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Lorenzana GP, Figueiró HV, Coutinho LL, Villela PMS, Eizirik E. Comparative assessment of genotyping-by-sequencing and whole-exome sequencing for estimating genetic diversity and geographic structure in small sample sizes: insights from wild jaguar populations. Genetica 2024:10.1007/s10709-024-00212-5. [PMID: 39322785 DOI: 10.1007/s10709-024-00212-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 09/12/2024] [Indexed: 09/27/2024]
Abstract
Biologists currently have an assortment of high-throughput sequencing techniques allowing the study of population dynamics in increasing detail. The utility of genetic estimates depends on their ability to recover meaningful approximations while filtering out noise produced by artifacts. In this study, we empirically compared the congruence of two reduced representation approaches (genotyping-by-sequencing, GBS, and whole-exome sequencing, WES) in estimating genetic diversity and population structure using SNP markers typed in a small number of wild jaguar (Panthera onca) samples from South America. Due to its targeted nature, WES allowed for a more straightforward reconstruction of loci compared to GBS, facilitating the identification of true polymorphisms across individuals. We therefore used WES-derived metrics as a benchmark against which GBS-derived indicators were compared, adjusting parameters for locus assembly and SNP filtering in the latter. We observed significant variation in SNP call rates across samples in GBS datasets, leading to a recurrent miscalling of heterozygous sites. This issue was further amplified by small sample sizes, ultimately impacting the consistency of summary statistics between genotyping methods. Recognizing that the genetic markers obtained from GBS and WES are intrinsically different due to varying evolutionary pressures, particularly selection, we consider that our empirical comparison offers valuable insights and highlights critical considerations for estimating population genetic attributes using reduced representation datasets. Our results emphasize the critical need for careful evaluation of missing data and stringent filtering to achieve reliable estimates of genetic diversity and differentiation in elusive wildlife species.
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Affiliation(s)
- Gustavo P Lorenzana
- Laboratório de Biologia Genômica e Molecular, Escola de Ciências da Saúde e da Vida, PUCRS, Porto Alegre, Brazil.
- School of Forestry, Northern Arizona University, Flagstaff, AZ, USA.
| | - Henrique V Figueiró
- Laboratório de Biologia Genômica e Molecular, Escola de Ciências da Saúde e da Vida, PUCRS, Porto Alegre, Brazil
- Environmental Genomics Group, Vale Institute of Technology, Belem, Brazil
| | | | - Priscilla M S Villela
- Centro de Genômica Funcional, ESALQ-USP, Piracicaba, Brazil
- EcoMol Consultoria e Projetos, Piracicaba, Brazil
| | - Eduardo Eizirik
- Laboratório de Biologia Genômica e Molecular, Escola de Ciências da Saúde e da Vida, PUCRS, Porto Alegre, Brazil
- Instituto Pró-Carnívoros, Atibaia, Brazil
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2
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Potter S, Moritz C, Piggott MP, Bragg JG, Afonso Silva AC, Bi K, McDonald-Spicer C, Turakulov R, Eldridge MDB. Museum Skins Enable Identification of Introgression Associated with Cytonuclear Discordance. Syst Biol 2024; 73:579-593. [PMID: 38577768 PMCID: PMC11377193 DOI: 10.1093/sysbio/syae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 03/14/2024] [Accepted: 04/03/2024] [Indexed: 04/06/2024] Open
Abstract
Increased sampling of genomes and populations across closely related species has revealed that levels of genetic exchange during and after speciation are higher than previously thought. One obvious manifestation of such exchange is strong cytonuclear discordance, where the divergence in mitochondrial DNA (mtDNA) differs from that for nuclear genes more (or less) than expected from differences between mtDNA and nuclear DNA (nDNA) in population size and mutation rate. Given genome-scale data sets and coalescent modeling, we can now confidently identify cases of strong discordance and test specifically for historical or recent introgression as the cause. Using population sampling, combining exon capture data from historical museum specimens and recently collected tissues we showcase how genomic tools can resolve complex evolutionary histories in the brachyotis group of rock-wallabies (Petrogale). In particular, applying population and phylogenomic approaches we can assess the role of demographic processes in driving complex evolutionary patterns and assess a role of ancient introgression and hybridization. We find that described species are well supported as monophyletic taxa for nDNA genes, but not for mtDNA, with cytonuclear discordance involving at least 4 operational taxonomic units across 4 species which diverged 183-278 kya. ABC modeling of nDNA gene trees supports introgression during or after speciation for some taxon pairs with cytonuclear discordance. Given substantial differences in body size between the species involved, this evidence for gene flow is surprising. Heterogenous patterns of introgression were identified but do not appear to be associated with chromosome differences between species. These and previous results suggest that dynamic past climates across the monsoonal tropics could have promoted reticulation among related species.
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Affiliation(s)
- Sally Potter
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Macquarie Park, NSW 2109, Australia
- Division of Ecology and Evolution, Research School of Biology, 134 Linnaeus Way, The Australian National University, Acton, ACT 2601, Australia
- Australian Museum Research Institute, Australian Museum, 1 William St, Sydney, NSW 2010, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology, 134 Linnaeus Way, The Australian National University, Acton, ACT 2601, Australia
| | - Maxine P Piggott
- Division of Ecology and Evolution, Research School of Biology, 134 Linnaeus Way, The Australian National University, Acton, ACT 2601, Australia
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Casuarina, NT 0811, Australia
| | - Jason G Bragg
- National Herbarium of New South Wales, The Royal Botanical Gardens and Domain Trust, Mrs Macquaries Road, Sydney, NSW 2000, Australia
| | | | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Christiana McDonald-Spicer
- Division of Ecology and Evolution, Research School of Biology, 134 Linnaeus Way, The Australian National University, Acton, ACT 2601, Australia
| | - Rustamzhon Turakulov
- Australian Genome Research Facility, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia
- Earth Sciences, College of Science and Engineering, Flinders University GPO Box 2100, Adelaide, SA 5001, Australia
| | - Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, 1 William St, Sydney, NSW 2010, Australia
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3
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Zhang W, Fan Y, Deng W, Chen Y, Wang S, Kang S, Steenwyk JL, Xiang M, Liu X. Characterization of genome-wide phylogenetic conflict uncovers evolutionary modes of carnivorous fungi. mBio 2024:e0213324. [PMID: 39207102 DOI: 10.1128/mbio.02133-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024] Open
Abstract
Mass extinction has often paved the way for rapid evolutionary radiation, resulting in the emergence of diverse taxa within specific lineages. The emergence and diversification of carnivorous nematode-trapping fungi (NTF) in Ascomycota have been linked to the Permian-Triassic (PT) extinction, but the processes underlying NTF radiation remain unclear. We conducted phylogenomic analyses using 23 genomes that represent three NTF lineages, each employing distinct nematode traps-mechanical traps (Drechslerella spp.), three-dimensional (3D) adhesive traps (Arthrobotrys spp.), and two-dimensional (2D) adhesive traps (Dactylellina spp.), and the genome of one non-NTF species as the outgroup. These analyses revealed multiple mechanisms that likely contributed to the tempo of the NTF evolution and rapid radiation. The species tree of NTFs based on 2,944 single-copy orthologous genes suggested that Drechslerella emerged earlier than Arthrobotrys and Dactylellina. Extensive genome-wide phylogenetic discordance was observed, mainly due to incomplete lineage sorting (ILS) between lineages. Two modes of non-vertical evolution (introgression and horizontal gene transfer) also contributed to phylogenetic discordance. The ILS genes that are associated with hyphal growth and trap morphogenesis (e.g., those associated with the cell membrane system and polarized cell division) exhibited signs of positive selection.IMPORTANCEBy conducting a comprehensive phylogenomic analysis of 23 genomes across three NTF lineages, the research reveals how diverse evolutionary mechanisms, including ILS and non-vertical evolution (introgression and horizontal gene transfer), contribute to the swift diversification of NTFs. These findings highlight the complex evolutionary dynamics that drive the rapid radiation of NTFs, providing valuable insights into the processes underlying their diversity and adaptation.
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Affiliation(s)
- Weiwei Zhang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology, and Department of Microbiology, College of Life Science, Nankai University, Tianjin, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yani Fan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Deng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology, and Department of Microbiology, College of Life Science, Nankai University, Tianjin, China
| | - Yue Chen
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology, and Department of Microbiology, College of Life Science, Nankai University, Tianjin, China
| | - Shunxian Wang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology, and Department of Microbiology, College of Life Science, Nankai University, Tianjin, China
| | - Seogchan Kang
- Department of Plant Pathology & Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Jacob Lucas Steenwyk
- Howards Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Meichun Xiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xingzhong Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology, and Department of Microbiology, College of Life Science, Nankai University, Tianjin, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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4
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Srigyan M, Schubert BW, Bushell M, Santos SHD, Figueiró HV, Sacco S, Eizirik E, Shapiro B. Mitogenomic analysis of a late Pleistocene jaguar from North America. J Hered 2024; 115:424-431. [PMID: 38150503 PMCID: PMC11235123 DOI: 10.1093/jhered/esad082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 12/02/2023] [Accepted: 12/22/2023] [Indexed: 12/29/2023] Open
Abstract
The jaguar (Panthera onca) is the largest living cat species native to the Americas and one of few large American carnivorans to have survived into the Holocene. However, the extent to which jaguar diversity declined during the end-Pleistocene extinction event remains unclear. For example, Pleistocene jaguar fossils from North America are notably larger than the average extant jaguar, leading to hypotheses that jaguars from this continent represent a now-extinct subspecies (Panthera onca augusta) or species (Panthera augusta). Here, we used a hybridization capture approach to recover an ancient mitochondrial genome from a large, late Pleistocene jaguar from Kingston Saltpeter Cave, Georgia, United States, which we sequenced to 26-fold coverage. We then estimated the evolutionary relationship between the ancient jaguar mitogenome and those from other extinct and living large felids, including multiple jaguars sampled across the species' current range. The ancient mitogenome falls within the diversity of living jaguars. All sampled jaguar mitogenomes share a common mitochondrial ancestor ~400 thousand years ago, indicating that the lineage represented by the ancient specimen dispersed into North America from the south at least once during the late Pleistocene. While genomic data from additional and older specimens will continue to improve understanding of Pleistocene jaguar diversity in the Americas, our results suggest that this specimen falls within the variation of extant jaguars despite the relatively larger size and geographic location and does not represent a distinct taxon.
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Affiliation(s)
- Megha Srigyan
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Blaine W Schubert
- Department of Geosciences, Center of Excellence in Paleontology, East Tennessee State University, Johnson City, TN, United States
| | - Matthew Bushell
- Department of Geosciences, Center of Excellence in Paleontology, East Tennessee State University, Johnson City, TN, United States
| | - Sarah H D Santos
- Department of Biology, University of Western Ontario, London, ON, Canada
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Henrique Vieira Figueiró
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
- Environmental Genomics Group, Vale Institute of Technology, Belem, PA, Brazil
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, United States
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5
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Murphy WJ, Harris AJ. Toward telomere-to-telomere cat genomes for precision medicine and conservation biology. Genome Res 2024; 34:655-664. [PMID: 38849156 PMCID: PMC11216403 DOI: 10.1101/gr.278546.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
Abstract
Genomic data from species of the cat family Felidae promise to stimulate veterinary and human medical advances, and clarify the coherence of genome organization. We describe how interspecies hybrids have been instrumental in the genetic analysis of cats, from the first genetic maps to propelling cat genomes toward the T2T standard set by the human genome project. Genotype-to-phenotype mapping in cat models has revealed dozens of health-related genetic variants, the molecular basis for mammalian pigmentation and patterning, and species-specific adaptations. Improved genomic surveillance of natural and captive populations across the cat family tree will increase our understanding of the genetic architecture of traits, population dynamics, and guide a future of genome-enabled biodiversity conservation.
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Affiliation(s)
- William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA;
- Department of Biology, Texas A&M University, College Station, Texas 77843-4458, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843-4458, USA
| | - Andrew J Harris
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843-4458, USA
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6
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Chatar N, Michaud M, Tamagnini D, Fischer V. Evolutionary patterns of cat-like carnivorans unveil drivers of the sabertooth morphology. Curr Biol 2024; 34:2460-2473.e4. [PMID: 38759651 DOI: 10.1016/j.cub.2024.04.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/10/2024] [Accepted: 04/24/2024] [Indexed: 05/19/2024]
Abstract
The sabertooth morphology stands as a classic case of convergence, manifesting recurrently across various vertebrate groups, prominently within two carnivorans clades: felids and nimravids. Nonetheless, the evolutionary mechanisms driving these recurring phenotypes remain insufficiently understood, lacking a robust phylogenetic and spatiotemporal framework. We reconstruct the tempo and mode of craniomandibular evolution of Felidae and Nimravidae and evaluate the strength of the dichotomy between conical and saber-toothed species, as well as within saber-toothed morphotypes. To do so, we investigate morphological variation, convergence, phenotypic integration, and evolutionary rates, employing a comprehensive dataset of nearly 200 3D models encompassing mandibles and crania from both extinct and extant feline-like carnivorans, spanning their entire evolutionary timeline. Our results reject the hypothesis of a distinctive sabertooth morphology, revealing instead a continuous spectrum of feline-like phenotypes in both the cranium and mandible, with sporadic instances of unequivocal convergence. Disparity peaked at the end of the Miocene and is usually higher in clades containing taxa with extreme sabertoothed adaptations. We show that taxa with saberteeth exhibit a lower degree of craniomandibular integration, allowing to exhibit a greater range of phenotypes. Those same groups usually show a burst of morphological evolutionary rate at the beginning of their evolutionary history. Consequently, we propose that a reduced degree of integration coupled with rapid evolutionary rates emerge as key components in the development of a sabertooth morphology in multiple clades.
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Affiliation(s)
- Narimane Chatar
- Evolution and Diversity Dynamics Lab, Université de Liège, Allée du six août 14, 4000 Liège, Belgium; Functional Anatomy and Vertebrate Evolution Lab, Department of Integrative Biology, University of California, Berkeley, 3040 Valley Life Sciences Building, Berkeley, CA 94720, USA.
| | - Margot Michaud
- Evolution and Diversity Dynamics Lab, Université de Liège, Allée du six août 14, 4000 Liège, Belgium; Département Formation et Recherche Sciences et Technologie, Université de Guyane, WMMX+5Q3, Cayenne 97300, Guyane
| | - Davide Tamagnini
- Department of Biology and Biotechnologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Valentin Fischer
- Evolution and Diversity Dynamics Lab, Université de Liège, Allée du six août 14, 4000 Liège, Belgium
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7
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Liu G, Pan Q, Dai Y, Wang X, Li M, Zhu P, Zhou X. Phylogenomics of Afrotherian mammals and improved resolution of extant Paenungulata. Mol Phylogenet Evol 2024; 195:108047. [PMID: 38460890 DOI: 10.1016/j.ympev.2024.108047] [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: 10/25/2023] [Revised: 02/19/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
Molecular investigations have gathered a diverse set of mammals-predominantly African natives like elephants, hyraxes, and aardvarks-into a clade known as Afrotheria. Nevertheless, the precise phylogenetic relationships among these species remain contentious. Here, we sourced orthologous markers and ultraconserved elements to discern the interordinal connections among Afrotherian mammals. Our phylogenetic analyses bolster the common origin of Afroinsectiphilia and Paenungulata, and propose Afrosoricida as the closer relative to Macroscelidea rather than Tubulidentata, while also challenging the notion of Sirenia and Hyracoidea as sister taxa. The approximately unbiased test and the gene concordance factor uniformly recognized the alliance of Proboscidea with Hyracoidea as the dominant topology within Paenungulata. Investigation into sites with extremly high phylogenetic signal unveiled their potential to intensify conflicts in the Paenungulata topology. Subsequent exploration suggested that incomplete lineage sorting was predominantly responsible for the observed contentious relationships, whereas introgression exerted a subsidiary influence. The divergence times estimated in our study hint at the Cretaceous-Paleogene (K-Pg) extinction event as a catalyst for Afrotherian diversification. Overall, our findings deliver a tentative but insightful overview of Afrotheria phylogeny and divergence, elucidating these relationships through the lens of phylogenomics.
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Affiliation(s)
- Gaoming Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Pan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yichen Dai
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiao Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Meng Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Pingfen Zhu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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8
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Pang XX, Zhang DY. Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information. Syst Biol 2024; 73:207-222. [PMID: 38224495 PMCID: PMC11129598 DOI: 10.1093/sysbio/syad077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 12/17/2023] [Accepted: 12/27/2023] [Indexed: 01/17/2024] Open
Abstract
In recent years, the study of hybridization and introgression has made significant progress, with ghost introgression-the transfer of genetic material from extinct or unsampled lineages to extant species-emerging as a key area for research. Accurately identifying ghost introgression, however, presents a challenge. To address this issue, we focused on simple cases involving 3 species with a known phylogenetic tree. Using mathematical analyses and simulations, we evaluated the performance of popular phylogenetic methods, including HyDe and PhyloNet/MPL, and the full-likelihood method, Bayesian Phylogenetics and Phylogeography (BPP), in detecting ghost introgression. Our findings suggest that heuristic approaches relying on site-pattern counts or gene-tree topologies struggle to differentiate ghost introgression from introgression between sampled non-sister species, frequently leading to incorrect identification of donor and recipient species. The full-likelihood method BPP uses multilocus sequence alignments directly-hence taking into account both gene-tree topologies and branch lengths, by contrast, is capable of detecting ghost introgression in phylogenomic datasets. We analyzed a real-world phylogenomic dataset of 14 species of Jaltomata (Solanaceae) to showcase the potential of full-likelihood methods for accurate inference of introgression.
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Affiliation(s)
- Xiao-Xu Pang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Da-Yong Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
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9
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Morris DR, McWhorter TJ, Boardman WSJ, Simpson G, Wentzel J, Coetzee J, Moodley Y. Unravelling the maternal evolutionary history of the African leopard ( Panthera pardus pardus). PeerJ 2024; 12:e17018. [PMID: 38618571 PMCID: PMC11016244 DOI: 10.7717/peerj.17018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 02/06/2024] [Indexed: 04/16/2024] Open
Abstract
The African leopard (Panthera pardus pardus) has lost a significant proportion of its historical range, notably in north-western Africa and South Africa. Recent studies have explored the genetic diversity and population structure of African leopards across the continent. A notable genetic observation is the presence of two divergent mitochondrial lineages, PAR-I and PAR-II. Both lineages appeared to be distributed widely, with PAR-II frequently found in southern Africa. Until now, no study has attempted to date the emergence of either lineage, assess haplotype distribution, or explore their evolutionary histories in any detail. To investigate these underappreciated questions, we compiled the largest and most geographically representative leopard data set of the mitochondrial NADH-5 gene to date. We combined samples (n = 33) collected in an altitudinal transect across the Mpumalanga province of South Africa, where two populations of leopard are known to be in genetic contact, with previously published sequences of African leopard (n = 211). We estimate that the maternal PAR-I and PAR-II lineages diverged approximately 0.7051 (0.4477-0.9632) million years ago (Ma). Through spatial and demographic analyses, we show that while PAR-I underwent a mid-Pleistocene population expansion resulting in several closely related haplotypes with little geographic structure across much of its range, PAR-II remained at constant size and may even have declined slightly in the last 0.1 Ma. The higher genetic drift experienced within PAR-II drove a greater degree of structure with little haplotype sharing and unique haplotypes in central Africa, the Cape, KwaZulu-Natal and the South African Highveld. The phylogeographic structure of PAR-II, with its increasing frequency southward and its exclusive occurrence in south-eastern South Africa, suggests that this lineage may have been isolated in South Africa during the mid-Pleistocene. This hypothesis is supported by historical changes in paleoclimate that promoted intense aridification around the Limpopo Basin between 1.0-0.6 Ma, potentially reducing gene flow and promoting genetic drift. Interestingly, we ascertained that the two nuclear DNA populations identified by a previous study as East and West Mpumalanga correspond to PAR-I and PAR-II, respectively, and that they have come into secondary contact in the Lowveld region of South Africa. Our results suggest a subdivision of African leopard mtDNA into two clades, with one occurring almost exclusively in South Africa, and we identify the potential environmental drivers of this observed structure. We caution that our results are based on a single mtDNA locus, but it nevertheless provides a hypothesis that can be further tested with a dense sample of nuclear DNA data, preferably whole genomes. If our interpretation holds true, it would provide the first genetic explanation for the smaller observed size of leopards at the southernmost end of their range in Africa.
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Affiliation(s)
- Declan R. Morris
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - Todd J. McWhorter
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - Wayne S. J. Boardman
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - Gregory Simpson
- Department of Wildlife Studies, Faculty of Veterinary of Science, University of Pretoria, Onderstepoort, Gauteng, South Africa
| | - Jeanette Wentzel
- Department of Wildlife Studies, Faculty of Veterinary of Science, University of Pretoria, Onderstepoort, Gauteng, South Africa
- Department of Veterinary Tropical Diseases, Hans Hoheisen Wildlife Research Station, University of Pretoria, Onderstepoort, Gauteng, South Africa
| | - Jannie Coetzee
- Mpumalanga Tourism and Parks Agency, Nelspruit, Mpumalanga, South Africa
| | - Yoshan Moodley
- Department of Biological Sciences, University of Venda, Thohoyandou, Limpopo, South Africa
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10
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Bertola LD, Quinn L, Hanghøj K, Garcia-Erill G, Rasmussen MS, Balboa RF, Meisner J, Bøggild T, Wang X, Lin L, Nursyifa C, Liu X, Li Z, Chege M, Moodley Y, Brüniche-Olsen A, Kuja J, Schubert M, Agaba M, Santander CG, Sinding MHS, Muwanika V, Masembe C, Siegismund HR, Moltke I, Albrechtsen A, Heller R. Giraffe lineages are shaped by major ancient admixture events. Curr Biol 2024; 34:1576-1586.e5. [PMID: 38479386 DOI: 10.1016/j.cub.2024.02.051] [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: 06/11/2023] [Revised: 09/29/2023] [Accepted: 02/21/2024] [Indexed: 04/11/2024]
Abstract
Strong genetic structure has prompted discussion regarding giraffe taxonomy,1,2,3 including a suggestion to split the giraffe into four species: Northern (Giraffa c. camelopardalis), Reticulated (G. c. reticulata), Masai (G. c. tippelskirchi), and Southern giraffes (G. c. giraffa).4,5,6 However, their evolutionary history is not yet fully resolved, as previous studies used a simple bifurcating model and did not explore the presence or extent of gene flow between lineages. We therefore inferred a model that incorporates various evolutionary processes to assess the drivers of contemporary giraffe diversity. We analyzed whole-genome sequencing data from 90 wild giraffes from 29 localities across their current distribution. The most basal divergence was dated to 280 kya. Genetic differentiation, FST, among major lineages ranged between 0.28 and 0.62, and we found significant levels of ancient gene flow between them. In particular, several analyses suggested that the Reticulated lineage evolved through admixture, with almost equal contribution from the Northern lineage and an ancestral lineage related to Masai and Southern giraffes. These new results highlight a scenario of strong differentiation despite gene flow, providing further context for the interpretation of giraffe diversity and the process of speciation in general. They also illustrate that conservation measures need to target various lineages and sublineages and that separate management strategies are needed to conserve giraffe diversity effectively. Given local extinctions and recent dramatic declines in many giraffe populations, this improved understanding of giraffe evolutionary history is relevant for conservation interventions, including reintroductions and reinforcements of existing populations.
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Affiliation(s)
- Laura D Bertola
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Renzo F Balboa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Meisner
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Bøggild
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xi Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Long Lin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Casia Nursyifa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xiaodong Liu
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Zilong Li
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mumbi Chege
- Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands; Wildlife Research and Training Institute, Naivasha, Kenya
| | - Yoshan Moodley
- Department of Biological Sciences, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa
| | | | - Josiah Kuja
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Schubert
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Morris Agaba
- School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, Nelson Mandela Road, Arusha, Tanzania
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Vincent Muwanika
- College of Agricultural and Environmental Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Charles Masembe
- College of Natural Sciences, Makerere University, P O. Box 7062, Kampala, Uganda
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | | | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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11
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Kaelin CB, McGowan KA, Hutcherson AD, Delay JM, Li JH, Kiener S, Jagannathan V, Leeb T, Murphy WJ, Barsh GS. Ancestry dynamics and trait selection in a designer cat breed. Curr Biol 2024; 34:1506-1518.e7. [PMID: 38531359 PMCID: PMC11162505 DOI: 10.1016/j.cub.2024.02.075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/10/2024] [Accepted: 02/28/2024] [Indexed: 03/28/2024]
Abstract
The Bengal cat breed was developed from intercrosses between the Asian leopard cat, Prionailurus bengalensis, and the domestic cat, Felis catus, with a last common ancestor approximately 6 million years ago. Predicted to derive ∼94% of their genome from domestic cats, regions of the leopard cat genome are thought to account for the unique pelage traits and ornate color patterns of the Bengal breed, which are similar to those of ocelots and jaguars. We explore ancestry distribution and selection signatures in the Bengal breed by using reduced representation and whole-genome sequencing from 947 cats. The mean proportion of leopard cat DNA in the Bengal breed is 3.48%, lower than predicted from breed history, and is broadly distributed, covering 93% of the Bengal genome. Overall, leopard cat introgressions do not show strong signatures of selection across the Bengal breed. However, two popular color traits in Bengal cats, charcoal and pheomelanin intensity, are explained by selection of leopard cat genes whose expression is reduced in a domestic cat background, consistent with genetic incompatibility resulting from hybridization. We characterize several selective sweeps in the Bengal genome that harbor candidate genes for pelage and color pattern and that are associated with domestic, rather than leopard, cat haplotypes. We identify the molecular and phenotypic basis of one selective sweep as reduced expression of the Fgfr2 gene, which underlies glitter, a trait desired by breeders that affects hair texture and light reflectivity.
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Affiliation(s)
- Christopher B Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kelly A McGowan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - John M Delay
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Sarah Kiener
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; Dermfocus, University of Bern, 3001 Bern, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; Dermfocus, University of Bern, 3001 Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; Dermfocus, University of Bern, 3001 Bern, Switzerland
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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12
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Pisciottano F, Campos MC, Penna C, Bruque CD, Gabaldón T, Saragüeta P. Positive selection in gamete interaction proteins in Carnivora. Mol Ecol 2024; 33:e17263. [PMID: 38318732 DOI: 10.1111/mec.17263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 12/15/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024]
Abstract
The absence of robust interspecific isolation barriers among pantherines, including the iconic South American jaguar (Panthera onca), led us to study molecular evolution of typically rapidly evolving reproductive proteins within this subfamily and related groups. In this study, we delved into the evolutionary forces acting on the zona pellucida (ZP) gamete interaction protein family and the sperm-oocyte fusion protein pair IZUMO1-JUNO across the Carnivora order, distinguishing between Caniformia and Feliformia suborders and anticipating few significant diversifying changes in the Pantherinae subfamily. A chromosome-resolved jaguar genome assembly facilitated coding sequences, enabling the reconstruction of protein evolutionary histories. Examining sequence variability across more than 30 Carnivora species revealed that Feliformia exhibited significantly lower diversity compared to its sister taxa, Caniformia. Molecular evolution analyses of ZP2 and ZP3, subunits directly involved in sperm-recognition, unveiled diversifying positive selection in Feliformia, Caniformia and Pantherinae, although no significant changes were linked to sperm binding. Structural cross-linking ZP subunits, ZP4 and ZP1 exhibited lower levels or complete absence of positive selection. Notably, the fusion protein IZUMO1 displayed prominent positive selection signatures and sites in basal lineages of both Caniformia and Feliformia, extending along the Caniformia subtree but absent in Pantherinae. Conversely, JUNO did not exhibit any positive selection signatures across tested lineages and clades. Eight Caniformia-specific positive selected sites in IZUMO1 were detected within two JUNO-interaction clusters. Our findings provide for the first time insights into the evolutionary trajectories of ZP proteins and the IZUMO1-JUNO gamete interaction pair within the Carnivora order.
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Affiliation(s)
- Francisco Pisciottano
- Instituto de Biología y Medicina Experimental (IByME-CONICET), Buenos Aires, Argentina
| | - María Clara Campos
- Instituto de Biología y Medicina Experimental (IByME-CONICET), Buenos Aires, Argentina
| | - Clementina Penna
- Instituto de Biología y Medicina Experimental (IByME-CONICET), Buenos Aires, Argentina
| | - Carlos David Bruque
- Unidad de Conocimiento Traslacional Hospitalaria Patagónica, Hospital de Alta Complejidad El Calafate SAMIC, El Calafate, Santa Cruz, Argentina
| | - Toni Gabaldón
- Barcelona Supercomputing Center (BSC), Institute for Research in Biomedicine (IRB), and Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Patricia Saragüeta
- Instituto de Biología y Medicina Experimental (IByME-CONICET), Buenos Aires, Argentina
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13
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Barazandeh M, Kriti D, Fickel J, Nislow C. The Addis Ababa Lions: Whole-Genome Sequencing of a Rare and Precious Population. Genome Biol Evol 2024; 16:evae021. [PMID: 38302110 PMCID: PMC10871700 DOI: 10.1093/gbe/evae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 12/18/2023] [Accepted: 01/23/2024] [Indexed: 02/03/2024] Open
Abstract
Lions are widely known as charismatic predators that once roamed across the globe, but their populations have been greatly affected by environmental factors and human activities over the last 150 yr. Of particular interest is the Addis Ababa lion population, which has been maintained in captivity at around 20 individuals for over 75 yr, while many wild African lion populations have become extinct. In order to understand the molecular features of this unique population, we conducted a whole-genome sequencing study on 15 Addis Ababa lions and detected 4.5 million distinct genomic variants compared with the reference African lion genome. Using functional annotation, we identified several genes with mutations that potentially impact various traits such as mane color, body size, reproduction, gastrointestinal functions, cardiovascular processes, and sensory perception. These findings offer valuable insights into the genetics of this threatened lion population.
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Affiliation(s)
- Marjan Barazandeh
- Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Divya Kriti
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jörns Fickel
- Institute for Biochemistry and Biology, University Potsdam, Potsdam, Germany
- Department of Evolutionary Genetics, Research Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Corey Nislow
- Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
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14
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Jensen A, Swift F, de Vries D, Beck RMD, Kuderna LFK, Knauf S, Chuma IS, Keyyu JD, Kitchener AC, Farh K, Rogers J, Marques-Bonet T, Detwiler KM, Roos C, Guschanski K. Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation. Mol Biol Evol 2023; 40:msad247. [PMID: 37987553 PMCID: PMC10691879 DOI: 10.1093/molbev/msad247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/17/2023] [Accepted: 11/09/2023] [Indexed: 11/22/2023] Open
Abstract
Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation.
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Affiliation(s)
- Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala SE-75236, Sweden
| | - Frances Swift
- School of Biological Sciences, Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Lukas F K Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald – Insel Riems 17493, Germany
| | | | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh EH1 1JF, UK
- School of Geosciences, University of Edinburgh, Edinburgh EH8 9XP, UK
| | - Kyle Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona 08003, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Barcelona 08010, Spain
| | - Kate M Detwiler
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, USA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala SE-75236, Sweden
- School of Biological Sciences, Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
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15
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Lescroart J, Bonilla-Sánchez A, Napolitano C, Buitrago-Torres DL, Ramírez-Chaves HE, Pulido-Santacruz P, Murphy WJ, Svardal H, Eizirik E. Extensive Phylogenomic Discordance and the Complex Evolutionary History of the Neotropical Cat Genus Leopardus. Mol Biol Evol 2023; 40:msad255. [PMID: 37987559 PMCID: PMC10701098 DOI: 10.1093/molbev/msad255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/22/2023] Open
Abstract
Even in the genomics era, the phylogeny of Neotropical small felids comprised in the genus Leopardus remains contentious. We used whole-genome resequencing data to construct a time-calibrated consensus phylogeny of this group, quantify phylogenomic discordance, test for interspecies introgression, and assess patterns of genetic diversity and demographic history. We infer that the Leopardus radiation started in the Early Pliocene as an initial speciation burst, followed by another in its subgenus Oncifelis during the Early Pleistocene. Our findings challenge the long-held notion that ocelot (Leopardus pardalis) and margay (L. wiedii) are sister species and instead indicate that margay is most closely related to the enigmatic Andean cat (L. jacobita), whose whole-genome data are reported here for the first time. In addition, we found that the newly sampled Andean tiger cat (L. tigrinus pardinoides) population from Colombia associates closely with Central American tiger cats (L. tigrinus oncilla). Genealogical discordance was largely attributable to incomplete lineage sorting, yet was augmented by strong gene flow between ocelot and the ancestral branch of Oncifelis, as well as between Geoffroy's cat (L. geoffroyi) and southern tiger cat (L. guttulus). Contrasting demographic trajectories have led to disparate levels of current genomic diversity, with a nearly tenfold difference in heterozygosity between Andean cat and ocelot, spanning the entire range of variability found in extant felids. Our analyses improved our understanding of the speciation history and diversity patterns in this felid radiation, and highlight the benefits to phylogenomic inference of embracing the many heterogeneous signals scattered across the genome.
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Affiliation(s)
- Jonas Lescroart
- Department of Biology, University of Antwerp, Antwerp, Belgium
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Alejandra Bonilla-Sánchez
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
- Faculty of Exact and Natural Sciences, University of Antioquia, Medellín, Colombia
| | - Constanza Napolitano
- Department of Biological Sciences and Biodiversity, University of Los Lagos, Osorno, Chile
- Institute of Ecology and Biodiversity, Concepción, Chile
- Cape Horn International Center, Puerto Williams, Chile
- Andean Cat Alliance, Villa Carlos Paz, Argentina
| | - Diana L Buitrago-Torres
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Héctor E Ramírez-Chaves
- Department of Biological Sciences, University of Caldas, Manizales, Colombia
- Centro de Museos, Museo de Historia Natural, University of Caldas, Manizales, Colombia
| | | | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Hannes Svardal
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Naturalis Biodiversity Center, Leiden, Netherlands
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
- Instituto Pró-Carnívoros, Atibaia, Brazil
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16
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Tan X, Qi J, Liu Z, Fan P, Liu G, Zhang L, Shen Y, Li J, Roos C, Zhou X, Li M. Phylogenomics Reveals High Levels of Incomplete Lineage Sorting at the Ancestral Nodes of the Macaque Radiation. Mol Biol Evol 2023; 40:msad229. [PMID: 37823401 PMCID: PMC10638670 DOI: 10.1093/molbev/msad229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/06/2023] [Accepted: 10/08/2023] [Indexed: 10/13/2023] Open
Abstract
The genus Macaca includes 23 species assigned into 4 to 7 groups. It exhibits the largest geographic range and represents the most successful example of adaptive radiation of nonhuman primates. However, intrageneric phylogenetic relationships among species remain controversial and have not been resolved so far. In this study, we conducted a phylogenomic analysis on 16 newly generated and 8 published macaque genomes. We found strong evidence supporting the division of this genus into 7 species groups. Incomplete lineage sorting (ILS) was the primary factor contributing to the discordance observed among gene trees; however, we also found evidence of hybridization events, specifically between the ancestral arctoides/sinica and silenus/nigra lineages that resulted in the hybrid formation of the fascicularis/mulatta group. Combined with fossil data, our phylogenomic data were used to establish a scenario for macaque radiation. These findings provide insights into ILS and potential ancient introgression events that were involved in the radiation of macaques, which will lead to a better understanding of the rapid speciation occurring in nonhuman primates.
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Affiliation(s)
- Xinxin Tan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Geneplus-Beijing Institute, Beijing 102206, China
| | - Jiwei Qi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhijin Liu
- College of Life Sciences, Capital Normal University, Beijing 100049, China
| | - Pengfei Fan
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Gaoming Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liye Zhang
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
| | - Ying Shen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Li
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
| | - Xuming Zhou
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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17
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Bredemeyer KR, Hillier L, Harris AJ, Hughes GM, Foley NM, Lawless C, Carroll RA, Storer JM, Batzer MA, Rice ES, Davis BW, Raudsepp T, O'Brien SJ, Lyons LA, Warren WC, Murphy WJ. Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution. Nat Genet 2023; 55:1953-1963. [PMID: 37919451 PMCID: PMC10845050 DOI: 10.1038/s41588-023-01548-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/20/2023] [Indexed: 11/04/2023]
Abstract
The role of structurally dynamic genomic regions in speciation is poorly understood due to challenges inherent in diploid genome assembly. Here we reconstructed the evolutionary dynamics of structural variation in five cat species by phasing the genomes of three interspecies F1 hybrids to generate near-gapless single-haplotype assemblies. We discerned that cat genomes have a paucity of segmental duplications relative to great apes, explaining their remarkable karyotypic stability. X chromosomes were hotspots of structural variation, including enrichment with inversions in a large recombination desert with characteristics of a supergene. The X-linked macrosatellite DXZ4 evolves more rapidly than 99.5% of the genome clarifying its role in felid hybrid incompatibility. Resolved sensory gene repertoires revealed functional copy number changes associated with ecomorphological adaptations, sociality and domestication. This study highlights the value of gapless genomes to reveal structural mechanisms underpinning karyotypic evolution, reproductive isolation and ecological niche adaptation.
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Affiliation(s)
- Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - LaDeana Hillier
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Andrew J Harris
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Graham M Hughes
- School of Biology & Environmental Sciences, University College Dublin, Dublin, Ireland
| | - Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Colleen Lawless
- School of Biology & Environmental Sciences, University College Dublin, Dublin, Ireland
| | - Rachel A Carroll
- Department of Animal Sciences, University of Missouri, Columbia, MO, USA
| | | | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Edward S Rice
- Department of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Brian W Davis
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Terje Raudsepp
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Stephen J O'Brien
- Guy Harvey Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine & Surgery, University of Missouri, Columbia, MO, USA
| | - Wesley C Warren
- Department of Animal Sciences, University of Missouri, Columbia, MO, USA.
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA.
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18
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Flouri T, Jiao X, Huang J, Rannala B, Yang Z. Efficient Bayesian inference under the multispecies coalescent with migration. Proc Natl Acad Sci U S A 2023; 120:e2310708120. [PMID: 37871206 PMCID: PMC10622872 DOI: 10.1073/pnas.2310708120] [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: 06/25/2023] [Accepted: 08/15/2023] [Indexed: 10/25/2023] Open
Abstract
Analyses of genome sequence data have revealed pervasive interspecific gene flow and enriched our understanding of the role of gene flow in speciation and adaptation. Inference of gene flow using genomic data requires powerful statistical methods. Yet current likelihood-based methods involve heavy computation and are feasible for small datasets only. Here, we implement the multispecies-coalescent-with-migration model in the Bayesian program bpp, which can be used to test for gene flow and estimate migration rates, as well as species divergence times and population sizes. We develop Markov chain Monte Carlo algorithms for efficient sampling from the posterior, enabling the analysis of genome-scale datasets with thousands of loci. Implementation of both introgression and migration models in the same program allows us to test whether gene flow occurred continuously over time or in pulses. Analyses of genomic data from Anopheles mosquitoes demonstrate rich information in typical genomic datasets about the mode and rate of gene flow.
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Affiliation(s)
- Tomáš Flouri
- Department of Genetics, Evolution, and Environment, University College London, LondonWC1E 6BT, United Kingdom
| | - Xiyun Jiao
- Department of Statistics and Data Science, China Southern University of Science and Technology, Shenzhen518055, China
| | - Jun Huang
- Department of Intelligent Medical Engineering, School of Biomedical Engineering, Capital Medical University, Beijing100069, China
| | - Bruce Rannala
- Department of Evolution and Ecology, University of California, Davis, CA95616
| | - Ziheng Yang
- Department of Genetics, Evolution, and Environment, University College London, LondonWC1E 6BT, United Kingdom
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19
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Yuan J, Wang G, Zhao L, Kitchener AC, Sun T, Chen W, Huang C, Wang C, Xu X, Wang J, Lu H, Xu L, Jiangzuo Q, Murphy WJ, Wu D, Li G. How genomic insights into the evolutionary history of clouded leopards inform their conservation. SCIENCE ADVANCES 2023; 9:eadh9143. [PMID: 37801506 PMCID: PMC10558132 DOI: 10.1126/sciadv.adh9143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
Clouded leopards (Neofelis spp.), a morphologically and ecologically distinct lineage of big cats, are severely threatened by habitat loss and fragmentation, targeted hunting, and other human activities. The long-held poor understanding of their genetics and evolution has undermined the effectiveness of conservation actions. Here, we report a comprehensive investigation of the whole genomes, population genetics, and adaptive evolution of Neofelis. Our results indicate the genus Neofelis arose during the Pleistocene, coinciding with glacial-induced climate changes to the distributions of savannas and rainforests, and signatures of natural selection associated with genes functioning in tooth, pigmentation, and tail development, associated with clouded leopards' unique adaptations. Our study highlights high-altitude adaptation as the main factor driving nontaxonomic population differentiation in Neofelis nebulosa. Population declines and inbreeding have led to reduced genetic diversity and the accumulation of deleterious variation that likely affect reproduction of clouded leopards, highlighting the urgent need for effective conservation efforts.
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Affiliation(s)
- Jiaqing Yuan
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Guiqiang Wang
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Le Zhao
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
- QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK
- School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH9 3PX, UK
| | - Ting Sun
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Wu Chen
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou, China
| | - Chen Huang
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Chen Wang
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou, China
| | - Xiao Xu
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Jinhong Wang
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Huimeng Lu
- School of Life Sciences, Northwestern Polytechnical University, Xi’an, China
| | - Lulu Xu
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Qigao Jiangzuo
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - William J. Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou, China
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20
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Heighton SP, Allio R, Murienne J, Salmona J, Meng H, Scornavacca C, Bastos ADS, Njiokou F, Pietersen DW, Tilak MK, Luo SJ, Delsuc F, Gaubert P. Pangolin Genomes Offer Key Insights and Resources for the World's Most Trafficked Wild Mammals. Mol Biol Evol 2023; 40:msad190. [PMID: 37794645 PMCID: PMC10551234 DOI: 10.1093/molbev/msad190] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023] Open
Abstract
Pangolins form a group of scaly mammals that are trafficked at record numbers for their meat and purported medicinal properties. Despite their conservation concern, knowledge of their evolution is limited by a paucity of genomic data. We aim to produce exhaustive genomic resources that include 3,238 orthologous genes and whole-genome polymorphisms to assess the evolution of all eight extant pangolin species. Robust orthologous gene-based phylogenies recovered the monophyly of the three genera and highlighted the existence of an undescribed species closely related to Southeast Asian pangolins. Signatures of middle Miocene admixture between an extinct, possibly European, lineage and the ancestor of Southeast Asian pangolins, provide new insights into the early evolutionary history of the group. Demographic trajectories and genome-wide heterozygosity estimates revealed contrasts between continental versus island populations and species lineages, suggesting that conservation planning should consider intraspecific patterns. With the expected loss of genomic diversity from recent, extensive trafficking not yet realized in pangolins, we recommend that populations be genetically surveyed to anticipate any deleterious impact of the illegal trade. Finally, we produce a complete set of genomic resources that will be integral for future conservation management and forensic endeavors for pangolins, including tracing their illegal trade. These comprise the completion of whole-genomes for pangolins through the hybrid assembly of the first reference genome for the giant pangolin (Smutsia gigantea) and new draft genomes (∼43x-77x) for four additional species, as well as a database of orthologous genes with over 3.4 million polymorphic sites.
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Affiliation(s)
- Sean P Heighton
- Laboratoire Evolution et Diversité Biologique (EDB)— IRD-UPS-CNRS, Université Toulouse III, Toulouse, France
| | - Rémi Allio
- Institut des Sciences de l'Évolution de Montpellier (ISEM), Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Jérôme Murienne
- Laboratoire Evolution et Diversité Biologique (EDB)— IRD-UPS-CNRS, Université Toulouse III, Toulouse, France
| | - Jordi Salmona
- Laboratoire Evolution et Diversité Biologique (EDB)— IRD-UPS-CNRS, Université Toulouse III, Toulouse, France
| | - Hao Meng
- The State Key Laboratory of Protein and Plant Gene Research of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Céline Scornavacca
- Institut des Sciences de l'Évolution de Montpellier (ISEM), Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Armanda D S Bastos
- Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Pretoria, South Africa
| | - Flobert Njiokou
- Laboratoire de Parasitologie et Ecologie, Faculté des Sciences, Université de Yaoundé I, Yaoundé, Cameroon
| | - Darren W Pietersen
- Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Pretoria, South Africa
| | - Marie-Ka Tilak
- Institut des Sciences de l'Évolution de Montpellier (ISEM), Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Shu-Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Frédéric Delsuc
- Institut des Sciences de l'Évolution de Montpellier (ISEM), Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique (EDB)— IRD-UPS-CNRS, Université Toulouse III, Toulouse, France
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade 16 do Porto, Terminal de Cruzeiros do Porto de Leixões, Porto, Portugal
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21
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Hrabina P, Pernerová L, Suchomel J, Robovský J. Utility of cytochrome c oxidase I for the deciphering of unstable phylogeny and taxonomy of gorals, genus Nemorhaedus Hamilton Smith, 1827 (Bovidae, Ovibovina). Zookeys 2023; 1181:81-110. [PMID: 38313159 PMCID: PMC10838175 DOI: 10.3897/zookeys.1181.108019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/04/2023] [Indexed: 02/06/2024] Open
Abstract
Gorals represent ungulate mammals of the Palearctic and Indo-Malayan realms that face habitat destruction and intense hunting pressure. Their classification has been the subject of various (mainly genetic) assessments in the last decade, but some results are conflicting, hampering some conservation-based decisions. Genetic sampling of gorals has increased considerably in recent years, at least for mitochondrial (mt) DNA. Results based on two mt genes (cytochrome b and the D-loop) are currently available. Still, the utility of cytochrome oxidase subunit I remains unanalysed, even though it belongs among the gene markers that enable a correct species identification in mammals. This study examines phylogenetic relationships and species delimitation in gorals using all currently available cytochrome oxidase subunit I sequences, including the not yet analysed goral population from Pakistan. Our results of various phylogenetic approaches, such as maximum parsimony, likelihood and Bayesian inference, and exploration of species boundaries via species delimitation support the validity of six species of goral, namely N.baileyi, N.caudatus, N.cranbrooki, N.evansi, N.goral, and N.griseus. This result accords well with results based on other mt genes, especially the cytochrome b from the highly exhaustive data sampling. Our study also summarises common sources of errors in the assessment of goral phylogeny and taxonomy and highlights future priorities in understanding goral diversification.
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Affiliation(s)
- Petr Hrabina
- Department of Zoology, Fisheries, Hydrobiology and Apiculture, Mendel University in Brno, Zemědělská 1, Brno, 61300, Czech Republic Mendel University in Brno Brno Czech Republic
| | - Ludmila Pernerová
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, 37005, Czech Republic University of South Bohemia České Budějovice Czech Republic
| | - Josef Suchomel
- Department of Zoology, Fisheries, Hydrobiology and Apiculture, Mendel University in Brno, Zemědělská 1, Brno, 61300, Czech Republic Mendel University in Brno Brno Czech Republic
| | - Jan Robovský
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, 37005, Czech Republic University of South Bohemia České Budějovice Czech Republic
- Liberec Zoo, Lidové sady 425/1, Liberec, 46001, Czech Republic Liberec Zoo Liberec Czech Republic
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22
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Mochales-Riaño G, Fontsere C, de Manuel M, Talavera A, Burriel-Carranza B, Tejero-Cicuéndez H, AlGethami RHM, Shobrak M, Marques-Bonet T, Carranza S. Genomics reveals introgression and purging of deleterious mutations in the Arabian leopard ( Panthera pardus nimr). iScience 2023; 26:107481. [PMID: 37601769 PMCID: PMC10432787 DOI: 10.1016/j.isci.2023.107481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/21/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2023] Open
Abstract
In endangered species, low-genetic variation and inbreeding result from recent population declines. Genetic screenings in endangered populations help to assess their vulnerability to extinction and to create informed management actions toward their conservation efforts. The leopard, Panthera pardus, is a highly generalist predator with currently eight different subspecies. Yet, genomic data are still lacking for the Critically Endangered Arabian leopard (P. p. nimr). Here, we sequenced the whole genome of two Arabian leopards and assembled the most complete genomic dataset for leopards to date. Our phylogenomic analyses show that leopards are divided into two deeply divergent clades: the African and the Asian. Conservation genomic analyses indicate a prolonged population decline, which has led to an increase in inbreeding and runs of homozygosity, with consequent purging of deleterious mutations in both Arabian individuals. Our study represents the first attempt to genetically inform captive breeding programmes for this Critically Endangered subspecies.
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Affiliation(s)
| | - Claudia Fontsere
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Øster Farimagsgade 5A, 1352 Copenhagen, Denmark
| | - Marc de Manuel
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Adrián Talavera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | | | - Héctor Tejero-Cicuéndez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense de Madrid, Madrid, Spain
| | - Raed Hamoud M. AlGethami
- National Center for Wildlife, Prince Saud Al-Faisal for Wildlife Research, P. O Box 1086, Taif, Taif 21944, Saudi Arabia
| | - Mohammed Shobrak
- National Center for Wildlife, Prince Saud Al-Faisal for Wildlife Research, P. O Box 1086, Taif, Taif 21944, Saudi Arabia
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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23
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Powell DM. Losing the forest for the tree? On the wisdom of subpopulation management. Zoo Biol 2023; 42:591-604. [PMID: 37218348 DOI: 10.1002/zoo.21776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 03/24/2023] [Accepted: 04/26/2023] [Indexed: 05/24/2023]
Abstract
Animal habitats are changing around the world in many ways, presenting challenges to the survival of species. Zoo animal populations are also challenged by small population sizes and limited genetic diversity. Some ex situ populations are managed as subpopulations based on presumed subspecies or geographic locality and related concerns over genetic purity or taxonomic integrity. However, these decisions can accelerate the loss of genetic diversity and increase the likelihood of population extinction. Here I challenge the wisdom of subpopulation management, pointing out significant concerns in the literature with delineation of species, subspecies, and evolutionarily significant units. I also review literature demonstrating the value of gene flow for preserving adaptive potential, the often-misunderstood role of hybridization in evolution, and the likely overstated concerns about outbreeding depression, and preservation of local adaptations. I argue that the most effective way to manage animal populations for the long term be they in human care, in the wild, or if a captive population is being managed for reintroduction, is to manage for maximum genetic diversity rather than managing subpopulations focusing on taxonomic integrity, genetic purity, or geographic locale because selection in the future, rather than the past, will determine what genotypes and phenotypes are the most fit. Several case studies are presented to challenge the wisdom of subpopulation management and stimulate thinking about the preservation of genomes rather than species, subspecies, or lineages because those units evolved in habitats that are likely very different from those habitats today and in the future.
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Affiliation(s)
- David M Powell
- Department of Reproductive & Behavioral Sciences, Saint Louis Zoo, Saint Louis, Missouri, USA
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24
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Sørensen EF, Harris RA, Zhang L, Raveendran M, Kuderna LFK, Walker JA, Storer JM, Kuhlwilm M, Fontsere C, Seshadri L, Bergey CM, Burrell AS, Bergman J, Phillips-Conroy JE, Shiferaw F, Chiou KL, Chuma IS, Keyyu JD, Fischer J, Gingras MC, Salvi S, Doddapaneni H, Schierup MH, Batzer MA, Jolly CJ, Knauf S, Zinner D, Farh KKH, Marques-Bonet T, Munch K, Roos C, Rogers J. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons. Science 2023; 380:eabn8153. [PMID: 37262153 DOI: 10.1126/science.abn8153] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 09/27/2022] [Indexed: 06/03/2023]
Abstract
Baboons (genus Papio) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically and genetically distinct phylogenetic species. We used high-coverage whole-genome sequences from 225 wild baboons representing 19 geographic localities to investigate population genomics and interspecies gene flow. Our analyses provide an expanded picture of evolutionary reticulation among species and reveal patterns of population structure within and among species, including differential admixture among conspecific populations. We describe the first example of a baboon population with a genetic composition that is derived from three distinct lineages. The results reveal processes, both ancient and recent, that produced the observed mismatch between phylogenetic relationships based on matrilineal, patrilineal, and biparental inheritance. We also identified several candidate genes that may contribute to species-specific phenotypes.
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Affiliation(s)
- Erik F Sørensen
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Liye Zhang
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lukas F K Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Artificial Intelligence Lab, Illumina Inc., San Diego, CA 92122, USA
| | - Jerilyn A Walker
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | | | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030 Vienna, Austria
| | - Claudia Fontsere
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Lakshmi Seshadri
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Christina M Bergey
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Andrew S Burrell
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Jane E Phillips-Conroy
- Department of Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | - Kenneth L Chiou
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | | | | | - Julia Fischer
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37077 Göttingen, Germany
| | - Marie-Claude Gingras
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sejal Salvi
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harshavardhan Doddapaneni
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
| | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Clifford J Jolly
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37077 Göttingen, Germany
| | - Kyle K-H Farh
- Artificial Intelligence Lab, Illumina Inc., San Diego, CA 92122, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluis Companys, 23, 08010 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Baldiri i Reixac 4, 08028 Barcelona, Spain
- Institut Catala de Paleontologia Miquel Crusafont, Universitat Autonoma de Barcelona, Edifici ICTA-ICP, cl Columnes s/n, 08193 Cerdanyola del Valles, Barcelona, Spain
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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25
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Vinkler M, Fiddaman SR, Těšický M, O'Connor EA, Savage AE, Lenz TL, Smith AL, Kaufman J, Bolnick DI, Davies CS, Dedić N, Flies AS, Samblás MMG, Henschen AE, Novák K, Palomar G, Raven N, Samaké K, Slade J, Veetil NK, Voukali E, Höglund J, Richardson DS, Westerdahl H. Understanding the evolution of immune genes in jawed vertebrates. J Evol Biol 2023; 36:847-873. [PMID: 37255207 PMCID: PMC10247546 DOI: 10.1111/jeb.14181] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 06/01/2023]
Abstract
Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.
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Affiliation(s)
- Michal Vinkler
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Martin Těšický
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Anna E. Savage
- Department of BiologyUniversity of Central FloridaFloridaOrlandoUSA
| | - Tobias L. Lenz
- Research Unit for Evolutionary ImmunogenomicsDepartment of BiologyUniversity of HamburgHamburgGermany
| | | | - Jim Kaufman
- Institute for Immunology and Infection ResearchUniversity of EdinburghEdinburghUK
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - Daniel I. Bolnick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | | | - Neira Dedić
- Department of Botany and ZoologyMasaryk UniversityBrnoCzech Republic
| | - Andrew S. Flies
- Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTasmaniaAustralia
| | - M. Mercedes Gómez Samblás
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
- Department of ParasitologyUniversity of GranadaGranadaSpain
| | | | - Karel Novák
- Department of Genetics and BreedingInstitute of Animal SciencePragueUhříněvesCzech Republic
| | - Gemma Palomar
- Faculty of BiologyInstitute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - Nynke Raven
- Department of ScienceEngineering and Build EnvironmentDeakin UniversityVictoriaWaurn PondsAustralia
| | - Kalifa Samaké
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Joel Slade
- Department of BiologyCalifornia State UniversityFresnoCaliforniaUSA
| | | | - Eleni Voukali
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Jacob Höglund
- Department of Ecology and GeneticsUppsala UniversitetUppsalaSweden
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26
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Sørensen EF, Harris RA, Zhang L, Raveendran M, Kuderna LFK, Walker JA, Storer JM, Kuhlwilm M, Fontsere C, Seshadri L, Bergey CM, Burrell AS, Bergmann J, Phillips-Conroy JE, Shiferaw F, Chiou KL, Chuma IS, Keyyu JD, Fischer J, Gingras MC, Salvi S, Doddapaneni H, Schierup MH, Batzer MA, Jolly CJ, Knauf S, Zinner D, Farh KKH, Marques-Bonet T, Munch K, Roos C, Rogers J. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539112. [PMID: 37205419 PMCID: PMC10187195 DOI: 10.1101/2023.05.02.539112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Baboons (genus Papio ) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically and genetically distinct phylogenetic species. We used high coverage whole genome sequences from 225 wild baboons representing 19 geographic localities to investigate population genomics and inter-species gene flow. Our analyses provide an expanded picture of evolutionary reticulation among species and reveal novel patterns of population structure within and among species, including differential admixture among conspecific populations. We describe the first example of a baboon population with a genetic composition that is derived from three distinct lineages. The results reveal processes, both ancient and recent, that produced the observed mismatch between phylogenetic relationships based on matrilineal, patrilineal, and biparental inheritance. We also identified several candidate genes that may contribute to species-specific phenotypes. One-Sentence Summary Genomic data for 225 baboons reveal novel sites of inter-species gene flow and local effects due to differences in admixture.
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27
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Schöneberg Y, Winter S, Arribas O, Riccardo Di Nicola M, Master M, Benjamin Owens J, Rovatsos M, Wüster W, Janke A, Fritz U. Genomics reveals broad hybridization in deeply divergent Palearctic grass and water snakes (Natrix spp.). Mol Phylogenet Evol 2023; 184:107787. [PMID: 37080398 DOI: 10.1016/j.ympev.2023.107787] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/03/2023] [Accepted: 04/13/2023] [Indexed: 04/22/2023]
Abstract
Understanding speciation is one of the cornerstones of biological diversity research. Currently, speciation is often understood as a continuous process of divergence that continues until genetic or other incompatibilities minimize or prevent interbreeding. The Palearctic snake genus Natrix is an ideal group to study speciation, as it comprises taxa representing distinct stages of the speciation process, ranging from widely interbreeding parapatric taxa through parapatric species with very limited gene flow in narrow hybrid zones to widely sympatric species. To understand the evolution of reproductive isolation through time, we have sequenced the genomes of all five species within this genus and two additional subspecies. We used both long-read and short-read methods to sequence and de-novo-assemble two high-quality genomes (Natrix h. helvetica, Natrix n. natrix) to their 1.7 Gb length with a contig N50 of 4.6 Mbp and 1.5 Mbp, respectively, and used these as references to assemble the remaining short-read-based genomes. Our phylogenomic analyses yielded a well-supported dated phylogeny and evidence for a surprisingly complex history of interspecific gene flow, including between widely sympatric species. Furthermore, evidence for gene flow was also found for currently allopatric species pairs. Genetic exchange among these well-defined, distinct, and several million-year-old reptile species emphasizes that speciation and maintenance of species distinctness can occur despite continued genetic exchange.
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Affiliation(s)
- Yannis Schöneberg
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 9, 60325 Frankfurt am Main, Germany
| | - Sven Winter
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstraße 1, 1160 Vienna, Austria
| | - Oscar Arribas
- IES Castilla, Junta de Castilla, Castilla y León, 42003 Soria, Spain
| | | | - Maya Master
- Molecular Ecology and Evolution at Bangor (MEEB), School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor LL57 2UW, Wales, UK
| | - John Benjamin Owens
- Molecular Ecology and Evolution at Bangor (MEEB), School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor LL57 2UW, Wales, UK
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Praha 2, Czech Republic
| | - Wolfgang Wüster
- Molecular Ecology and Evolution at Bangor (MEEB), School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor LL57 2UW, Wales, UK
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 9, 60325 Frankfurt am Main, Germany; LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Uwe Fritz
- Senckenberg Dresden, Museum of Zoology, A. B. Meyer Building, 01109 Dresden, Germany.
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28
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De León LF, Silva B, Avilés-Rodríguez KJ, Buitrago-Rosas D. Harnessing the omics revolution to address the global biodiversity crisis. Curr Opin Biotechnol 2023; 80:102901. [PMID: 36773576 DOI: 10.1016/j.copbio.2023.102901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/10/2023] [Accepted: 01/18/2023] [Indexed: 02/12/2023]
Abstract
Human disturbances are altering global biodiversity in unprecedented ways. We identify three fundamental challenges underpinning our understanding of global biodiversity (namely discovery, loss, and preservation), and discuss how the omics revolution (e.g. genomics, transcriptomics, proteomics, metabolomics, and meta-omics) can help address these challenges. We also discuss how omics tools can illuminate the major drivers of biodiversity loss, including invasive species, pollution, urbanization, overexploitation, and climate change, with a special focus on highly diverse tropical environments. Although omics tools are transforming the traditional toolkit of biodiversity research, their application to addressing the current biodiversity crisis remains limited and may not suffice to offset current rates of biodiversity loss. Despite technical and logistical challenges, omics tools need to be fully integrated into global biodiversity research, and better strategies are needed to improve their translation into biodiversity policy and practice. It is also important to recognize that although the omics revolution can be considered the biologist's dream, socioeconomic disparity limits their application in biodiversity research.
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Affiliation(s)
- Luis F De León
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA.
| | - Bruna Silva
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Kevin J Avilés-Rodríguez
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA; Department of Biology, Fordham University, Bronx, NY, USA
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29
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Hu Y, Wang X, Xu Y, Yang H, Tong Z, Tian R, Xu S, Yu L, Guo Y, Shi P, Huang S, Yang G, Shi S, Wei F. Molecular mechanisms of adaptive evolution in wild animals and plants. SCIENCE CHINA. LIFE SCIENCES 2023; 66:453-495. [PMID: 36648611 PMCID: PMC9843154 DOI: 10.1007/s11427-022-2233-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 08/30/2022] [Indexed: 01/18/2023]
Abstract
Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning. In this study, we reviewed the latest research advances in wild animals and plants, focusing on adaptive traits, convergent evolution, and coevolution. Firstly, we focused on the adaptive evolution of morphological, behavioral, and physiological traits. Secondly, we reviewed the phenotypic convergences of life history traits and responding to environmental pressures, and the underlying molecular convergence mechanisms. Thirdly, we summarized the advances of coevolution, including the four main types: mutualism, parasitism, predation and competition. Overall, these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction, demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies. Finally, we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.
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Affiliation(s)
- Yibo Hu
- CAS Key Lab of Animal Ecology and Conservation Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xiaoping Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Yongchao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hui Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zeyu Tong
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Ran Tian
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China.
| | - Yalong Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Peng Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Shuangquan Huang
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
| | - Guang Yang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Fuwen Wei
- CAS Key Lab of Animal Ecology and Conservation Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
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30
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Cui B, Guo Z, Cao H, Calus M, Zhang Q. The computational implementation of a platform of relative identity-by-descent scores algorithm for introgressive mapping. Front Genet 2023; 13:1028662. [PMID: 36761695 PMCID: PMC9903072 DOI: 10.3389/fgene.2022.1028662] [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: 08/26/2022] [Accepted: 11/15/2022] [Indexed: 01/25/2023] Open
Abstract
With the development of genotyping and sequencing technology, researchers working in the area of conservation genetics are able to obtain the genotypes or even the sequences of a representative sample of individuals from the population. It is of great importance to examine the genomic variants and genes that are highly preferred or pruned during the process of adaptive introgression or long-term hybridization. To the best of our knowledge, we are the first to develop a platform with computational integration of a relative identity-by-descent (rIBD) scores algorithm for introgressive mapping. The rIBD algorithm is designed for mapping the fine-scaled genomic regions under adaptive introgression between the source breeds and the admixed breed. Our rIBD calculation platform provides compact functions including reading input information and uploading of files, rIBD calculation, and presentation of the rIBD scores. We analyzed the simulated data using the rIBD calculation platform and calculated the average IBD score of 0.061 with a standard deviation of 0.124. The rIBD scores generally follow a normal distribution, and a cut-off of 0.432 and -0.310 for both positive and negative rIBD scores is derived to enable the identification of genomic regions showing significant introgression signals from the source breed to the admixed breed. A list of genomic regions with detailed calculated rIBD scores is reported, and all the rIBD scores for each of the considered windows are presented in plots on the rIBD calculation platform. Our rIBD calculation platform provides a user-friendly tool for the calculation of fine-scaled rIBD scores for each of the genomic regions to map possible functional genomic variants due to adaptive introgression or long-term hybridization.
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Affiliation(s)
- Bo Cui
- School of Chemistry and Biological Engineering, University of Science and Technology, Beijing, China
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing, China
- Institute of Biotechnology, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Zhongxu Guo
- School of Chemistry and Biological Engineering, University of Science and Technology, Beijing, China
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing, China
- Institute of Biotechnology, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Hongbo Cao
- School of Chemistry and Biological Engineering, University of Science and Technology, Beijing, China
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing, China
- Institute of Biotechnology, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Mario Calus
- Department of Animal Science, Animal Breeding and Genetics Group, Wageningen University, Wageningen, Netherlands
| | - Qianqian Zhang
- School of Chemistry and Biological Engineering, University of Science and Technology, Beijing, China
- Institute of Biotechnology, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
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31
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Owens GL, Huang K, Todesco M, Rieseberg LH. Re-evaluating Homoploid Reticulate Evolution in Helianthus Sunflowers. Mol Biol Evol 2023; 40:6989481. [PMID: 36648104 PMCID: PMC9907532 DOI: 10.1093/molbev/msad013] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/03/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Sunflowers of the genus Helianthus are models for hybridization research and contain three of the best-studied examples of homoploid hybrid speciation. To understand a broader picture of hybridization within the annual sunflowers, we used whole-genome resequencing to conduct a phylogenomic analysis and test for gene flow between lineages. We find that all annual sunflower species tested have evidence of admixture, suggesting hybridization was common during the radiation of the genus. Support for the major species tree decreases with increasing recombination rate, consistent with hybridization and introgression contributing to discordant topologies. Admixture graphs found hybridization to be associated with the origins of the three putative hybrid species (Helianthus anomalus, Helianthus deserticola, and Helianthus paradoxus). However, the hybridization events are more ancient than suggested by previous work. Furthermore, H. anomalus and H. deserticola appear to have arisen from a single hybridization event involving an unexpected donor, rather than through multiple independent events as previously proposed. This means our results are consistent with, but not definitive proof of, two ancient independent homoploid hybrid speciation events in the genus. Using a broader data set that covers the whole Helianthus genus, including perennial species, we find that signals of introgression span the genus and beyond, suggesting highly divergent introgression and/or the sorting of ancient haplotypes. Thus, Helianthus can be viewed as a syngameon in which largely reproductively isolated species are linked together by occasional or frequent gene flow.
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Affiliation(s)
| | - Kaichi Huang
- Department of Botany and Beaty Biodiversity Center, University of British Columbia, Vancouver, BC, Canada
| | - Marco Todesco
- Department of Botany and Beaty Biodiversity Center, University of British Columbia, Vancouver, BC, Canada
| | - Loren H Rieseberg
- Department of Botany and Beaty Biodiversity Center, University of British Columbia, Vancouver, BC, Canada
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32
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Shukla H, Suryamohan K, Khan A, Mohan K, Perumal RC, Mathew OK, Menon R, Dixon MD, Muraleedharan M, Kuriakose B, Michael S, Krishnankutty SP, Zachariah A, Seshagiri S, Ramakrishnan U. Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation. Gigascience 2022; 12:giac112. [PMID: 36576130 PMCID: PMC9795480 DOI: 10.1093/gigascience/giac112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/17/2022] [Accepted: 10/20/2022] [Indexed: 12/29/2022] Open
Abstract
The tiger, a poster child for conservation, remains an endangered apex predator. Continued survival and recovery will require a comprehensive understanding of genetic diversity and the use of such information for population management. A high-quality tiger genome assembly will be an important tool for conservation genetics, especially for the Indian tiger, the most abundant subspecies in the wild. Here, we present high-quality near-chromosomal genome assemblies of a female and a male wild Indian tiger (Panthera tigris tigris). Our assemblies had a scaffold N50 of >140 Mb, with 19 scaffolds corresponding to the 19 numbered chromosomes, containing 95% of the genome. Our assemblies also enabled detection of longer stretches of runs of homozygosity compared to previous assemblies, which will help improve estimates of genomic inbreeding. Comprehensive genome annotation identified 26,068 protein-coding genes, including several gene families involved in key morphological features such as the teeth, claws, vision, olfaction, taste, and body stripes. We also identified 301 microRNAs, 365 small nucleolar RNAs, 632 transfer RNAs, and other noncoding RNA elements, several of which are predicted to regulate key biological pathways that likely contribute to the tiger's apex predatory traits. We identify signatures of positive selection in the tiger genome that are consistent with the Panthera lineage. Our high-quality genome will enable use of noninvasive samples for comprehensive assessment of genetic diversity, thus supporting effective conservation and management of wild tiger populations.
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Affiliation(s)
- Harsh Shukla
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Kushal Suryamohan
- MedGenome Inc., Department of Research and Development, Foster City, CA 94404, USA
- SciGenom Research Foundation, Narayana Health City, Bangalore, Karnataka 560099, India
| | - Anubhab Khan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Krishna Mohan
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Rajadurai C Perumal
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Oommen K Mathew
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Ramesh Menon
- MedGenome Labs Ltd., Narayana Health City, Bangalore, Karnataka 560099, India
| | - Mandumpala Davis Dixon
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Megha Muraleedharan
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Boney Kuriakose
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Saju Michael
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Sajesh P Krishnankutty
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Arun Zachariah
- SciGenom Research Foundation, Narayana Health City, Bangalore, Karnataka 560099, India
- Wayanad Wildlife Sanctuary, Sultan Bathery, Kerala 673592, India
| | - Somasekar Seshagiri
- SciGenom Research Foundation, Narayana Health City, Bangalore, Karnataka 560099, India
- MedGenome Labs Ltd., Narayana Health City, Bangalore, Karnataka 560099, India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
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33
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Baeza JA. Mitochondrial genomes assembled from non-invasive eDNA metagenomic scat samples in the endangered Amur tiger Panthera tigris altaica. PeerJ 2022; 10:e14428. [PMID: 36523460 PMCID: PMC9745948 DOI: 10.7717/peerj.14428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/30/2022] [Indexed: 12/12/2022] Open
Abstract
The Amur or Siberian tiger Panthera tigris altaica (Temminck, 1844) is currently restricted to a small region of its original geographical range in northwestern Asia and is considered 'endangered' by the IUCN Red List of Threatened Species. This solitary, territorial, and large top predator is in major need of genomic resources to inform conservation management strategies. This study formally tested if complete mitochondrial genomes of P. tigris altaica can be assembled from non-enriched metagenomic libraries generated from scat eDNA samples using the Illumina sequencing platform and open-access bioinformatics pipelines. The mitogenome of P. tigris altaica was assembled and circularized using the pipeline GetOrganelle with a coverage ranging from 322.7x to 17.6x in four different scat eDNA samples. A nearly complete mitochondrial genome (101x) was retrieved from a fifth scat eDNA sample. The complete or nearly complete mitochondrial genomes of P. tigris altaica were AT-rich and composed of 13 protein coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Synteny observed in all assembled mitogenomes was identical to that reported before for P. tigris altaica and other felids. A phylogenomic analysis based on all PCGs demonstrated that the mitochondrial genomes assembled from scat eDNA reliably identify the sequenced samples as belonging to P. tigris and distinguished the same samples from closely and distantly related congeneric species. This study demonstrates that it is viable to retrieve accurate whole and nearly complete mitochondrial genomes of P. tigris altaica (and probably other felids) from scat eDNA samples without library enrichment protocols and using open-access bioinformatics workflows. This new genomic resource represents a new tool to support conservation strategies (bio-prospecting and bio-monitoring) in this iconic cat.
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Affiliation(s)
- J. Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC, United States,Smithsonian Marine Station at Fort Pierce, Fort Pierce, Florida, United States,Departamento de Biologia Marina, Universidad Catolica del Norte, Coquimbo, IV Region, Chile
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34
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Armstrong EE, Campana MG, Solari KA, Morgan SR, Ryder OA, Naude VN, Samelius G, Sharma K, Hadly EA, Petrov DA. Genome report: chromosome-level draft assemblies of the snow leopard, African leopard, and tiger (Panthera uncia, Panthera pardus pardus, and Panthera tigris). G3 (BETHESDA, MD.) 2022; 12:jkac277. [PMID: 36250809 PMCID: PMC9713438 DOI: 10.1093/g3journal/jkac277] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/14/2022] [Indexed: 04/07/2024]
Abstract
The big cats (genus Panthera) represent some of the most popular and charismatic species on the planet. Although some reference genomes are available for this clade, few are at the chromosome level, inhibiting high-resolution genomic studies. We assembled genomes from 3 members of the genus, the tiger (Panthera tigris), the snow leopard (Panthera uncia), and the African leopard (Panthera pardus pardus), at chromosome or near-chromosome level. We used a combination of short- and long-read technologies, as well as proximity ligation data from Hi-C technology, to achieve high continuity and contiguity for each individual. We hope that these genomes will aid in further evolutionary and conservation research of this iconic group of mammals.
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Affiliation(s)
- Ellie E Armstrong
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Biology, Washington State University, Pullman, WA 99164, USA
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, DC 20008, USA
| | | | - Simon R Morgan
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Wildlife ACT Fund Trust, Cape Town 8001, South Africa
| | - Oliver A Ryder
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, San Diego, CA 92027, USA
| | - Vincent N Naude
- Department of Conservation Ecology and Entomology, University of Stellenbosch, Stellenbosch, 7602, South Africa
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | | | - Koustubh Sharma
- Snow Leopard Trust, Seattle, WA 98103, USA
- Nature Conservation Foundation, Mysore 570 017, India
| | | | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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35
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vonHoldt BM, Brzeski KE, Aardema ML, Schell CJ, Rutledge LY, Fain SR, Shutt AC, Linderholm A, Murphy WJ. Persistence and expansion of cryptic endangered red wolf genomic ancestry along the American Gulf coast. Mol Ecol 2022; 31:5440-5454. [PMID: 34585803 DOI: 10.1111/mec.16200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/03/2021] [Accepted: 09/22/2021] [Indexed: 12/24/2022]
Abstract
Admixture and introgression play a critical role in adaptation and genetic rescue that has only recently gained a deeper appreciation. Here, we explored the geographical and genomic landscape of cryptic ancestry of the endangered red wolf that persists within the genome of a ubiquitous sister taxon, the coyote, all while the red wolf has been extinct in the wild since the early 1980s. We assessed admixture across 120,621 single nucleotiode polymorphism (SNP) loci genotyped in 293 canid genomes. We found support for increased red wolf ancestry along a west-to-east gradient across the southern United States associated with historical admixture in the past 100 years. Southwestern Louisiana and southeastern Texas, the geographical zone where the last red wolves were known prior to extinction in the wild, contained the highest and oldest levels of red wolf ancestry. Further, given the paucity of inferences based on chromosome types, we compared patterns of ancestry on the X chromosome and autosomes. We additionally aimed to explore the relationship between admixture timing and recombination rate variation to investigate gene flow events. We found that X-linked regions of low recombination rates were depleted of introgression, relative to the autosomes, consistent with the large X effect and enrichment with loci involved in maintaining reproductive isolation. Recombination rate was positively correlated with red wolf ancestry across coyote genomes, consistent with theoretical predictions. The geographical and genomic extent of cryptic red wolf ancestry can provide novel genomic resources for recovery plans targeting the conservation of the endangered red wolf.
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Affiliation(s)
- Bridgett M vonHoldt
- Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Kristin E Brzeski
- College of Forest Resources and Environment Science, Michigan Technological University, Houghton, Michigan, USA
| | - Matthew L Aardema
- Department of Biology, Montclair State University, Montclair, New Jersey, USA.,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Christopher J Schell
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
| | - Linda Y Rutledge
- Biology Department, Trent University, Peterborough, Ontario, Canada
| | - Steven R Fain
- USFWS, Clark R. Bavin National Forensics Laboratory, Ashland, Oregon, USA
| | | | - Anna Linderholm
- Department of Anthropology, Texas A&M University, College Station, Texas, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
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36
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Harvati K, Ackermann RR. Merging morphological and genetic evidence to assess hybridization in Western Eurasian late Pleistocene hominins. Nat Ecol Evol 2022; 6:1573-1585. [PMID: 36064759 DOI: 10.1038/s41559-022-01875-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/08/2022] [Indexed: 11/09/2022]
Abstract
Previous scientific consensus saw human evolution as defined by adaptive differences (behavioural and/or biological) and the emergence of Homo sapiens as the ultimate replacement of non-modern groups by a modern, adaptively more competitive group. However, recent research has shown that the process underlying our origins was considerably more complex. While archaeological and fossil evidence suggests that behavioural complexity may not be confined to the modern human lineage, recent palaeogenomic work shows that gene flow between distinct lineages (for example, Neanderthals, Denisovans, early H. sapiens) occurred repeatedly in the late Pleistocene, probably contributing elements to our genetic make-up that might have been crucial to our success as a diverse, adaptable species. Following these advances, the prevailing human origins model has shifted from one of near-complete replacement to a more nuanced view of partial replacement with considerable reticulation. Here we provide a brief introduction to the current genetic evidence for hybridization among hominins, its prevalence in, and effects on, comparative mammal groups, and especially how it manifests in the skull. We then explore the degree to which cranial variation seen in the fossil record of late Pleistocene hominins from Western Eurasia corresponds with our current genetic and comparative data. We are especially interested in understanding the degree to which skeletal data can reflect admixture. Our findings indicate some correspondence between these different lines of evidence, flag individual fossils as possibly admixed, and suggest that different cranial regions may preserve hybridization signals differentially. We urge further studies of the phenotype to expand our ability to detect the ways in which migration, interaction and genetic exchange have shaped the human past, beyond what is currently visible with the lens of ancient DNA.
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Affiliation(s)
- K Harvati
- Paleoanthropology section, Senckenberg Centre for Human Evolution and Palaeoenvironment, Institute for Archaeological Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany.
- DFG Centre for Advanced Studies 'Words, Bones, Genes, Tools', Eberhard Karls Universität Tübingen, Tübingen, Germany.
| | - R R Ackermann
- Human Evolution Research Institute, University of Cape Town, Cape Town, South Africa.
- Department of Archaeology, University of Cape Town, Cape Town, South Africa.
- DFG Centre for Advanced Studies 'Words, Bones, Genes, Tools', Eberhard Karls Universität Tübingen, Tübingen, Germany.
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37
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Collaborative behaviour and coalitions in male jaguars (Panthera onca)—evidence and comparison with other felids. Behav Ecol Sociobiol 2022. [DOI: 10.1007/s00265-022-03232-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Abstract
Most large felids are classified as solitary species, with only lions (Panthera leo) and cheetahs (Acinonyx jubatus) exhibiting social, collaborative behaviours. Herein, we present evidence of the formation of male coalitions by jaguars (Panthera onca), based on data from five studies conducted with camera trapping, GPS telemetry, and direct observations in the Venezuelan Llanos and Brazilian Pantanal. Out of 7062 male records obtained with camera traps or visual observations, we detected 105 cases of male-male interactions, of which we classified 18 as aggression, nine as tolerance, 70 as cooperation/coalition, and eight as unidentified. In two studies, two male jaguars formed stable coalitions lasting over 7 years each. In the Llanos, each coalition male paired and mated with several females. For male jaguar coalitions, we documented similar behaviours as recorded earlier in lions or cheetahs, which included patrolling and marking territory together, invading territories of other males, collaborative chasing and killing other jaguars, and sharing prey. However, different from lions or cheetahs, associated male jaguars spent less time together, did not cooperate with females, and did not hunt cooperatively together. Our analysis of literature suggested that male jaguar coalitions were more likely to form when females had small home range size, a proxy of females’ concentration, while in lions, the male group size was directly correlated with the female group size. Similarly, locally concentrated access to females may drive formation of male coalitions in cheetahs. We conclude that high biomass and aggregation of prey are likely drivers of sociality in felids.
Significance statement
The division into social and solitary species in large felids has so far seemed unambiguous, with only lions and cheetahs classified as social species, in which male coalitions also occurred. Our data show that, under certain conditions, male coalitions may also form in jaguar populations. Factors that drive formation of male coalitions in lions and cheetahs, but not in other species of large cats, have not been clear until now. Our analyses indicate that in jaguars, lions, and cheetahs, the concentration of females likely plays the most important role. In jaguars, the probability of male coalition occurrence is highest in populations with the smallest mean female home range size (and thus likely high local density of females), while in lions, male group size is most strongly correlated with female group size.
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Voronova AN, Vainutis KS, Tabakaeva TV, Sapotsky MV, Kakareka NN, Volkov YG, Galkina IV, Shchelkanov MY. Molecular identification of the trematode P. ichunensis stat. n. from lungs of siberian tigers justified reappraisal of Paragonimus westermani species complex. J Parasit Dis 2022; 46:744-753. [PMID: 36091260 PMCID: PMC9458828 DOI: 10.1007/s12639-022-01481-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 03/07/2022] [Indexed: 10/18/2022] Open
Abstract
Flukes from the genus Paragonimus Braun, 1899 are medically important foodborne trematodes predominantly occurring throughout Asian countries. Providing molecular genetic characteristics based on ITS2 and partial 28 S rDNA of the paragonimids from the Russian Far East, Northeast, South, and Southeast Asian countries, we performed a partial reappraisal of Paragonimus westermani species complex. Members of this complex are genetically distinct worms with different divergence times and explosive expansion during Miocene-Pliocene epochs. We confirm the taxonomic status as valid species for P. ichunensis stat. n. (from the Russian Far East and Northern China), and P. filipinus (from the Philippines), which were previously considered subspecies of P. westermani, and reinstated the species name P. pulmonalis (from Japan). We suggest considering the worms from South Korea the Korean variety of P. ichunensis, because Korean specimens are sister and genetically closest to P. ichunensis from Northeast China and Primorsky region of Russia. Worms from South (India (type 2), Sri Lanka), Southeast (Malaysia, Vietnam, Thailand (types 1 and 2)) and East Asia (Taiwan) were left in the paragonimid systematics as Paragonimus sp. We propose to consider Indian worms of type 1 as true P. westermani, but in further revisions, due to the lack of holotype and unknown exact type locality, new type specimens (neotype) should be established.
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Affiliation(s)
- Anastasia N. Voronova
- G.P. Somov Institute of Epidemiology and Microbiology, Russian Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 1, Selskaya st, 690087 Vladivostok, Russia
| | - Konstantin S. Vainutis
- G.P. Somov Institute of Epidemiology and Microbiology, Russian Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 1, Selskaya st, 690087 Vladivostok, Russia
| | - Tatiana V. Tabakaeva
- G.P. Somov Institute of Epidemiology and Microbiology, Russian Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 1, Selskaya st, 690087 Vladivostok, Russia
- Far Eastern Federal University, Sukhanova st., 8, 690091 Vladivostok, Russia
| | - Mikhail V. Sapotsky
- Federal Scientific Centre of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, pr. Stoletiya Vladivostoka, 159, 690022 Vladivostok, Russia
| | - Nadezhda N. Kakareka
- Federal Scientific Centre of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, pr. Stoletiya Vladivostoka, 159, 690022 Vladivostok, Russia
| | - Yury G. Volkov
- Federal Scientific Centre of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, pr. Stoletiya Vladivostoka, 159, 690022 Vladivostok, Russia
| | - Irina V. Galkina
- Far Eastern Federal University, Sukhanova st., 8, 690091 Vladivostok, Russia
| | - Mikhail Yu. Shchelkanov
- G.P. Somov Institute of Epidemiology and Microbiology, Russian Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 1, Selskaya st, 690087 Vladivostok, Russia
- Far Eastern Federal University, Sukhanova st., 8, 690091 Vladivostok, Russia
- Federal Scientific Centre of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, pr. Stoletiya Vladivostoka, 159, 690022 Vladivostok, Russia
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39
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Helleu Q, Roux C, Ross KG, Keller L. Radiation and hybridization underpin the spread of the fire ant social supergene. Proc Natl Acad Sci U S A 2022; 119:e2201040119. [PMID: 35969752 PMCID: PMC9407637 DOI: 10.1073/pnas.2201040119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/04/2022] [Indexed: 11/18/2022] Open
Abstract
Supergenes are clusters of tightly linked genes that jointly produce complex phenotypes. Although widespread in nature, how such genomic elements are formed and how they spread are in most cases unclear. In the fire ant Solenopsis invicta and closely related species, a "social supergene controls whether a colony maintains one or multiple queens. Here, we show that the three inversions constituting the Social b (Sb) supergene emerged sequentially during the separation of the ancestral lineages of S. invicta and Solenopsis richteri. The two first inversions arose in the ancestral population of both species, while the third one arose in the S. richteri lineage. Once completely assembled in the S. richteri lineage, the supergene first introgressed into S. invicta, and from there into the other species of the socially polymorphic group of South American fire ant species. Surprisingly, the introgression of this large and important genomic element occurred despite recent hybridization being uncommon between several of the species. These results highlight how supergenes can readily move across species boundaries, possibly because of fitness benefits they provide and/or expression of selfish properties favoring their transmission.
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Affiliation(s)
- Quentin Helleu
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Camille Roux
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Kenneth G. Ross
- Department of Entomology, University of Georgia, Athens, GA 30605
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
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40
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Wang RJ, Raveendran M, Harris RA, Murphy WJ, Lyons LA, Rogers J, Hahn MW. De novo Mutations in Domestic Cat are Consistent with an Effect of Reproductive Longevity on Both the Rate and Spectrum of Mutations. Mol Biol Evol 2022; 39:msac147. [PMID: 35771663 PMCID: PMC9290555 DOI: 10.1093/molbev/msac147] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The mutation rate is a fundamental evolutionary parameter with direct and appreciable effects on the health and function of individuals. Here, we examine this important parameter in the domestic cat, a beloved companion animal as well as a valuable biomedical model. We estimate a mutation rate of 0.86 × 10-8 per bp per generation for the domestic cat (at an average parental age of 3.8 years). We find evidence for a significant paternal age effect, with more mutations transmitted by older sires. Our analyses suggest that the cat and the human have accrued similar numbers of mutations in the germline before reaching sexual maturity. The per-generation mutation rate in the cat is 28% lower than what has been observed in humans, but is consistent with the shorter generation time in the cat. Using a model of reproductive longevity, which takes into account differences in the reproductive age and time to sexual maturity, we are able to explain much of the difference in per-generation rates between species. We further apply our reproductive longevity model in a novel analysis of mutation spectra and find that the spectrum for the cat resembles the human mutation spectrum at a younger age of reproduction. Together, these results implicate changes in life-history as a driver of mutation rate evolution between species. As the first direct observation of the paternal age effect outside of rodents and primates, our results also suggest a phenomenon that may be universal among mammals.
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Affiliation(s)
- Richard J Wang
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN, USA
- Department of Computer Science, Indiana University, Bloomington, IN, USA
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41
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Burbrink FT, Crother BI, Murray CM, Smith BT, Ruane S, Myers EA, Pyron RA. Empirical and philosophical problems with the subspecies rank. Ecol Evol 2022; 12:e9069. [PMID: 35845367 PMCID: PMC9271888 DOI: 10.1002/ece3.9069] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/01/2022] [Accepted: 06/10/2022] [Indexed: 11/12/2022] Open
Abstract
Species-level taxonomy derives from empirical sources (data and techniques) that assess the existence of spatiotemporal evolutionary lineages via various species "concepts." These concepts determine if observed lineages are independent given a particular methodology and ontology, which relates the metaphysical species concept to what "kind" of thing a species is in reality. Often, species concepts fail to link epistemology back to ontology. This lack of coherence is in part responsible for the persistence of the subspecies rank, which in modern usage often functions as a placeholder between the evolutionary events of divergence or collapse of incipient species. Thus, prospective events like lineages merging or diverging require information from unknowable future information. This is also conditioned on evidence that the lineage already has a detectably distinct evolutionary history. Ranking these lineages as subspecies can seem attractive given that many lineages do not exhibit intrinsic reproductive isolation. We argue that using subspecies is indefensible on philosophical and empirical grounds. Ontologically, the rank of subspecies is either identical to that of species or undefined in the context of evolutionary lineages representing spatiotemporally defined individuals. Some species concepts more inclined to consider subspecies, like the Biological Species Concept, are disconnected from evolutionary ontology and do not consider genealogy. Even if ontology is ignored, methods addressing reproductive isolation are often indirect and fail to capture the range of scenarios linking gene flow to species identity over space and time. The use of subspecies and reliance on reproductive isolation as a basis for an operational species concept can also conflict with ethical issues governing the protection of species. We provide a way forward for recognizing and naming species that links theoretical and operational species concepts regardless of the magnitude of reproductive isolation.
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Affiliation(s)
- Frank T. Burbrink
- Department of HerpetologyAmerican Museum of Natural HistoryNew YorkNew YorkUSA
| | - Brian I. Crother
- Department of Biological SciencesSoutheastern Louisiana UniversityHammondLouisianaUSA
| | - Christopher M. Murray
- Department of Biological SciencesSoutheastern Louisiana UniversityHammondLouisianaUSA
| | - Brian Tilston Smith
- Department of OrnithologyAmerican Museum of Natural HistoryNew YorkNew YorkUSA
| | - Sara Ruane
- Life Sciences Section, Negaunee Integrative Research CenterField Museum of Natural HistoryChicagoIllinoisUSA
| | - Edward A. Myers
- Department of HerpetologyAmerican Museum of Natural HistoryNew YorkNew YorkUSA
- Department of Biological SciencesClemson UniversityClemsonSouth CarolinaUSA
- Department of Vertebrate ZoologySmithsonian Institution, National Museum of Natural HistoryWashingtonDistrict of ColumbiaUSA
| | - Robert Alexander Pyron
- Department of Vertebrate ZoologySmithsonian Institution, National Museum of Natural HistoryWashingtonDistrict of ColumbiaUSA
- Department of Biological SciencesThe George Washington UniversityWashingtonDistrict of ColumbiaUSA
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42
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Harris AJ, Foley NM, Williams TL, Murphy WJ. Tree House Explorer: A Novel Genome Browser for Phylogenomics. Mol Biol Evol 2022; 39:msac130. [PMID: 35700217 PMCID: PMC9246335 DOI: 10.1093/molbev/msac130] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/09/2022] [Accepted: 06/02/2022] [Indexed: 11/22/2022] Open
Abstract
Tree House Explorer (THEx) is a genome browser that integrates phylogenomic data and genomic annotations into a single interactive platform for combined analysis. THEx allows users to visualize genome-wide variation in evolutionary histories and genetic divergence on a chromosome-by-chromosome basis, with continuous sliding window comparisons to gene annotations (GFF/GTF), recombination rates, and other user-specified, highly customizable feature annotations. THEx provides a new platform for interactive phylogenomic data visualization to analyze and interpret the diverse evolutionary histories woven throughout genomes. Hosted on Conda, THEx integrates seamlessly into new or pre-existing workflows.
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Affiliation(s)
- Andrew J Harris
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Tiffani L Williams
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
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43
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Ramirez JL, Lescroart J, Figueiró HV, Torres-Florez JP, Villela PMS, Coutinho LL, Freitas PD, Johnson WE, Antunes A, Galetti PM, Eizirik E. Genomic signatures of divergent ecological strategies in a recent radiation of Neotropical wild cats. Mol Biol Evol 2022; 39:6594307. [PMID: 35639983 PMCID: PMC9189605 DOI: 10.1093/molbev/msac117] [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] [Indexed: 11/14/2022] Open
Abstract
Ecological differentiation among diverging species is an important component of the evolutionary process and can be investigated in rapid and recent radiations. Here we use whole genome sequences of five species from the genus Leopardus, a recently diversified Neotropical lineage with species bearing distinctive morphological, ecological and behavioral features, to investigate genome-wide diversity, comparative demographic history and signatures of positive selection. Our results show that divergent ecological strategies are reflected in genomic features, e.g. a generalist species shows historically larger effective population size and higher heterozygosity than habitat specialists. The demographic history of these cats seems to have been jointly driven by climate fluctuations and habitat specialization, with different ecological adaptations leading to distinct trajectories. Finally, a gene involved in vertebrate retinal neurogenesis (POU4F2) was found to be under positive selection in the margay, a cat with notoriously large eyes that are likely associated with its nocturnal and arboreal specializations.
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Affiliation(s)
- Jorge L Ramirez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Peru
| | - Jonas Lescroart
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.,Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Henrique V Figueiró
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.,Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, USA
| | - Juan Pablo Torres-Florez
- Instituto Chico Mendes de Conservação da Biodiversidade/Centro Nacional de Pesquisa e Conservação de Mamíferos Aquáticos (ICMBio/CMA), Santos, Brazil
| | | | - Luiz L Coutinho
- Centro de Genômica Funcional, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Patricia D Freitas
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Pedro M Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.,Instituto Pró-Carnívoros, Atibaia, SP, Brazil.,INCT-EECBio, Goiânia, GO, Brazil
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44
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Thawornwattana Y, Seixas FA, Yang Z, Mallet J. OUP accepted manuscript. Syst Biol 2022; 71:1159-1177. [PMID: 35169847 PMCID: PMC9366460 DOI: 10.1093/sysbio/syac009] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 02/01/2022] [Accepted: 02/08/2022] [Indexed: 11/21/2022] Open
Abstract
Introgressive hybridization plays a key role in adaptive evolution and species diversification in many groups of species. However, frequent hybridization and gene flow between species make estimation of the species phylogeny and key population parameters challenging. Here, we show that by accounting for phasing and using full-likelihood methods, introgression histories and population parameters can be estimated reliably from whole-genome sequence data. We employ the multispecies coalescent (MSC) model with and without gene flow to infer the species phylogeny and cross-species introgression events using genomic data from six members of the erato-sara clade of Heliconius butterflies. The methods naturally accommodate random fluctuations in genealogical history across the genome due to deep coalescence. To avoid heterozygote phasing errors in haploid sequences commonly produced by genome assembly methods, we process and compile unphased diploid sequence alignments and use analytical methods to average over uncertainties in heterozygote phase resolution. There is robust evidence for introgression across the genome, both among distantly related species deep in the phylogeny and between sister species in shallow parts of the tree. We obtain chromosome-specific estimates of key population parameters such as introgression directions, times and probabilities, as well as species divergence times and population sizes for modern and ancestral species. We confirm ancestral gene flow between the sara clade and an ancestral population of Heliconius telesiphe, a likely hybrid speciation origin for Heliconius hecalesia, and gene flow between the sister species Heliconius erato and Heliconius himera. Inferred introgression among ancestral species also explains the history of two chromosomal inversions deep in the phylogeny of the group. This study illustrates how a full-likelihood approach based on the MSC makes it possible to extract rich historical information of species divergence and gene flow from genomic data. [3s; bpp; gene flow; Heliconius; hybrid speciation; introgression; inversion; multispecies coalescent]
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Affiliation(s)
- Yuttapong Thawornwattana
- Correspondence to be sent to: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; E-mail: ; (Y.T. and J.M.); Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK; E-mail: (Z.Y.)
| | - Fernando A Seixas
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ziheng Yang
- Correspondence to be sent to: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; E-mail: ; (Y.T. and J.M.); Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK; E-mail: (Z.Y.)
| | - James Mallet
- Correspondence to be sent to: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; E-mail: ; (Y.T. and J.M.); Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK; E-mail: (Z.Y.)
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45
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Santos SHD, Peery RM, Miller JM, Dao A, Lyu FH, Li X, Li MH, Coltman DW. Ancient hybridization patterns between bighorn and thinhorn sheep. Mol Ecol 2021; 30:6273-6288. [PMID: 34845798 DOI: 10.1111/mec.16136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 07/27/2021] [Accepted: 08/18/2021] [Indexed: 12/12/2022]
Abstract
Whole-genome sequencing has advanced the study of species evolution, including the detection of genealogical discordant events such as ancient hybridization and incomplete lineage sorting (ILS). The evolutionary history of bighorn (Ovis canadensis) and thinhorn (Ovis dalli) sheep present an ideal system to investigate evolutionary discordance due to their recent and rapid radiation and putative secondary contact between bighorn and thinhorn sheep subspecies, specifically the dark pelage Stone sheep (O. dalli stonei) and predominately white Dall sheep (O. dalli dalli), during the last ice age. Here, we used multiple genomes of bighorn and thinhorn sheep, together with snow (O. nivicola) and the domestic sheep (O. aries) as outgroups, to assess their phylogenomic history, potential introgression patterns and their adaptive consequences. Among the Pachyceriforms (snow, bighorn and thinhorn sheep) a consistent monophyletic species tree was retrieved; however, many genealogical discordance patterns were observed. Alternative phylogenies frequently placed Stone and bighorn as sister clades. This relationship occurred more often and was less divergent than that between Dall and bighorn. We also observed many blocks containing introgression signal between Stone and bighorn genomes in which coat colour genes were present. Introgression signals observed between Dall and bighorn were more random and less frequent, and therefore probably due to ILS or intermediary secondary contact. These results strongly suggest that Stone sheep originated from a complex series of events, characterized by multiple, ancient periods of secondary contact with bighorn sheep.
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Affiliation(s)
- Sarah H D Santos
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Rhiannon M Peery
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Joshua M Miller
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Anh Dao
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Feng-Hua Lyu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xin Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Chinese Academy of Sciences (CAS), Beijing, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Chinese Academy of Sciences (CAS), Beijing, China
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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46
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Abstract
Alleles that introgress between species can influence the evolutionary and ecological fate of species exposed to novel environments. Hybrid offspring of different species are often unfit, and yet it has long been argued that introgression can be a potent force in evolution, especially in plants. Over the last two decades, genomic data have increasingly provided evidence that introgression is a critically important source of genetic variation and that this additional variation can be useful in adaptive evolution of both animals and plants. Here, we review factors that influence the probability that foreign genetic variants provide long-term benefits (so-called adaptive introgression) and discuss their potential benefits. We find that introgression plays an important role in adaptive evolution, particularly when a species is far from its fitness optimum, such as when they expand their range or are subject to changing environments.
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Affiliation(s)
- Nathaniel B Edelman
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Current affiliation: Yale Institute for Biospheric Studies and Yale School of the Environment, Yale University, New Haven, Connecticut 06511, USA;
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA;
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47
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Chen ZH, Xu YX, Xie XL, Wang DF, Aguilar-Gómez D, Liu GJ, Li X, Esmailizadeh A, Rezaei V, Kantanen J, Ammosov I, Nosrati M, Periasamy K, Coltman DW, Lenstra JA, Nielsen R, Li MH. Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep. Commun Biol 2021; 4:1307. [PMID: 34795381 PMCID: PMC8602413 DOI: 10.1038/s42003-021-02817-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/27/2021] [Indexed: 02/06/2023] Open
Abstract
The domestication and subsequent development of sheep are crucial events in the history of human civilization and the agricultural revolution. However, the impact of interspecific introgression on the genomic regions under domestication and subsequent selection remains unclear. Here, we analyze the whole genomes of domestic sheep and their wild relative species. We found introgression from wild sheep such as the snow sheep and its American relatives (bighorn and thinhorn sheep) into urial, Asiatic and European mouflons. We observed independent events of adaptive introgression from wild sheep into the Asiatic and European mouflons, as well as shared introgressed regions from both snow sheep and argali into Asiatic mouflon before or during the domestication process. We revealed European mouflons might arise through hybridization events between a now extinct sheep in Europe and feral domesticated sheep around 6000-5000 years BP. We also unveiled later introgressions from wild sheep to their sympatric domestic sheep after domestication. Several of the introgression events contain loci with candidate domestication genes (e.g., PAPPA2, NR6A1, SH3GL3, RFX3 and CAMK4), associated with morphological, immune, reproduction or production traits (wool/meat/milk). We also detected introgression events that introduced genes related to nervous response (NEURL1), neurogenesis (PRUNE2), hearing ability (USH2A), and placental viability (PAG11 and PAG3) into domestic sheep and their ancestral wild species from other wild species.
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Affiliation(s)
- Ze-Hui Chen
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China ,grid.22935.3f0000 0004 0530 8290College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ya-Xi Xu
- grid.22935.3f0000 0004 0530 8290College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xing-Long Xie
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Dong-Feng Wang
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Diana Aguilar-Gómez
- grid.47840.3f0000 0001 2181 7878Center for Computational Biology, University of California at Berkeley, Berkeley, CA 94720 USA
| | | | - Xin Li
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ali Esmailizadeh
- grid.412503.10000 0000 9826 9569Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Vahideh Rezaei
- grid.412503.10000 0000 9826 9569Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Juha Kantanen
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Innokentyi Ammosov
- grid.495192.2Laboratory of Reindeer Husbandry and Traditional Industries, Yakut Scientific Research Institute of Agriculture, The Sakha Republic (Yakutia), Yakutsk, Russia
| | - Maryam Nosrati
- grid.412462.70000 0000 8810 3346Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Kathiravan Periasamy
- grid.420221.70000 0004 0403 8399Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria
| | - David W. Coltman
- grid.17089.37Department of Biological Sciences, University of Alberta, Edmonton, AB T6G2E9 Canada
| | - Johannes A. Lenstra
- grid.5477.10000000120346234Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California at Berkeley, Berkeley, CA, 94720, USA. .,Department of Statistics, UC Berkeley, Berkeley, CA, 94707, USA. .,Globe Institute, University of Copenhagen, 1350, København K, Denmark.
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, China.
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48
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Extensive Interspecific Gene Flow Shaped Complex Evolutionary History and Underestimated Species Diversity in Rapidly Radiated Dolphins. J MAMM EVOL 2021. [DOI: 10.1007/s10914-021-09581-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractRecently diverged taxa are often characterized by high rates of hybridization, which can complicate phylogenetic reconstruction. For this reason, the phylogenetic relationships and evolutionary history of dolphins are still not very well resolved; the question of whether the genera Tursiops and Stenella are monophyletic is especially controversial. Here, we performed re-sequencing of six dolphin genomes and combined them with eight previously published dolphin SRA datasets and six whole-genome datasets to investigate the phylogenetic relationships of dolphins and test the monophyly hypothesis of Tursiops and Stenella. Phylogenetic reconstruction with the maximum likelihood and Bayesian methods of concatenated loci, as well as with coalescence analyses of sliding window trees, produced a concordant and well-supported tree. Our studies support the non-monophyletic status of Tursiops and Stenella because the species referred these genera do not form exclusive monophyletic clades. This suggests that the current taxonomy of both genera might not reflect their evolutionary history and may underestimate their diversity. A four-taxon D-statistic (ABBA-BABA) test, five-taxon DFOIL test, and tree-based PhyloNet analyses all showed extensive gene flow across dolphin species, which could explain the instability in resolving phylogenetic relationship of oceanic dolphins with different and limited markers. This study could be a good case to demonstrate how genomic data can reveal complex speciation and phylogeny in rapidly radiating animal groups.
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49
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Fuentes D, Molina M, Chorostecki U, Capella-Gutiérrez S, Marcet-Houben M, Gabaldón T. PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies. Nucleic Acids Res 2021; 50:D1062-D1068. [PMID: 34718760 PMCID: PMC8728271 DOI: 10.1093/nar/gkab966] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/02/2021] [Accepted: 10/05/2021] [Indexed: 12/20/2022] Open
Abstract
PhylomeDB is a unique knowledge base providing public access to minable and browsable catalogues of pre-computed genome-wide collections of annotated sequences, alignments and phylogenies (i.e. phylomes) of homologous genes, as well as to their corresponding phylogeny-based orthology and paralogy relationships. In addition, PhylomeDB trees and alignments can be downloaded for further processing to detect and date gene duplication events, infer past events of inter-species hybridization and horizontal gene transfer, as well as to uncover footprints of selection, introgression, gene conversion, or other relevant evolutionary processes in the genes and organisms of interest. Here, we describe the latest evolution of PhylomeDB (version 5). This new version includes a newly implemented web interface and several new functionalities such as optimized searching procedures, the possibility to create user-defined phylome collections, and a fully redesigned data structure. This release also represents a significant core data expansion, with the database providing access to 534 phylomes, comprising over 8 million trees, and homology relationships for genes in over 6000 species. This makes PhylomeDB the largest and most comprehensive public repository of gene phylogenies. PhylomeDB is available at http://www.phylomedb.org.
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Affiliation(s)
- Diego Fuentes
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Manuel Molina
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Uciel Chorostecki
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | | | - Marina Marcet-Houben
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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50
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The evolutionary genomics of species' responses to climate change. Nat Ecol Evol 2021; 5:1350-1360. [PMID: 34373621 DOI: 10.1038/s41559-021-01526-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 07/05/2021] [Indexed: 02/06/2023]
Abstract
Climate change is a threat to biodiversity. One way that this threat manifests is through pronounced shifts in the geographical range of species over time. To predict these shifts, researchers have primarily used species distribution models. However, these models are based on assumptions of niche conservatism and do not consider evolutionary processes, potentially limiting their accuracy and value. To incorporate evolution into the prediction of species' responses to climate change, researchers have turned to landscape genomic data and examined information about local genetic adaptation using climate models. Although this is an important advancement, this approach currently does not include other evolutionary processes-such as gene flow, population dispersal and genomic load-that are critical for predicting the fate of species across the landscape. Here, we briefly review the current practices for the use of species distribution models and for incorporating local adaptation. We next discuss the rationale and theory for considering additional processes, reviewing how they can be incorporated into studies of species' responses to climate change. We summarize with a conceptual framework of how manifold layers of information can be combined to predict the potential response of specific populations to climate change. We illustrate all of the topics using an exemplar dataset and provide the source code as potential tutorials. This Perspective is intended to be a step towards a more comprehensive integration of population genomics with climate change science.
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