu Y, Zhang J, Chen L, Corlett RT, Hughes AC, Pimm S, Schmid B, Shi S, Svenning JC, Ma K. The global significance of biodiversity science in China: an overview. Natl Sci Rev 2021; 8:nwab032. [PMID: 34694304 PMCID: PMC8310773 DOI: 10.1093/nsr/nwab032] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 01/03/2021] [Accepted: 02/14/2021] [Indexed: 01/13/2023] Open
Abstract
Biodiversity science in China has seen rapid growth over recent decades, ranging from baseline biodiversity studies to understanding the processes behind evolution across dynamic regions such as the Qinghai-Tibetan Plateau. We review research, including species catalogues; biodiversity monitoring; the origins, distributions, maintenance and threats to biodiversity; biodiversity-related ecosystem function and services; and species and ecosystems' responses to global change. Next, we identify priority topics and offer suggestions and priorities for future biodiversity research in China. These priorities include (i) the ecology and biogeography of the Qinghai-Tibetan Plateau and surrounding mountains, and that of subtropical and tropical forests across China; (ii) marine and inland aquatic biodiversity; and (iii) effective conservation and management to identify and maintain synergies between biodiversity and socio-economic development to fulfil China's vision for becoming an ecological civilization. In addition, we propose three future strategies: (i) translate advanced biodiversity science into practice for biodiversity conservation; (ii) strengthen capacity building and application of advanced technologies, including high-throughput sequencing, genomics and remote sensing; and (iii) strengthen and expand international collaborations. Based on the recent rapid progress of biodiversity research, China is well positioned to become a global leader in biodiversity research in the near future.
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Affiliation(s)
- Xiangcheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Gang Feng
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Yibo Hu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Zhang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Lei Chen
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Richard T Corlett
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, 666303, China
| | - Alice C Hughes
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, 666303, China
| | - Stuart Pimm
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Bernhard Schmid
- Department of Geography, Remote Sensing Laboratories, University of Zurich, Zurich 8057, Switzerland
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jens-Christian Svenning
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE) and Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Keping Ma
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Universityof Chinese Academy of Sciences, Beijing 100049, China
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29
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Lei Y, Yang L, Zhou Y, Wang C, Lv W, Li L, He S. Hb adaptation to hypoxia in high-altitude fishes: Fresh evidence from schizothoracinae fishes in the Qinghai-Tibetan Plateau. Int J Biol Macromol 2021; 185:471-484. [PMID: 34214574 DOI: 10.1016/j.ijbiomac.2021.06.186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/27/2021] [Indexed: 10/21/2022]
Abstract
Uncovering the genetic basis of hypoxic adaptation is one of the most active research areas in evolutionary biology. Among air-breathing vertebrates, modifications of hemoglobin (Hb) play a pivotal role in mediating an adaptive response to high-altitude hypoxia. However, the relative contributions in water-breathing organisms are still unclear. Here, we tested the Hb concentration of fish at different altitudes. All species showed species-specific Hb concentration, which has a non-positive correlation with altitude. Moreover, we investigated the expression of Hb genes by the RNA-seq and quantitative real-time PCR (qRT-PCR), and Hb composition by two-dimensional electrophoresis (2-DE). The results showed that the multiple Hb genes and isoforms are co-expressed in schizothoracinae fishes endemic to the Qinghai-Tibetan Plateau (QTP). Phylogenetic analyses of Hb genes indicated that the evolutionary relationships are not easily reconciled with the organismal phylogeny. Furthermore, evidence of positive selection was found in the Hb genes of schizothoracinae fishes through the selection pressure analysis. We demonstrated that positively selected sites likely facilitated the functional divergence of Hb isoforms. Taken together, this study indicated that the long-term maintenance of high Hb concentration may be a disadvantage for physiologically acclimating to high altitude hypoxia. Meanwhile, the genetically based modification of Hb-O2 affinity in schizothoracinae fishes might facilitate the evolutionary adaptation to Tibetan aqueous environments.
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Affiliation(s)
- Yi Lei
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhou
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenqi Lv
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Li
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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30
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Storz JF, Signore AV. Introgressive Hybridization and Hypoxia Adaptation in High-Altitude Vertebrates. Front Genet 2021; 12:696484. [PMID: 34239546 PMCID: PMC8258166 DOI: 10.3389/fgene.2021.696484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
In natural populations of animals, a growing body of evidence suggests that introgressive hybridization may often serve as an important source of adaptive genetic variation. Population genomic studies of high-altitude vertebrates have provided strong evidence of positive selection on introgressed allelic variants, typically involving a long-term highland species as the donor and a more recently arrived colonizing species as the recipient. In high-altitude humans and canids from the Tibetan Plateau, case studies of adaptive introgression involving the HIF transcription factor, EPAS1, have provided insights into complex histories of ancient introgression, including examples of admixture from now-extinct source populations. In Tibetan canids and Andean waterfowl, directed mutagenesis experiments involving introgressed hemoglobin variants successfully identified causative amino acid mutations and characterized their phenotypic effects, thereby providing insights into the functional properties of selectively introgressed alleles. We review case studies of adaptive introgression in high-altitude vertebrates and we highlight findings that may be of general significance for understanding mechanisms of environmental adaptation involving different sources of genetic variation.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE, United States
| | - Anthony V Signore
- School of Biological Sciences, University of Nebraska, Lincoln, NE, United States
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31
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Xie VC, Pu J, Metzger BP, Thornton JW, Dickinson BC. Contingency and chance erase necessity in the experimental evolution of ancestral proteins. eLife 2021; 10:67336. [PMID: 34061027 PMCID: PMC8282340 DOI: 10.7554/elife.67336] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/30/2021] [Indexed: 12/13/2022] Open
Abstract
The roles of chance, contingency, and necessity in evolution are unresolved because they have never been assessed in a single system or on timescales relevant to historical evolution. We combined ancestral protein reconstruction and a new continuous evolution technology to mutate and select proteins in the B-cell lymphoma-2 (BCL-2) family to acquire protein–protein interaction specificities that occurred during animal evolution. By replicating evolutionary trajectories from multiple ancestral proteins, we found that contingency generated over long historical timescales steadily erased necessity and overwhelmed chance as the primary cause of acquired sequence variation; trajectories launched from phylogenetically distant proteins yielded virtually no common mutations, even under strong and identical selection pressures. Chance arose because many sets of mutations could alter specificity at any timepoint; contingency arose because historical substitutions changed these sets. Our results suggest that patterns of variation in BCL-2 sequences – and likely other proteins, too – are idiosyncratic products of a particular and unpredictable course of historical events. One of the most fundamental and unresolved questions in evolutionary biology is whether the outcomes of evolution are predictable. Is the diversity of life we see today the expected result of organisms adapting to their environment throughout history (also known as natural selection) or the product of random chance? Or did chance events early in history shape the paths that evolution could take next, determining the biological forms that emerged under natural selection much later? These questions are hard to study because evolution happened only once, long ago. To overcome this barrier, Xie, Pu, Metzger et al. developed an experimental approach that can evolve reconstructed ancestral proteins that existed deep in the past. Using this method, it is possible to replay evolution multiple times, from various historical starting points, under conditions similar to those that existed long ago. The end products of the evolutionary trajectories can then be compared to determine how predictable evolution actually is. Xie, Pu, Metzger et al. studied proteins belonging to the BCL-2 family, which originated some 800 million years ago. These proteins have diversified greatly over time in both their genetic sequences and their ability to bind to specific partner proteins called co-regulators. Xie, Pu, Metzger et al. synthesized BCL-2 proteins that existed at various times in the past. Each ancestral protein was then allowed to evolve repeatedly under natural selection to acquire the same co-regulator binding functions that evolved during history. At the end of each evolutionary trajectory, the genetic sequence of the resulting BCL-2 proteins was recorded. This revealed that the outcomes of evolution were almost completely unpredictable: trajectories initiated from the same ancestral protein produced proteins with very different sequences, and proteins launched from different ancestral starting points were even more dissimilar. Further experiments identified the mutations in each trajectory that caused changes in coregulator binding. When these mutations were introduced into other ancestral proteins, they did not yield the same change in function. This suggests that early chance events influenced each protein’s evolution in an unpredictable way by opening and closing the paths available to it in the future. This research expands our understanding of evolution on a molecular level whilst providing a new experimental approach for studying evolutionary drivers in more detail. The results suggest that BCL-2 proteins, in all their various forms, are unique products of a particular, unpredictable course of history set in motion by ancient chance events.
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Affiliation(s)
| | - Jinyue Pu
- Department of Chemistry, University of Chicago, Chicago, United States
| | - Brian Ph Metzger
- Department of Ecology and Evolution, University of Chicago, Chicago, United States
| | - Joseph W Thornton
- Department of Ecology and Evolution, University of Chicago, Chicago, United States.,Department of Human Genetics, University of Chicago, Chicago, United States
| | - Bryan C Dickinson
- Department of Chemistry, University of Chicago, Chicago, United States
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32
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Sendell-Price AT, Ruegg KC, Robertson BC, Clegg SM. An island-hopping bird reveals how founder events shape genome-wide divergence. Mol Ecol 2021; 30:2495-2510. [PMID: 33826187 DOI: 10.1111/mec.15898] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/09/2021] [Accepted: 03/18/2021] [Indexed: 12/16/2022]
Abstract
When populations colonize new areas, both strong selection and strong drift can be experienced due to novel environments and small founding populations, respectively. Empirical studies have predominantly focused on the phenotype when assessing the role of selection, and limited neutral-loci when assessing founder-induced loss of diversity. Consequently, the extent to which processes interact to influence evolutionary trajectories is difficult to assess. Genomic-level approaches provide the opportunity to simultaneously consider these processes. Here, we examine the roles of selection and drift in shaping genomic diversity and divergence in historically documented sequential island colonizations by the silvereye (Zosterops lateralis). We provide the first empirical demonstration of the rapid appearance of highly diverged genomic regions following population founding, the position of which are highly idiosyncratic. As these regions rarely contained loci putatively under selection, it is most likely that these differences arise via the stochastic nature of the founding process. However, selection is required to explain rapid evolution of larger body size in insular silvereyes. Reconciling our genomic data with these phenotypic patterns suggests there may be many genomic routes to the island phenotype, which vary across populations. Finally, we show that accelerated divergence associated with multiple founding steps is the product of genome-wide rather than localized differences, and that diversity erodes due to loss of rare alleles. However, even multiple founder events do not result in divergence and diversity levels seen in evolutionary older subspecies, and therefore do not provide a shortcut to speciation as proposed by founder-effect speciation models.
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Affiliation(s)
- Ashley T Sendell-Price
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
| | - Kristen C Ruegg
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK.,Department of Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Sonya M Clegg
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK.,Environmental Futures Research Institute, Griffith University, Nathan, Qld, Australia
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33
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Qu Y, Chen C, Chen X, Hao Y, She H, Wang M, Ericson PGP, Lin H, Cai T, Song G, Jia C, Chen C, Zhang H, Li J, Liang L, Wu T, Zhao J, Gao Q, Zhang G, Zhai W, Zhang C, Zhang YE, Lei F. The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai-Tibet Plateau. Proc Natl Acad Sci U S A 2021; 118:e2012398118. [PMID: 33753478 PMCID: PMC8020664 DOI: 10.1073/pnas.2012398118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Species in a shared environment tend to evolve similar adaptations under the influence of their phylogenetic context. Using snowfinches, a monophyletic group of passerine birds (Passeridae), we study the relative roles of ancestral and species-specific adaptations to an extreme high-elevation environment, the Qinghai-Tibet Plateau. Our ancestral trait reconstruction shows that the ancestral snowfinch occupied high elevations and had a larger body mass than most nonsnowfinches in Passeridae. Subsequently, this phenotypic adaptation diversified in the descendant species. By comparing high-quality genomes from representatives of the three phylogenetic lineages, we find that about 95% of genes under positive selection in the descendant species are different from those in the ancestor. Consistently, the biological functions enriched for these species differ from those of their ancestor to various degrees (semantic similarity values ranging from 0.27 to 0.5), suggesting that the three descendant species have evolved divergently from the initial adaptation in their common ancestor. Using a functional assay to a highly selective gene, DTL, we demonstrate that the nonsynonymous substitutions in the ancestor and descendant species have improved the repair capacity of ultraviolet-induced DNA damage. The repair kinetics of the DTL gene shows a twofold to fourfold variation across the ancestor and the descendants. Collectively, this study reveals an exceptional case of adaptive evolution to high-elevation environments, an evolutionary process with an initial adaptation in the common ancestor followed by adaptive diversification of the descendant species.
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Affiliation(s)
- Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China;
| | - Chunhai Chen
- BGI Genomics, BGI-Shenzhen, 518084 Shenzhen, China
| | - Xiumin Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Huishang She
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Mengxia Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
| | - Haiyan Lin
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Tianlong Cai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Chunyan Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Hailin Zhang
- BGI Genomics, BGI-Shenzhen, 518084 Shenzhen, China
| | - Jiang Li
- BGI Genomics, BGI-Shenzhen, 518084 Shenzhen, China
| | - Liping Liang
- BGI Genomics, BGI-Shenzhen, 518084 Shenzhen, China
| | - Tianyu Wu
- BGI Genomics, BGI-Shenzhen, 518084 Shenzhen, China
| | - Jinyang Zhao
- BGI Genomics, BGI-Shenzhen, 518084 Shenzhen, China
| | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, 518084 Shenzhen, China
| | - Guojie Zhang
- BGI-Shenzhen, 518083 Shenzhen, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China
| | - Chi Zhang
- BGI Genomics, BGI-Shenzhen, 518084 Shenzhen, China;
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China;
- College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China
- Chinese Institute for Brain Research, 102206 Beijing, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China;
- College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China
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Evolved increases in hemoglobin-oxygen affinity and the Bohr effect coincided with the aquatic specialization of penguins. Proc Natl Acad Sci U S A 2021; 118:2023936118. [PMID: 33753505 PMCID: PMC8020755 DOI: 10.1073/pnas.2023936118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In diving birds like penguins, physiologic considerations suggest that increased hemoglobin (Hb)-O2 affinity may improve pulmonary O2 extraction and enhance dive capacity. We integrated experimental tests on whole-blood and native Hbs of penguins with protein engineering experiments on reconstructed ancestral Hbs. The experiments involving ancestral protein resurrection enabled us to test for evolved changes in Hb function in the stem lineage of penguins after divergence from their closest nondiving relatives. We demonstrate that penguins evolved an increased Hb-O2 affinity in conjunction with a greatly augmented Bohr effect (i.e., reduction in Hb-O2 affinity at low pH) that should maximize pulmonary O2 extraction without compromising O2 delivery at systemic capillaries. Dive capacities of air-breathing vertebrates are dictated by onboard O2 stores, suggesting that physiologic specialization of diving birds such as penguins may have involved adaptive changes in convective O2 transport. It has been hypothesized that increased hemoglobin (Hb)-O2 affinity improves pulmonary O2 extraction and enhances the capacity for breath-hold diving. To investigate evolved changes in Hb function associated with the aquatic specialization of penguins, we integrated comparative measurements of whole-blood and purified native Hb with protein engineering experiments based on site-directed mutagenesis. We reconstructed and resurrected ancestral Hb representing the common ancestor of penguins and the more ancient ancestor shared by penguins and their closest nondiving relatives (order Procellariiformes, which includes albatrosses, shearwaters, petrels, and storm petrels). These two ancestors bracket the phylogenetic interval in which penguin-specific changes in Hb function would have evolved. The experiments revealed that penguins evolved a derived increase in Hb-O2 affinity and a greatly augmented Bohr effect (i.e., reduced Hb-O2 affinity at low pH). Although an increased Hb-O2 affinity reduces the gradient for O2 diffusion from systemic capillaries to metabolizing cells, this can be compensated by a concomitant enhancement of the Bohr effect, thereby promoting O2 unloading in acidified tissues. We suggest that the evolved increase in Hb-O2 affinity in combination with the augmented Bohr effect maximizes both O2 extraction from the lungs and O2 unloading from the blood, allowing penguins to fully utilize their onboard O2 stores and maximize underwater foraging time.
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35
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Moreno JM, Jesus TF, Coelho MM, Sousa VC. Adaptation and convergence in circadian-related genes in Iberian freshwater fish. BMC Ecol Evol 2021; 21:38. [PMID: 33685402 PMCID: PMC7941933 DOI: 10.1186/s12862-021-01767-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 02/16/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The circadian clock is a biological timing system that improves the ability of organisms to deal with environmental fluctuations. At the molecular level it consists of a network of transcription-translation feedback loops, involving genes that activate (bmal and clock - positive loop) and repress expression (cryptochrome (cry) and period (per) - negative loop). This is regulated by daily alternations of light but can also be affected by temperature. Fish, as ectothermic, depend on the environmental temperature and thus are good models to study its integration within the circadian system. Here, we studied the molecular evolution of circadian genes in four Squalius freshwater fish species, distributed across Western Iberian rivers affected by two climatic types with different environmental conditions (e.g., light and temperature). S. carolitertii and S. pyrenaicus inhabit the colder northern region under Atlantic climate type, while S. torgalensis, S. aradensis and some populations of S. pyrenaicus inhabit the warmer southern region affected by summer droughts, under Mediterranean climate type. RESULTS We identified 16 circadian-core genes in the Squalius species using a comparative transcriptomics approach. We detected evidence of positive selection in 12 of these genes using methods based on dN/dS. Positive selection was mainly found in cry and per genes of the negative loop, with 55 putatively adaptive substitutions, 16 located on protein domains. Evidence for positive selection is predominant in southern populations affected by the Mediterranean climate type. By predicting protein features we found that changes at sites under positive selection can impact protein thermostability by changing their aliphatic index and isoelectric point. Additionally, in nine genes, the phylogenetic clustering of species that belong to different clades but inhabit southern basins with similar environmental conditions indicated evolutionary convergence. We found evidence for increased nonsynonymous substitution rate in convergent lineages, likely due to positive selection at 27 sites, mostly in cry genes. CONCLUSIONS Our results support that temperature may be a selective pressure driving the evolution of genes involved in the circadian system. By integrating sequence-based functional protein prediction with dN/dS-based methods to detect selection we uncovered adaptive convergence in the southern populations, probably related to their similar thermal conditions.
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Affiliation(s)
- João M Moreno
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Tiago F Jesus
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Maria M Coelho
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Vitor C Sousa
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.
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Storz JF. High-Altitude Adaptation: Mechanistic Insights from Integrated Genomics and Physiology. Mol Biol Evol 2021; 38:2677-2691. [PMID: 33751123 PMCID: PMC8233491 DOI: 10.1093/molbev/msab064] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Population genomic analyses of high-altitude humans and other vertebrates have identified numerous candidate genes for hypoxia adaptation, and the physiological pathways implicated by such analyses suggest testable hypotheses about underlying mechanisms. Studies of highland natives that integrate genomic data with experimental measures of physiological performance capacities and subordinate traits are revealing associations between genotypes (e.g., hypoxia-inducible factor gene variants) and hypoxia-responsive phenotypes. The subsequent search for causal mechanisms is complicated by the fact that observed genotypic associations with hypoxia-induced phenotypes may reflect second-order consequences of selection-mediated changes in other (unmeasured) traits that are coupled with the focal trait via feedback regulation. Manipulative experiments to decipher circuits of feedback control and patterns of phenotypic integration can help identify causal relationships that underlie observed genotype–phenotype associations. Such experiments are critical for correct inferences about phenotypic targets of selection and mechanisms of adaptation.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
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37
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Effect of NH2-terminal acetylation on the oxygenation properties of vertebrate haemoglobin. Biochem J 2021; 477:3839-3850. [PMID: 32936244 DOI: 10.1042/bcj20200623] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/08/2020] [Accepted: 09/15/2020] [Indexed: 01/07/2023]
Abstract
In vertebrate haemoglobin (Hb), the NH2-terminal residues of the α- and β-chain subunits are thought to play an important role in the allosteric binding of protons (Bohr effect), CO2 (as carbamino derivatives), chloride ions, and organic phosphates. Accordingly, acetylation of the α- and/or β-chain NH2-termini may have significant effects on the oxygenation properties of Hb. Here we investigate the effect of NH2-terminal acetylation by using a newly developed expression plasmid system that enables us to compare recombinantly expressed Hbs that are structurally identical except for the presence or absence of NH2-terminal acetyl groups. Experiments with native and recombinant Hbs of representative vertebrates reveal that NH2-terminal acetylation does not impair the Bohr effect, nor does it significantly diminish responsiveness to allosteric cofactors, such as chloride ions or organic phosphates. These results suggest that observed variation in the oxygenation properties of vertebrate Hbs is principally explained by amino acid divergence in the constituent globin chains rather than post-translational modifications of the globin chain NH2-termini.
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Abstract
Population genomic studies of humans and other animals at high altitude have generated many hypotheses about the genes and pathways that may have contributed to hypoxia adaptation. Future advances require experimental tests of such hypotheses to identify causal mechanisms. Studies to date illustrate the challenge of moving from lists of candidate genes to the identification of phenotypic targets of selection, as it can be difficult to determine whether observed genotype-phenotype associations reflect causal effects or secondary consequences of changes in other traits that are linked via homeostatic regulation. Recent work on high-altitude models such as deer mice has revealed both plastic and evolved changes in respiratory, cardiovascular, and metabolic traits that contribute to aerobic performance capacity in hypoxia, and analyses of tissue-specific transcriptomes have identified changes in regulatory networks that mediate adaptive changes in physiological phenotype. Here we synthesize recent results and discuss lessons learned from studies of high-altitude adaptation that lie at the intersection of genomics and physiology.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588, USA;
| | - Zachary A Cheviron
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA;
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Ivy CM, Scott GR. Life-long exposure to hypoxia affects metabolism and respiratory physiology across life stages in high-altitude deer mice ( Peromyscus maniculatus). ACTA ACUST UNITED AC 2021; 224:jeb.237024. [PMID: 33268530 DOI: 10.1242/jeb.237024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022]
Abstract
Hypoxia exposure can have distinct physiological effects between early developmental and adult life stages, but it is unclear how the effects of hypoxia may progress during continuous exposure throughout life. We examined this issue in deer mice (Peromyscus maniculatus) from a population native to high altitude. Mice were bred in captivity in one of three treatment groups: normoxia (controls), life-long hypoxia (∼12 kPa O2 from conception to adulthood) and parental hypoxia (normoxia from conception to adulthood, but parents previously exposed to hypoxia). Metabolic, thermoregulatory and ventilatory responses to progressive stepwise hypoxia and haematology were then measured at post-natal day (P) 14 and 30 and/or in adulthood. Life-long hypoxia had consistent effects across ages on metabolism, attenuating the declines in O2 consumption rate (V̇ O2 ) and body temperature during progressive hypoxia compared with control mice. However, life-long hypoxia had age-specific effects on breathing, blunting the hypoxia-induced increases in air convection requirement (quotient of total ventilation and V̇ O2 ) at P14 and P30 only, but then shifting breathing pattern towards deeper and/or less frequent breaths at P30 and adulthood. Hypoxia exposure also increased blood-O2 affinity at P14 and P30, in association with an increase in arterial O2 saturation in hypoxia at P30. In contrast, parental hypoxia had no effects on metabolism or breathing, but it increased blood-O2 affinity and decreased red cell haemoglobin content at P14 (but not P30). Therefore, hypoxia exposure has some consistent effects across early life and adulthood, and some other effects that are unique to specific life stages.
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Affiliation(s)
- 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
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40
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Lu B, Jin H, Fu J. Molecular convergent and parallel evolution among four high-elevation anuran species from the Tibetan region. BMC Genomics 2020; 21:839. [PMID: 33246413 PMCID: PMC7694343 DOI: 10.1186/s12864-020-07269-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/23/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To date, evidence for the relative prevalence or rarity of molecular convergent and parallel evolution is conflicting, and understanding of how these processes contribute to adaptation is limited. We compared four high-elevation anuran species (Bufo tibetanus, Nanorana parkeri, Rana kukunoris and Scutiger boulengeri) from the Tibetan region, and examined convergent and parallel amino acid substitutions between them and how they may have contributed to high-elevation adaptation. RESULTS Genomic data of the four high-elevation species and eight of their low-elevation close relatives were gathered. A total of 1098 orthologs shared by all species were identified. We first conducted pairwise comparisons using Zhang and Kumar's test. Then, the Rconv index was calculated and convergence/divergence correlation plotting was conducted. Furthermore, genes under positive selection and with elevated evolutionary rate were examined. We detected a large number of amino acid sites with convergent or parallel substitutions. Several pairs of high-elevation species, in particular, R. kukunoris vs N. parkeri and B. tibetanus vs S. boulengeri, had excessive amounts of convergent substitutions compared to neutral expectation. Nevertheless, these sites were mostly concentrated in a small number of genes (3-32), and no genome-wide convergence was detected. Furthermore, the majority of these convergent genes were neither under detectable positive selection nor had elevated evolutionary rates, although functional prediction analysis suggested some of the convergent genes could potentially contribute to high-elevation adaptation. CONCLUSIONS There is a substantial amount of convergent evolution at the amino-acid level among high-elevation amphibians, although these sites are concentrated in a few genes, not widespread across the genomes. This may attribute to the fact that all the target species are from the same environment. The relative prevalence of convergent substitutions among high-elevation amphibians provides an excellent opportunity for further study of molecular convergent evolution.
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Affiliation(s)
- Bin Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Hong Jin
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Jinzhong Fu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China. .,Department of Integrative Biology, University of Guelph, Guelph, Canada.
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41
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Lei Y, Yang L, Jiang H, Chen J, Sun N, Lv W, He S. Recent genome duplications facilitate the phenotypic diversity of Hb repertoire in the Cyprinidae. SCIENCE CHINA-LIFE SCIENCES 2020; 64:1149-1164. [PMID: 33051703 DOI: 10.1007/s11427-020-1809-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022]
Abstract
Whole-genome duplications (WGDs) are an important contributor to phenotypic innovations in evolutionary history. The diversity of blood oxygen transport traits is the perfect reflection of physiological versatility for evolutionary success among vertebrates. In this study, the evolutionary changes of hemoglobin (Hb) repertoire driven by the recent genome duplications were detected in representative Cyprinidae fish, including eight diploid and four tetraploid species. Comparative genomic analysis revealed a substantial variation in both membership composition and intragenomic organization of Hb genes in these species. Phylogenetic reconstruction analyses were conducted to characterize the evolutionary history of these genes. Data were integrated with the expression profiles of the genes during ontogeny. Our results indicated that genome duplications facilitated the phenotypic diversity of the Hb gene family; each was associated with species-specific changes in gene content via gene loss and fusion after genome duplications. This led to repeated evolutionary transitions in the ontogenic regulation of Hb gene expression. Our results revealed that genome duplications helped to generate phenotypic changes in Cyprinidae Hb systems.
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Affiliation(s)
- Yi Lei
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haifeng Jiang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ning Sun
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenqi Lv
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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42
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Natarajan C, Signore AV, Kumar V, Storz JF. Synthesis of Recombinant Human Hemoglobin With NH 2 -Terminal Acetylation in Escherichia coli. ACTA ACUST UNITED AC 2020; 101:e112. [PMID: 32687676 DOI: 10.1002/cpps.112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The development of new technologies for the efficient expression of recombinant hemoglobin (rHb) is of interest for experimental studies of protein biochemistry and the development of cell-free blood substitutes in transfusion medicine. Expression of rHb in Escherichia coli host cells has numerous advantages, but one disadvantage of using prokaryotic systems to express eukaryotic proteins is that they are incapable of performing post-translational modifications such as NH2 -terminal acetylation. One possible solution is to coexpress additional enzymes that can perform the necessary modifications in the host cells. Here, we report a new method for synthesizing human rHb with proper NH2 -terminal acetylation. Mass spectrometry experiments involving native and recombinant human Hb confirmed the efficacy of the new technique in producing correctly acetylated globin chains. Finally, functional experiments provided insights into the effects of NH2 -terminal acetylation on O2 binding properties. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Gene synthesis and cloning the cassette to the expression plasmid Basic Protocol 2: Selection of E. coli expression strains for coexpression Basic Protocol 3: Large-scale recombinant hemoglobin expression and purification Support Protocol 1: Measuring O2 equilibration curves Support Protocol 2: Mass spectrometry to confirm NH2 -terminal acetylation.
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Affiliation(s)
| | - Anthony V Signore
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska
| | - Vikas Kumar
- Mass Spectrometry and Proteomics Core Facility, University of Nebraska Medical Center, Omaha, Nebraska
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska
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43
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Feijó A, Ge D, Wen Z, Xia L, Yang Q. Divergent adaptations in resource‐use traits explain how pikas thrive on the roof of the world. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13609] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anderson Feijó
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
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44
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Li D, Davis JE, Sun Y, Wang G, Nabi G, Wingfield JC, Lei F. Coping with extremes: convergences of habitat use, territoriality, and diet in summer but divergences in winter between two sympatric snow finches on the Qinghai-Tibet Plateau. Integr Zool 2020; 15:533-543. [PMID: 32627943 DOI: 10.1111/1749-4877.12462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
On the Qinghai-Tibet Plateau, extreme environmental conditions have imposed intense selective pressure on the evolution of phenotypic traits of wild animals. To date, limited information is available on behavioral and ecological traits concerning niche differentiation among sympatric animals on the Qinghai-Tibet Plateau, especially during winter when the environments are most severe. Here, we studied the seasonal variations in habitat occurrence, territorial behavior, and diet in two sympatric snow finches (the white-rumped snow finch, Onychostruthus taczanowskii, WRSF; and the rufous-necked snow finch, Pyrgilauda ruficollis, RNSF) to determine convergence and divergence of ecological traits in such severe climatic conditions. Our results showed that: (i) WRSF occupied rural areas as a dominant species throughout the annual cycle while RNSF occupied the rural areas in summer and then shifted to human-occupied areas in winter and spring; (ii) WRSFs exhibited robust aggressive behavior and territoriality during winter relative to RNSFs; (iii) the diets of both species varied with the season but did not vary between species except that WRSF ate significantly more seeds but RNSF consumed more starchy material derived from human food waste during winter. Therefore, the separations in the spatial niche and territoriality between WRSF and RNSF, especially in winter, may contribute to alleviating the pressure of interspecific competition, and promoting the coexistence of the two sympatric snow finches in the extreme environments on the Qinghai-Tibet Plateau.
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Affiliation(s)
- Dongming Li
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei Province, China.,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Department of Neurobiology, Physiology and Behavior, University of California, Davis, California, USA
| | - Jason E Davis
- Department of Biology, Radford University, Radford, Virginia, USA
| | - Yanfeng Sun
- Ocean College, Hebei Agricultural University, Qinhuangdao, Hebei Province, China
| | - Gang Wang
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, California, USA
| | - Ghulam Nabi
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei Province, China
| | - John C Wingfield
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, California, USA
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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45
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Signore AV, Storz JF. Biochemical pedomorphosis and genetic assimilation in the hypoxia adaptation of Tibetan antelope. SCIENCE ADVANCES 2020; 6:eabb5447. [PMID: 32596473 PMCID: PMC7299627 DOI: 10.1126/sciadv.abb5447] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/11/2020] [Indexed: 05/17/2023]
Abstract
Developmental shifts in stage-specific gene expression can provide a ready mechanism of phenotypic change by altering the rate or timing of ontogenetic events. We found that the high-altitude Tibetan antelope (Panthelops hodgsonii) has evolved an adaptive increase in blood-O2 affinity by truncating the ancestral ontogeny of globin gene expression such that a high-affinity juvenile hemoglobin isoform (isoHb) completely supplants the lower-affinity isoHb that is expressed in the adult red blood cells of other bovids. This juvenilization of blood properties represents a canalization of an acclimatization response to hypoxia that has been well documented in adult goats and sheep. We also found the genomic mechanism underlying this regulatory isoHb switch, revealing how a reversible acclimatization response became genetically assimilated as an irreversible adaptation to chronic hypoxia.
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Affiliation(s)
- Anthony V. Signore
- University of Nebraska, School of Biological Sciences, Lincoln, NE 68588, USA
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46
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Wang W, Wang F, Hao R, Wang A, Sharshov K, Druzyaka A, Lancuo Z, Shi Y, Feng S. First de novo whole genome sequencing and assembly of the bar-headed goose. PeerJ 2020; 8:e8914. [PMID: 32292659 PMCID: PMC7144584 DOI: 10.7717/peerj.8914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 03/15/2020] [Indexed: 12/23/2022] Open
Abstract
Background The bar-headed goose (Anser indicus) mainly inhabits the plateau wetlands of Asia. As a specialized high-altitude species, bar-headed geese can migrate between South and Central Asia and annually fly twice over the Himalayan mountains along the central Asian flyway. The physiological, biochemical and behavioral adaptations of bar-headed geese to high-altitude living and flying have raised much interest. However, to date, there is still no genome assembly information publicly available for bar-headed geese. Methods In this study, we present the first de novo whole genome sequencing and assembly of the bar-headed goose, along with gene prediction and annotation. Results 10X Genomics sequencing produced a total of 124 Gb sequencing data, which can cover the estimated genome size of bar-headed goose for 103 times (average coverage). The genome assembly comprised 10,528 scaffolds, with a total length of 1.143 Gb and a scaffold N50 of 10.09 Mb. Annotation of the bar-headed goose genome assembly identified a total of 102 Mb (8.9%) of repetitive sequences, 16,428 protein-coding genes, and 282 tRNAs. In total, we determined that there were 63 expanded and 20 contracted gene families in the bar-headed goose compared with the other 15 vertebrates. We also performed a positive selection analysis between the bar-headed goose and the closely related low-altitude goose, swan goose (Anser cygnoides), to uncover its genetic adaptations to the Qinghai-Tibetan Plateau. Conclusion We reported the currently most complete genome sequence of the bar-headed goose. Our assembly will provide a valuable resource to enhance further studies of the gene functions of bar-headed goose. The data will also be valuable for facilitating studies of the evolution, population genetics and high-altitude adaptations of the bar-headed geese at the genomic level.
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Affiliation(s)
- Wen Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xi'ning, Qinghai, China
| | - Fang Wang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xi'ning, Qinghai, China
| | - Rongkai Hao
- Novogene Bioinformatics Institute, Beijing, China
| | - Aizhen Wang
- College of Eco-Environmental Engineering, Qinghai University, Xi'ning, Qinghai, China
| | - Kirill Sharshov
- Research Institute of Experimental and Clinical Medicine, Novosibirsk, Russia
| | - Alexey Druzyaka
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Zhuoma Lancuo
- School of Finance and Economics, Qinghai University, Xi'ning, Qinghai, China
| | - Yuetong Shi
- KunLun College of Qinghai University, Xi'ning, Qinghai, China
| | - Shuo Feng
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xi'ning, Qinghai, China
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47
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DuBay SG, Wu Y, Scott GR, Qu Y, Liu Q, Smith JH, Xin C, Hart Reeve A, Juncheng C, Meyer D, Wang J, Johnson J, Cheviron ZA, Lei F, Bates J. Life history predicts flight muscle phenotype and function in birds. J Anim Ecol 2020; 89:1262-1276. [PMID: 32124424 DOI: 10.1111/1365-2656.13190] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 12/19/2019] [Indexed: 11/30/2022]
Abstract
Functional traits are the essential phenotypes that underlie an organism's life history and ecology. Although biologists have long recognized that intraspecific variation is consequential to an animals' ecology, studies of functional variation are often restricted to species-level comparisons, ignoring critical variation within species. In birds, interspecific comparisons have been foundational in connecting flight muscle phenotypes to species-level ecology, but intraspecific variation has remained largely unexplored. We asked how age- and sex-dependent demands on flight muscle function are reconciled in birds. The flight muscle is an essential multifunctional organ, mediating a large range of functions associated with powered flight and thermoregulation. These functions must be balanced over an individual's lifetime. We leveraged within- and between-species comparisons in a clade of small passerines (Tarsiger bush-robins) from the eastern edge of the Qinghai-Tibet Plateau. We integrated measurements of flight muscle physiology, morphology, behaviour, phenology and environmental data, analysing trait data within a context of three widespread, adaptive life-history strategies-sexual dichromatism, age and sex-structured migration, and delayed plumage maturation. This approach provides a framework of the selective forces that shape functional variation within and between species. We found more variation in flight muscle traits within species than has been previously described between species of birds under 20 g. This variation was associated with the discovery of mixed muscle fibre types (i.e. both fast glycolytic and fast oxidative fibres), which differ markedly in their physiological and functional attributes. This result is surprising given that the flight muscles of small birds are generally thought to contain only fast oxidative fibres, suggesting a novel ecological context for glycolytic muscle fibres in small birds. Within each species, flight muscle phenotypes varied by age and sex, reflecting the functional demands at different life-history stages and the pressures that individuals face as a result of their multi-class identity (i.e. species, age and sex). Our findings reveal new links between avian physiology, ecology, behaviour and life history, while demonstrating the importance of demographic-dependent selection in shaping functional phenotypic variation.
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Affiliation(s)
- Shane G DuBay
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL, USA.,Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA
| | - Yongjie Wu
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Graham R Scott
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qiao Liu
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, China
| | - Joel H Smith
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Chao Xin
- Laboratory of Molecular Evolution and Molecular Phylogeny, College of Life Sciences, Shannxi Normal University, Xi'an, China
| | - Andrew Hart Reeve
- Biosystematics Section, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Chen Juncheng
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Dylan Meyer
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Jing Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jacob Johnson
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Zachary A Cheviron
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - John Bates
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA
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48
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Qu Y, Chen C, Xiong Y, She H, Zhang YE, Cheng Y, DuBay S, Li D, Ericson PGP, Hao Y, Wang H, Zhao H, Song G, Zhang H, Yang T, Zhang C, Liang L, Wu T, Zhao J, Gao Q, Zhai W, Lei F. Rapid phenotypic evolution with shallow genomic differentiation during early stages of high elevation adaptation in Eurasian Tree Sparrows. Natl Sci Rev 2019; 7:113-127. [PMID: 34692022 PMCID: PMC8289047 DOI: 10.1093/nsr/nwz138] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 08/31/2019] [Accepted: 09/01/2019] [Indexed: 02/06/2023] Open
Abstract
Abstract
Known as the ‘third polar region’, the Qinghai-Tibet Plateau represents one of the harshest highland environments in the world and yet a number of organisms thrive there. Previous studies of birds, animals and humans have focused on well-differentiated populations in later stages of phenotypic divergence. The adaptive processes during the initial phase of highland adaptation remain poorly understood. We studied a human commensal, the Eurasian Tree Sparrow, which has followed human agriculture to the Qinghai-Tibet Plateau. Despite strong phenotypic differentiation at multiple levels, in particular in muscle-related phenotypes, highland and lowland populations show shallow genomic divergence and the colonization event occurred within the past few thousand years. In a one-month acclimation experiment investigating phenotypic plasticity, we exposed adult lowland tree sparrows to a hypoxic environment and did not observe muscle changes. Through population genetic analyses, we identified a signature of polygenic adaptation, whereby shifts in allele frequencies are spread across multiple loci, many of which are associated with muscle-related processes. Our results reveal a case of positive selection in which polygenic adaptation appears to drive rapid phenotypic evolution, shedding light on early stages of adaptive evolution to a novel environment.
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Affiliation(s)
- Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunhai Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen 518084, China
| | - Ying Xiong
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huishang She
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shane DuBay
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637, USA
- Life Sciences Section, Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA
| | - Dongming Li
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongyuan Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Hongfeng Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hailin Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518084, China
| | - Ting Yang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Chi Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518084, China
| | - Liping Liang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518084, China
| | - Tianyu Wu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518084, China
| | - Jinyang Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen 518084, China
| | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen 518084, China
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Human Genetics, Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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49
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Storz JF, Scott GR. Life Ascending: Mechanism and Process in Physiological Adaptation to High-Altitude Hypoxia. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2019; 50:503-526. [PMID: 33033467 DOI: 10.1146/annurev-ecolsys-110218-025014] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
To cope with the reduced availability of O2 at high altitude, air-breathing vertebrates have evolved myriad adjustments in the cardiorespiratory system to match tissue O2 delivery with metabolic O2 demand. We explain how changes at interacting steps of the O2 transport pathway contribute to plastic and evolved changes in whole-animal aerobic performance under hypoxia. In vertebrates native to high altitude, enhancements of aerobic performance under hypoxia are attributable to a combination of environmentally induced and evolved changes in multiple steps of the pathway. Additionally, evidence suggests that many high-altitude natives have evolved mechanisms for attenuating maladaptive acclimatization responses to hypoxia, resulting in counter-gradient patterns of altitudinal variation for key physiological phenotypes. For traits that exhibit counteracting environmental and genetic effects, evolved changes in phenotype may be cryptic under field conditions and can only be revealed by rearing representatives of high-and low-altitude populations under standardized environmental conditions to control for plasticity.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588, USA
| | - Graham R Scott
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
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50
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Rey C, Lanore V, Veber P, Guéguen L, Lartillot N, Sémon M, Boussau B. Detecting adaptive convergent amino acid evolution. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180234. [PMID: 31154974 PMCID: PMC6560273 DOI: 10.1098/rstb.2018.0234] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2019] [Indexed: 11/12/2022] Open
Abstract
In evolutionary genomics, researchers have taken an interest in identifying substitutions that subtend convergent phenotypic adaptations. This is a difficult question that requires distinguishing foreground convergent substitutions that are involved in the convergent phenotype from background convergent substitutions. Those may be linked to other adaptations, may be neutral or may be the consequence of mutational biases. Furthermore, there is no generally accepted definition of convergent substitutions. Various methods that use different definitions have been proposed in the literature, resulting in different sets of candidate foreground convergent substitutions. In this article, we first describe the processes that can generate foreground convergent substitutions in coding sequences, separating adaptive from non-adaptive processes. Second, we review methods that have been proposed to detect foreground convergent substitutions in coding sequences and expose the assumptions that underlie them. Finally, we examine their power on simulations of convergent changes-including in the presence of a change in the efficacy of selection-and on empirical alignments. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Carine Rey
- ENS de Lyon, CNRS UMR 5239, INSERM U1210, LBMC, Univ Lyon, Université Claude Bernard Lyon 1, F-69007 Lyon, France
| | - Vincent Lanore
- CNRS UMR 5558, LBBE, Univ Lyon, Université Claude Bernard Lyon 1, F-69100 Villeurbanne, France
| | - Philippe Veber
- CNRS UMR 5558, LBBE, Univ Lyon, Université Claude Bernard Lyon 1, F-69100 Villeurbanne, France
| | - Laurent Guéguen
- CNRS UMR 5558, LBBE, Univ Lyon, Université Claude Bernard Lyon 1, F-69100 Villeurbanne, France
| | - Nicolas Lartillot
- CNRS UMR 5558, LBBE, Univ Lyon, Université Claude Bernard Lyon 1, F-69100 Villeurbanne, France
| | - Marie Sémon
- ENS de Lyon, CNRS UMR 5239, INSERM U1210, LBMC, Univ Lyon, Université Claude Bernard Lyon 1, F-69007 Lyon, France
| | - Bastien Boussau
- CNRS UMR 5558, LBBE, Univ Lyon, Université Claude Bernard Lyon 1, F-69100 Villeurbanne, France
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