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Blumstein D, MacManes M. The multi-tissue gene expression and physiological responses of water deprived Peromyscus eremicus. BMC Genomics 2024; 25:770. [PMID: 39118009 PMCID: PMC11308687 DOI: 10.1186/s12864-024-10629-z] [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: 03/06/2024] [Accepted: 07/17/2024] [Indexed: 08/10/2024] Open
Abstract
The harsh and dry conditions of desert environments have resulted in genomic adaptations, allowing for desert organisms to withstand prolonged drought, extreme temperatures, and limited food resources. Here, we present a comprehensive exploration of gene expression across five tissues (kidney, liver, lung, gastrointestinal tract, and hypothalamus) and 19 phenotypic measurements to explore the whole-organism physiological and genomic response to water deprivation in the desert-adapted cactus mouse (Peromyscus eremicus). The findings encompass the identification of differentially expressed genes and correlative analysis between phenotypes and gene expression patterns across multiple tissues. Specifically, we found robust activation of the vasopressin renin-angiotensin-aldosterone system (RAAS) pathways, whose primary function is to manage water and solute balance. Animals reduced food intake during water deprivation, and upregulation of PCK1 highlights the adaptive response to reduced oral intake via its actions aimed at maintained serum glucose levels. Even with such responses to maintain water balance, hemoconcentration still occurred, prompting a protective downregulation of genes responsible for the production of clotting factors while simultaneously enhancing angiogenesis which is thought to maintain tissue perfusion. In this study, we elucidate the complex mechanisms involved in water balance in the desert-adapted cactus mouse, P. eremicus. By prioritizing a comprehensive analysis of whole-organism physiology and multi-tissue gene expression in a simulated desert environment, we describe the complex response of regulatory processes.
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Affiliation(s)
- Danielle Blumstein
- Biomedical Sciences Department, University of New Hampshire, Molecular, Cellular, Durham, NH, DMB, 03824, USA.
| | - Matthew MacManes
- Biomedical Sciences Department, University of New Hampshire, Molecular, Cellular, Durham, NH, DMB, 03824, USA
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2
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Li Z, Fang B, Dong P, Shan W. Selective sweep analysis of the adaptability of the Yarkand hare (Lepus yarkandensis) to hot arid environments using SLAF-seq. Anim Genet 2024; 55:681-686. [PMID: 38722026 DOI: 10.1111/age.13440] [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: 03/06/2023] [Revised: 03/06/2024] [Accepted: 04/22/2024] [Indexed: 07/04/2024]
Abstract
The Yarkand hare (Lepus yarkandensis) inhabits arid desert areas and is endemic to China. It has evolved various adaptations to survive in hot arid environments, including stress responses, the ability to maintain water homeostasis and heat tolerance. Here, we performed a selective sweep analysis to identify the candidate genes for adaptation to hot arid environments in the Yarkand hare. A total of 397 237 single-nucleotide polymorphisms were obtained from 80 Yarkand hares, which inhabit hot arid environments, and 36 Tolai hares (Lepus tolai), which inhabit environments with a mild climate, via specific-locus amplified fragment sequencing. We identified several candidate genes that were associated with the heat stress response (HSPE1), oxidative stress response (SLC23A and GLRX2), immune response (IL1R1 and IRG1), central nervous system development (FGF13, THOC2, FMR1 and MECP2) and regulation of water homeostasis (CDK1) according to fixation index values and θπ ratios in the selective sweep analysis, and six of these genes (GLRX2, IRG1, FGF13, FMR1, MECP2 and CDK1) are newly discovered genes. To the best of our knowledge, this is the first study to identify candidate genes for adaptation to hot arid environments in the Yarkand hare. The results of this study enhance our understanding of the adaptation of the Yarkand hare to hot arid environments and will aid future studies aiming to functionally verify these candidate genes.
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Affiliation(s)
- Zurui Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Bingwa Fang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Pengcheng Dong
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Wenjuan Shan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
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Blumstein DM, MacManes MD. Impacts of dietary fat on multi tissue gene expression in the desert-adapted cactus mouse. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592397. [PMID: 38746252 PMCID: PMC11092757 DOI: 10.1101/2024.05.03.592397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Understanding the relationship between dietary fat and physiological responses is crucial in species adapted to arid environments where water scarcity is common. In this study, we present a comprehensive exploration of gene expression across five tissues (kidney, liver, lung, gastrointestinal tract, and hypothalamus) and 19 phenotypic measurements, investigating the effects of dietary fat in the desert-adapted cactus mouse ( Peromyscus eremicus ). We show impacts on immune function, circadian gene regulation, and mitochondrial function for mice fed a lower-fat diet compared to mice fed a higher-fat diet. In arid environments with severe water scarcity, even subtle changes in organismal health and water balance can affect physical performance, potentially impacting survival and reproductive success. The study sheds light on the complex interplay between diet, physiological processes, and environmental adaptation, providing valuable insights into the multifaceted impacts of dietary choices on organismal well-being and adaptation strategies in arid habitats.
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Blumstein DM, MacManes MD. When the tap runs dry: The multi-tissue gene expression and physiological responses of water deprived Peromyscus eremicus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576658. [PMID: 38328088 PMCID: PMC10849551 DOI: 10.1101/2024.01.22.576658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The harsh and dry conditions of desert environments have resulted in genomic adaptations, allowing for desert organisms to withstand prolonged drought, extreme temperatures, and limited food resources. Here, we present a comprehensive exploration of gene expression across five tissues (kidney, liver, lung, gastrointestinal tract, and hypothalamus) and 19 phenotypic measurements to explore the whole-organism physiological and genomic response to water deprivation in the desert-adapted cactus mouse (Peromyscus eremicus). The findings encompass the identification of differentially expressed genes and correlative analysis between phenotypes and gene expression patterns across multiple tissues. Specifically, we found robust activation of the vasopressin renin-angiotensin-aldosterone system (RAAS) pathways, whose primary function is to manage water and solute balance. Animals reduce food intake during water deprivation, and upregulation of PCK1 highlights the adaptive response to reduced oral intake via its actions aimed at maintained serum glucose levels. Even with such responses to maintain water balance, hemoconcentration still occurred, prompting a protective downregulation of genes responsible for the production of clotting factors while simultaneously enhancing angiogenesis which is thought to maintains tissue perfusion. In this study, we elucidate the complex mechanisms involved in water balance in the desert-adapted cactus mouse, P. eremicus. By prioritizing a comprehensive analysis of whole-organism physiology and multi-tissue gene expression in a simulated desert environment, we describe the complex and successful response of regulatory processes.
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Affiliation(s)
- Danielle M Blumstein
- University of New Hampshire, Molecular, Cellular, and Biomedical Sciences Department, Durham, NH 03824
| | - Matthew D MacManes
- University of New Hampshire, Molecular, Cellular, and Biomedical Sciences Department, Durham, NH 03824
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5
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Blumstein DM, MacManes MD. When the tap runs dry: the physiological effects of acute experimental dehydration in Peromyscus eremicus. J Exp Biol 2023; 226:jeb246386. [PMID: 37921453 PMCID: PMC10714145 DOI: 10.1242/jeb.246386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/12/2023] [Indexed: 11/04/2023]
Abstract
Desert organisms have evolved physiological, biochemical and genomic mechanisms to survive the extreme aridity of desert environments. Studying desert-adapted species provides a unique opportunity to investigate the survival strategies employed by organisms in some of the harshest habitats on Earth. Two of the primary challenges faced in desert environments are maintaining water balance and thermoregulation. We collected data in a simulated desert environment and a captive colony of cactus mice (Peromyscus eremicus) and used lab-based experiments with real time physiological measurements; energy expenditure, water loss rate and respiratory exchange rate, to characterize the response to water deprivation. Mice without access to water had significantly lower energy expenditures and in turn, reduced water loss compared to mice with access to water after the first 24 h of the experiment. Additionally, we observed significant mass loss that is probably due to dehydration-associated anorexia a response to limit fluid loss by reducing waste and the solute load as well as allowing water reabsorption from the kidneys and gastrointestinal tract. Finally, we observed body temperature correlated with sex, with males without access to water maintaining body temperature when compared with hydrated males, whereas body temperature decreased for females without access to water, suggesting daily metabolic depression in females.
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Affiliation(s)
- Danielle M. Blumstein
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Matthew D. MacManes
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
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Peng X, Cheng J, Li H, Feijó A, Xia L, Ge D, Wen Z, Yang Q. Whole-genome sequencing reveals adaptations of hairy-footed jerboas (Dipus, Dipodidae) to diverse desert environments. BMC Biol 2023; 21:182. [PMID: 37649052 PMCID: PMC10469962 DOI: 10.1186/s12915-023-01680-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/10/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND Environmental conditions vary among deserts across the world, spanning from hyper-arid to high-elevation deserts. However, prior genomic studies on desert adaptation have focused on desert and non-desert comparisons overlooking the complexity of conditions within deserts. Focusing on the adaptation mechanisms to diverse desert environments will advance our understanding of how species adapt to extreme desert environments. The hairy-footed jerboas are well adapted to diverse desert environments, inhabiting high-altitude arid regions, hyper-arid deserts, and semi-deserts, but the genetic basis of their adaptation to different deserts remains unknown. RESULTS Here, we sequenced the whole genome of 83 hairy-footed jerboas from distinct desert zones in China to assess how they responded under contrasting conditions. Population genomics analyses reveal the existence of three species in hairy-footed jerboas distributed in China: Dipus deasyi, Dipus sagitta, and Dipus sowerbyi. Analyses of selection between high-altitude desert (elevation ≥ 3000m) and low-altitude desert (< 500m) populations identified two strongly selected genes, ATR and HIF1AN, associated with intense UV radiation and hypoxia in high-altitude environments. A number of candidate genes involved in energy and water homeostasis were detected in the comparative genomic analyses of hyper-arid desert (average annual precipitation < 70mm) and arid desert (< 200mm) populations versus semi-desert (> 360mm) populations. Hyper-arid desert animals also exhibited stronger adaptive selection in energy homeostasis, suggesting water and resource scarcity may be the main drivers of desert adaptation in hairy-footed jerboas. CONCLUSIONS Our study challenges the view of deserts as homogeneous environments and shows that distinct genomic adaptations can be found among desert animals depending on their habitats.
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Affiliation(s)
- Xingwen Peng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, 100049, China
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Hong Li
- Novogene Bioinformatics Institute, Haidian District, Beijing, 100083, China
| | - Anderson Feijó
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, 60605, USA
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China.
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Blumstein DM, MacManes MD. When the tap runs dry: The physiological effects of acute experimental dehydration in Peromyscus eremicus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.03.547568. [PMID: 37461486 PMCID: PMC10349944 DOI: 10.1101/2023.07.03.547568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Desert organisms have evolved physiological, biochemical, and genomic mechanisms to survive the extreme aridity of desert environments. Studying desert-adapted species provides a unique opportunity to investigate the survival strategies employed by organisms in some of the harshest habitats on Earth. Two of the primary challenges faced in desert environments are maintaining water balance and thermoregulation. We collected data in a simulated desert environment and a captive colony of cactus mice (Peromyscus eremicus) and used lab-based experiments with real time physiological measurements to characterize the response to water-deprivation. Mice without access to water had significantly lower energy expenditures and in turn, reduced water loss compared to mice with access to water after the first 24 hours of the experiment. Additionally, we observed significant weight loss likely related to dehydration-associated anorexia a response to limit fluid loss by reducing waste and the solute load as well as allowing water reabsorption from the kidneys and gastrointestinal tract. Finally, we observed body temperature correlated with sex, with males without access to water maintaining body temperature when compared to hydrated males while body temperature decreased for females without access to water compared to hydrated, suggesting daily torpor in females.
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Affiliation(s)
- Danielle M Blumstein
- University of New Hampshire, Molecular, Cellular, and Biomedical Sciences Department, Durham, NH 03824
| | - Matthew D MacManes
- University of New Hampshire, Molecular, Cellular, and Biomedical Sciences Department, Durham, NH 03824
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8
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Sørensen EF, Harris RA, Zhang L, Raveendran M, Kuderna LFK, Walker JA, Storer JM, Kuhlwilm M, Fontsere C, Seshadri L, Bergey CM, Burrell AS, Bergman J, Phillips-Conroy JE, Shiferaw F, Chiou KL, Chuma IS, Keyyu JD, Fischer J, Gingras MC, Salvi S, Doddapaneni H, Schierup MH, Batzer MA, Jolly CJ, Knauf S, Zinner D, Farh KKH, Marques-Bonet T, Munch K, Roos C, Rogers J. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons. Science 2023; 380:eabn8153. [PMID: 37262153 DOI: 10.1126/science.abn8153] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 09/27/2022] [Indexed: 06/03/2023]
Abstract
Baboons (genus Papio) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically and genetically distinct phylogenetic species. We used high-coverage whole-genome sequences from 225 wild baboons representing 19 geographic localities to investigate population genomics and interspecies gene flow. Our analyses provide an expanded picture of evolutionary reticulation among species and reveal patterns of population structure within and among species, including differential admixture among conspecific populations. We describe the first example of a baboon population with a genetic composition that is derived from three distinct lineages. The results reveal processes, both ancient and recent, that produced the observed mismatch between phylogenetic relationships based on matrilineal, patrilineal, and biparental inheritance. We also identified several candidate genes that may contribute to species-specific phenotypes.
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Affiliation(s)
- Erik F Sørensen
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Liye Zhang
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lukas F K Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Artificial Intelligence Lab, Illumina Inc., San Diego, CA 92122, USA
| | - Jerilyn A Walker
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | | | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030 Vienna, Austria
| | - Claudia Fontsere
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Lakshmi Seshadri
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Christina M Bergey
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Andrew S Burrell
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Jane E Phillips-Conroy
- Department of Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | - Kenneth L Chiou
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | | | | | - Julia Fischer
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37077 Göttingen, Germany
| | - Marie-Claude Gingras
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sejal Salvi
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harshavardhan Doddapaneni
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
| | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Clifford J Jolly
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37077 Göttingen, Germany
| | - Kyle K-H Farh
- Artificial Intelligence Lab, Illumina Inc., San Diego, CA 92122, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluis Companys, 23, 08010 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Baldiri i Reixac 4, 08028 Barcelona, Spain
- Institut Catala de Paleontologia Miquel Crusafont, Universitat Autonoma de Barcelona, Edifici ICTA-ICP, cl Columnes s/n, 08193 Cerdanyola del Valles, Barcelona, Spain
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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9
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Sørensen EF, Harris RA, Zhang L, Raveendran M, Kuderna LFK, Walker JA, Storer JM, Kuhlwilm M, Fontsere C, Seshadri L, Bergey CM, Burrell AS, Bergmann J, Phillips-Conroy JE, Shiferaw F, Chiou KL, Chuma IS, Keyyu JD, Fischer J, Gingras MC, Salvi S, Doddapaneni H, Schierup MH, Batzer MA, Jolly CJ, Knauf S, Zinner D, Farh KKH, Marques-Bonet T, Munch K, Roos C, Rogers J. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539112. [PMID: 37205419 PMCID: PMC10187195 DOI: 10.1101/2023.05.02.539112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Baboons (genus Papio ) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically and genetically distinct phylogenetic species. We used high coverage whole genome sequences from 225 wild baboons representing 19 geographic localities to investigate population genomics and inter-species gene flow. Our analyses provide an expanded picture of evolutionary reticulation among species and reveal novel patterns of population structure within and among species, including differential admixture among conspecific populations. We describe the first example of a baboon population with a genetic composition that is derived from three distinct lineages. The results reveal processes, both ancient and recent, that produced the observed mismatch between phylogenetic relationships based on matrilineal, patrilineal, and biparental inheritance. We also identified several candidate genes that may contribute to species-specific phenotypes. One-Sentence Summary Genomic data for 225 baboons reveal novel sites of inter-species gene flow and local effects due to differences in admixture.
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10
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Cheng J, Peng X, Li H, Feijó A, Xia L, Shenbrot GI, Ge D, Wen Z, Wang D, Yang Q. Similar adaptative mechanism but divergent demographic history of four sympatric desert rodents in Eurasian inland. Commun Biol 2023; 6:33. [PMID: 36635382 PMCID: PMC9837166 DOI: 10.1038/s42003-023-04415-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 01/03/2023] [Indexed: 01/13/2023] Open
Abstract
Phenotypes associated with metabolism and water retention are thought to be key to the adaptation of desert species. However, knowledge on the genetic changes and selective regimes on the similar and divergent ways to desert adaptation in sympatric and phylogenetically close desert organisms remains limited. Here, we generate a chromosome level genome assembly for Northern three-toed jerboa (Dipus sagitta) and three other high-quality genome assemblies for Siberian jerboa (Orientallactaga sibirica), Midday jird (Meriones meridianus), and Desert hamster (Phodopus roborovskii). Genomic analyses unveil that desert adaptation of the four species mainly result from similar metabolic pathways, such as arachidonic acid metabolism, thermogenesis, oxidative phosphorylation, insulin related pathway, DNA repair and protein synthesis and degradation. However, the specific evolved genes in the same adaptative molecular pathway often differ in the four species. We also reveal similar niche selection but different demographic histories and sensitivity to climate changes, which may be related to the diversified genomic adaptative features. In addition, our study suggests that nocturnal rodents have evolved some specific adaptative mechanism to desert environments compared to large desert animals. Our genomic resources will provide an important foundation for further research on desert genetic adaptations.
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Affiliation(s)
- Jilong Cheng
- grid.9227.e0000000119573309Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101 China
| | - Xingwen Peng
- grid.9227.e0000000119573309Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419College of Life Sciences, University of Chinese Academy of Sciences, Shijingshan District, Beijing, 100049 China
| | - Hong Li
- grid.410753.4Novogene Bioinformatics Institute, Beijing, 100083 China
| | - Anderson Feijó
- grid.9227.e0000000119573309Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101 China
| | - Lin Xia
- grid.9227.e0000000119573309Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101 China
| | - Georgy I. Shenbrot
- grid.7489.20000 0004 1937 0511Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Negev, 84990 Israel
| | - Deyan Ge
- grid.9227.e0000000119573309Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101 China
| | - Zhixin Wen
- grid.9227.e0000000119573309Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101 China
| | - Dehua Wang
- grid.9227.e0000000119573309State Key Lab of Integrated management for Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101 China
| | - Qisen Yang
- grid.9227.e0000000119573309Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101 China
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11
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Tigano A, Khan R, Omer AD, Weisz D, Dudchenko O, Multani AS, Pathak S, Behringer RR, Aiden EL, Fisher H, MacManes MD. Chromosome size affects sequence divergence between species through the interplay of recombination and selection. Evolution 2022; 76:782-798. [PMID: 35271737 PMCID: PMC9314927 DOI: 10.1111/evo.14467] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 12/12/2021] [Indexed: 01/21/2023]
Abstract
The structure of the genome shapes the distribution of genetic diversity and sequence divergence. To investigate how the relationship between chromosome size and recombination rate affects sequence divergence between species, we combined empirical analyses and evolutionary simulations. We estimated pairwise sequence divergence among 15 species from three different mammalian clades-Peromyscus rodents, Mus mice, and great apes-from chromosome-level genome assemblies. We found a strong significant negative correlation between chromosome size and sequence divergence in all species comparisons within the Peromyscus and great apes clades but not the Mus clade, suggesting that the dramatic chromosomal rearrangements among Mus species may have masked the ancestral genomic landscape of divergence in many comparisons. Our evolutionary simulations showed that the main factor determining differences in divergence among chromosomes of different sizes is the interplay of recombination rate and selection, with greater variation in larger populations than in smaller ones. In ancestral populations, shorter chromosomes harbor greater nucleotide diversity. As ancestral populations diverge, diversity present at the onset of the split contributes to greater sequence divergence in shorter chromosomes among daughter species. The combination of empirical data and evolutionary simulations revealed that chromosomal rearrangements, demography, and divergence times may also affect the relationship between chromosome size and divergence, thus deepening our understanding of the role of genome structure in the evolution of species divergence.
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Affiliation(s)
- Anna Tigano
- Molecular, Cellular, and Biomedical Sciences DepartmentUniversity of New HampshireDurhamNH03824USA,Hubbard Center for Genome StudiesUniversity of New HampshireDurhamNH03824USA,Current address: Department of BiologyUniversity of British Columbia – Okanagan CampusKelownaBCV1 V 1V7Canada
| | - Ruqayya Khan
- The Center for Genome ArchitectureDepartment of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
| | - Arina D. Omer
- The Center for Genome ArchitectureDepartment of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
| | - David Weisz
- The Center for Genome ArchitectureDepartment of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
| | - Olga Dudchenko
- The Center for Genome ArchitectureDepartment of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA,Department of Computer ScienceDepartment of Computational and Applied MathematicsRice UniversityHoustonTX77030USA
| | - Asha S. Multani
- Department of GeneticsM.D. Anderson Cancer CenterUniversity of TexasHoustonTX77030USA
| | - Sen Pathak
- Department of GeneticsM.D. Anderson Cancer CenterUniversity of TexasHoustonTX77030USA
| | - Richard R. Behringer
- Department of GeneticsM.D. Anderson Cancer CenterUniversity of TexasHoustonTX77030USA
| | - Erez L. Aiden
- The Center for Genome ArchitectureDepartment of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA,Department of Computer ScienceDepartment of Computational and Applied MathematicsRice UniversityHoustonTX77030USA,Center for Theoretical and Biological PhysicsRice UniversityHoustonTX77030USA,Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China,School of Agriculture and EnvironmentUniversity of Western AustraliaPerthWA6009Australia
| | - Heidi Fisher
- Department of BiologyUniversity of MarylandCollege ParkMD20742USA
| | - Matthew D. MacManes
- Molecular, Cellular, and Biomedical Sciences DepartmentUniversity of New HampshireDurhamNH03824USA,Hubbard Center for Genome StudiesUniversity of New HampshireDurhamNH03824USA
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12
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Mallatt J, Feinberg TE. Multiple Routes to Animal Consciousness: Constrained Multiple Realizability Rather Than Modest Identity Theory. Front Psychol 2021; 12:732336. [PMID: 34630245 PMCID: PMC8497802 DOI: 10.3389/fpsyg.2021.732336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/13/2021] [Indexed: 11/13/2022] Open
Abstract
The multiple realizability thesis (MRT) is an important philosophical and psychological concept. It says any mental state can be constructed by multiple realizability (MR), meaning in many distinct ways from different physical parts. The goal of our study is to find if the MRT applies to the mental state of consciousness among animals. Many things have been written about MRT but the ones most applicable to animal consciousness are by Shapiro in a 2004 book called The Mind Incarnate and by Polger and Shapiro in their 2016 work, The Multiple Realization Book. Standard, classical MRT has been around since 1967 and it says that a mental state can have very many different physical realizations, in a nearly unlimited manner. To the contrary, Shapiro's book reasoned that physical, physiological, and historical constraints force mental traits to evolve in just a few, limited directions, which is seen as convergent evolution of the associated neural traits in different animal lineages. This is his mental constraint thesis (MCT). We examined the evolution of consciousness in animals and found that it arose independently in just three animal clades-vertebrates, arthropods, and cephalopod mollusks-all of which share many consciousness-associated traits: elaborate sensory organs and brains, high capacity for memory, directed mobility, etc. These three constrained, convergently evolved routes to consciousness fit Shapiro's original MCT. More recently, Polger and Shapiro's book presented much the same thesis but changed its name from MCT to a "modest identity thesis." Furthermore, they argued against almost all the classically offered instances of MR in animal evolution, especially against the evidence of neural plasticity and the differently expanded cerebrums of mammals and birds. In contrast, we argue that some of these classical examples of MR are indeed valid and that Shapiro's original MCT correction of MRT is the better account of the evolution of consciousness in animal clades. And we still agree that constraints and convergence refute the standard, nearly unconstrained, MRT.
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Affiliation(s)
- Jon Mallatt
- The University of Washington WWAMI Medical Education Program at The University of Idaho, Moscow, ID, United States
| | - Todd E Feinberg
- Department of Psychiatry and Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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13
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Colella JP, Blumstein DM, MacManes MD. Disentangling environmental drivers of circadian metabolism in desert-adapted mice. J Exp Biol 2021; 224:jeb242529. [PMID: 34495305 PMCID: PMC8502254 DOI: 10.1242/jeb.242529] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/13/2021] [Indexed: 01/21/2023]
Abstract
Metabolism is a complex phenotype shaped by natural environmental rhythms, as well as behavioral, morphological and physiological adaptations. Metabolism has been historically studied under constant environmental conditions, but new methods of continuous metabolic phenotyping now offer a window into organismal responses to dynamic environments, and enable identification of abiotic controls and the timing of physiological responses relative to environmental change. We used indirect calorimetry to characterize metabolic phenotypes of the desert-adapted cactus mouse (Peromyscus eremicus) in response to variable environmental conditions that mimic their native environment versus those recorded under constant warm and constant cool conditions, with a constant photoperiod and full access to resources. We found significant sexual dimorphism, with males being more prone to dehydration than females. Under circadian environmental variation, most metabolic shifts occurred prior to physical environmental change and the timing was disrupted under both constant treatments. The ratio of CO2 produced to O2 consumed (the respiratory quotient) reached greater than 1.0 only during the light phase under diurnally variable conditions, a pattern that strongly suggests that lipogenesis contributes to the production of energy and endogenous water. Our results are consistent with historical descriptions of circadian torpor in this species (torpid by day, active by night), but reject the hypothesis that torpor is initiated by food restriction or negative water balance.
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Affiliation(s)
| | | | - Matthew D. MacManes
- University of New Hampshire, Department of Molecular, Cellular, and Biomedical Sciences, Durham, NH 03824, USA
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14
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Rocha JL, Godinho R, Brito JC, Nielsen R. Life in Deserts: The Genetic Basis of Mammalian Desert Adaptation. Trends Ecol Evol 2021; 36:637-650. [PMID: 33863602 DOI: 10.1016/j.tree.2021.03.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/13/2022]
Abstract
Deserts are among the harshest environments on Earth. The multiple ages of different deserts and their global distribution provide a unique opportunity to study repeated adaptation at different timescales. Here, we summarize recent genomic research on the genetic mechanisms underlying desert adaptations in mammals. Several studies on different desert mammals show large overlap in functional classes of genes and pathways, consistent with the complexity and variety of phenotypes associated with desert adaptation to water and food scarcity and extreme temperatures. However, studies of desert adaptation are also challenged by a lack of accurate genotype-phenotype-environment maps. We encourage development of systems that facilitate functional analyses, but also acknowledge the need for more studies on a wider variety of desert mammals.
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Affiliation(s)
- Joana L Rocha
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal.
| | - Raquel Godinho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal; Department of Zoology, University of Johannesburg, PO Box 534, Auckland Park 2006, South Africa
| | - José C Brito
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Rasmus Nielsen
- Department of Integrative Biology and Department of Statistics, University of California Berkeley, Berkeley, CA 94820, USA; Globe Institute, University of Copenhagen, DK-1165 Copenhagen, Denmark.
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