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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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Cao Y, Zeng T, Han W, Ma X, Gu T, Chen L, Tian Y, Xu W, Yin J, Li G, Lu L, Gun S. Comparative analysis of liver transcriptome reveals adaptive responses to hypoxia environmental condition in Tibetan chicken. Anim Biosci 2024; 37:28-38. [PMID: 37641844 PMCID: PMC10766467 DOI: 10.5713/ab.23.0126] [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: 04/05/2023] [Revised: 05/25/2023] [Accepted: 07/11/2023] [Indexed: 08/31/2023] Open
Abstract
OBJECTIVE Tibetan chickens, which have unique adaptations to extreme high-altitude environments, exhibit phenotypic and physiological characteristics that are distinct from those of lowland chickens. However, the mechanisms underlying hypoxic adaptation in the liver of chickens remain unknown. METHODS RNA-sequencing (RNA-Seq) technology was used to assess the differentially expressed genes (DEGs) involved in hypoxia adaptation in highland chickens (native Tibetan chicken [HT]) and lowland chickens (Langshan chicken [LS], Beijing You chicken [BJ], Qingyuan Partridge chicken [QY], and Chahua chicken [CH]). RESULTS A total of 352 co-DEGs were specifically screened between HT and four native lowland chicken breeds. Gene ontology and Kyoto encyclopedia of genes and genomes enrichment analyses indicated that these co-DEGs were widely involved in lipid metabolism processes, such as the peroxisome proliferator-activated receptors (PPAR) signaling pathway, fatty acid degradation, fatty acid metabolism and fatty acid biosynthesis. To further determine the relationship from the 352 co-DEGs, protein-protein interaction network was carried out and identified eight genes (ACSL1, CPT1A, ACOX1, PPARC1A, SCD, ACSBG2, ACACA, and FASN) as the potential regulating genes that are responsible for the altitude difference between the HT and other four lowland chicken breeds. CONCLUSION This study provides novel insights into the molecular mechanisms regulating hypoxia adaptation via lipid metabolism in Tibetan chickens and other highland animals.
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Affiliation(s)
- Yongqing Cao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070,
China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
| | - Tao Zeng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
| | - Wei Han
- Jiangsu Institute of Poultry Science, Yangzhou 225125,
China
- Technology Innovation Co., Ltd., Jiangsu Institute of Poultry Science, Yangzhou 211412,
China
| | - Xueying Ma
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy Agricultural and Animal Husbandry Sciences, Lhasa 850004,
China
| | - Tiantian Gu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
| | - Li Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
- China-Ukraine Joint Research Center for Protection, Exploitation and Utilization of Poultry Germplasm Resources, Hangzhou 310021,
China
| | - Yong Tian
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
| | - Wenwu Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
| | - Jianmei Yin
- Jiangsu Institute of Poultry Science, Yangzhou 225125,
China
- Technology Innovation Co., Ltd., Jiangsu Institute of Poultry Science, Yangzhou 211412,
China
| | - Guohui Li
- Jiangsu Institute of Poultry Science, Yangzhou 225125,
China
- Technology Innovation Co., Ltd., Jiangsu Institute of Poultry Science, Yangzhou 211412,
China
| | - Lizhi Lu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070,
China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
- China-Ukraine Joint Research Center for Protection, Exploitation and Utilization of Poultry Germplasm Resources, Hangzhou 310021,
China
| | - Shuangbao Gun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070,
China
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Sun Y, Hao Y, Zhang Q, Liu X, Wang L, Li J, Li M, Li D. Coping with extremes: Alternations in diet, gut microbiota, and hepatic metabolic functions in a highland passerine. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167079. [PMID: 37714349 DOI: 10.1016/j.scitotenv.2023.167079] [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: 06/26/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/17/2023]
Abstract
In wild animals, diet and gut microbiota interactions are critical moderators of metabolic functions and are highly contingent on habitat conditions. Challenged by the extreme conditions of high-altitude environments, the strategies implemented by highland animals to adjust their diet and gut microbial composition and modulate their metabolic substrates remain largely unexplored. By employing a typical human commensal species, the Eurasian tree sparrow (Passer montanus, ETS), as a model species, we studied the differences in diet, digestive tract morphology and enzyme activity, gut microbiota, and metabolic energy profiling between highland (the Qinghai-Tibet Plateau, QTP; 3230 m) and lowland (Shijiazhuang, Hebei; 80 m) populations. Our results showed that highland ETSs had enlarged digestive organs and longer small intestinal villi, while no differences in key digestive enzyme activities were observed between the two populations. The 18S rRNA sequencing results revealed that the dietary composition of highland ETSs were more animal-based and less plant-based than those of the lowland ones. Furthermore, 16S rRNA sequencing results suggested that the intestinal microbial communities were structurally segregated between populations. PICRUSt metagenome predictions further indicated that the expression patterns of microbial genes involved in material and energy metabolism, immune system and infection, and xenobiotic biodegradation were strikingly different between the two populations. Analysis of liver metabolomics revealed significant metabolic differences between highland and lowland ETSs in terms of substrate utilization, as well as distinct sex-specific alterations in glycerophospholipids. Furthermore, the interplay between diet, liver metabolism, and gut microbiota suggests a dietary shift resulting in corresponding changes in gut microbiota and metabolic functions. Our findings indicate that highland ETSs have evolved to optimize digestion and absorption, rely on more protein-rich foods, and possess gut microbiota tailored to their dietary composition, likely adaptive physiological and ecological strategies adopted to cope with extreme highland environments.
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Affiliation(s)
- Yanfeng Sun
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China; Ocean College, Hebei Agricultural University, Qinhuangdao 066003, China; Hebei Collaborative Innovation Center for Eco-Environment, Hebei Normal University, Shijiazhuang 050024, China
| | - Yaotong Hao
- Ocean College, Hebei Agricultural University, Qinhuangdao 066003, China
| | - Qian Zhang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Xu Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Limin Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Juyong Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Mo Li
- College of Life Sciences, Cangzhou Normal University, Cangzhou 061001, China.
| | - Dongming Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China; Hebei Collaborative Innovation Center for Eco-Environment, Hebei Normal University, Shijiazhuang 050024, China.
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Li W, Chen Y, Zhang Y, Zhao N, Zhang W, Shi M, Zhao Y, Cai C, Lu C, Gao P, Guo X, Li B, Kim SW, Yang Y, Cao G. Transcriptome Analysis Revealed Potential Genes of Skeletal Muscle Thermogenesis in Mashen Pigs and Large White Pigs under Cold Stress. Int J Mol Sci 2023; 24:15534. [PMID: 37958518 PMCID: PMC10650474 DOI: 10.3390/ijms242115534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
Pigs are susceptible to cold stress due to the absence of brown fat caused by the partial deletion of uncoupling protein 1 during their evolution. Some local pig breeds in China exhibit potential cold adaptability, but research has primarily focused on fat and intestinal tissues. Skeletal muscle plays a key role in adaptive thermogenesis in mammals, yet the molecular mechanism of cold adaptation in porcine skeletal muscle remains poorly understood. This study investigated the cold adaptability of two pig breeds, Mashen pigs (MS) and Large White pigs (LW), in a four-day cold (4 °C) or normal temperature (25 °C) environment. We recorded phenotypic changes and collected blood and longissimus dorsi muscle for transcriptome sequencing. Finally, the PRSS8 gene was randomly selected for functional exploration in porcine skeletal muscle satellite cells. A decrease in body temperature and body weight in both LW and MS pigs under cold stress, accompanied by increased shivering frequency and respiratory frequency, were observed. However, the MS pigs demonstrated stable physiological homeostasis, indicating a certain level of cold adaptability. The LW pigs primarily responded to cold stress by regulating their heat production and glycolipid energy metabolism. The MS pigs exhibited a distinct response to cold stress, involving the regulation of heat production, energy metabolism pathways, and robust mitochondrial activity, as well as a stronger immune response. Furthermore, the functional exploration of PRSS8 in porcine skeletal muscle satellite cells revealed that it affected cellular energy metabolism and thermogenesis by regulating ERK phosphorylation. These findings shed light on the diverse transcriptional responses of skeletal muscle in LW and MS pigs under cold stress, offering valuable insights into the molecular mechanisms underlying cold adaptation in pigs.
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Affiliation(s)
- Wenxia Li
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (W.L.)
| | - Yufen Chen
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (W.L.)
| | - Yunting Zhang
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (W.L.)
| | - Ning Zhao
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (W.L.)
| | - Wanfeng Zhang
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (W.L.)
| | - Mingyue Shi
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (W.L.)
| | - Yan Zhao
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (W.L.)
| | - Chunbo Cai
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (W.L.)
| | - Chang Lu
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (W.L.)
| | - Pengfei Gao
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (W.L.)
| | - Xiaohong Guo
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (W.L.)
| | - Bugao Li
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (W.L.)
| | - Sung-Woo Kim
- Department of Animal Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Yang Yang
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (W.L.)
| | - Guoqing Cao
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (W.L.)
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Zhang Q, Li M, Yin Y, Ge S, Li D, Ahmad IM, Nabi G, Sun Y, Luo X, Li D. Physiological but not morphological adjustments along latitudinal gradients in a human commensal species, the Eurasian tree sparrow. Integr Zool 2023; 18:891-905. [PMID: 36880561 DOI: 10.1111/1749-4877.12709] [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] [Indexed: 03/08/2023]
Abstract
Human commensal species take advantage of anthropogenic conditions that are less likely to be challenged by the selective pressures of natural environments. Their morphological and physiological phenotypes can therefore dissociate from habitat characteristics. Understanding how these species adjust their morphological and physiological traits across latitudinal gradients is fundamental to uncovering the eco-physiological strategies underlying coping mechanisms. Here, we studied morphological traits in breeding Eurasian tree sparrows (ETSs; Passer montanus) among low-latitude (Yunnan and Hunan) and middle-latitude (Hebei) localities in China. We then compared body mass; lengths of bill, tarsometatarsus, wing, total body, and tail feather; and baseline and capture stress-induced levels of plasma corticosterone (CORT) and the metabolites including glucose (Glu), total triglyceride (TG), free fatty acid (FFA), total protein, and uric acid (UA). None of the measured morphological parameters varied with latitude except in the Hunan population, which demonstrated longer bills than those in other populations. Stress-induced CORT levels significantly exceeded baseline levels and decreased with increasing latitude, but total integrated CORT levels did not vary with latitude. Capture stress-induced significantly increased Glu levels and decreased TG levels, independent of site. However, the Hunan population had significantly higher baseline CORT, baseline and stress-induced FFA levels, but lower UA levels, which differed from other populations. Our results suggest that rather than morphological adjustments, physiological adjustments are mainly involved in coping mechanisms for middle-latitude adaptation in ETSs. It is worth investigating whether other avian species also exhibit such dissociation from external morphological designs while depending on physiological adjustments.
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Affiliation(s)
- Qian Zhang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaborative Innovation Center for Eco-Environment, Hebei Normal University, Shijiazhuang, China
| | - Mo Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaborative Innovation Center for Eco-Environment, Hebei Normal University, Shijiazhuang, China
| | - Yuan Yin
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaborative Innovation Center for Eco-Environment, Hebei Normal University, Shijiazhuang, China
| | - Shiyong Ge
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaborative Innovation Center for Eco-Environment, Hebei Normal University, Shijiazhuang, China
| | - Danjie Li
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Faculty of Biodiversity and Conservation, Southwest Forestry University, Kunming, China
| | - Ibrahim M Ahmad
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaborative Innovation Center for Eco-Environment, Hebei Normal University, Shijiazhuang, China
| | - Ghulam Nabi
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaborative Innovation Center for Eco-Environment, Hebei Normal University, Shijiazhuang, China
| | - Yanfeng Sun
- Ocean College, Hebei Agricultural University, Qinhuangdao, China
| | - Xu Luo
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Faculty of Biodiversity and Conservation, Southwest Forestry University, Kunming, China
| | - Dongming Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaborative Innovation Center for Eco-Environment, Hebei Normal University, Shijiazhuang, China
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