1
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Ellis S, Franks DW, Nielsen MLK, Weiss MN, Croft DP. The evolution of menopause in toothed whales. Nature 2024; 627:579-585. [PMID: 38480878 PMCID: PMC10954554 DOI: 10.1038/s41586-024-07159-9] [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: 02/23/2023] [Accepted: 02/05/2024] [Indexed: 03/20/2024]
Abstract
Understanding how and why menopause has evolved is a long-standing challenge across disciplines. Females can typically maximize their reproductive success by reproducing for the whole of their adult life. In humans, however, women cease reproduction several decades before the end of their natural lifespan1,2. Although progress has been made in understanding the adaptive value of menopause in humans3,4, the generality of these findings remains unclear. Toothed whales are the only mammal taxon in which menopause has evolved several times5, providing a unique opportunity to test the theories of how and why menopause evolves in a comparative context. Here, we assemble and analyse a comparative database to test competing evolutionary hypotheses. We find that menopause evolved in toothed whales by females extending their lifespan without increasing their reproductive lifespan, as predicted by the 'live-long' hypotheses. We further show that menopause results in females increasing their opportunity for intergenerational help by increasing their lifespan overlap with their grandoffspring and offspring without increasing their reproductive overlap with their daughters. Our results provide an informative comparison for the evolution of human life history and demonstrate that the same pathway that led to menopause in humans can also explain the evolution of menopause in toothed whales.
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Affiliation(s)
- Samuel Ellis
- Centre for Research in Animal Behaviour, Department of Psychology, University of Exeter, Exeter, UK.
| | | | | | - Michael N Weiss
- Centre for Research in Animal Behaviour, Department of Psychology, University of Exeter, Exeter, UK
- Center for Whale Research, Friday Harbor, WA, USA
| | - Darren P Croft
- Centre for Research in Animal Behaviour, Department of Psychology, University of Exeter, Exeter, UK
- Center for Whale Research, Friday Harbor, WA, USA
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2
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Freudiger A, Jovanovic VM, Huang Y, Snyder-Mackler N, Conrad DF, Miller B, Montague MJ, Westphal H, Stadler PF, Bley S, Horvath JE, Brent LJN, Platt ML, Ruiz-Lambides A, Tung J, Nowick K, Ringbauer H, Widdig A. Taking identity-by-descent analysis into the wild: Estimating realized relatedness in free-ranging macaques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574911. [PMID: 38260273 PMCID: PMC10802400 DOI: 10.1101/2024.01.09.574911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Biological relatedness is a key consideration in studies of behavior, population structure, and trait evolution. Except for parent-offspring dyads, pedigrees capture relatedness imperfectly. The number and length of DNA segments that are identical-by-descent (IBD) yield the most precise estimates of relatedness. Here, we leverage novel methods for estimating locus-specific IBD from low coverage whole genome resequencing data to demonstrate the feasibility and value of resolving fine-scaled gradients of relatedness in free-living animals. Using primarily 4-6× coverage data from a rhesus macaque (Macaca mulatta) population with available long-term pedigree data, we show that we can call the number and length of IBD segments across the genome with high accuracy even at 0.5× coverage. The resulting estimates demonstrate substantial variation in genetic relatedness within kin classes, leading to overlapping distributions between kin classes. They identify cryptic genetic relatives that are not represented in the pedigree and reveal elevated recombination rates in females relative to males, which allows us to discriminate maternal and paternal kin using genotype data alone. Our findings represent a breakthrough in the ability to understand the predictors and consequences of genetic relatedness in natural populations, contributing to our understanding of a fundamental component of population structure in the wild.
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Affiliation(s)
- Annika Freudiger
- Behavioral Ecology Research Group, Faculty of Life Sciences, Institute of Biology, Leipzig University, Leipzig, Germany
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Vladimir M Jovanovic
- Human Biology and Primate Evolution, Institut für Zoologie, Freie Universität Berlin, Berlin, Germany
- Bioinformatics Solution Center, Freie Universität Berlin, Berlin, Germany
| | - Yilei Huang
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Bioinformatics Group, Institute of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Noah Snyder-Mackler
- Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, USA
| | - Donald F Conrad
- Division of Genetics, Oregon National Primate Research Center, Portland, Oregon, USA
| | - Brian Miller
- Division of Genetics, Oregon National Primate Research Center, Portland, Oregon, USA
| | - Michael J Montague
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hendrikje Westphal
- Behavioral Ecology Research Group, Faculty of Life Sciences, Institute of Biology, Leipzig University, Leipzig, Germany
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Bioinformatics Group, Institute of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Institute of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, Austria
- Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
- Santa Fe Institute, Santa Fe, NM, USA
| | - Stefanie Bley
- Behavioral Ecology Research Group, Faculty of Life Sciences, Institute of Biology, Leipzig University, Leipzig, Germany
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Julie E Horvath
- Department of Biological and Biomedical Sciences, North Carolina Central University, North Carolina, Durham, USA
- Research and Collections Section, North Carolina Museum of Natural Sciences, North Carolina, Raleigh, USA
- Department of Biological Sciences, North Carolina State University, North Carolina, Raleigh, USA
- Department of Evolutionary Anthropology, Duke University, North Carolina, Durham, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lauren J N Brent
- Centre for Research in Animal Behaviour, University of Exeter, Exeter, UK
| | - Michael L Platt
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Marketing Department, the Wharton School of Business, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Angelina Ruiz-Lambides
- Cayo Santiago Field Station, Caribbean Primate Research Center, University of Puerto Rico, Punta Santiago, Puerto Rico
| | - Jenny Tung
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Evolutionary Anthropology, Duke University, North Carolina, Durham, USA
- Department of Biology, Duke University, Durham, North Carolina, USA
- Duke University Population Research Institute, Durham, North Carolina, USA
| | - Katja Nowick
- Human Biology and Primate Evolution, Institut für Zoologie, Freie Universität Berlin, Berlin, Germany
- Bioinformatics Solution Center, Freie Universität Berlin, Berlin, Germany
| | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anja Widdig
- Behavioral Ecology Research Group, Faculty of Life Sciences, Institute of Biology, Leipzig University, Leipzig, Germany
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Germany
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3
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Mann J. Animal behavior: Killer whale mamas' boys. Curr Biol 2023; 33:R194-R197. [PMID: 36917944 DOI: 10.1016/j.cub.2023.01.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Long-term study of killer whales reveals that sons stay with their mothers for life, and although this benefits sons, it negatively impacts the mother's reproductive output.
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Affiliation(s)
- Janet Mann
- Department of Biology, Department of Psychology, Georgetown University, Washington, Washington DC 20057, USA.
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4
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Weiss MN, Ellis S, Franks DW, Nielsen MLK, Cant MA, Johnstone RA, Ellifrit DK, Balcomb KC, Croft DP. Costly lifetime maternal investment in killer whales. Curr Biol 2023; 33:744-748.e3. [PMID: 36758545 DOI: 10.1016/j.cub.2022.12.057] [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: 09/23/2022] [Revised: 11/07/2022] [Accepted: 12/21/2022] [Indexed: 02/11/2023]
Abstract
Parents often sacrifice their own future reproductive success to boost the survival of their offspring, a phenomenon referred to as parental investment. In several social mammals, mothers continue to improve the survival of their offspring well into adulthood;1,2,3,4,5 however, whether this extended care comes at a reproductive costs to mothers, and therefore represents maternal investment, is not well understood. We tested whether lifetime maternal care is a form of parental investment in fish-eating "resident" killer whales. Adult killer whales, particularly males, are known to receive survival benefits from their mothers;3 however, whether this comes at a cost to mothers' reproductive success is not known. Using multiple decades of complete census data from the "southern resident" population, we found a strong negative correlation between females' number of surviving weaned sons and their annual probability of producing a viable calf. This negative effect did not attenuate as sons grew older, and the cost of sons could not be explained by long-term costs of lactation or group composition effects, supporting the hypothesis that caring for adult sons is reproductively costly. This is the first direct evidence of lifetime maternal investment in an iteroparous animal, revealing a previously unknown life history strategy.
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Affiliation(s)
- Michael N Weiss
- Centre for Research in Animal Behaviour, University of Exeter, EX4 4QG, Exeter, UK; Center for Whale Research, Friday Harbor, WA 98250, USA.
| | - Samuel Ellis
- Centre for Research in Animal Behaviour, University of Exeter, EX4 4QG, Exeter, UK
| | - Daniel W Franks
- Department of Biology, University of York, YO10 5DD, York, UK; Department of Computer Science, University of York, YO10 5DD, York, UK
| | | | - Michael A Cant
- College of Life and Environmental Sciences, University of Exeter, Penryn, TR10 9FE, UK
| | - Rufus A Johnstone
- Department of Zoology, University of Cambridge, CB2 3EJ, Cambridge, UK
| | | | | | - Darren P Croft
- Centre for Research in Animal Behaviour, University of Exeter, EX4 4QG, Exeter, UK
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5
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Onoufriou AB, Gaggiotti OE, Aguilar de Soto N, McCarthy ML, Morin PA, Rosso M, Dalebout M, Davison N, Baird RW, Baker CS, Berrow S, Brownlow A, Burns D, Caurant F, Claridge D, Constantine R, Demaret F, Dreyer S, Ðuras M, Durban JW, Frantzis A, Freitas L, Genty G, Galov A, Hansen SS, Kitchener AC, Martin V, Mignucci-Giannoni AA, Montano V, Moulins A, Olavarría C, Poole MM, Reyes Suárez C, Rogan E, Ryan C, Schiavi A, Tepsich P, Urban R. J, West K, Olsen MT, Carroll EL. Biogeography in the deep: Hierarchical population genomic structure of two beaked whale species. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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6
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Dynamics of short-finned pilot whales long-term social structure in Madeira. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00280-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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7
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Proposing a framework for monitoring demographic parameters in local cetacean populations: the case of short-finned pilot whales in Madeira. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00266-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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8
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Vargas-Fonseca OA, Yates P, Kirkman SP, Pistorius PA, Moore DM, Natoli A, Cockcroft V, Hoelzel AR. Population structure associated with bioregion and seasonal prey distribution for Indo-Pacific bottlenose dolphins (Tursiops aduncus) in South Africa. Mol Ecol 2021; 30:4642-4659. [PMID: 34289192 DOI: 10.1111/mec.16086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 06/19/2021] [Accepted: 06/29/2021] [Indexed: 11/28/2022]
Abstract
Many marine species exhibit fine-scale population structure despite high mobility and a lack of physical barriers to dispersal, but the evolutionary drivers of differentiation in these systems are generally poorly understood. Here we investigate the potential role of habitat transitions and seasonal prey distributions on the evolution of population structure in the Indo-Pacific bottlenose dolphin, Tursiops aduncus, off South Africa's coast, using double-digest restriction-site associated DNA sequencing. Population structure was identified between the eastern and southern coasts and correlated with the habitat transition between the temperate Agulhas (southern) and subtropical Natal (eastern) Bioregions, suggesting differentiation driven by resource specializations. Differentiation along the Natal coast was comparatively weak, but was evident in some analyses and varied depending on whether the samples were collected during or outside the seasonal sardine (Sardinops sagax) run. This local abundance of prey could influence the ranging patterns and apparent genetic structure of T. aduncus. These findings have significant and transferable management implications, most importantly in terms of differentiating populations inhabiting distinct bioregions and seasonal structural patterns within a region associated with the movement of prey resources.
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Affiliation(s)
- O Alejandra Vargas-Fonseca
- Department of Zoology, Nelson Mandela University, Port Elizabeth, South Africa.,Marine Apex Predator Research Unit (MAPRU), Institute for Coastal and Marine Research, Nelson Mandela University, Port Elizabeth, South Africa
| | - Paige Yates
- Department of Biosciences, University of Durham, Durham, UK
| | - Stephan P Kirkman
- Marine Apex Predator Research Unit (MAPRU), Institute for Coastal and Marine Research, Nelson Mandela University, Port Elizabeth, South Africa.,Branch: Oceans and Coasts, Department of Environment, Forestry and Fisheries (DEFF), Cape Town, South Africa
| | - Pierre A Pistorius
- Department of Zoology, Nelson Mandela University, Port Elizabeth, South Africa.,Marine Apex Predator Research Unit (MAPRU), Institute for Coastal and Marine Research, Nelson Mandela University, Port Elizabeth, South Africa
| | - Daniel M Moore
- Department of Biosciences, University of Durham, Durham, UK
| | - Ada Natoli
- Department of Life and Environmental Sciences, College of Natural and Health Sciences, Zayed University, United Arab Emirates.,UAE Dolphin Project, Dubai, United Arab Emirates
| | - Victor Cockcroft
- Department of Zoology, Nelson Mandela University, Port Elizabeth, South Africa
| | - A Rus Hoelzel
- Department of Biosciences, University of Durham, Durham, UK
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9
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Sarano F, Girardet J, Sarano V, Vitry H, Preud'homme A, Heuzey R, Garcia-Cegarra AM, Madon B, Delfour F, Glotin H, Adam O, Jung JL. Kin relationships in cultural species of the marine realm: case study of a matrilineal social group of sperm whales off Mauritius island, Indian Ocean. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201794. [PMID: 33972866 PMCID: PMC8074673 DOI: 10.1098/rsos.201794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/11/2021] [Indexed: 05/14/2023]
Abstract
Understanding the organization and dynamics of social groups of marine mammals through the study of kin relationships is particularly challenging. Here, we studied a stable social group of sperm whales off Mauritius, using underwater observations, individual-specific identification, non-invasive sampling and genetic analyses based on mitochondrial sequencing and microsatellite profiling. Twenty-four sperm whales were sampled between 2017 and 2019. All individuals except one adult female shared the same mitochondrial DNA (mtDNA) haplotype-one that is rare in the western Indian Ocean-thus confirming with near certainty the matrilineality of the group. All probable first- and second-degree kin relationships were depicted in the sperm whale social group: 13 first-degree and 27 second-degree relationships were identified. Notably, we highlight the likely case of an unrelated female having been integrated into a social unit, in that she presented a distinct mtDNA haplotype and no close relationships with any members of the group. Investigating the possible matrilineality of sperm whale cultural units (i.e. vocal clans) is the next step in our research programme to elucidate and better apprehend the complex organization of sperm whale social groups.
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Affiliation(s)
| | - Justine Girardet
- Université de Brest, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, ISYEB, Brest, France
| | | | - Hugues Vitry
- Marine Megafauna Conservation Organisation, Mauritius
| | | | | | - Ana M. Garcia-Cegarra
- Centro de Investigación de Fauna Marina y Avistamiento de Cetáceos, CIFAMAC, Mejillones, Chile
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomás, Antofagasta, Chile
| | - Bénédicte Madon
- Université de Brest, AMURE - Aménagement des Usages des Ressources et des Espaces marins et littoraux - Centre de droit et d'économie de la mer, Plouzané, France
| | - Fabienne Delfour
- Laboratoire d'Ethologie Expérimentale et Comparée EA 4443, Université Paris 13, Sorbonne Paris Cité, Villetaneuse, France
| | - Hervé Glotin
- Toulon University, Aix Marseille Université, CNRS, LIS, DYNI Team, Marseille, France
| | - Olivier Adam
- Sorbonne Université, CNRS, Institut Jean Le Rond d'Alembert, UMR 7190, Paris, France
- Institute of Neurosciences Paris-Saclay, Bioacoustics Team, CNRS UMR 9197, Université Paris Sud, Orsay, France
| | - Jean-Luc Jung
- Université de Brest, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, ISYEB, Brest, France
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10
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Petty LE, Phillippi-Falkenstein K, Kubisch HM, Raveendran M, Harris RA, Vallender EJ, Huff CD, Bohm RP, Rogers J, Below JE. Pedigree reconstruction and distant pairwise relatedness estimation from genome sequence data: A demonstration in a population of rhesus macaques (Macaca mulatta). Mol Ecol Resour 2021; 21:1333-1346. [PMID: 33386679 PMCID: PMC8247968 DOI: 10.1111/1755-0998.13317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/13/2020] [Accepted: 12/07/2020] [Indexed: 12/30/2022]
Abstract
A primary challenge in the analysis of free‐ranging animal populations is the accurate estimation of relatedness among individuals. Many aspects of population analysis rely on knowledge of relatedness patterns, including socioecology, demography, heritability and gene mapping analyses, wildlife conservation and the management of breeding colonies. Methods for determining relatedness using genome‐wide data have improved our ability to determine kinship and reconstruct pedigrees in humans. However, methods for reconstructing complex pedigree structures and estimating distant relatedness (beyond third‐degree) have not been widely applied to other species. We sequenced the genomes of 150 male rhesus macaques from the Tulane National Primate Research Center colony to estimate pairwise relatedness, reconstruct closely related pedigrees, estimate more distant relationships and augment colony records. Methods for determining relatedness developed for human genetic data were applied and evaluated in the analysis of nonhuman primates, including identity‐by‐descent‐based methods for pedigree reconstruction and shared segment‐based inference of more distant relatedness. We compared the genotype‐based pedigrees and estimated relationships to available colony pedigree records and found high concordance (95.5% agreement) between expected and identified relationships for close relatives. In addition, we detected distant relationships not captured in colony records, including some as distant as twelfth‐degree. Furthermore, while deep sequence coverage is preferable, we show that this approach can also provide valuable information when only low‐coverage (5×) sequence data is available. Our findings demonstrate the value of these methods for determination of relatedness in various animal populations, with diverse applications to conservation biology, evolutionary and ecological research and biomedical studies.
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Affiliation(s)
- Lauren E Petty
- Vanderbilt Genetics Institute and Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - H Michael Kubisch
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Eric J Vallender
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA, USA.,Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, USA
| | - Chad D Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rudolf P Bohm
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute and Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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11
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Li YL, Wang L, Wu JW, Ye XP, Garber PA, Yan Y, Liu JH, Li BG, Qi XG. Bachelor groups in primate multilevel society facilitate gene flow across fragmented habitats. Curr Zool 2020; 66:113-122. [PMID: 32211037 PMCID: PMC7083096 DOI: 10.1093/cz/zoaa006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/10/2020] [Indexed: 11/25/2022] Open
Abstract
In the face of ongoing habitat fragmentation, many primate species have experienced reduced gene flow resulting in a reduction of genetic diversity, population bottlenecks, and inbreeding depression, including golden snub-nosed monkeys Rhinopithecus roxellana. Golden snub-nosed monkeys live in a multilevel society composed of several 1 male harem units that aggregate to form a cohesive breeding band, which is followed by one or more bachelor groups composed of juvenile, subadult, and adult male members. In this research, we examine the continuous landscape resistance surface, the genetic diversity and patterns of gene flow among 4 isolated breeding bands and 1 all-male band in the Qinling Mountains, China. Landscape surface modeling suggested that human activities and ecological factors severely limit the movement of individuals among breeding bands. Although these conditions are expected to result in reduced gene flow, reduced genetic diversity, and an increased opportunity for a genetic bottleneck, based on population genetic analyses of 13 microsatellite loci from 188 individuals inhabiting 4 isolated breeding bands and 1 all-male band, we found high levels of genetic diversity but low levels of genetic divergence, as well as high rates of gene flow between males residing in the all-male band and each of the 4 breeding bands. Our results indicate that the movement of bachelor males across the landscape, along with their association with several different breeding bands, appears to provide a mechanism for promoting gene flows and maintaining genetic diversity that may counteract the otherwise isolating effects of habitat fragmentation.
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Affiliation(s)
- Yu-Li Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Science, Northwest University, Xi'an, 710069, China
| | - Lu Wang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Science, Northwest University, Xi'an, 710069, China
| | - Jin-Wei Wu
- Shaanxi Key Laboratory for Animal Conservation, College of Life Science, Northwest University, Xi'an, 710069, China
| | - Xin-Ping Ye
- College of Life Science, Shaanxi Normal University, Xi'an, 710119, China
| | - Paul A Garber
- Anthropology Department, University of Illinois, Urbana, IL, 61801, USA
| | - Ying Yan
- Shaanxi Key Laboratory for Animal Conservation, College of Life Science, Northwest University, Xi'an, 710069, China
| | - Jia-Hui Liu
- Shaanxi Key Laboratory for Animal Conservation, College of Life Science, Northwest University, Xi'an, 710069, China
| | - Bao-Guo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Science, Northwest University, Xi'an, 710069, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Science, Kumming, 650223, China
| | - Xiao-Guang Qi
- Shaanxi Key Laboratory for Animal Conservation, College of Life Science, Northwest University, Xi'an, 710069, China
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12
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Foroughirad V, Levengood AL, Mann J, Frère CH. Quality and quantity of genetic relatedness data affect the analysis of social structure. Mol Ecol Resour 2019; 19:1181-1194. [PMID: 31056823 DOI: 10.1111/1755-0998.13028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 02/06/2023]
Abstract
Kinship plays a fundamental role in the evolution of social systems and is considered a key driver of group living. To understand the role of kinship in the formation and maintenance of social bonds, accurate measures of genetic relatedness are critical. Genotype-by-sequencing technologies are rapidly advancing the accuracy and precision of genetic relatedness estimates for wild populations. The ability to assign kinship from genetic data varies depending on a species' or population's mating system and pattern of dispersal, and empirical data from longitudinal studies are crucial to validate these methods. We use data from a long-term behavioural study of a polygynandrous, bisexually philopatric marine mammal to measure accuracy and precision of parentage and genetic relatedness estimation against a known partial pedigree. We show that with moderate but obtainable sample sizes of approximately 4,235 SNPs and 272 individuals, highly accurate parentage assignments and genetic relatedness coefficients can be obtained. Additionally, we subsample our data to quantify how data availability affects relatedness estimation and kinship assignment. Lastly, we conduct a social network analysis to investigate the extent to which accuracy and precision of relatedness estimation improve statistical power to detect an effect of relatedness on social structure. Our results provide practical guidance for minimum sample sizes and sequencing depth for future studies, as well as thresholds for post hoc interpretation of previous analyses.
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Affiliation(s)
- Vivienne Foroughirad
- Division of Marine Science and Conservation, Duke University Marine Laboratory, Beaufort, North Carolina
| | - Alexis L Levengood
- Global Change Ecology Research Group, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
| | - Janet Mann
- Departments of Biology and Psychology, Georgetown University, Washington, District of Columbia
| | - Céline H Frère
- Global Change Ecology Research Group, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
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13
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Van Cise AM, Baird RW, Baker CS, Cerchio S, Claridge D, Fielding R, Hancock-Hanser B, Marrero J, Martien KK, Mignucci-Giannoni AA, Oleson EM, Oremus M, Poole MM, Rosel PE, Taylor BL, Morin PA. Oceanographic barriers, divergence, and admixture: Phylogeography and taxonomy of two putative subspecies of short-finned pilot whale. Mol Ecol 2019; 28:2886-2902. [PMID: 31002212 DOI: 10.1111/mec.15107] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 04/10/2019] [Indexed: 12/11/2022]
Abstract
Genomic phylogeography plays an important role in describing evolutionary processes and their geographic, ecological, or cultural drivers. These drivers are often poorly understood in marine environments, which have fewer obvious barriers to mixing than terrestrial environments. Taxonomic uncertainty of some taxa (e.g., cetaceans), due to the difficulty in obtaining morphological data, can hamper our understanding of these processes. One such taxon, the short-finned pilot whale, is recognized as a single global species but includes at least two distinct morphological forms described from stranding and drive hunting in Japan, the "Naisa" and "Shiho" forms. Using samples (n = 735) collected throughout their global range, we examine phylogeographic patterns of divergence by comparing mitogenomes and nuclear SNP loci. Our results suggest three types within the species: an Atlantic Ocean type, a western/central Pacific and Indian Ocean (Naisa) type, and an eastern Pacific Ocean and northern Japan (Shiho) type. mtDNA control region differentiation indicates these three types form two subspecies, separated by the East Pacific Barrier: Shiho short-finned pilot whale, in the eastern Pacific Ocean and northern Japan, and Naisa short-finned pilot whale, throughout the remainder of the species' distribution. Our data further indicate two diverging populations within the Naisa subspecies, in the Atlantic Ocean and western/central Pacific and Indian Oceans, separated by the Benguela Barrier off South Africa. This study reveals a process of divergence and speciation within a globally-distributed, mobile marine predator, and indicates the importance of the East Pacific Barrier to this evolutionary process.
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Affiliation(s)
- Amy M Van Cise
- Scripps Institution of Oceanography, La Jolla, California.,Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, California.,Woods Hole Oceanographic Institution, Woods Hole, Massachusetts
| | | | - Charles Scott Baker
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Newport, Oregon
| | | | - Diane Claridge
- Bahamas Marine Mammal Research Organisation, Abaco, Bahamas
| | - Russell Fielding
- Department of Earth & Environmental Systems, University of the South, Sewanee, Tennessee
| | - Brittany Hancock-Hanser
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, California
| | - Jacobo Marrero
- Asociación Tonina, Investigación y Divulgación del medio natural Marino, San Cristóbal de La Laguna, Spain.,BIOECOMAC, Department of Animal Biology, La Laguna University, La Laguna, Tenerife, Canary Islands, Spain
| | - Karen K Martien
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, California
| | | | - Erin M Oleson
- Pacific Islands Fisheries Science Center, National Marine Fisheries Service, NOAA, Honolulu, Hawaii
| | - Marc Oremus
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Newport, Oregon
| | | | - Patricia E Rosel
- Southeast Fisheries Science Center, National Marine Fisheries Service, NOAA, Lafayette, Louisiana
| | - Barbara L Taylor
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, California
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, California
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Van Cise AM, Mahaffy SD, Baird RW, Mooney TA, Barlow J. Song of my people: dialect differences among sympatric social groups of short-finned pilot whales in Hawai’i. Behav Ecol Sociobiol 2018. [DOI: 10.1007/s00265-018-2596-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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