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Liao BY, Weng MP, Chang TY, Chang AYF, Ching YH, Wu CH. Degeneration of the Olfactory System in a Murid Rodent that Evolved Diurnalism. Mol Biol Evol 2024; 41:msae037. [PMID: 38376543 PMCID: PMC10906987 DOI: 10.1093/molbev/msae037] [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: 10/19/2022] [Revised: 01/03/2024] [Accepted: 02/13/2024] [Indexed: 02/21/2024] Open
Abstract
In mammalian research, it has been debated what can initiate an evolutionary tradeoff between different senses, and the phenomenon of sensory tradeoff in rodents, the most abundant mammalian clade, is not evident. The Nile rat (Arvicanthis niloticus), a murid rodent, recently adapted to a diurnal niche through an evolutionary acquisition of daylight vision with enhanced visual acuity. As such, this model provides an opportunity for a cross-species investigation where comparative morphological and multi-omic analyses of the Nile rat are made with its closely related nocturnal species, e.g. the mouse (Mus musculus) and the rat (Rattus norvegicus). Thus, morphological examinations were performed, and evolutionary reductions in relative sizes of turbinal bone surfaces, the cribriform plate, and the olfactory bulb were discovered in Nile rats. Subsequently, we compared multiple murid genomes, and profiled olfactory epithelium transcriptomes of mice and Nile rats at various ages with RNA sequencing. The results further demonstrate that, in comparison with mouse olfactory receptor (OR) genes, Nile rat OR genes have experienced less frequent gain, more frequent loss, and more frequent expression reduction during their evolution. Furthermore, functional degeneration of coding sequences in the Nile rat lineage was found in OR genes, yet not in other genes. Taken together, these results suggest that acquisition of improved vision in the Nile rat has been accompanied by degeneration of both olfaction-related anatomical structures and OR gene repertoires, consistent with the hypothesis of an olfaction-vision tradeoff initiated by the switch from a nocturnal to a diurnal lifestyle in mammals.
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Affiliation(s)
- Ben-Yang Liao
- Institute of Population Health Sciences, National Health Research Institutes, Taiwan, Republic of China
| | - Meng-Pin Weng
- Institute of Population Health Sciences, National Health Research Institutes, Taiwan, Republic of China
| | - Ting-Yan Chang
- Institute of Population Health Sciences, National Health Research Institutes, Taiwan, Republic of China
| | - Andrew Ying-Fei Chang
- Institute of Population Health Sciences, National Health Research Institutes, Taiwan, Republic of China
| | - Yung-Hao Ching
- Department of Molecular Biology and Human Genetics, Tzu Chi University, Taiwan, Republic of China
| | - Chia-Hwa Wu
- Laboratory Animal Center, National Health Research Institutes, Taiwan, Republic of China
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2
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Liu W, Zhu P, Li M, Li Z, Yu Y, Liu G, Du J, Wang X, Yang J, Tian R, Seim I, Kaya A, Li M, Li M, Gladyshev VN, Zhou X. Large-scale across species transcriptomic analysis identifies genetic selection signatures associated with longevity in mammals. EMBO J 2023; 42:e112740. [PMID: 37427458 PMCID: PMC10476176 DOI: 10.15252/embj.2022112740] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 05/12/2023] [Accepted: 05/22/2023] [Indexed: 07/11/2023] Open
Abstract
Lifespan varies significantly among mammals, with more than 100-fold difference between the shortest and longest living species. This natural difference may uncover the evolutionary forces and molecular features that define longevity. To understand the relationship between gene expression variation and longevity, we conducted a comparative transcriptomics analysis of liver, kidney, and brain tissues of 103 mammalian species. We found that few genes exhibit common expression patterns with longevity in the three organs analyzed. However, pathways related to translation fidelity, such as nonsense-mediated decay and eukaryotic translation elongation, correlated with longevity across mammals. Analyses of selection pressure found that selection intensity related to the direction of longevity-correlated genes is inconsistent across organs. Furthermore, expression of methionine restriction-related genes correlated with longevity and was under strong selection in long-lived mammals, suggesting that a common strategy is utilized by natural selection and artificial intervention to control lifespan. Our results indicate that lifespan regulation via gene expression is driven through polygenic and indirect natural selection.
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Affiliation(s)
- Weiqiang Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Pingfen Zhu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Meng Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Zihao Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yang Yu
- School of Life SciencesUniversity of Science and Technology of ChinaAnhuiChina
| | - Gaoming Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Juan Du
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiao Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Jing Yang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ran Tian
- Integrative Biology Laboratory, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Inge Seim
- Integrative Biology Laboratory, College of Life SciencesNanjing Normal UniversityNanjingChina
- School of Biology and Environmental ScienceQueensland University of TechnologyBrisbaneQLDAustralia
| | - Alaattin Kaya
- Department of BiologyVirginia Commonwealth UniversityRichmondVAUSA
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityChengduChina
| | - Ming Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's HospitalHarvard Medical SchoolBostonMAUSA
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
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3
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Zhu P, Liu W, Zhang X, Li M, Liu G, Yu Y, Li Z, Li X, Du J, Wang X, Grueter CC, Li M, Zhou X. Correlated evolution of social organization and lifespan in mammals. Nat Commun 2023; 14:372. [PMID: 36720880 PMCID: PMC9889386 DOI: 10.1038/s41467-023-35869-7] [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: 05/09/2022] [Accepted: 01/05/2023] [Indexed: 02/02/2023] Open
Abstract
Discerning the relationship between sociality and longevity would permit a deeper understanding of how animal life history evolved. Here, we perform a phylogenetic comparative analysis of ~1000 mammalian species on three states of social organization (solitary, pair-living, and group-living) and longevity. We show that group-living species generally live longer than solitary species, and that the transition rate from a short-lived state to a long-lived state is higher in group-living than non-group-living species, altogether supporting the correlated evolution of social organization and longevity. The comparative brain transcriptomes of 94 mammalian species identify 31 genes, hormones and immunity-related pathways broadly involved in the association between social organization and longevity. Further selection features reveal twenty overlapping pathways under selection for both social organization and longevity. These results underscore a molecular basis for the influence of the social organization on longevity.
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Affiliation(s)
- Pingfen Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Weiqiang Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxiao Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meng Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Gaoming Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Yang Yu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Zihao Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuanjing Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Du
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Cyril C Grueter
- School of Human Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Centre for Evolutionary Biology, School of Biological Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,International Center of Biodiversity and Primate Conservation, Dali University, Dali, Yunnan, 671003, China
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Xuming Zhou
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.
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4
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Chen F, Yi WM, Wang SY, Yuan MH, Wen J, Li HY, Zou Q, Liu S, Cai ZY. A long-term high-fat diet influences brain damage and is linked to the activation of HIF-1α/AMPK/mTOR/p70S6K signalling. Front Neurosci 2022; 16:978431. [PMID: 36188454 PMCID: PMC9524849 DOI: 10.3389/fnins.2022.978431] [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: 06/26/2022] [Accepted: 08/30/2022] [Indexed: 12/02/2022] Open
Abstract
High-fat diets (HFDs) are related to the incidence of obesity and diabetes, but the effect of high-fat diet-induced brain damage remains to be clarified. In our study, we found that 24 weeks of a HFD effectively induced obesity and a change in fur color in mice. In addition, the mice also exhibited deficits in learning and memory. We further found that autophagic flux was impaired in mice after HFD feeding. Hypoxia-inducible factor 1α (HIF-1α) expression was significantly increased in HFD-fed mice, and HFD feeding inhibited adenosine monophosphate-activated protein kinase (AMPK) phosphorylation and induced mechanistic target of rapamycin (mTOR) phosphorylation and p70S6K expression. Treatment of HFD-induced BV2 cell model with palmitic acid (PA) was used to further verify a similar result. We concluded that improving tissue hypoxia or enhancing autophagy through the AMPK/mTOR/p70S6K pathway may be a relevant strategy for improving obesity- and ageing-related disorders.
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Affiliation(s)
- Fei Chen
- Department of Neurology, Chongqing Medical University, Chongqing, China
- Chongqing Institute Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing, China
- Department of Neurology, Chongqing General Hospital, Chongqing, China
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, China
| | - Wen-min Yi
- Department of Neurology, Chongqing Medical University, Chongqing, China
- Chongqing Institute Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing, China
- Department of Neurology, Chongqing General Hospital, Chongqing, China
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, China
| | - Sheng-yuan Wang
- Department of Neurology, Chongqing Medical University, Chongqing, China
- Chongqing Institute Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing, China
- Department of Neurology, Chongqing General Hospital, Chongqing, China
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, China
| | - Ming-hao Yuan
- Department of Neurology, Chongqing Medical University, Chongqing, China
- Chongqing Institute Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing, China
- Department of Neurology, Chongqing General Hospital, Chongqing, China
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, China
| | - Jie Wen
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, China
- Department of Neurology, Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Hong-Yan Li
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, China
- Department of Neurology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Qian Zou
- Department of Neurology, Chongqing General Hospital, Chongqing, China
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, China
| | - Shu Liu
- Department of Neurology, Chongqing Medical University, Chongqing, China
- Chongqing Institute Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing, China
- Department of Neurology, Chongqing General Hospital, Chongqing, China
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, China
| | - Zhi-you Cai
- Department of Neurology, Chongqing Medical University, Chongqing, China
- Chongqing Institute Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing, China
- Department of Neurology, Chongqing General Hospital, Chongqing, China
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, China
- *Correspondence: Zhi-you Cai, ; orcid.org/0000-0002-9552-4020
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5
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Chavez DE, Gronau I, Hains T, Dikow RB, Frandsen PB, Figueiró HV, Garcez FS, Tchaicka L, de Paula RC, Rodrigues FHG, Jorge RSP, Lima ES, Songsasen N, Johnson WE, Eizirik E, Koepfli KP, Wayne RK. Comparative genomics uncovers the evolutionary history, demography, and molecular adaptations of South American canids. Proc Natl Acad Sci U S A 2022; 119:e2205986119. [PMID: 35969758 PMCID: PMC9407222 DOI: 10.1073/pnas.2205986119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/28/2022] [Indexed: 11/18/2022] Open
Abstract
The remarkable radiation of South American (SA) canids produced 10 extant species distributed across diverse habitats, including disparate forms such as the short-legged, hypercarnivorous bush dog and the long-legged, largely frugivorous maned wolf. Despite considerable research spanning nearly two centuries, many aspects of their evolutionary history remain unknown. Here, we analyzed 31 whole genomes encompassing all extant SA canid species to assess phylogenetic relationships, interspecific hybridization, historical demography, current genetic diversity, and the molecular bases of adaptations in the bush dog and maned wolf. We found that SA canids originated from a single ancestor that colonized South America 3.9 to 3.5 Mya, followed by diversification east of the Andes and then a single colonization event and radiation of Lycalopex species west of the Andes. We detected extensive historical gene flow between recently diverged lineages and observed distinct patterns of genomic diversity and demographic history in SA canids, likely induced by past climatic cycles compounded by human-induced population declines. Genome-wide scans of selection showed that disparate limb proportions in the bush dog and maned wolf may derive from mutations in genes regulating chondrocyte proliferation and enlargement. Further, frugivory in the maned wolf may have been enabled by variants in genes associated with energy intake from short-chain fatty acids. In contrast, unique genetic variants detected in the bush dog may underlie interdigital webbing and dental adaptations for hypercarnivory. Our analyses shed light on the evolution of a unique carnivoran radiation and how it was shaped by South American topography and climate change.
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Affiliation(s)
- Daniel E. Chavez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095
- Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Ilan Gronau
- Efi Arazi School of Computer Science, Reichman University, Herzliya 46150, Israel
| | - Taylor Hains
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637
| | - Rebecca B. Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20560
| | - Paul B. Frandsen
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20560
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602
| | - Henrique V. Figueiró
- Smithsonian’s National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA 22630
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, 90619-900, Brazil
| | - Fabrício S. Garcez
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, 90619-900, Brazil
| | - Ligia Tchaicka
- Rede de Biodiversidade e Biotecnologia da Amazônia, Curso de Pós-Graduação em Recursos Aquáticos e Pesca, Universidade Estadual do Maranhão, São Luis, 2016-8100, Brazil
| | - Rogério C. de Paula
- Centro Nacional de Pesquisa e Conservação de Mamíferos Carnívoros, Instituto Chico Mendes de Conservação da Biodiversidade, 12952-011, Atibaia, Brazil
| | - Flávio H. G. Rodrigues
- Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Rodrigo S. P. Jorge
- Centro Nacional de Avaliação da Biodiversidade e de Pesquisa e Conservação do Cerrado, Instituto Chico Mendes de Conservação da Biodiversidade, Brasilia, 70670-350, Brazil
| | - Edson S. Lima
- Private address, Nova Xavantina, MT, 78690-000, Brazil
| | - Nucharin Songsasen
- Smithsonian’s National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA 22630
| | - Warren E. Johnson
- Smithsonian’s National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA 22630
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, 90619-900, Brazil
- Instituto Pró-Carnívoros, Atibaia, 12945-010, Brazil
- Instituto Nacional de Ciência e Tecnologia em Ecologia Evolução Conservação da Biodiverside, Universidade Federal de GoiásGoiânia, 74690-900, Brazil
| | - Klaus-Peter Koepfli
- Smithsonian’s National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA 22630
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095
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6
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Hartfield M, Poulsen NA, Guldbrandtsen B, Bataillon T. Using singleton densities to detect recent selection in Bos taurus. Evol Lett 2021; 5:595-606. [PMID: 34917399 PMCID: PMC8645200 DOI: 10.1002/evl3.263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 11/05/2022] Open
Abstract
Many quantitative traits are subject to polygenic selection, where several genomic regions undergo small, simultaneous changes in allele frequency that collectively alter a phenotype. The widespread availability of genome data, along with novel statistical techniques, has made it easier to detect these changes. We apply one such method, the "Singleton Density Score" (SDS), to the Holstein breed of Bos taurus to detect recent selection (arising up to around 740 years ago). We identify several genes as candidates for targets of recent selection, including some relating to cell regulation, catabolic processes, neural-cell adhesion and immunity. We do not find strong evidence that three traits that are important to humans-milk protein content, milk fat content, and stature-have been subject to directional selection. Simulations demonstrate that because B. taurus recently experienced a population bottleneck, singletons are depleted so the power of SDS methods is reduced. These results inform on which genes underlie recent genetic change in B. taurus, while providing information on how polygenic selection can be best investigated in future studies.
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Affiliation(s)
- Matthew Hartfield
- Bioinformatics Research CentreAarhus UniversityAarhusDK‐8000Denmark
- Institute of Evolutionary BiologyUniversity of EdinburghEdinburghEH9 3FLUnited Kingdom
| | | | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and GeneticsAarhus UniversityTjeleDK‐8830Denmark
- Rheinische Friedrich‐Wilhelms‐Universität BonnInstitut für TierwissenschaftenBonnDE‐53115Germany
- Department of Veterinary SciencesCopenhagen UniversityFrederiksberg CDK‐1870Denmark
| | - Thomas Bataillon
- Bioinformatics Research CentreAarhus UniversityAarhusDK‐8000Denmark
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7
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Trigila AP, Pisciottano F, Franchini LF. Hearing loss genes reveal patterns of adaptive evolution at the coding and non-coding levels in mammals. BMC Biol 2021; 19:244. [PMID: 34784928 PMCID: PMC8594068 DOI: 10.1186/s12915-021-01170-6] [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: 11/20/2020] [Accepted: 10/21/2021] [Indexed: 11/26/2022] Open
Abstract
Background Mammals possess unique hearing capacities that differ significantly from those of the rest of the amniotes. In order to gain insights into the evolution of the mammalian inner ear, we aim to identify the set of genetic changes and the evolutionary forces that underlie this process. We hypothesize that genes that impair hearing when mutated in humans or in mice (hearing loss (HL) genes) must play important roles in the development and physiology of the inner ear and may have been targets of selective forces across the evolution of mammals. Additionally, we investigated if these HL genes underwent a human-specific evolutionary process that could underlie the evolution of phenotypic traits that characterize human hearing. Results We compiled a dataset of HL genes including non-syndromic deafness genes identified by genetic screenings in humans and mice. We found that many genes including those required for the normal function of the inner ear such as LOXHD1, TMC1, OTOF, CDH23, and PCDH15 show strong signatures of positive selection. We also found numerous noncoding accelerated regions in HL genes, and among them, we identified active transcriptional enhancers through functional enhancer assays in transgenic zebrafish. Conclusions Our results indicate that the key inner ear genes and regulatory regions underwent adaptive evolution in the basal branch of mammals and along the human-specific branch, suggesting that they could have played an important role in the functional remodeling of the cochlea. Altogether, our data suggest that morphological and functional evolution could be attained through molecular changes affecting both coding and noncoding regulatory regions. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01170-6.
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Affiliation(s)
- Anabella P Trigila
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428, Buenos Aires, Argentina
| | - Francisco Pisciottano
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428, Buenos Aires, Argentina.,Current address: Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428, Buenos Aires, Argentina
| | - Lucía F Franchini
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428, Buenos Aires, Argentina.
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8
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Lu H, Li F, Yuan L, Domenzain I, Yu R, Wang H, Li G, Chen Y, Ji B, Kerkhoven EJ, Nielsen J. Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection. Mol Syst Biol 2021; 17:e10427. [PMID: 34676984 PMCID: PMC8532513 DOI: 10.15252/msb.202110427] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 10/02/2021] [Accepted: 10/04/2021] [Indexed: 12/24/2022] Open
Abstract
Yeasts are known to have versatile metabolic traits, while how these metabolic traits have evolved has not been elucidated systematically. We performed integrative evolution analysis to investigate how genomic evolution determines trait generation by reconstructing genome-scale metabolic models (GEMs) for 332 yeasts. These GEMs could comprehensively characterize trait diversity and predict enzyme functionality, thereby signifying that sequence-level evolution has shaped reaction networks towards new metabolic functions. Strikingly, using GEMs, we can mechanistically map different evolutionary events, e.g. horizontal gene transfer and gene duplication, onto relevant subpathways to explain metabolic plasticity. This demonstrates that gene family expansion and enzyme promiscuity are prominent mechanisms for metabolic trait gains, while GEM simulations reveal that additional factors, such as gene loss from distant pathways, contribute to trait losses. Furthermore, our analysis could pinpoint to specific genes and pathways that have been under positive selection and relevant for the formulation of complex metabolic traits, i.e. thermotolerance and the Crabtree effect. Our findings illustrate how multidimensional evolution in both metabolic network structure and individual enzymes drives phenotypic variations.
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Affiliation(s)
- Hongzhong Lu
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Feiran Li
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Le Yuan
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Iván Domenzain
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Rosemary Yu
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Hao Wang
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
- National Bioinformatics Infrastructure SwedenScience for Life LaboratoryChalmers University of TechnologyGothenburgSweden
| | - Gang Li
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Yu Chen
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Boyang Ji
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkLyngbyDenmark
| | - Eduard J Kerkhoven
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Jens Nielsen
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkLyngbyDenmark
- BioInnovation InstituteCopenhagen NDenmark
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9
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Huang YF. Dissecting genomic determinants of positive selection with an evolution-guided regression model. Mol Biol Evol 2021; 39:6379733. [PMID: 34597406 PMCID: PMC8763110 DOI: 10.1093/molbev/msab291] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In evolutionary genomics, it is fundamentally important to understand how characteristics of genomic sequences, such as gene expression level, determine the rate of adaptive evolution. While numerous statistical methods, such as the McDonald–Kreitman (MK) test, are available to examine the association between genomic features and the rate of adaptation, we currently lack a statistical approach to disentangle the independent effect of a genomic feature from the effects of other correlated genomic features. To address this problem, I present a novel statistical model, the MK regression, which augments the MK test with a generalized linear model. Analogous to the classical multiple regression model, the MK regression can analyze multiple genomic features simultaneously to infer the independent effect of a genomic feature, holding constant all other genomic features. Using the MK regression, I identify numerous genomic features driving positive selection in chimpanzees. These features include well-known ones, such as local mutation rate, residue exposure level, tissue specificity, and immune genes, as well as new features not previously reported, such as gene expression level and metabolic genes. In particular, I show that highly expressed genes may have a higher adaptation rate than their weakly expressed counterparts, even though a higher expression level may impose stronger negative selection. Also, I show that metabolic genes may have a higher adaptation rate than their nonmetabolic counterparts, possibly due to recent changes in diet in primate evolution. Overall, the MK regression is a powerful approach to elucidate the genomic basis of adaptation.
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Affiliation(s)
- Yi-Fei Huang
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.,Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
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10
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Upadhyay M, Kunz E, Sandoval-Castellanos E, Hauser A, Krebs S, Graf A, Blum H, Dotsev A, Okhlopkov I, Shakhin A, Bagirov V, Brem G, Fries R, Zinovieva N, Medugorac I. Whole genome sequencing reveals a complex introgression history and the basis of adaptation to subarctic climate in wild sheep. Mol Ecol 2021; 30:6701-6717. [PMID: 34534381 DOI: 10.1111/mec.16184] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/01/2021] [Accepted: 09/07/2021] [Indexed: 11/29/2022]
Abstract
To predict species responses to anthropogenic disturbances and climate change, it is reasonable to use species with high sensitivity to such factors. Snow sheep (Ovis nivicola) could represent a good candidate for this; as the only large herbivore species adapted to the cold and alpine habitats of northeastern Siberia, it plays a crucial role in its ecosystem. Despite having an extensive geographical distribution among all ovine species, it is one of the least studied. In this study, we sequenced and analysed six genomes of snow sheep in combination with all other wild sheep species to infer key aspects of their evolutionary history and unveil the genetic basis of their adaptation to subarctic environments. Despite their large census population size, snow sheep genomes showed remarkably low heterozygosity, which could reflect the effect of isolation and historical bottlenecks that we inferred using the pairwise sequential Markovian coalescent and runs of homozygosity. F4 -statistics indicated instances of introgression involving snow sheep with argali (Ovis ammon) and Dall (Ovis dalli) sheep, suggesting that these species might have been more widespread during the Pleistocene. Furthermore, the introgressed segments, which were identified using mainly minimum relative node depth, covered genes associated with immunity, adipogenesis and morphology-related traits, representing potential targets of adaptive introgression. Genes related to mitochondrial functions and thermogenesis associated with adipose tissue were identified to be under selection. Overall, our data suggest introgression as a mechanism facilitating adaptation in wild sheep species and provide insights into the genetic mechanisms underlying cold adaptation in snow sheep.
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Affiliation(s)
- Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Elisabeth Kunz
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | | | - Andreas Hauser
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Arsen Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia
| | | | - Alexey Shakhin
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia
| | - Vugar Bagirov
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, VMU, Vienna, Austria
| | - Ruedi Fries
- Lehrstuhl für Tierzucht, Technische Universität München, Freising, Germany
| | - Natalia Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Munich, Germany
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11
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Modulation of bioelectric cues in the evolution of flying fishes. Curr Biol 2021; 31:5052-5061.e8. [PMID: 34534441 DOI: 10.1016/j.cub.2021.08.054] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 07/09/2021] [Accepted: 08/20/2021] [Indexed: 01/03/2023]
Abstract
Changes to allometry, or the relative proportions of organs and tissues within organisms, is a common means for adaptive character change in evolution. However, little is understood about how relative size is specified during development and shaped during evolution. Here, through a phylogenomic analysis of genome-wide variation in 35 species of flying fishes and relatives, we identify genetic signatures in both coding and regulatory regions underlying the convergent evolution of increased paired fin size and aerial gliding behaviors. To refine our analysis, we intersected convergent phylogenomic signatures with mutants with altered fin size identified in distantly related zebrafish. Through these paired approaches, we identify a surprising role for an L-type amino acid transporter, lat4a, and the potassium channel, kcnh2a, in the regulation of fin proportion. We show that interaction between these genetic loci in zebrafish closely phenocopies the observed fin proportions of flying fishes. The congruence of experimental and phylogenomic findings point to conserved, non-canonical signaling integrating bioelectric cues and amino acid transport in the establishment of relative size in development and evolution.
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12
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Yousaf A, Liu J, Ye S, Chen H. Current Progress in Evolutionary Comparative Genomics of Great Apes. Front Genet 2021; 12:657468. [PMID: 34456962 PMCID: PMC8385753 DOI: 10.3389/fgene.2021.657468] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 07/15/2021] [Indexed: 12/04/2022] Open
Abstract
The availability of high-quality genome sequences of great ape species provides unprecedented opportunities for genomic analyses. Herein, we reviewed the recent progress in evolutionary comparative genomic studies of the existing great ape species, including human, chimpanzee, bonobo, gorilla, and orangutan. We elaborate discovery on evolutionary history, natural selection, structural variations, and new genes of these species, which is informative for understanding the origin of human-specific phenotypes.
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Affiliation(s)
- Aisha Yousaf
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Junfeng Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China
| | - Sicheng Ye
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hua Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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13
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Moreira A, Croze M, Delehelle F, Cussat-Blanc S, Luga H, Mollereau C, Balaresque P. Hearing Sensitivity of Primates: Recurrent and Episodic Positive Selection in Hair Cells and Stereocilia Protein-Coding Genes. Genome Biol Evol 2021; 13:6302699. [PMID: 34137817 PMCID: PMC8358225 DOI: 10.1093/gbe/evab133] [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] [Accepted: 06/06/2021] [Indexed: 12/29/2022] Open
Abstract
The large spectrum of hearing sensitivity observed in primates results from the impact of environmental and behavioral pressures to optimize sound perception and localization. Although evidence of positive selection in auditory genes has been detected in mammals including in Hominoids, selection has never been investigated in other primates. We analyzed 123 genes highly expressed in the inner ear of 27 primate species and tested to what extent positive selection may have shaped these genes in the order Primates tree. We combined both site and branch-site tests to obtain a comprehensive picture of the positively selected genes (PSGs) involved in hearing sensitivity, and drew a detailed description of the most affected branches in the tree. We chose a conservative approach, and thus focused on confounding factors potentially affecting PSG signals (alignment, GC-biased gene conversion, duplications, heterogeneous sequencing qualities). Using site tests, we showed that around 12% of these genes are PSGs, an α selection value consistent with average human genome estimates (10-15%). Using branch-site tests, we showed that the primate tree is heterogeneously affected by positive selection, with the black snub-nosed monkey, the bushbaby, and the orangutan, being the most impacted branches. A large proportion of these genes is inclined to shape hair cells and stereocilia, which are involved in the mechanotransduction process, known to influence frequency perception. Adaptive selection, and more specifically recurrent adaptive evolution, could have acted in parallel on a set of genes (ADGRV1, USH2A, PCDH15, PTPRQ, and ATP8A2) involved in stereocilia growth and the whole complex of bundle links connecting them, in species across different habitats, including high altitude and nocturnal environments.
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Affiliation(s)
- Andreia Moreira
- Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Faculté de Médecine Purpan, CNRS UMR5288, Université de Toulouse, Université Toulouse III Paul Sabatier, France.,Institut de Recherche en Informatique de Toulouse (IRIT), CNRS UMR5505, Université Toulouse III Paul Sabatier, France
| | - Myriam Croze
- Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Faculté de Médecine Purpan, CNRS UMR5288, Université de Toulouse, Université Toulouse III Paul Sabatier, France
| | - Franklin Delehelle
- Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Faculté de Médecine Purpan, CNRS UMR5288, Université de Toulouse, Université Toulouse III Paul Sabatier, France.,Institut de Recherche en Informatique de Toulouse (IRIT), CNRS UMR5505, Université Toulouse III Paul Sabatier, France
| | - Sylvain Cussat-Blanc
- Institut de Recherche en Informatique de Toulouse (IRIT), CNRS UMR5505, Université Toulouse III Paul Sabatier, France
| | - Hervé Luga
- Institut de Recherche en Informatique de Toulouse (IRIT), CNRS UMR5505, Université Toulouse III Paul Sabatier, France
| | - Catherine Mollereau
- Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Faculté de Médecine Purpan, CNRS UMR5288, Université de Toulouse, Université Toulouse III Paul Sabatier, France
| | - Patricia Balaresque
- Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Faculté de Médecine Purpan, CNRS UMR5288, Université de Toulouse, Université Toulouse III Paul Sabatier, France
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14
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Jovanovic VM, Sarfert M, Reyna-Blanco CS, Indrischek H, Valdivia DI, Shelest E, Nowick K. Positive Selection in Gene Regulatory Factors Suggests Adaptive Pleiotropic Changes During Human Evolution. Front Genet 2021; 12:662239. [PMID: 34079582 PMCID: PMC8166252 DOI: 10.3389/fgene.2021.662239] [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] [Received: 01/31/2021] [Accepted: 04/19/2021] [Indexed: 01/09/2023] Open
Abstract
Gene regulatory factors (GRFs), such as transcription factors, co-factors and histone-modifying enzymes, play many important roles in modifying gene expression in biological processes. They have also been proposed to underlie speciation and adaptation. To investigate potential contributions of GRFs to primate evolution, we analyzed GRF genes in 27 publicly available primate genomes. Genes coding for zinc finger (ZNF) proteins, especially ZNFs with a Krüppel-associated box (KRAB) domain were the most abundant TFs in all genomes. Gene numbers per TF family differed between all species. To detect signs of positive selection in GRF genes we investigated more than 3,000 human GRFs with their more than 70,000 orthologs in 26 non-human primates. We implemented two independent tests for positive selection, the branch-site-model of the PAML suite and aBSREL of the HyPhy suite, focusing on the human and great ape branch. Our workflow included rigorous procedures to reduce the number of false positives: excluding distantly similar orthologs, manual corrections of alignments, and considering only genes and sites detected by both tests for positive selection. Furthermore, we verified the candidate sites for selection by investigating their variation within human and non-human great ape population data. In order to approximately assign a date to positively selected sites in the human lineage, we analyzed archaic human genomes. Our work revealed with high confidence five GRFs that have been positively selected on the human lineage and one GRF that has been positively selected on the great ape lineage. These GRFs are scattered on different chromosomes and have been previously linked to diverse functions. For some of them a role in speciation and/or adaptation can be proposed based on the expression pattern or association with human diseases, but it seems that they all contributed independently to human evolution. Four of the positively selected GRFs are KRAB-ZNF proteins, that induce changes in target genes co-expression and/or through arms race with transposable elements. Since each positively selected GRF contains several sites with evidence for positive selection, we suggest that these GRFs participated pleiotropically to phenotypic adaptations in humans.
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Affiliation(s)
- Vladimir M Jovanovic
- Human Biology and Primate Evolution, Freie Universität Berlin, Berlin, Germany.,Bioinformatics Solution Center, Freie Universität Berlin, Berlin, Germany
| | - Melanie Sarfert
- Human Biology and Primate Evolution, Freie Universität Berlin, Berlin, Germany
| | - Carlos S Reyna-Blanco
- Department of Biology, University of Fribourg, Fribourg, Switzerland.,Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Henrike Indrischek
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - Dulce I Valdivia
- Evolutionary Genomics Laboratory and Genome Topology and Regulation Laboratory, Genetic Engineering Department, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-Irapuato), Irapuato, Mexico
| | - Ekaterina Shelest
- Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, United Kingdom
| | - Katja Nowick
- Human Biology and Primate Evolution, Freie Universität Berlin, Berlin, Germany
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15
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Brázda V, Bartas M, Bowater RP. Evolution of Diverse Strategies for Promoter Regulation. Trends Genet 2021; 37:730-744. [PMID: 33931265 DOI: 10.1016/j.tig.2021.04.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 12/15/2022]
Abstract
DNA is fundamentally important for all cellular organisms due to its role as a store of hereditary genetic information. The precise and accurate regulation of gene transcription depends primarily on promoters, which vary significantly within and between genomes. Some promoters are rich in specific types of bases, while others have more varied, complex sequence characteristics. However, it is not only base sequence but also epigenetic modifications and altered DNA structure that regulate promoter activity. Significantly, many promoters across all organisms contain sequences that can form intrastrand hairpins (cruciforms) or four-stranded structures (G-quadruplex or i-motif). In this review we integrate recent studies on promoter regulation that highlight the importance of DNA structure in the evolutionary adaptation of promoter sequences.
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Affiliation(s)
- Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Martin Bartas
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Richard P Bowater
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
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16
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Anthropological Prosociality via Sub-Group Level Selection. Integr Psychol Behav Sci 2021; 56:180-205. [PMID: 33893612 DOI: 10.1007/s12124-021-09606-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] [Accepted: 03/01/2021] [Indexed: 10/21/2022]
Abstract
A perennial challenge of evolutionary psychology is explaining prosocial traits such as a preference for fairness rather than inequality, compassion towards suffering, and an instinctive ability to coordinate within small teams. Considering recent fossil evidence and a novel logical test, we deem present explanations insufficiently explanatory of the divergence of hominins. In answering this question, we focus on the divergence of hominins from the last common ancestor (LCA) shared with Pan. We consider recent fossil discoveries that indicate the LCA was bipedal, which reduces the cogency of this explanation for hominin development. We also review evolutionary theory that claims to explain how hominins developed into modern humans, however it is found that no mechanism differentiates hominins from other primates. Either the mechanism was available to the last common ancestor (LCA) (with P. troglodytes as its proxy), or because early hominins had insufficient cognition to utilise the mechanism. A novel mechanism, sub-group level selection (sGLS) is hypothesised by triangulating two pieces of data rarely considered by evolutionary biologists. These are behavioural dimorphism of Pan (chimpanzees and bonobos) that remain identifiable in modern humans, and the social behaviour of primate troops in a savannah ecology. We then contend that sGLS supplied an exponential effect which was available to LCA who left the forest, but was not sufficiently available to any other primates. In conclusion, while only indirectly supported by various evidence, sGLS is found to be singularly and persuasively explanatory of human's unique evolutionary story.
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17
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Liu J, Robinson-Rechavi M. Robust inference of positive selection on regulatory sequences in the human brain. SCIENCE ADVANCES 2020; 6:6/48/eabc9863. [PMID: 33246961 PMCID: PMC7695467 DOI: 10.1126/sciadv.abc9863] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/16/2020] [Indexed: 05/07/2023]
Abstract
A longstanding hypothesis is that divergence between humans and chimpanzees might have been driven more by regulatory level adaptations than by protein sequence adaptations. This has especially been suggested for regulatory adaptations in the evolution of the human brain. We present a new method to detect positive selection on transcription factor binding sites on the basis of measuring predicted affinity change with a machine learning model of binding. Unlike other methods, this approach requires neither defining a priori neutral sites nor detecting accelerated evolution, thus removing major sources of bias. We scanned the signals of positive selection for CTCF binding sites in 29 human and 11 mouse tissues or cell types. We found that human brain-related cell types have the highest proportion of positive selection. This result is consistent with the view that adaptive evolution to gene regulation has played an important role in evolution of the human brain.
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Affiliation(s)
- Jialin Liu
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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18
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Daane JM, Auvinet J, Stoebenau A, Yergeau D, Harris MP, Detrich HW. Developmental constraint shaped genome evolution and erythrocyte loss in Antarctic fishes following paleoclimate change. PLoS Genet 2020; 16:e1009173. [PMID: 33108368 PMCID: PMC7660546 DOI: 10.1371/journal.pgen.1009173] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/12/2020] [Accepted: 10/06/2020] [Indexed: 02/07/2023] Open
Abstract
In the frigid, oxygen-rich Southern Ocean (SO), Antarctic icefishes (Channichthyidae; Notothenioidei) evolved the ability to survive without producing erythrocytes and hemoglobin, the oxygen-transport system of virtually all vertebrates. Here, we integrate paleoclimate records with an extensive phylogenomic dataset of notothenioid fishes to understand the evolution of trait loss associated with climate change. In contrast to buoyancy adaptations in this clade, we find relaxed selection on the genetic regions controlling erythropoiesis evolved only after sustained cooling in the SO. This pattern is seen not only within icefishes but also occurred independently in other high-latitude notothenioids. We show that one species of the red-blooded dragonfish clade evolved a spherocytic anemia that phenocopies human patients with this disease via orthologous mutations. The genomic imprint of SO climate change is biased toward erythrocyte-associated conserved noncoding elements (CNEs) rather than to coding regions, which are largely preserved through pleiotropy. The drift in CNEs is specifically enriched near genes that are preferentially expressed late in erythropoiesis. Furthermore, we find that the hematopoietic marrow of icefish species retained proerythroblasts, which indicates that early erythroid development remains intact. Our results provide a framework for understanding the interactions between development and the genome in shaping the response of species to climate change. Our climate is rapidly changing. To better understand how species can adapt to major climate disturbance, we looked back into the past at a group of fishes that have encountered dramatic climate upheavals and thrived: Antarctic notothenioid fishes. In particular, we focus on the icefishes, which lost the ability to produce red blood cells in the frigid environment of the Southern Ocean. By integrating past climate records with a large genetic dataset of Antarctic fishes, we show that the loss of red blood cells occurred only after sustained cooling of the Southern Ocean. As cooling continued into the modern era, we discover that even some of the “red-blooded” relatives of the icefishes show early genetic and morphological signs of erythrocyte loss. This cooling event left a non-random imprint on the genome of icefishes. With few exceptions, the genetic toolkit underlying red cell development has remained intact in icefishes because many “erythroid” genes perform important functions in other tissues. Rather, mutations have accumulated in gene regulatory regions near genes that control terminal erythroid maturation, such that icefishes continue to produce red cell progenitors but not mature erythrocytes. These results show that the genetic constraints regulating embryonic development shaped the evolutionary response of this fish group to climate change.
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Affiliation(s)
- Jacob M. Daane
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, United States of America
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, MA, United States of America
- Department of Genetics, Harvard Medical School, Boston, MA, United States of America
- * E-mail: (JMD); (HWD)
| | - Juliette Auvinet
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, United States of America
| | - Alicia Stoebenau
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, United States of America
| | - Donald Yergeau
- Department of Biology, Northeastern University, Boston, MA, United States of America
| | - Matthew P. Harris
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, MA, United States of America
- Department of Genetics, Harvard Medical School, Boston, MA, United States of America
| | - H. William Detrich
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, United States of America
- Department of Biology, Northeastern University, Boston, MA, United States of America
- * E-mail: (JMD); (HWD)
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19
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Adaptive evolution of peptidoglycan recognition protein family regulates the innate signaling against microbial pathogens in vertebrates. Microb Pathog 2020; 147:104361. [PMID: 32622926 DOI: 10.1016/j.micpath.2020.104361] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 04/28/2020] [Accepted: 06/22/2020] [Indexed: 12/16/2022]
Abstract
The innate immune system is the first line of defense in vertebrates against microbial pathogens. This defense system depends on the peptidoglycan pathogen recognition of receptors (PGRPs) existing in both invertebrates and vertebrates. Although some studies revealed the structural and functional differences between them, however, the evolutionary history and the selection pressures on these genes during adaptive evolution are poorly understood. In this study, we examined four (PGLYRP1, PGLYRP2, PGLYRP3, and PGLYRP4) genes of 127 vertebrates' species, conserved across vertebrates to evaluate positive selection pressure drives by adaptive evolution. The codons under positive selection were recognized through likelihood tests by comparing different models based on ω ratios in these genes across the vertebrate species. The positive selection test used two sets of models M1a vs. M2a and M7 vs. M8. The results showed that the test of these genes in M1a vs. M2a was not significant with the likelihood value 2ΔlnL = 0, while the likelihood ratios (2ΔlnL) were 2ΔlnL = 12.386, 2ΔlnL = 4.9283, 2ΔlnL = 24.031, and 2ΔlnL = 103.39 for PGLYRP1, PGLYRP2, PGLYRP3, and PGLYRP4 in M7 vs. M8, respectively. Our study identified the evidence of robust positive selection for these four genes across the vertebrates. These protuberant changes in PGRPs evolution of vertebrates reveal their role in innate immunity. Our study provides an insight based on PGRP genes to understand the evolution of host and pathogens interaction that leads to the progress of the novel conducts for immune diseases that include proteins linked to the recognition of pathogens.
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20
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Rees JS, Castellano S, Andrés AM. The Genomics of Human Local Adaptation. Trends Genet 2020; 36:415-428. [DOI: 10.1016/j.tig.2020.03.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 01/23/2023]
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21
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Singh RS, Gupta BP. Genes and genomes and unnecessary complexity in precision medicine. NPJ Genom Med 2020; 5:21. [PMID: 32377378 PMCID: PMC7198588 DOI: 10.1038/s41525-020-0128-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/27/2020] [Indexed: 02/07/2023] Open
Abstract
The sequencing of the human genome heralded the new age of 'genetic medicine' and raised the hope of precision medicine facilitating prolonged and healthy lives. Recent studies have dampened this expectation, as the relationships among mutations (termed 'risk factors'), biological processes, and diseases have emerged to be more complex than initially anticipated. In this review, we elaborate upon the nature of the relationship between genotype and phenotype, between chance-laden molecular complexity and the evolution of complex traits, and the relevance of this relationship to precision medicine. Molecular contingency, i.e., chance-driven molecular changes, in conjunction with the blind nature of evolutionary processes, creates genetic redundancy or multiple molecular pathways to the same phenotype; as time goes on, these pathways become more complex, interconnected, and hierarchically integrated. Based on the proposition that gene-gene interactions provide the major source of variation for evolutionary change, we present a theory of molecular complexity and posit that it consists of two parts, necessary and unnecessary complexity, both of which are inseparable and increase over time. We argue that, unlike necessary complexity, comprising all aspects of the organism's genetic program, unnecessary complexity is evolutionary baggage: the result of molecular constraints, historical circumstances, and the blind nature of evolutionary forces. In the short term, unnecessary complexity can give rise to similar risk factors with different genetic backgrounds; in the long term, genes become functionally interconnected and integrated, directly or indirectly, affecting multiple traits simultaneously. We reason that in addition to personal genomics and precision medicine, unnecessary complexity has consequences in evolutionary biology.
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Affiliation(s)
- Rama S. Singh
- Department of Biology, Origins Institute, McMaster University, 1280 Main Street West, Hamilton, ON Canada
| | - Bhagwati P. Gupta
- Department of Biology, Origins Institute, McMaster University, 1280 Main Street West, Hamilton, ON Canada
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22
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McGowen MR, Tsagkogeorga G, Williamson J, Morin PA, Rossiter ASJ. Positive Selection and Inactivation in the Vision and Hearing Genes of Cetaceans. Mol Biol Evol 2020; 37:2069-2083. [DOI: 10.1093/molbev/msaa070] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Abstract
The transition to an aquatic lifestyle in cetaceans (whales and dolphins) resulted in a radical transformation in their sensory systems. Toothed whales acquired specialized high-frequency hearing tied to the evolution of echolocation, whereas baleen whales evolved low-frequency hearing. More generally, all cetaceans show adaptations for hearing and seeing underwater. To determine the extent to which these phenotypic changes have been driven by molecular adaptation, we performed large-scale targeted sequence capture of 179 sensory genes across the Cetacea, incorporating up to 54 cetacean species from all major clades as well as their closest relatives, the hippopotamuses. We screened for positive selection in 167 loci related to vision and hearing and found that the diversification of cetaceans has been accompanied by pervasive molecular adaptations in both sets of genes, including several loci implicated in nonsyndromic hearing loss. Despite these findings, however, we found no direct evidence of positive selection at the base of odontocetes coinciding with the origin of echolocation, as found in studies examining fewer taxa. By using contingency tables incorporating taxon- and gene-based controls, we show that, although numbers of positively selected hearing and nonsyndromic hearing loss genes are disproportionately high in cetaceans, counts of vision genes do not differ significantly from expected values. Alongside these adaptive changes, we find increased evidence of pseudogenization of genes involved in cone-mediated vision in mysticetes and deep-diving odontocetes.
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Affiliation(s)
- Michael R McGowen
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
| | - Joseph Williamson
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA
| | - and Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
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23
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Ahmad HI, Zhou J, Ahmad MJ, Afzal G, Jiang H, Zhang X, Elokil AA, Khan MA, Li L, Li H, Ping L, Chen J. Adaptive selection in the evolution of programmed cell death-1 and its ligands in vertebrates. Aging (Albany NY) 2020; 12:3516-3557. [PMID: 32045365 PMCID: PMC7066927 DOI: 10.18632/aging.102827] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/28/2020] [Indexed: 12/14/2022]
Abstract
Programmed cell death-1 (PD-1) and its ligands, particularly PD-L1 and PD-L2, are the most important proteins responsible for signaling T-cell inhibition and arbitrating immune homeostasis and tolerance mechanisms. However, the adaptive evolution of these genes is poorly understood. In this study, we aligned protein-coding genes from vertebrate species to evaluate positive selection constraints and evolution in the PD1, PD-L1 and PD-L2 genes conserved across up to 166 vertebrate species, with an average of 55 species per gene. We determined that although the positive selection was obvious, an average of 5.3% of codons underwent positive selection in the three genes across vertebrate lineages, and increased positive selection pressure was detected in both the Ig-like domains and transmembrane domains of the proteins. Moreover, the PD1, PD-L1 and PD-L2 genes were highly expressed in almost all tissues of the selected species indicating a distinct expression pattern in different tissues among most species. Our study reveals that adaptive selection plays a key role in the evolution of PD1 and its ligands in the majority of vertebrate species, which is in agreement with the contribution of these residues to the mechanisms of pathogen identification and coevolution in the complexity and novelties of vertebrate immune systems.
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Affiliation(s)
- Hafiz Ishfaq Ahmad
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Jiabin Zhou
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Muhammad Jamil Ahmad
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Gulnaz Afzal
- Department of Zoology, The Islamia University, Bahawalpur, Pakistan
| | - Haiying Jiang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Xiujuan Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Abdelmotaleb A. Elokil
- Department of Zoology, The Islamia University, Bahawalpur, Pakistan
- Animal Production Department, Faculty of Agriculture, Benha University, Moshtohor, Egypt
| | - Musarrat Abbas Khan
- Department of Animal Breeding and Genetics, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Linmiao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Huiming Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Liu Ping
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
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24
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Hämälä T, Guiltinan MJ, Marden JH, Maximova SN, dePamphilis CW, Tiffin P. Gene Expression Modularity Reveals Footprints of Polygenic Adaptation in Theobroma cacao. Mol Biol Evol 2020; 37:110-123. [PMID: 31501906 DOI: 10.1093/molbev/msz206] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Separating footprints of adaptation from demography is challenging. When selection has acted on a single locus with major effect, this issue can be alleviated through signatures left by selective sweeps. However, as adaptation is often driven by small allele frequency shifts at many loci, studies focusing on single genes are able to identify only a small portion of genomic variants responsible for adaptation. In face of this challenge, we utilize coexpression information to search for signals of polygenetic adaptation in Theobroma cacao, a tropical tree species that is the source of chocolate. Using transcriptomics and a weighted correlation network analysis, we group genes with similar expression patterns into functional modules. We then ask whether modules enriched for specific biological processes exhibit cumulative effects of differential selection in the form of high FST and dXY between populations. Indeed, modules putatively involved in protein modification, flowering, and water transport show signs of polygenic adaptation even though individual genes that are members of those groups do not bear strong signatures of selection. Modeling of demography, background selection, and the effects of genomic features reveal that these patterns are unlikely to arise by chance. We also find that specific modules are enriched for signals of strong or relaxed purifying selection, with one module bearing signs of adaptive differentiation and an excess of deleterious mutations. Our results provide insight into polygenic adaptation and contribute to understanding of population structure, demographic history, and genome evolution in T. cacao.
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Affiliation(s)
- Tuomas Hämälä
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN
| | - Mark J Guiltinan
- Department of Plant Sciences, The Pennsylvania State University, University Park, PA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA
| | - James H Marden
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA.,Department of Biology, The Pennsylvania State University, University Park, PA
| | - Siela N Maximova
- Department of Plant Sciences, The Pennsylvania State University, University Park, PA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA
| | - Claude W dePamphilis
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA.,Department of Biology, The Pennsylvania State University, University Park, PA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN
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25
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Zu W, Zhang H, Lan X, Tan X. Genome-wide evolution analysis reveals low CpG contents of fast-evolving genes and identifies antiviral microRNAs. J Genet Genomics 2020; 47:49-60. [DOI: 10.1016/j.jgg.2019.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/11/2019] [Accepted: 12/03/2019] [Indexed: 01/28/2023]
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26
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Mayol M, Riba M, Cavers S, Grivet D, Vincenot L, Cattonaro F, Vendramin GG, González‐Martínez SC. A multiscale approach to detect selection in nonmodel tree species: Widespread adaptation despite population decline in Taxus baccata L. Evol Appl 2020; 13:143-160. [PMID: 31892949 PMCID: PMC6935595 DOI: 10.1111/eva.12838] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 06/18/2019] [Accepted: 06/24/2019] [Indexed: 01/03/2023] Open
Abstract
Detecting the molecular basis of local adaptation and identifying selective drivers is still challenging in nonmodel species. The use of purely population genetic approaches is limited by some characteristics of genetic systems, such as pleiotropy and polygenic control, and parallel evidence from phenotypic-based experimental comparisons is required. In long-lived organisms, the detection of selective pressures might also be precluded by evolutionary lag times in response to the environment. Here, we used the English yew to showcase an example of a multiscale integrative approach in a nonmodel species with limited plant and genomic resources. We combined information from two independent sources, phenotypes in a common environment and genomic data in natural populations, to investigate the signature of selection. Growth differences among populations in a common environment, and phenological patterns of both shoot elongation and male strobili maturation, were associated with climate clines, providing evidence for local adaptation and guiding us in the selection of populations for genomic analyses. We used information on over 25,000 SNPs from c. 1,200 genes to infer the demographic history and to test for molecular signatures of selection at different levels: SNP, gene, and biological pathway. Our results confirmed an overall demographic history of population decline, but we also found evidence for putative local adaptation at the molecular level. We identified or confirmed several candidate genes for positive and negative selection in forest trees, including the pseudo-response regulator 7 (PRR7), an essential component of the circadian clock in plants. In addition, we successfully tested an approach to detect polygenic adaptation in biological pathways, allowing us to identify the flavonoid biosynthesis pathway as a candidate stress-response pathway that deserves further attention in other plants. Finally, our study contributes to the emerging view that explaining contemporary standing genetic variation requires considering adaptation to past climates, especially for long-lived trees.
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Affiliation(s)
| | - Miquel Riba
- CREAFCerdanyola del VallèsSpain
- Univ. Autònoma BarcelonaCerdanyola del VallèsSpain
| | | | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research CentreINIA‐CIFORMadridSpain
- Sustainable Forest Management Research Institute, INIA‐University of ValladolidMadridSpain
| | | | | | - Giovanni G. Vendramin
- Institute of Biosciences and Bioresources, Division of FlorenceNational Research CouncilSesto FiorentinoItaly
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27
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Beichman AC, Koepfli KP, Li G, Murphy W, Dobrynin P, Kliver S, Tinker MT, Murray MJ, Johnson J, Lindblad-Toh K, Karlsson EK, Lohmueller KE, Wayne RK. Aquatic Adaptation and Depleted Diversity: A Deep Dive into the Genomes of the Sea Otter and Giant Otter. Mol Biol Evol 2019; 36:2631-2655. [PMID: 31212313 PMCID: PMC7967881 DOI: 10.1093/molbev/msz101] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Despite its recent invasion into the marine realm, the sea otter (Enhydra lutris) has evolved a suite of adaptations for life in cold coastal waters, including limb modifications and dense insulating fur. This uniquely dense coat led to the near-extinction of sea otters during the 18th-20th century fur trade and an extreme population bottleneck. We used the de novo genome of the southern sea otter (E. l. nereis) to reconstruct its evolutionary history, identify genes influencing aquatic adaptation, and detect signals of population bottlenecks. We compared the genome of the southern sea otter with the tropical freshwater-living giant otter (Pteronura brasiliensis) to assess common and divergent genomic trends between otter species, and with the closely related northern sea otter (E. l. kenyoni) to uncover population-level trends. We found signals of positive selection in genes related to aquatic adaptations, particularly limb development and polygenic selection on genes related to hair follicle development. We found extensive pseudogenization of olfactory receptor genes in both the sea otter and giant otter lineages, consistent with patterns of sensory gene loss in other aquatic mammals. At the population level, the southern sea otter and the northern sea otter showed extremely low genomic diversity, signals of recent inbreeding, and demographic histories marked by population declines. These declines may predate the fur trade and appear to have resulted in an increase in putatively deleterious variants that could impact the future recovery of the sea otter.
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Affiliation(s)
- Annabel C Beichman
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
| | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Gang Li
- College of Life Science, Shaanxi Normal University, Xi’an, Shaanxi, China
| | - William Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
| | - Pasha Dobrynin
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Sergei Kliver
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Martin T Tinker
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA
| | | | - Jeremy Johnson
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Kerstin Lindblad-Toh
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, MA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Elinor K Karlsson
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, MA
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
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28
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Davydov II, Salamin N, Robinson-Rechavi M. Large-Scale Comparative Analysis of Codon Models Accounting for Protein and Nucleotide Selection. Mol Biol Evol 2019; 36:1316-1332. [PMID: 30847475 PMCID: PMC6526913 DOI: 10.1093/molbev/msz048] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
There are numerous sources of variation in the rate of synonymous substitutions inside genes, such as direct selection on the nucleotide sequence, or mutation rate variation. Yet scans for positive selection rely on codon models which incorporate an assumption of effectively neutral synonymous substitution rate, constant between sites of each gene. Here we perform a large-scale comparison of approaches which incorporate codon substitution rate variation and propose our own simple yet effective modification of existing models. We find strong effects of substitution rate variation on positive selection inference. More than 70% of the genes detected by the classical branch-site model are presumably false positives caused by the incorrect assumption of uniform synonymous substitution rate. We propose a new model which is strongly favored by the data while remaining computationally tractable. With the new model we can capture signatures of nucleotide level selection acting on translation initiation and on splicing sites within the coding region. Finally, we show that rate variation is highest in the highly recombining regions, and we propose that recombination and mutation rate variation, such as high CpG mutation rate, are the two main sources of nucleotide rate variation. Although we detect fewer genes under positive selection in Drosophila than without rate variation, the genes which we detect contain a stronger signal of adaptation of dynein, which could be associated with Wolbachia infection. We provide software to perform positive selection analysis using the new model.
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Affiliation(s)
- Iakov I Davydov
- Department of Computational Biology, Biophore, University of Lausanne, Lausanne, Switzerland.,Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, Biophore, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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29
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Liu J, Robinson-Rechavi M. Adaptive Evolution of Animal Proteins over Development: Support for the Darwin Selection Opportunity Hypothesis of Evo-Devo. Mol Biol Evol 2019; 35:2862-2872. [PMID: 30184095 PMCID: PMC6278863 DOI: 10.1093/molbev/msy175] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A driving hypothesis of evolutionary developmental biology is that animal morphological diversity is shaped both by adaptation and by developmental constraints. Here, we have tested Darwin’s “selection opportunity” hypothesis, according to which high evolutionary divergence in late development is due to strong positive selection. We contrasted it to a “developmental constraint” hypothesis, according to which late development is under relaxed negative selection. Indeed, the highest divergence between species, both at the morphological and molecular levels, is observed late in embryogenesis and postembryonically. To distinguish between adaptation and relaxation hypotheses, we investigated the evidence of positive selection on protein-coding genes in relation to their expression over development, in fly Drosophila melanogaster, zebrafish Danio rerio, and mouse Mus musculus. First, we found that genes specifically expressed in late development have stronger signals of positive selection. Second, over the full transcriptome, genes with evidence for positive selection trend to be expressed in late development. Finally, genes involved in pathways with cumulative evidence of positive selection have higher expression in late development. Overall, there is a consistent signal that positive selection mainly affects genes and pathways expressed in late embryonic development and in adult. Our results imply that the evolution of embryogenesis is mostly conservative, with most adaptive evolution affecting some stages of postembryonic gene expression, and thus postembryonic phenotypes. This is consistent with the diversity of environmental challenges to which juveniles and adults are exposed.
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Affiliation(s)
- Jialin Liu
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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30
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Daane JM, Dornburg A, Smits P, MacGuigan DJ, Brent Hawkins M, Near TJ, William Detrich Iii H, Harris MP. Historical contingency shapes adaptive radiation in Antarctic fishes. Nat Ecol Evol 2019; 3:1102-1109. [PMID: 31182814 PMCID: PMC7147983 DOI: 10.1038/s41559-019-0914-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 05/02/2019] [Indexed: 12/02/2022]
Abstract
Adaptive radiation illustrates links between ecological opportunity, natural selection and the generation of biodiversity. Central to adaptive radiation is the association between a diversifying lineage and the evolution of phenotypic variation that facilitates the use of new environments or resources. However, is not clear whether adaptive evolution or historical contingency is more important for the origin of key phenotypic traits in adaptive radiation. Here we use targeted sequencing of >250,000 loci across 46 species to examine hypotheses concerning the origin and diversification of key traits in the adaptive radiation of Antarctic notothenioid fishes. Contrary to expectations of adaptive evolution, we show that notothenioids experienced a punctuated burst of genomic diversification and evolved key skeletal modifications before the onset of polar conditions in the Southern Ocean. We show that diversifying selection in pathways associated with human skeletal dysplasias facilitates ecologically important variation in buoyancy among Antarctic notothenioid species, and demonstrate the sufficiency of altered trip11, col1a2 and col1a1a function in zebrafish (Danio rerio) to phenocopy skeletal reduction in Antarctic notothenioids. Rather than adaptation being driven by the cooling of the Antarctic, our results highlight the role of historical contingency in shaping the adaptive radiation of notothenioids. Understanding the historical and environmental context for the origin of key traits in adaptive radiations extends beyond reconstructing events that result in evolutionary innovation, as it also provides a context in forecasting the effects of climate change on the stability and evolvability of natural populations.
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Affiliation(s)
- Jacob M Daane
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, USA.
| | - Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, NC, USA
| | - Patrick Smits
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, MA, USA
| | - Daniel J MacGuigan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - M Brent Hawkins
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, MA, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Peabody Museum of Natural History, Yale University, New Haven, CT, USA
| | - H William Detrich Iii
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, USA.
| | - Matthew P Harris
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
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31
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Fraser BA, Whiting JR. What can be learned by scanning the genome for molecular convergence in wild populations? Ann N Y Acad Sci 2019; 1476:23-42. [PMID: 31241191 PMCID: PMC7586825 DOI: 10.1111/nyas.14177] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/24/2019] [Accepted: 06/04/2019] [Indexed: 12/11/2022]
Abstract
Convergent evolution, where independent lineages evolve similar phenotypes in response to similar challenges, can provide valuable insight into how selection operates and the limitations it encounters. However, it has only recently become possible to explore how convergent evolution is reflected at the genomic level. The overlapping outlier approach (OOA), where genome scans of multiple independent lineages are used to find outliers that overlap and therefore identify convergently evolving loci, is becoming popular. Here, we present a quantitative analysis of 34 studies that used this approach across many sampling designs, taxa, and sampling intensities. We found that OOA studies with increased biological sampling power within replicates have increased likelihood of finding overlapping, "convergent" signals of adaptation between them. When identifying convergent loci as overlapping outliers, it is tempting to assume that any false-positive outliers derived from individual scans will fail to overlap across replicates, but this cannot be guaranteed. We highlight how population demographics and genomic context can contribute toward both true convergence and false positives in OOA studies. We finish with an exploration of emerging methods that couple genome scans with phenotype and environmental measures, leveraging added information from genome data to more directly test hypotheses of the likelihood of convergent evolution.
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Affiliation(s)
- Bonnie A Fraser
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - James R Whiting
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
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32
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Chavez DE, Gronau I, Hains T, Kliver S, Koepfli KP, Wayne RK. Comparative genomics provides new insights into the remarkable adaptations of the African wild dog (Lycaon pictus). Sci Rep 2019; 9:8329. [PMID: 31171819 PMCID: PMC6554312 DOI: 10.1038/s41598-019-44772-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/22/2019] [Indexed: 12/02/2022] Open
Abstract
Within the Canidae, the African wild dog (Lycaon pictus) is the most specialized with regards to cursorial adaptations (specialized for running), having only four digits on their forefeet. In addition, this species is one of the few canids considered to be an obligate meat-eater, possessing a robust dentition for taking down large prey, and displays one of the most variable coat colorations amongst mammals. Here, we used comparative genomic analysis to investigate the evolutionary history and genetic basis for adaptations associated with cursoriality, hypercanivory, and coat color variation in African wild dogs. Genome-wide scans revealed unique amino acid deletions that suggest a mode of evolutionary digit loss through expanded apoptosis in the developing first digit. African wild dog-specific signals of positive selection also uncovered a putative mechanism of molar cusp modification through changes in genes associated with the sonic hedgehog (SHH) signaling pathway, required for spatial patterning of teeth, and three genes associated with pigmentation. Divergence time analyses suggest the suite of genomic changes we identified evolved ~1.7 Mya, coinciding with the diversification of large-bodied ungulates. Our results show that comparative genomics is a powerful tool for identifying the genetic basis of evolutionary changes in Canidae.
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Affiliation(s)
- Daniel E Chavez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, 90095, USA.
| | - Ilan Gronau
- Efi Arazi School of Computer Science, Herzliya Interdisciplinary Center (IDC), Herzliya, 46150, Israel
| | - Taylor Hains
- Environmental Science and Policy, Johns Hopkins University, Washington, D.C., 20036, USA
| | - Sergei Kliver
- Institute of Molecular and Cellular Biology, Novosibirsk, 630090, Russian Federation
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, D.C., 20008, USA
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, 90095, USA
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33
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Marcionetti A, Rossier V, Roux N, Salis P, Laudet V, Salamin N. Insights into the Genomics of Clownfish Adaptive Radiation: Genetic Basis of the Mutualism with Sea Anemones. Genome Biol Evol 2019; 11:869-882. [PMID: 30830203 PMCID: PMC6430985 DOI: 10.1093/gbe/evz042] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2019] [Indexed: 02/06/2023] Open
Abstract
Clownfishes are an iconic group of coral reef fishes, especially known for their mutualism with sea anemones. This mutualism is particularly interesting as it likely acted as the key innovation that triggered clownfish adaptive radiation. Indeed, after the acquisition of the mutualism, clownfishes diversified into multiple ecological niches linked with host and habitat use. However, despite the importance of this mutualism, the genetic mechanisms allowing clownfishes to interact with sea anemones are still unclear. Here, we used a comparative genomics and molecular evolutionary analyses to investigate the genetic basis of clownfish mutualism with sea anemones. We assembled and annotated the genome of nine clownfish species and one closely related outgroup. Orthologous genes inferred between these species and additional publicly available teleost genomes resulted in almost 16,000 genes that were tested for positively selected substitutions potentially involved in the adaptation of clownfishes to live in sea anemones. We identified 17 genes with a signal of positive selection at the origin of clownfish radiation. Two of them (Versican core protein and Protein O-GlcNAse) show particularly interesting functions associated with N-acetylated sugars, which are known to be involved in sea anemone discharge of toxins. This study provides the first insights into the genetic mechanisms of clownfish mutualism with sea anemones. Indeed, we identified the first candidate genes likely to be associated with clownfish protection form sea anemones, and thus the evolution of their mutualism. Additionally, the genomic resources acquired represent a valuable resource for further investigation of the genomic basis of clownfish adaptive radiation.
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Affiliation(s)
- Anna Marcionetti
- Department of Computational Biology, Génopode, University of Lausanne, Switzerland
| | - Victor Rossier
- Department of Computational Biology, Génopode, University of Lausanne, Switzerland
| | - Natacha Roux
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne University, Banyuls-sur-Mer, France
| | - Pauline Salis
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne University, Banyuls-sur-Mer, France
| | - Vincent Laudet
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne University, Banyuls-sur-Mer, France
| | - Nicolas Salamin
- Department of Computational Biology, Génopode, University of Lausanne, Switzerland
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Delaye L, Ruiz-Ruiz S, Calderon E, Tarazona S, Conesa A, Moya A. Evidence of the Red-Queen Hypothesis from Accelerated Rates of Evolution of Genes Involved in Biotic Interactions in Pneumocystis. Genome Biol Evol 2018; 10:1596-1606. [PMID: 29893833 PMCID: PMC6012782 DOI: 10.1093/gbe/evy116] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2018] [Indexed: 01/15/2023] Open
Abstract
Pneumocystis species are ascomycete fungi adapted to live inside the lungs of mammals. These ascomycetes show extensive stenoxenism, meaning that each species of Pneumocystis infects a single species of host. Here, we study the effect exerted by natural selection on gene evolution in the genomes of three Pneumocystis species. We show that genes involved in host interaction evolve under positive selection. In the first place, we found strong evidence of episodic diversifying selection in Major surface glycoproteins (Msg). These proteins are located on the surface of Pneumocystis and are used for host attachment and probably for immune system evasion. Consistent with their function as antigens, most sites under diversifying selection in Msg code for residues with large relative surface accessibility areas. We also found evidence of positive selection in part of the cell machinery used to export Msg to the cell surface. Specifically, we found that genes participating in glycosylphosphatidylinositol (GPI) biosynthesis show an increased rate of nonsynonymous substitutions (dN) versus synonymous substitutions (dS). GPI is a molecule synthesized in the endoplasmic reticulum that is used to anchor proteins to membranes. We interpret the aforementioned findings as evidence of selective pressure exerted by the host immune system on Pneumocystis species, shaping the evolution of Msg and several proteins involved in GPI biosynthesis. We suggest that genome evolution in Pneumocystis is well described by the Red-Queen hypothesis whereby genes relevant for biotic interactions show accelerated rates of evolution.
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Affiliation(s)
- Luis Delaye
- Departamento de Ingeniería Genética, CINVESTAV Irapuato, Guanajuato, México
| | - Susana Ruiz-Ruiz
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Pública, València, Spain
| | - Enrique Calderon
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla.,Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Sonia Tarazona
- Centro de Investigacion Principe Felipe, València, Spain.,Departamento de Estadística e Investigación Operativa Aplicadas y Calidad, Universitat Politècnica de València, Spain
| | - Ana Conesa
- Centro de Investigacion Principe Felipe, València, Spain.,Microbiology and Cell Science, University of Florida
| | - Andrés Moya
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Pública, València, Spain.,Institute for Integrative Systems Biology, Universitat de València, Spain
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35
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Reales G, Paixão-Côrtes VR, Cybis GB, Gonçalves GL, Pissinatti A, Salzano FM, Bortolini MC. Serotonin, behavior, and natural selection in New World monkeys. J Evol Biol 2018; 31:1180-1192. [DOI: 10.1111/jeb.13295] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 05/16/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Guillermo Reales
- Departamento de Genética; Instituto de Biociências; Universidade Federal do Rio Grande do Sul; Porto Alegre RS Brazil
| | | | - Gabriela B. Cybis
- Departamento de Estatística; Universidade Federal do Rio Grande do Sul; Porto Alegre RS Brazil
| | - Gislene L. Gonçalves
- Departamento de Genética; Instituto de Biociências; Universidade Federal do Rio Grande do Sul; Porto Alegre RS Brazil
| | | | - Francisco M. Salzano
- Departamento de Genética; Instituto de Biociências; Universidade Federal do Rio Grande do Sul; Porto Alegre RS Brazil
| | - Maria Cátira Bortolini
- Departamento de Genética; Instituto de Biociências; Universidade Federal do Rio Grande do Sul; Porto Alegre RS Brazil
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36
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Csilléry K, Rodríguez-Verdugo A, Rellstab C, Guillaume F. Detecting the genomic signal of polygenic adaptation and the role of epistasis in evolution. Mol Ecol 2018; 27:606-612. [DOI: 10.1111/mec.14499] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/19/2018] [Accepted: 01/22/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Katalin Csilléry
- Department of Evolutionary Biology and Environmental Studies; University of Zürich; Zürich Switzerland
- Biodiversity and Conservation Biology; WSL Swiss Federal Research Institute; Birmensdorf Switzerland
| | - Alejandra Rodríguez-Verdugo
- Center for Adaptation to a Changing Environment (ACE); ETH Zürich; Zürich Switzerland
- Department of Environmental Microbiology; Eawag; Dübendorf Switzerland
| | - Christian Rellstab
- Biodiversity and Conservation Biology; WSL Swiss Federal Research Institute; Birmensdorf Switzerland
| | - Frédéric Guillaume
- Department of Evolutionary Biology and Environmental Studies; University of Zürich; Zürich Switzerland
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Levy Karin E, Shkedy D, Ashkenazy H, Cartwright RA, Pupko T. Inferring Rates and Length-Distributions of Indels Using Approximate Bayesian Computation. Genome Biol Evol 2018; 9:1280-1294. [PMID: 28453624 PMCID: PMC5438127 DOI: 10.1093/gbe/evx084] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2017] [Indexed: 02/07/2023] Open
Abstract
The most common evolutionary events at the molecular level are single-base substitutions, as well as insertions and deletions (indels) of short DNA segments. A large body of research has been devoted to develop probabilistic substitution models and to infer their parameters using likelihood and Bayesian approaches. In contrast, relatively little has been done to model indel dynamics, probably due to the difficulty in writing explicit likelihood functions. Here, we contribute to the effort of modeling indel dynamics by presenting SpartaABC, an approximate Bayesian computation (ABC) approach to infer indel parameters from sequence data (either aligned or unaligned). SpartaABC circumvents the need to use an explicit likelihood function by extracting summary statistics from simulated sequences. First, summary statistics are extracted from the input sequence data. Second, SpartaABC samples indel parameters from a prior distribution and uses them to simulate sequences. Third, it computes summary statistics from the simulated sets of sequences. By computing a distance between the summary statistics extracted from the input and each simulation, SpartaABC can provide an approximation to the posterior distribution of indel parameters as well as point estimates. We study the performance of our methodology and show that it provides accurate estimates of indel parameters in simulations. We next demonstrate the utility of SpartaABC by studying the impact of alignment errors on the inference of positive selection. A C ++ program implementing SpartaABC is freely available in http://spartaabc.tau.ac.il.
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Affiliation(s)
- Eli Levy Karin
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel.,Department of Molecular Biology & Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
| | - Dafna Shkedy
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
| | - Haim Ashkenazy
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
| | - Reed A Cartwright
- The Biodesign Institute, Arizona State University, Tempe, AZ.,School of Life Sciences, Arizona State University, Tempe, AZ
| | - Tal Pupko
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
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