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Ishizuka S, Inoue E, Kaji Y. Paternity success for resident and non-resident males and their influences on paternal sibling cohorts in Japanese macaques (Macaca fuscata) on Shodoshima Island. PLoS One 2024; 19:e0309056. [PMID: 39298461 DOI: 10.1371/journal.pone.0309056] [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: 07/01/2024] [Accepted: 08/06/2024] [Indexed: 09/21/2024] Open
Abstract
Reproductive success can be attributed to both resident and non-resident males in non-human primates. However, reproductive success of non-resident males has rarely been investigated at an individual level. As resident males achieve different degree of reproductive success with regard to various factors, such as male dominance relationships or female mate choice, the degree of reproductive success for non-resident males may vary between individuals. As male reproductive success is highly skewed towards specific individuals, the percentage of similar-aged paternal siblings within groups is expected to increase. However, the extent to which each male contributes to the production of cohorts of paternal siblings remains unclear. Here we examined the paternity of offspring born over five consecutive years in a free-ranging group of Japanese macaques Macaca fuscata on Shodoshima Island, Kagawa Prefecture. Genotypes of 87 individuals at 16 autosomal microsatellite loci were analyzed and paternity of 34 offspring was successfully assigned to a single candidate father. We quantitatively assessed paternity success for resident and a few non-resident males whose genetic samples were successfully collected. We quantitatively assessed the percentages of paternal siblings in the same age cohorts produced by those males. Non-resident males sired similar percentage of offspring compared to resident males. A large prime-aged non-resident male was the most successful sire among males in two of the five years. These results provide new insights that male reproductive success could be highly skewed toward a specific non-resident male. Subadult males had a lower percentage of paternity success, which may be because females may prefer physically mature males. Various males, including non-resident males, contributed to the creation of paternal sibling in the same age cohort. The overall results highlighted that not only resident but also non-resident males play an important role in shaping within-group kin structures.
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Affiliation(s)
- Shintaro Ishizuka
- Faculty of Life Science and Technology, Department of Biological Science, Fukuyama University, Fukuyama, Hiroshima, Japan
- Faculty of Science, Department of Biology, Toho University, Funabashi, Chiba, Japan
- Japan Society for Promotion of Science, Kojimachi Business Center Building, Chiyoda-ku, Tokyo, Japan
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Eiji Inoue
- Faculty of Science, Department of Biology, Toho University, Funabashi, Chiba, Japan
| | - Yuki Kaji
- Choshikei Monkey Park, Tonosho, Kagawa, Japan
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2
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Scott AM, Banes GL, Setiadi W, Saragih JR, Susanto TW, Mitra Setia T, Knott CD. Flanged males have higher reproductive success in a completely wild orangutan population. PLoS One 2024; 19:e0296688. [PMID: 38335166 PMCID: PMC10857694 DOI: 10.1371/journal.pone.0296688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/17/2023] [Indexed: 02/12/2024] Open
Abstract
Male orangutans (Pongo spp.) exhibit bimaturism, an alternative reproductive tactic, with flanged and unflanged males displaying two distinct morphological and behavioral phenotypes. Flanged males are larger than unflanged males and display secondary sexual characteristics which unflanged males lack. The evolutionary explanation for alternative reproductive tactics in orangutans remains unclear because orangutan paternity studies to date have been from sites with ex-captive orangutans, provisioning via feeding stations and veterinary care, or that lack data on the identity of mothers. Here we demonstrate, using the first long-term paternity data from a site free of these limitations, that alternative reproductive tactics in orangutans are condition-dependent, not frequency-dependent. We found higher reproductive success by flanged males than by unflanged males, a pattern consistent with other Bornean orangutan (Pongo pygmaeus) paternity studies. Previous paternity studies disagree on the degree of male reproductive skew, but we found low reproductive skew among flanged males. We compare our findings and previous paternity studies from both Bornean and Sumatran orangutans (Pongo abelii) to understand why these differences exist, examining the possible roles of species differences, ecology, and human intervention. Additionally, we use long-term behavioral data to demonstrate that while flanged males can displace unflanged males in association with females, flanged males are unable to keep other males from associating with a female, and thus they are unable to completely mate guard females. Our results demonstrate that alternative reproductive tactics in Bornean orangutans are condition-dependent, supporting the understanding that the flanged male morph is indicative of good condition. Despite intense male-male competition and direct sexual coercion by males, female mate choice is effective in determining reproductive outcomes in this population of wild orangutans.
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Affiliation(s)
- Amy M. Scott
- Department of Anthropology, Boston University, Boston, Massachusetts, United States of America
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, United States of America
| | - Graham L. Banes
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- The Orang-Utan Conservation Genetics Project, Madison, Wisconsin, United States of America
| | - Wuryantari Setiadi
- Eijkman Research Center for Molecular Biology, National Agency for Research and Innovation (BRIN), The Science and Technology Center of Soekarno, Cibinong, West Java, Indonesia
| | - Jessica R. Saragih
- Eijkman Research Center for Molecular Biology, National Agency for Research and Innovation (BRIN), The Science and Technology Center of Soekarno, Cibinong, West Java, Indonesia
| | - Tri Wahyu Susanto
- Departemen of Biology, Faculty of Biology and Agricultural, Universitas Nasional, Kota Jakarta Selatan, Daerah Khusus Ibukota Jakarta, Indonesia
| | - Tatang Mitra Setia
- Departemen of Biology, Faculty of Biology and Agricultural, Universitas Nasional, Kota Jakarta Selatan, Daerah Khusus Ibukota Jakarta, Indonesia
| | - Cheryl D. Knott
- Department of Anthropology, Boston University, Boston, Massachusetts, United States of America
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
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3
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Tkaczynski PJ, Mafessoni F, Girard-Buttoz C, Samuni L, Ackermann CY, Fedurek P, Gomes C, Hobaiter C, Löhrich T, Manin V, Preis A, Valé PD, Wessling EG, Wittiger L, Zommers Z, Zuberbuehler K, Vigilant L, Deschner T, Wittig RM, Crockford C. Shared community effects and the non-genetic maternal environment shape cortisol levels in wild chimpanzees. Commun Biol 2023; 6:565. [PMID: 37237178 DOI: 10.1038/s42003-023-04909-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
Mechanisms of inheritance remain poorly defined for many fitness-mediating traits, especially in long-lived animals with protracted development. Using 6,123 urinary samples from 170 wild chimpanzees, we examined the contributions of genetics, non-genetic maternal effects, and shared community effects on variation in cortisol levels, an established predictor of survival in long-lived primates. Despite evidence for consistent individual variation in cortisol levels across years, between-group effects were more influential and made an overwhelming contribution to variation in this trait. Focusing on within-group variation, non-genetic maternal effects accounted for 8% of the individual differences in average cortisol levels, significantly more than that attributable to genetic factors, which was indistinguishable from zero. These maternal effects are consistent with a primary role of a shared environment in shaping physiology. For chimpanzees, and perhaps other species with long life histories, community and maternal effects appear more relevant than genetic inheritance in shaping key physiological traits.
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Affiliation(s)
- Patrick J Tkaczynski
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire.
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK.
| | - Fabrizio Mafessoni
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Weizmann Institute of Science, Department of Plant and Environmental Sciences, Rehovot, Israel.
| | - Cédric Girard-Buttoz
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
- The Ape Social Mind Lab, Institut des Sciences Cognitives, CNRS UMR 5229, Lyon, France
| | - Liran Samuni
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Centre for Social Learning & Cognitive Evolution, School of Psychology & Neuroscience, University of St Andrews, St Andrews, UK
| | - Corinne Y Ackermann
- Universite de Neuchatel, Institut de Biologie, Cognition Compare, Neuchatel, Switzerland
| | - Pawel Fedurek
- Division of Psychology, University of Stirling, Stirling, UK
| | - Cristina Gomes
- Tropical Conservation Institute, Institute of Environment, College of Arts, Science and Education, Florida International University, Miami, FL, USA
| | - Catherine Hobaiter
- Centre for Social Learning & Cognitive Evolution, School of Psychology & Neuroscience, University of St Andrews, St Andrews, UK
| | - Therese Löhrich
- World Wide Fund for Nature, Dzanga Sangha Protected Areas, BP 1053, Bangui, Central African Republic
- Robert Koch Institute, Epidemiology of Highly Pathogenic Microorganisms, Berlin, Germany
| | - Virgile Manin
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
| | - Anna Preis
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
| | - Prince D Valé
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
- Unité de Formation et de Recherche Agroferesterie, Université Jean Lorougnon Guédé, Daloa, Côte d'Ivoire
| | - Erin G Wessling
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | - Zinta Zommers
- Perry World House, University of Pennsylvania, Philadelphia, USA
| | - Klaus Zuberbuehler
- Universite de Neuchatel, Institut de Biologie, Cognition Compare, Neuchatel, Switzerland
| | - Linda Vigilant
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tobias Deschner
- Institute of Cognitive Science, Comparative BioCognition, University of Osnabrück, Osnabrück, Germany
| | - Roman M Wittig
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
- The Ape Social Mind Lab, Institut des Sciences Cognitives, CNRS UMR 5229, Lyon, France
| | - Catherine Crockford
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
- The Ape Social Mind Lab, Institut des Sciences Cognitives, CNRS UMR 5229, Lyon, France
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Scully EJ, Liu W, Li Y, Ndjango JBN, Peeters M, Kamenya S, Pusey AE, Lonsdorf EV, Sanz CM, Morgan DB, Piel AK, Stewart FA, Gonder MK, Simmons N, Asiimwe C, Zuberbühler K, Koops K, Chapman CA, Chancellor R, Rundus A, Huffman MA, Wolfe ND, Duraisingh MT, Hahn BH, Wrangham RW. The ecology and epidemiology of malaria parasitism in wild chimpanzee reservoirs. Commun Biol 2022; 5:1020. [PMID: 36167977 PMCID: PMC9515101 DOI: 10.1038/s42003-022-03962-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 09/01/2022] [Indexed: 11/09/2022] Open
Abstract
Chimpanzees (Pan troglodytes) harbor rich assemblages of malaria parasites, including three species closely related to P. falciparum (sub-genus Laverania), the most malignant human malaria parasite. Here, we characterize the ecology and epidemiology of malaria infection in wild chimpanzee reservoirs. We used molecular assays to screen chimpanzee fecal samples, collected longitudinally and cross-sectionally from wild populations, for malaria parasite mitochondrial DNA. We found that chimpanzee malaria parasitism has an early age of onset and varies seasonally in prevalence. A subset of samples revealed Hepatocystis mitochondrial DNA, with phylogenetic analyses suggesting that Hepatocystis appears to cross species barriers more easily than Laverania. Longitudinal and cross-sectional sampling independently support the hypothesis that mean ambient temperature drives spatiotemporal variation in chimpanzee Laverania infection. Infection probability peaked at ~24.5 °C, consistent with the empirical transmission optimum of P. falciparum in humans. Forest cover was also positively correlated with spatial variation in Laverania prevalence, consistent with the observation that forest-dwelling Anophelines are the primary vectors. Extrapolating these relationships across equatorial Africa, we map spatiotemporal variation in the suitability of chimpanzee habitat for Laverania transmission, offering a hypothetical baseline indicator of human exposure risk.
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Affiliation(s)
- Erik J Scully
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Department of Immunology & Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Weimin Liu
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yingying Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jean-Bosco N Ndjango
- Department of Ecology and Management of Plant and Animal Resources, Faculty of Sciences, University of Kisangani, BP 2012, Kisangani, Democratic Republic of the Congo
| | - Martine Peeters
- Recherche Translationnelle Appliquée au VIH et aux Maladies Infectieuses, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34090, Montpellier, France
| | - Shadrack Kamenya
- Gombe Stream Research Centre, The Jane Goodall Institute, Tanzania, Kigoma, Tanzania
| | - Anne E Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, NC, 27708, USA
| | - Elizabeth V Lonsdorf
- Department of Psychology, Franklin and Marshall College, Lancaster, PA, 17604, USA
| | - Crickette M Sanz
- Department of Anthropology, Washington University in St. Louis, St Louis, MO, 63130, USA
- Congo Program, Wildlife Conservation Society, BP 14537, Brazzaville, Republic of the Congo
| | - David B Morgan
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, Chicago, IL, 60614, USA
| | - Alex K Piel
- Department of Anthropology, University College London, 14 Taviton St, Bloomsbury, WC1H OBW, London, UK
| | - Fiona A Stewart
- Department of Anthropology, University College London, 14 Taviton St, Bloomsbury, WC1H OBW, London, UK
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | - Mary K Gonder
- Department of Biology, Drexel University, Philadelphia, PA, 19104, USA
| | - Nicole Simmons
- Zoology Department, Makerere University, P.O. Box 7062, Kampala, Uganda
| | | | - Klaus Zuberbühler
- School of Psychology and Neuroscience, University of St Andrews, St Andrews, UK
- Department of Comparative Cognition, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Kathelijne Koops
- Department of Ape Behaviour & Ecology Group, University of Zurich, Zurich, Switzerland
| | - Colin A Chapman
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, George Washington University, Washington, DC, USA
- School of Life Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
| | - Rebecca Chancellor
- Department of Anthropology & Sociology, West Chester University, West Chester, PA, USA
- Department of Psychology, West Chester University, West Chester, PA, USA
| | - Aaron Rundus
- Department of Psychology, West Chester University, West Chester, PA, USA
| | - Michael A Huffman
- Center for International Collaboration and Advanced Studies in Primatology, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | | | - Manoj T Duraisingh
- Department of Immunology & Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA.
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Richard W Wrangham
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
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Genetic, maternal, and environmental influences on sociality in a pedigreed primate population. Heredity (Edinb) 2022; 129:203-214. [PMID: 36056208 PMCID: PMC9519975 DOI: 10.1038/s41437-022-00558-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 11/09/2022] Open
Abstract
Various aspects of sociality in mammals (e.g., dyadic connectedness) are linked with measures of biological fitness (e.g., longevity). How within- and between-individual variation in relevant social traits arises in uncontrolled wild populations is challenging to determine but is crucial for understanding constraints on the evolution of sociality. We use an advanced statistical method, known as the 'animal model', which incorporates pedigree information, to look at social, genetic, and environmental influences on sociality in a long-lived wild primate. We leverage a longitudinal database spanning 20 years of observation on individually recognized white-faced capuchin monkeys (Cebus capucinus imitator), with a multi-generational pedigree. We analyze two measures of spatial association, using repeat sampling of 376 individuals (mean: 53.5 months per subject, range: 6-185 months per subject). Conditioned on the effects of age, sex, group size, seasonality, and El Niño-Southern Oscillation phases, we show low to moderate long-term repeatability (across years) of the proportion of time spent social (posterior mode [95% Highest Posterior Density interval]: 0.207 [0.169, 0.265]) and of average number of partners (0.144 [0.113, 0.181]) (latent scale). Most of this long-term repeatability could be explained by modest heritability (h2social: 0.152 [0.094, 0.207]; h2partners: 0.113 [0.076, 0.149]) with small long-term maternal effects (m2social: 0.000 [0.000, 0.045]; m2partners: 0.000 [0.000, 0.041]). Our models capture the majority of variance in our behavioral traits, with much of the variance explained by temporally changing factors, such as group of residence, highlighting potential limits to the evolvability of our trait due to social and environmental constraints.
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Population dynamics and genetic connectivity in recent chimpanzee history. CELL GENOMICS 2022; 2:None. [PMID: 35711737 PMCID: PMC9188271 DOI: 10.1016/j.xgen.2022.100133] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 12/29/2021] [Accepted: 04/15/2022] [Indexed: 11/22/2022]
Abstract
Knowledge on the population history of endangered species is critical for conservation, but whole-genome data on chimpanzees (Pan troglodytes) is geographically sparse. Here, we produced the first non-invasive geolocalized catalog of genomic diversity by capturing chromosome 21 from 828 non-invasive samples collected at 48 sampling sites across Africa. The four recognized subspecies show clear genetic differentiation correlating with known barriers, while previously undescribed genetic exchange suggests that these have been permeable on a local scale. We obtained a detailed reconstruction of population stratification and fine-scale patterns of isolation, migration, and connectivity, including a comprehensive picture of admixture with bonobos (Pan paniscus). Unlike humans, chimpanzees did not experience extended episodes of long-distance migrations, which might have limited cultural transmission. Finally, based on local rare variation, we implement a fine-grained geolocalization approach demonstrating improved precision in determining the origin of confiscated chimpanzees.
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Abstract
Understanding variation in host-associated microbial communities is important given the relevance of microbiomes to host physiology and health. Using 560 fecal samples collected from wild chimpanzees (Pan troglodytes) across their range, we assessed how geography, genetics, climate, vegetation, and diet relate to gut microbial community structure (prokaryotes, eukaryotic parasites) at multiple spatial scales. We observed a high degree of regional specificity in the microbiome composition, which was associated with host genetics, available plant foods, and potentially with cultural differences in tool use, which affect diet. Genetic differences drove community composition at large scales, while vegetation and potentially tool use drove within-region differences, likely due to their influence on diet. Unlike industrialized human populations in the United States, where regional differences in the gut microbiome are undetectable, chimpanzee gut microbiomes are far more variable across space, suggesting that technological developments have decoupled humans from their local environments, obscuring regional differences that could have been important during human evolution. IMPORTANCE Gut microbial communities are drivers of primate physiology and health, but the factors that influence the gut microbiome in wild primate populations remain largely undetermined. We report data from a continent-wide survey of wild chimpanzee gut microbiota and highlight the effects of genetics, vegetation, and potentially even tool use at different spatial scales on the chimpanzee gut microbiome, including bacteria, archaea, and eukaryotic parasites. Microbial community dissimilarity was strongly correlated with chimpanzee population genetic dissimilarity, and vegetation composition and consumption of algae, honey, nuts, and termites were potentially associated with additional divergence in microbial communities between sampling sites. Our results suggest that host genetics, geography, and climate play a far stronger role in structuring the gut microbiome in chimpanzees than in humans.
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Masi S, Austerlitz F, Chabaud C, Lafosse S, Marchi N, Georges M, Dessarps‐Freichey F, Miglietta S, Sotto‐Mayor A, Galli AS, Meulman E, Pouydebat E, Krief S, Todd A, Fuh T, Breuer T, Ségurel L. No evidence for female kin association, indications for extragroup paternity, and sex-biased dispersal patterns in wild western gorillas. Ecol Evol 2021; 11:7634-7646. [PMID: 34188840 PMCID: PMC8216920 DOI: 10.1002/ece3.7596] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/02/2021] [Accepted: 04/04/2021] [Indexed: 02/05/2023] Open
Abstract
Characterizing animal dispersal patterns and the rational behind individuals' transfer choices is a long-standing question of interest in evolutionary biology. In wild western gorillas (Gorilla gorilla), a one-male polygynous species, previous genetic findings suggested that, when dispersing, females might favor groups with female kin to promote cooperation, resulting in higher-than-expected within-group female relatedness. The extent of male dispersal remains unclear with studies showing conflicting results. To investigate male and female dispersal patterns and extragroup paternity, we analyzed long-term field observations, including female spatial proximity data, together with genetic data (10 autosomal microsatellites) on individuals from a unique set of four habituated western gorilla groups, and four additional extragroup males (49 individuals in total). The majority of offspring (25 of 27) were sired by the group male. For two offspring, evidence for extragroup paternity was found. Contrarily to previous findings, adult females were not significantly more related within groups than across groups. Consistently, adult female relatedness within groups did not correlate with their spatial proximity inferred from behavioral data. Adult females were similarly related to adult males from their group than from other groups. Using R ST statistics, we found significant genetic structure and a pattern of isolation by distance, indicating limited dispersal in this species. Comparing relatedness among females and among males revealed that males disperse farer than females, as expected in a polygamous species. Our study on habituated western gorillas shed light on the dispersal dynamics and reproductive behavior of this polygynous species and challenge some of the previous results based on unhabituated groups.
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Affiliation(s)
- Shelly Masi
- UMR7206 Eco‐anthropologieMuséum national d’Histoire naturelleCNRSUniversité de Paris; Musée de l'HommeParisFrance
| | - Frédéric Austerlitz
- UMR7206 Eco‐anthropologieMuséum national d’Histoire naturelleCNRSUniversité de Paris; Musée de l'HommeParisFrance
| | - Chloé Chabaud
- UMR7206 Eco‐anthropologieMuséum national d’Histoire naturelleCNRSUniversité de Paris; Musée de l'HommeParisFrance
- Department of BiologyEcole normale supérieurePSL University ParisParisFrance
| | - Sophie Lafosse
- UMR7206 Eco‐anthropologieMuséum national d’Histoire naturelleCNRSUniversité de Paris; Musée de l'HommeParisFrance
| | - Nina Marchi
- UMR7206 Eco‐anthropologieMuséum national d’Histoire naturelleCNRSUniversité de Paris; Musée de l'HommeParisFrance
- Present address:
CMPGInstitute for Ecology and EvolutionUniversity of BerneBerneSwitzerland
| | - Myriam Georges
- UMR7206 Eco‐anthropologieMuséum national d’Histoire naturelleCNRSUniversité de Paris; Musée de l'HommeParisFrance
- Present address:
UMS2700 2AD ‐ Acquisition et Analyse de Données pour l'Histoire naturelleConcarneauFrance
| | - Françoise Dessarps‐Freichey
- UMR7206 Eco‐anthropologieMuséum national d’Histoire naturelleCNRSUniversité de Paris; Musée de l'HommeParisFrance
| | - Silvia Miglietta
- UMR7206 Eco‐anthropologieMuséum national d’Histoire naturelleCNRSUniversité de Paris; Musée de l'HommeParisFrance
| | - Andrea Sotto‐Mayor
- UMR7206 Eco‐anthropologieMuséum national d’Histoire naturelleCNRSUniversité de Paris; Musée de l'HommeParisFrance
| | - Aurore San Galli
- UMR7206 Eco‐anthropologieMuséum national d’Histoire naturelleCNRSUniversité de Paris; Musée de l'HommeParisFrance
| | - Ellen Meulman
- UMR7206 Eco‐anthropologieMuséum national d’Histoire naturelleCNRSUniversité de Paris; Musée de l'HommeParisFrance
| | | | - Sabrina Krief
- UMR7206 Eco‐anthropologieMuséum national d’Histoire naturelleCNRSUniversité de Paris; Musée de l'HommeParisFrance
| | - Angelique Todd
- Dzanga‐Sangha Protected AreasWorld Wide Fund for NatureBanguiCentral African Republic
- Present address:
Fauna & Flora InternationalCambridgeUK
| | - Terence Fuh
- Dzanga‐Sangha Protected AreasWorld Wide Fund for NatureBanguiCentral African Republic
| | - Thomas Breuer
- Wildlife Conservation SocietyGlobal Conservation ProgramBronxNYUSA
- Present address:
World Wide Fund for Nature –GermanyBerlinGermany
| | - Laure Ségurel
- UMR7206 Eco‐anthropologieMuséum national d’Histoire naturelleCNRSUniversité de Paris; Musée de l'HommeParisFrance
- Present address:
Laboratoire de Biométrie et Biologie EvolutiveCNRS ‐ Université de LyonVilleurbanneFrance
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Lester JD, Vigilant L, Gratton P, McCarthy MS, Barratt CD, Dieguez P, Agbor A, Álvarez-Varona P, Angedakin S, Ayimisin EA, Bailey E, Bessone M, Brazzola G, Chancellor R, Cohen H, Danquah E, Deschner T, Egbe VE, Eno-Nku M, Goedmakers A, Granjon AC, Head J, Hedwig D, Hernandez-Aguilar RA, Jeffery KJ, Jones S, Junker J, Kadam P, Kaiser M, Kalan AK, Kehoe L, Kienast I, Langergraber KE, Lapuente J, Laudisoit A, Lee K, Marrocoli S, Mihindou V, Morgan D, Muhanguzi G, Neil E, Nicholl S, Orbell C, Ormsby LJ, Pacheco L, Piel A, Robbins MM, Rundus A, Sanz C, Sciaky L, Siaka AM, Städele V, Stewart F, Tagg N, Ton E, van Schijndel J, Vyalengerera MK, Wessling EG, Willie J, Wittig RM, Yuh YG, Yurkiw K, Zuberbuehler K, Boesch C, Kühl HS, Arandjelovic M. Recent genetic connectivity and clinal variation in chimpanzees. Commun Biol 2021; 4:283. [PMID: 33674780 PMCID: PMC7935964 DOI: 10.1038/s42003-021-01806-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 02/04/2021] [Indexed: 01/31/2023] Open
Abstract
Much like humans, chimpanzees occupy diverse habitats and exhibit extensive behavioural variability. However, chimpanzees are recognized as a discontinuous species, with four subspecies separated by historical geographic barriers. Nevertheless, their range-wide degree of genetic connectivity remains poorly resolved, mainly due to sampling limitations. By analyzing a geographically comprehensive sample set amplified at microsatellite markers that inform recent population history, we found that isolation by distance explains most of the range-wide genetic structure of chimpanzees. Furthermore, we did not identify spatial discontinuities corresponding with the recognized subspecies, suggesting that some of the subspecies-delineating geographic barriers were recently permeable to gene flow. Substantial range-wide genetic connectivity is consistent with the hypothesis that behavioural flexibility is a salient driver of chimpanzee responses to changing environmental conditions. Finally, our observation of strong local differentiation associated with recent anthropogenic pressures portends future loss of critical genetic diversity if habitat fragmentation and population isolation continue unabated.
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Affiliation(s)
- Jack D Lester
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany.
| | - Linda Vigilant
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Paolo Gratton
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Maureen S McCarthy
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Christopher D Barratt
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Paula Dieguez
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Anthony Agbor
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Paula Álvarez-Varona
- Jane Goodall Institute Spain and Senegal, Dindefelo Biological Station, Dindefelo, Kedougou, Senegal
| | - Samuel Angedakin
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | | | - Emma Bailey
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Mattia Bessone
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Gregory Brazzola
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Rebecca Chancellor
- West Chester University, Depts of Anthropology & Sociology and Psychology, West Chester, PA, USA
| | - Heather Cohen
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Emmanuel Danquah
- Department of Wildlife and Range Management, Faculty of Renewable Natural Resources, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Tobias Deschner
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Villard Ebot Egbe
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | | | | | - Anne-Céline Granjon
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Josephine Head
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Daniela Hedwig
- Elephant Listening Project, Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA
| | - R Adriana Hernandez-Aguilar
- Jane Goodall Institute Spain and Senegal, Dindefelo Biological Station, Dindefelo, Kedougou, Senegal
- Department of Social Psychology and Quantitative Psychology, Faculty of Psychology, University of Barcelona, Barcelona, Spain
| | - Kathryn J Jeffery
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| | - Sorrel Jones
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Jessica Junker
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | | | - Michael Kaiser
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Ammie K Kalan
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Laura Kehoe
- Wild Chimpanzee Foundation (WCF), Leipzig, Germany
| | - Ivonne Kienast
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Kevin E Langergraber
- School of Human Evolution and Social Change, Arizona State University, 900 Cady Mall, Tempe, AZ 85287 Arizona State University, Tempe, AZ, USA
| | - Juan Lapuente
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
- Comoé Chimpanzee Conservation Project, Comoé National Park, Kakpin, Côte d'Ivoire
| | - Anne Laudisoit
- Ecohealth Alliance, New York, NY, USA
- University of Antwerp, Campus Drie Eiken, lokaal D.133, Universiteitsplein 1 - 2610, Antwerpen, Belgium
| | - Kevin Lee
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Sergio Marrocoli
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Vianet Mihindou
- Agence National des Parcs Nationaux (ANPN) Batterie 4, Libreville, Gabon
- Ministère des Eaux, des Forêts, de la Mer, de l'Environnement, Chargé du Plan Climat, des Objectifs de Développement Durable et du Plan d'Affectation des Terres, Libreville, Gabon
| | - David Morgan
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, Chicago, IL, USA
| | | | - Emily Neil
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Sonia Nicholl
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | | | - Lucy Jayne Ormsby
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Liliana Pacheco
- Jane Goodall Institute Spain and Senegal, Dindefelo Biological Station, Dindefelo, Kedougou, Senegal
| | - Alex Piel
- Department of Anthropology, University College London, London, UK
| | - Martha M Robbins
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Aaron Rundus
- West Chester University, Department of Psychology, West Chester, PA, USA
| | - Crickette Sanz
- Washington University in Saint Louis, Department of Anthropology, One Brookings Drive, St. Louis, MO, USA
- Wildlife Conservation Society, Congo Program, Brazzaville, Republic of Congo
| | - Lilah Sciaky
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Alhaji M Siaka
- National Protected Area Authority, Freetown, Sierra Leone
| | - Veronika Städele
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Fiona Stewart
- School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Nikki Tagg
- KMDA, Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Els Ton
- Chimbo Foundation, Amsterdam, Netherlands
| | | | | | - Erin G Wessling
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Jacob Willie
- KMDA, Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Roman M Wittig
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
| | - Yisa Ginath Yuh
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Kyle Yurkiw
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
- Pan Verus Project Outamba-Kilimi National Park, Freetown, Sierra Leone
| | - Klaus Zuberbuehler
- Budongo Conservation Field Station, Masindi, Uganda
- Université de Neuchâtel, Institut de Biologie, Neuchâtel, Switzerland
- School of Psychology and Neuroscience, University of St Andrews, St Andrews, UK
| | - Christophe Boesch
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
| | - Hjalmar S Kühl
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Mimi Arandjelovic
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Leipzig, Germany.
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10
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Female fertile phase synchrony, and male mating and reproductive skew, in the crested macaque. Sci Rep 2021; 11:4251. [PMID: 33608592 PMCID: PMC7896048 DOI: 10.1038/s41598-021-81163-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 12/03/2020] [Indexed: 01/31/2023] Open
Abstract
High social status is the primary determinant of reproductive success among group-living male mammals. Primates living in multimale-multifemale groups show the greatest variation in the strength of this link, with marked variation in reproductive skew by male dominance among species, dependent on the degree of female fertile phase synchrony, and the number of competing males. Here, we present data on two groups of wild crested macaques (Macaca nigra), living in the Tangkoko Reserve, Sulawesi, Indonesia. We investigated male monopolization of fertile females in 31 cycles of 19 females, and genetic paternity of 14 offspring conceived during the study period. We show that female fertile phase synchrony was low, that females had few mating partners in their fertile phase, and that dominant males monopolized a high proportion of consortships and matings, resulting in marked and steep mating and reproductive skew. We conclude that female cycle asynchrony provides the opportunity for strong direct male-male competition in crested macaques, resulting in monopolization of females by dominant males, consistent with their marked sexual dimorphism. Our study provides a test of the underlying factors that determine the relative occurrence and strength of different mechanisms of sexual selection, and the phenotypes that evolve as a result.
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11
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Group-level cooperation in chimpanzees is shaped by strong social ties. Nat Commun 2021; 12:539. [PMID: 33483482 PMCID: PMC7822919 DOI: 10.1038/s41467-020-20709-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 12/07/2020] [Indexed: 01/30/2023] Open
Abstract
Humans maintain extensive social ties of varying preferences, providing a range of opportunities for beneficial cooperative exchange that may promote collective action and our unique capacity for large-scale cooperation. Similarly, non-human animals maintain differentiated social relationships that promote dyadic cooperative exchange, but their link to cooperative collective action is little known. Here, we investigate the influence of social relationship properties on male and female chimpanzee participations in a costly form of group action, intergroup encounters. We find that intergroup encounter participation increases with a greater number of other participants as well as when participants are maternal kin or social bond partners, and that these effects are independent from one another and from the likelihood to associate with certain partners. Together, strong social relationships between kin and non-kin facilitate group-level cooperation in one of our closest living relatives, suggesting that social bonds may be integral to the evolution of cooperation in our own species.
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12
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Trede F, Kil N, Stranks J, Connell AJ, Fischer J, Ostner J, Schülke O, Zinner D, Roos C. A refined panel of 42 microsatellite loci to universally genotype catarrhine primates. Ecol Evol 2021; 11:498-505. [PMID: 33437445 PMCID: PMC7790618 DOI: 10.1002/ece3.7069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/28/2020] [Accepted: 11/03/2020] [Indexed: 11/30/2022] Open
Abstract
Microsatellite genotyping is an important genetic method for a number of research questions in biology. Given that the traditional fragment length analysis using polyacrylamide gel or capillary electrophoresis has several drawbacks, microsatellite genotyping-by-sequencing (GBS) has arisen as a promising alternative. Although GBS mitigates many of the problems of fragment length analysis, issues with allelic dropout and null alleles often remain due to mismatches in primer binding sites and unnecessarily long PCR products. This is also true for GBS in catarrhine primates where cross-species amplification of loci (often human derived) is common.We therefore redesigned primers for 45 microsatellite loci based on 17 available catarrhine reference genomes. Next, we tested them in singleplex and different multiplex settings in a panel of species representing all major lineages of Catarrhini and further validated them in wild Guinea baboons (Papio papio) using fecal samples.The final panel of 42 microsatellite loci can efficiently be amplified with primers distributed into three amplification pools.With our microsatellite panel, we provide a tool to universally genotype catarrhine primates via GBS from different sample sources in a cost- and time-efficient way, with higher resolution, and comparability among laboratories and species.
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Affiliation(s)
- Franziska Trede
- Cognitive Ethology LaboratoryGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
- Primate Genetics LaboratoryGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
| | - Niels Kil
- Primate Genetics LaboratoryGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
- Department of Behavioral EcologyUniversity of GöttingenGöttingenGermany
- Leibniz ScienceCampus Primate CognitionGöttingenGermany
- Research Group Primate Social EvolutionGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
| | - James Stranks
- Primate Genetics LaboratoryGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
- Department of Behavioral EcologyUniversity of GöttingenGöttingenGermany
- Leibniz ScienceCampus Primate CognitionGöttingenGermany
- Research Group Primate Social EvolutionGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
| | - Andrew Jesse Connell
- Department of MicrobiologyPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Julia Fischer
- Cognitive Ethology LaboratoryGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
- Leibniz ScienceCampus Primate CognitionGöttingenGermany
- Department of Primate CognitionGeorg‐August‐UniversityGöttingenGermany
| | - Julia Ostner
- Department of Behavioral EcologyUniversity of GöttingenGöttingenGermany
- Leibniz ScienceCampus Primate CognitionGöttingenGermany
- Research Group Primate Social EvolutionGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
| | - Oliver Schülke
- Department of Behavioral EcologyUniversity of GöttingenGöttingenGermany
- Leibniz ScienceCampus Primate CognitionGöttingenGermany
- Research Group Primate Social EvolutionGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
| | - Dietmar Zinner
- Cognitive Ethology LaboratoryGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
- Leibniz ScienceCampus Primate CognitionGöttingenGermany
- Department of Primate CognitionGeorg‐August‐UniversityGöttingenGermany
| | - Christian Roos
- Primate Genetics LaboratoryGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
- Gene Bank of PrimatesGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
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13
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Fontsere C, Alvarez-Estape M, Lester J, Arandjelovic M, Kuhlwilm M, Dieguez P, Agbor A, Angedakin S, Ayuk Ayimisin E, Bessone M, Brazzola G, Deschner T, Eno-Nku M, Granjon AC, Head J, Kadam P, Kalan AK, Kambi M, Langergraber K, Lapuente J, Maretti G, Jayne Ormsby L, Piel A, Robbins MM, Stewart F, Vergnes V, Wittig RM, Kühl HS, Marques-Bonet T, Hughes DA, Lizano E. Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments. Mol Ecol Resour 2020; 21:745-761. [PMID: 33217149 DOI: 10.1111/1755-0998.13300] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 10/15/2020] [Accepted: 11/13/2020] [Indexed: 11/30/2022]
Abstract
Noninvasive samples as a source of DNA are gaining interest in genomic studies of endangered species. However, their complex nature and low endogenous DNA content hamper the recovery of good quality data. Target capture has become a productive method to enrich the endogenous fraction of noninvasive samples, such as faeces, but its sensitivity has not yet been extensively studied. Coping with faecal samples with an endogenous DNA content below 1% is a common problem when prior selection of samples from a large collection is not possible. However, samples classified as unfavourable for target capture sequencing might be the only representatives of unique specific geographical locations, or to answer the question of interest. To explore how library complexity may be increased without repeating DNA extractions and generating new libraries, in this study we captured the exome of 60 chimpanzees (Pan troglodytes) using faecal samples with very low proportions of endogenous content (<1%). Our results indicate that by performing additional hybridizations of the same libraries, the molecular complexity can be maintained to achieve higher coverage. Also, whenever possible, the starting DNA material for capture should be increased. Finally, we specifically calculated the sequencing effort needed to avoid exhausting the library complexity of enriched faecal samples with low endogenous DNA content. This study provides guidelines, schemes and tools for laboratories facing the challenges of working with noninvasive samples containing extremely low amounts of endogenous DNA.
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Affiliation(s)
- Claudia Fontsere
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Marina Alvarez-Estape
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Jack Lester
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mimi Arandjelovic
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Martin Kuhlwilm
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Paula Dieguez
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anthony Agbor
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Samuel Angedakin
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Mattia Bessone
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Gregory Brazzola
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tobias Deschner
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | | | - Josephine Head
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Parag Kadam
- School of Biological and Environmental Sciences, Liverpool John Moores University, James Parsons Building, Liverpool, UK
| | - Ammie K Kalan
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mohamed Kambi
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Kevin Langergraber
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Institute of Human Origins, Arizona State University, Tempe, AZ, USA
| | - Juan Lapuente
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Comoé Chimpanzee Conservation Project, Kakpin, Comoé National Park, Ivory Coast, Côte d'Ivoire
| | - Giovanna Maretti
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Lucy Jayne Ormsby
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alex Piel
- Department of Anthropology, University College London, London, UK
| | - Martha M Robbins
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Fiona Stewart
- School of Biological and Environmental Sciences, Liverpool John Moores University, James Parsons Building, Liverpool, UK.,Department of Anthropology, University College London, London, UK
| | | | - Roman M Wittig
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
| | - Hjalmar S Kühl
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - David A Hughes
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Esther Lizano
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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14
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Crockford C, Samuni L, Vigilant L, Wittig RM. Postweaning maternal care increases male chimpanzee reproductive success. SCIENCE ADVANCES 2020; 6:6/38/eaaz5746. [PMID: 32948598 PMCID: PMC7500924 DOI: 10.1126/sciadv.aaz5746] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 07/28/2020] [Indexed: 06/01/2023]
Abstract
Humans are unusual among animals for continuing to provision and care for their offspring until adulthood. This "prolonged dependency" is considered key for the evolution of other notable human traits, such as large brains, complex societies, and extended postreproductive lifespans. Prolonged dependency must therefore have evolved under conditions in which reproductive success is gained with parental investment and diminished with early parental loss. We tested this idea using data from wild chimpanzees, which have similarly extended immature years as humans and prolonged mother-offspring associations. Males who lost their mothers after weaning but before maturity began reproducing later and had lower average reproductive success. Thus, persistent mother-immature son associations seem vital for enhancing male reproductive success, although mothers barely provision sons after weaning. We posit that these associations lead to social gains, crucial for successful reproduction in complex social societies, and offer insights into the evolution of prolonged dependency.
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Affiliation(s)
- Catherine Crockford
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Taï Chimpanzee Project, CSRS, Abidjan, Ivory Coast
- Human Behaviour, Ecology & Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Liran Samuni
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Taï Chimpanzee Project, CSRS, Abidjan, Ivory Coast
- Department of Human Evolutionary Biology, Harvard University, Cambridge, USA
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Roman M Wittig
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Taï Chimpanzee Project, CSRS, Abidjan, Ivory Coast
- Human Behaviour, Ecology & Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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15
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Genetic Diversity of Historical and Modern Populations of Russian Cattle Breeds Revealed by Microsatellite Analysis. Genes (Basel) 2020; 11:genes11080940. [PMID: 32824045 PMCID: PMC7463645 DOI: 10.3390/genes11080940] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/10/2020] [Accepted: 08/12/2020] [Indexed: 01/24/2023] Open
Abstract
Analysis of ancient and historical DNA has great potential to trace the genetic diversity of local cattle populations during their centuries-long development. Forty-nine specimens representing five cattle breeds (Kholmogor, Yaroslavl, Great Russian, Novgorod, and Holland), dated from the end of the 19th century to the first half of the 20th century, were genotyped for nine polymorphic microsatellite loci. Using a multiple-tube approach, we determined the consensus genotypes of all samples/loci analysed. Amplification errors, including allelic drop-out (ADO) and false alleles (FA), occurred with an average frequency of 2.35% and 0.79%, respectively. A significant effect of allelic length on ADO rate (r2 = 0.620, p = 0.05) was shown. We did not observe significant differences in genetic diversity among historical samples and modern representatives of Kholmogor and Yaroslavl breeds. The unbiased expected heterozygosity values were 0.726–0.774 and 0.708–0.739; the allelic richness values were 2.716–2.893 and 2.661–2.758 for the historical and modern samples, respectively. Analyses of FST and Jost’s D genetic distances, and the results of STRUCTURE clustering, showed the maintenance of a part of historical components in the modern populations of Kholmogor and Yaroslavl cattle. Our study contributes to the conservation of biodiversity in the local Russian genetic resources of cattle.
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16
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De Moor D, Roos C, Ostner J, Schülke O. Bonds of bros and brothers: Kinship and social bonding in postdispersal male macaques. Mol Ecol 2020; 29:3346-3360. [PMID: 32688434 DOI: 10.1111/mec.15560] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 07/01/2020] [Accepted: 07/10/2020] [Indexed: 12/17/2022]
Abstract
Group-living animals often maintain a few very close affiliative relationships-social bonds-that can buffer them against many of the inevitable costs of gregariousness. Kinship plays a central role in the development of such social bonds. The bulk of research on kin biases in sociality has focused on philopatric females, who typically live in deeply kin-structured systems, with matrilineal dominance rank inheritance and life-long familiarity between kin. Closely related males, in contrast, are usually not close in rank or familiar, which offers the opportunity to test the importance of kinship per se in the formation of social bonds. So far, however, kin biases in male social bonding have only been tested in philopatric males, where familiarity remains a confounding factor. Here, we studied bonds between male Assamese macaques, a species in which males disperse from their natal groups and in which male bonds are known to affect fitness. Combining extensive behavioural data on 43 adult males over a 10-year period with DNA microsatellite relatedness analyses, we find that postdispersal males form stronger relationships with the few close kin available in the group than with the average nonkin. However, males form the majority of their bonds with nonkin and may choose nonkin over available close kin to bond with. Our results show that kinship facilitates bond formation, but is not a prerequisite for it, which suggests that strong bonds are not restricted to kin in male mammals and that animals cooperate for both direct and indirect fitness benefits.
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Affiliation(s)
- Delphine De Moor
- Department of Behavioural Ecology, University of Goettingen, Goettingen, Germany
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
- Leibniz-ScienceCampus Primate Cognition, Goettingen, Germany
- Research Group Primate Social Evolution, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Julia Ostner
- Department of Behavioural Ecology, University of Goettingen, Goettingen, Germany
- Leibniz-ScienceCampus Primate Cognition, Goettingen, Germany
- Research Group Primate Social Evolution, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Oliver Schülke
- Department of Behavioural Ecology, University of Goettingen, Goettingen, Germany
- Leibniz-ScienceCampus Primate Cognition, Goettingen, Germany
- Research Group Primate Social Evolution, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
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17
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Muller MN, Blurton Jones NG, Colchero F, Thompson ME, Enigk DK, Feldblum JT, Hahn BH, Langergraber KE, Scully EJ, Vigilant L, Walker KK, Wrangham RW, Wroblewski EE, Pusey AE. Sexual dimorphism in chimpanzee (Pan troglodytes schweinfurthii) and human age-specific fertility. J Hum Evol 2020; 144:102795. [PMID: 32454364 PMCID: PMC7337577 DOI: 10.1016/j.jhevol.2020.102795] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 03/27/2020] [Accepted: 03/27/2020] [Indexed: 11/28/2022]
Abstract
Across vertebrates, species with intense male mating competition and high levels of sexual dimorphism in body size generally exhibit dimorphism in age-specific fertility. Compared with females, males show later ages at first reproduction and earlier reproductive senescence because they take longer to attain adult body size and musculature, and maintain peak condition for a limited time. This normally yields a shorter male duration of effective breeding, but this reduction might be attenuated in species that frequently use coalitionary aggression. Here, we present comparative genetic and demographic data on chimpanzees from three long-term study communities (Kanyawara: Kibale National Park, Uganda; Mitumba and Kasekela: Gombe National Park, Tanzania), comprising 581 male risk years and 112 infants, to characterize male age-specific fertility. For comparison, we update estimates from female chimpanzees in the same sites and append a sample of human foragers (the Tanzanian Hadza). Consistent with the idea that aggressive mating competition favors youth, chimpanzee males attained a higher maximum fertility than females, followed by a steeper decline with age. Males did not show a delay in reproduction compared with females, however, as adolescents in both sites successfully reproduced by targeting young, subfecund females, who were less attractive to adults. Gombe males showed earlier reproductive senescence and a shorter duration of effective breeding than Gombe females. By contrast, older males in Kanyawara generally continued to reproduce, apparently by forming coalitions with the alpha. Hadza foragers showed a distinct pattern of sexual dimorphism in age-specific fertility as, compared with women, men gained conceptions later but continued reproducing longer. In sum, both humans and chimpanzees showed sexual dimorphism in age-specific fertility that deviated from predictions drawn from primates with more extreme body size dimorphism, suggesting altered dynamics of male-male competition in the two lineages. In both species, coalitions appear important for extending male reproductive careers.
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Affiliation(s)
- Martin N Muller
- Department of Anthropology, University of New Mexico, MSC 01-1040, Albuquerque, NM, 87111, USA.
| | | | - Fernando Colchero
- Interdisciplinary Center on Population Dynamics, Department of Mathematics and Computer Science, University of Southern Denmark, Denmark
| | - Melissa Emery Thompson
- Department of Anthropology, University of New Mexico, MSC 01-1040, Albuquerque, NM, 87111, USA
| | - Drew K Enigk
- Department of Anthropology, University of New Mexico, MSC 01-1040, Albuquerque, NM, 87111, USA
| | - Joseph T Feldblum
- Department of Anthropology, Michigan Society of Fellows, University of Michigan, USA
| | - Beatrice H Hahn
- Perelman School of Medicine, University of Pennsylvania, USA
| | - Kevin E Langergraber
- School of Human Evolution and Social Change, and Institute of Human Origins, Arizona State University, USA
| | - Erik J Scully
- Department of Human Evolutionary Biology, Harvard University, USA
| | - Linda Vigilant
- Primatology Department, Max Planck Institute for Evolutionary Anthropology, Germany
| | - Kara K Walker
- College of Veterinary Medicine, North Carolina State University, USA
| | | | | | - Anne E Pusey
- Department of Evolutionary Anthropology, Duke University, USA
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18
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Akankunda T, To H, Rodriguez Lopez C, Leijs R, Hogendoorn K. A method to generate multilocus barcodes of pinned insect specimens using MiSeq. Mol Ecol Resour 2020; 20. [PMID: 32104992 DOI: 10.1111/1755-0998.13143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/20/2020] [Accepted: 02/03/2020] [Indexed: 01/03/2023]
Abstract
For molecular insect identification, amplicon sequencing methods are recommended because they offer a cost-effective approach for targeting small sets of informative genes from multiple samples. In this context, high-throughput multilocus amplicon sequencing has been achieved using the MiSeq Illumina sequencing platform. However, this approach generates short gene fragments of <500 bp, which then have to be overlapped using bioinformatics to achieve longer sequence lengths. This increases the risk of generating chimeric sequences or leads to the formation of incomplete loci. Here, we propose a modified nested amplicon sequencing method for targeting multiple loci from pinned insect specimens using the MiSeq Illumina platform. The modification exists in using a three-step nested PCR approach targeting near full-length loci in the initial PCR and subsequently amplifying short fragments of between 300 and 350 bp for high-throughput sequencing using Illumina chemistry. Using this method, we generated 407 sequences of three loci from 86% of all the specimens sequenced. Out of 103 pinned bee specimens of replicated species, 71% passed the 95% sequence similarity threshold between species replicates. This method worked best for pinned specimens aged between 0 and 5 years, with a limit of 10 years for pinned and 14 years for ethanol-preserved specimens. Hence, our method overcomes some of the challenges of amplicon sequencing using short read next generation sequencing and improves the possibility of creating high-quality multilocus barcodes from insect collections.
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Affiliation(s)
- Trace Akankunda
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Hien To
- The Bioinformatics Hub, The University of Adelaide, Adelaide, SA, Australia
| | - Carlos Rodriguez Lopez
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia.,Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Remko Leijs
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia.,South Australian Museum, North Terrace, Adelaide, SA, Australia
| | - Katja Hogendoorn
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
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19
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Ishizuka S, Takemoto H, Sakamaki T, Tokuyama N, Toda K, Hashimoto C, Furuichi T. Comparisons of between-group differentiation in male kinship between bonobos and chimpanzees. Sci Rep 2020; 10:251. [PMID: 31937864 PMCID: PMC6959343 DOI: 10.1038/s41598-019-57133-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/23/2019] [Indexed: 11/13/2022] Open
Abstract
Patterns of kinship among individuals in different groups have been rarely examined in animals. Two closest living relatives of humans, bonobos and chimpanzees share many characteristics of social systems including male philopatry, whereas one major difference between the two species is the nature of intergroup relationship. Intergroup relationship is basically antagonistic and males sometimes kill individuals of other groups in chimpanzees, whereas it is much more moderate in bonobos and copulations between individuals of different groups are often observed during intergroup encounters. Such behavioural differences may facilitate more frequent between-group male gene flow and greater between-group differentiation in male kinship in bonobos than in chimpanzees. Here we compared differences between average relatedness among males within groups and that among males of neighbouring groups, and between-group male genetic distance between bonobos and chimpanzees. Contrary to expectation, the differences between average relatedness among males within groups and that among males of neighbouring groups were significantly greater in bonobos than in chimpanzees. There were no significant differences in autosomal and Y-chromosomal between-group male genetic distance between the two species. Our results showed that intergroup male kinship is similarly or more differentiated in bonobos than in chimpanzees.
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Affiliation(s)
- Shintaro Ishizuka
- Primate Research Institute, Kyoto University, Inuyama, Japan.
- Japan Society for the Promotion of Science, Chiyoda-ku, Japan.
| | | | - Tetsuya Sakamaki
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Antwerp Zoo Foundation, Antwerp, Belgium
| | - Nahoko Tokuyama
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Japan Society for the Promotion of Science, Chiyoda-ku, Japan
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies, Yokosuka, Japan
| | - Kazuya Toda
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Japan Society for the Promotion of Science, Chiyoda-ku, Japan
| | - Chie Hashimoto
- Primate Research Institute, Kyoto University, Inuyama, Japan
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20
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Granjon A, Robbins MM, Arinaitwe J, Cranfield MR, Eckardt W, Mburanumwe I, Musana A, Robbins AM, Roy J, Sollmann R, Vigilant L, Hickey JR. Estimating abundance and growth rates in a wild mountain gorilla population. Anim Conserv 2020. [DOI: 10.1111/acv.12559] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- A.‐C. Granjon
- Department of Primatology Max Planck Institute for Evolutionary Anthropology Leipzig Germany
| | - M. M. Robbins
- Department of Primatology Max Planck Institute for Evolutionary Anthropology Leipzig Germany
| | - J. Arinaitwe
- Bwindi Mgahinga Conservation Area Uganda Wildlife Authority Kampala Uganda
| | - M. R. Cranfield
- Mountain Gorilla Veterinary Project School of Veterinary Medicine University of California Davis Davis CA USA
| | - W. Eckardt
- The Dian Fossey Gorilla Fund International Musanze Rwanda
| | - I. Mburanumwe
- Parc National des Virunga‐sud Institut Congolais pour la Conservation de la Nature Gisenyi Rwanda
| | - A. Musana
- Parc National des Volcans Rwanda Development Board Kigali Rwanda
| | - A. M. Robbins
- Department of Primatology Max Planck Institute for Evolutionary Anthropology Leipzig Germany
| | - J. Roy
- Department of Primatology Max Planck Institute for Evolutionary Anthropology Leipzig Germany
| | - R. Sollmann
- Department of Wildlife, Fish, and Conservation Biology University of California Davis Davis CA USA
| | - L. Vigilant
- Department of Primatology Max Planck Institute for Evolutionary Anthropology Leipzig Germany
| | - J. R. Hickey
- International Gorilla Conservation Programme Kigali Rwanda
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21
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De Moor D, Roos C, Ostner J, Schülke O. Female Assamese macaques bias their affiliation to paternal and maternal kin. Behav Ecol 2020. [DOI: 10.1093/beheco/arz213] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Abstract
Forming strong social bonds can lead to higher reproductive success, increased longevity, and/or increased infant survival in several mammal species. Given these adaptive benefits, understanding what determines partner preferences in social bonding is important. Maternal relatedness strongly predicts partner preference across many mammalian taxa. The role of paternal relatedness, however, has received relatively little attention, even though paternal and maternal kin share the same number of genes, and theoretically similar preferences would therefore be expected for paternal kin. Here, we investigate the role of maternal and paternal relatedness in female affiliation in Assamese macaques (Macaca assamensis), a species characterized by a relatively low male reproductive skew. We studied a wild population under natural conditions using extensive behavioral data and relatedness analyses based on pedigree reconstruction. We found stronger affiliative relationships and more time spent grooming between maternal kin and paternal half-sisters compared with nonkin, with no preference of maternal over paternal kin. Paternally related and nonrelated dyads did not form stronger relationships when they had less close maternal kin available, but we would need a bigger sample size to confirm this. As expected given the low reproductive skew, affiliative relationships between paternal half-sisters closer in age were not stronger than between paternal half-sisters with larger age differences, suggesting that the kin bias toward paternal kin was not mediated by age similarity. An alternative way through which paternal kin could get familiarized is mother- and/or father-mediated familiarity.
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Affiliation(s)
- Delphine De Moor
- Department of Behavioural Ecology, University of Goettingen, Kellnerweg, Goettingen, Germany
- Primate Genetics, German Primate Center Leibniz Institute for Primate Research, Kellnerweg, Goettingen, Germany
- Leibniz-ScienceCampus Primate Cognition, Kellnerweg, Goettingen, Germany
- Research Group Primate Social Evolution, Kellnerweg, German Primate Center Leibniz Institute for Primate Research, Goettingen, Germany
| | - Christian Roos
- Primate Genetics, German Primate Center Leibniz Institute for Primate Research, Kellnerweg, Goettingen, Germany
| | - Julia Ostner
- Department of Behavioural Ecology, University of Goettingen, Kellnerweg, Goettingen, Germany
- Leibniz-ScienceCampus Primate Cognition, Kellnerweg, Goettingen, Germany
- Research Group Primate Social Evolution, Kellnerweg, German Primate Center Leibniz Institute for Primate Research, Goettingen, Germany
| | - Oliver Schülke
- Department of Behavioural Ecology, University of Goettingen, Kellnerweg, Goettingen, Germany
- Leibniz-ScienceCampus Primate Cognition, Kellnerweg, Goettingen, Germany
- Research Group Primate Social Evolution, Kellnerweg, German Primate Center Leibniz Institute for Primate Research, Goettingen, Germany
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22
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Minkner MMI, Young C, Amici F, McFarland R, Barrett L, Grobler JP, Henzi SP, Widdig A. Assessment of Male Reproductive Skew via Highly Polymorphic STR Markers in Wild Vervet Monkeys, Chlorocebus pygerythrus. J Hered 2019; 109:780-790. [PMID: 30272235 DOI: 10.1093/jhered/esy048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 09/28/2018] [Indexed: 11/12/2022] Open
Abstract
Male reproductive strategies have been well studied in primate species where the ability of males to monopolize reproductive access is high. Less is known about species where males cannot monopolize mating access. Vervet monkeys (Chlorocebus pygerythrus) are interesting in this regard as female codominance reduces the potential for male monopolization. Under this condition, we assessed whether male dominance rank still influences male mating and reproductive success, by assigning paternities to infants in a population of wild vervets in the Eastern Cape, South Africa. To determine paternity, we established microsatellite markers from noninvasive fecal samples via cross-species amplification. In addition, we evaluated male mating and reproductive success for 3 groups over 4 mating seasons. We identified 21 highly polymorphic microsatellites (number of alleles = 7.5 ± 3.1 [mean ± SD], observed heterozygosity = 0.691 ± 0.138 [mean ± SD]) and assigned paternity to 94 of 97 sampled infants (96.9%) with high confidence. Matings pooled over 4 seasons were significantly skewed across 3 groups, although skew indices were low (B index = 0.023-0.030) and mating success did not correlate with male dominance. Paternities pooled over 4 seasons were not consistently significantly skewed (B index = 0.005-0.062), with high-ranking males siring more offspring than subordinates only in some seasons. We detected 6 cases of extra-group paternity (6.4%) and 4 cases of natal breeding (4.3%). Our results suggest that alternative reproductive strategies besides priority of access for dominant males are likely to affect paternity success, warranting further investigation into the determinants of paternity among species with limited male monopolization potential.
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Affiliation(s)
- Mirjam M I Minkner
- Behavioural Ecology, Institute of Biology, Faculty of Life Sciences, Leipzig University, Talstr, Leipzig, Germany.,Research Group Primate Kin Selection, Department of Primatology, Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany.,Applied Behavioural Ecology and Ecosystems Research Unit, University of South Africa, Christiaan de Wet Road and Pioneer Avenue, Florida, Gauteng, South Africa
| | - Christopher Young
- Applied Behavioural Ecology and Ecosystems Research Unit, University of South Africa, Christiaan de Wet Road and Pioneer Avenue, Florida, Gauteng, South Africa.,Department of Psychology, University of Lethbridge, Lethbridge, AB, Canada.,Department of Anatomy and Physiology, Faculty of Veterinary Science, University of Pretoria, Private Bag, Onderstepoort, South Africa
| | - Federica Amici
- Behavioural Ecology, Institute of Biology, Faculty of Life Sciences, Leipzig University, Talstr, Leipzig, Germany.,Research Group Primate Kin Selection, Department of Primatology, Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany
| | - Richard McFarland
- Department of Anthropology, University of Wisconsin-Madison, Madison, WI, USA.,Brain Function Research Group, School of Physiology, University of the Witwatersrand, Parktown, Johannesburg, Gauteng, South Africa
| | - Louise Barrett
- Applied Behavioural Ecology and Ecosystems Research Unit, University of South Africa, Christiaan de Wet Road and Pioneer Avenue, Florida, Gauteng, South Africa.,Department of Psychology, University of Lethbridge, Lethbridge, AB, Canada
| | - J Paul Grobler
- and Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, Nelson Mandela Drive, Park West, Bloemfontein, South Africa
| | - S Peter Henzi
- Applied Behavioural Ecology and Ecosystems Research Unit, University of South Africa, Christiaan de Wet Road and Pioneer Avenue, Florida, Gauteng, South Africa.,Department of Psychology, University of Lethbridge, Lethbridge, AB, Canada
| | - Anja Widdig
- Behavioural Ecology, Institute of Biology, Faculty of Life Sciences, Leipzig University, Talstr, Leipzig, Germany.,Research Group Primate Kin Selection, Department of Primatology, Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany
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23
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White LC, Fontsere C, Lizano E, Hughes DA, Angedakin S, Arandjelovic M, Granjon AC, Hans JB, Lester JD, Rabanus-Wallace MT, Rowney C, Städele V, Marques-Bonet T, Langergraber KE, Vigilant L. A roadmap for high-throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture. Mol Ecol Resour 2019; 19:609-622. [PMID: 30637963 DOI: 10.1111/1755-0998.12993] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 12/14/2018] [Accepted: 01/08/2019] [Indexed: 11/30/2022]
Abstract
Large-scale genomic studies of wild animal populations are often limited by access to high-quality DNA. Although noninvasive samples, such as faeces, can be readily collected, DNA from the sample producers is usually present in low quantities, fragmented, and contaminated by microorganism and dietary DNAs. Hybridization capture can help to overcome these impediments by increasing the proportion of subject DNA prior to high-throughput sequencing. Here we evaluate a key design variable for hybridization capture, the number of rounds of capture, by testing whether one or two rounds are most appropriate, given varying sample quality (as measured by the ratios of subject to total DNA). We used a set of 1,780 quality-assessed wild chimpanzee (Pan troglodytes schweinfurthii) faecal samples and chose 110 samples of varying quality for exome capture and sequencing. We used multiple regression to assess the effects of the ratio of subject to total DNA (sample quality), rounds of capture and sequencing effort on the number of unique exome reads sequenced. We not only show that one round of capture is preferable when the proportion of subject DNA in a sample is above ~2%-3%, but also explore various types of bias introduced by capture, and develop a model that predicts the sequencing effort necessary for a desired data yield from samples of a given quality. Thus, our results provide a useful guide and pave a methodological way forward for researchers wishing to plan similar hybridization capture studies.
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Affiliation(s)
- Lauren C White
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Claudia Fontsere
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Spain
| | - Esther Lizano
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Spain
| | - David A Hughes
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Samuel Angedakin
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mimi Arandjelovic
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anne-Céline Granjon
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jörg B Hans
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jack D Lester
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Carolyn Rowney
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Veronika Städele
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, 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, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Kevin E Langergraber
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona.,Institute of Human Origins, Arizona State University, Tempe, Arizona
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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24
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Gottfried H, Vigilant L, Mundry R, Behringer V, Surbeck M. Aggression by male bonobos against immature individuals does not fit with predictions of infanticide. Aggress Behav 2019; 45:300-309. [PMID: 30710459 DOI: 10.1002/ab.21819] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 11/20/2018] [Accepted: 12/04/2018] [Indexed: 12/27/2022]
Abstract
The selective advantage of male infanticide is enhancement of reproductive success of the aggressor. This implies that aggression is directed at individuals sired by others, infant loss shortens the mother's inter-birth interval, and the aggressor has a greater likelihood of siring the next offspring of the victims' mother. As these conditions are not always met, the occurrence of male infanticide is expected to vary, and hominoid primates offer an interesting example of variation in male infanticide. Infanticide has been reported in gorillas and chimpanzees but appears to be absent in orangutans and bonobos. One argument for the absence of infanticide in bonobos is reduction of male aggression. However, given that male aggression against immature individuals occurs and that females engage in behavior that is considered to be counterstrategy against male infanticide, the risk of male infanticide may pose a potential threat. Here, we explored whether aggression by male bonobos fits predictions of male infanticide. Male aggression toward immature individuals was rare and did not have lethal consequences, but the majority of observed cases exposed targets to risks of injury. Males did not target their own offspring less frequently than unrelated immatures, and the risk of being the target of male aggression increased with the targets' age. Overall, these results do not match the predictions of the adaptive male infanticide hypothesis. Instead, aggression by males may promote the emigration of the targets and older males may reinforce their superior status toward individuals that will soon compete for the same resources.
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Affiliation(s)
| | - Linda Vigilant
- Max‐Planck‐Institute for Evolutionary AnthropologyLeipzigGermany
| | - Roger Mundry
- Max‐Planck‐Institute for Evolutionary AnthropologyLeipzigGermany
| | - Verena Behringer
- Max‐Planck‐Institute for Evolutionary AnthropologyLeipzigGermany
| | - Martin Surbeck
- Max‐Planck‐Institute for Evolutionary AnthropologyLeipzigGermany
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25
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Infant carrying by a wild chimpanzee father at Bulindi, Uganda. Primates 2019; 60:333-338. [DOI: 10.1007/s10329-019-00726-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/08/2019] [Indexed: 02/07/2023]
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26
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Porter A, Eckardt W, Vecellio V, Guschanski K, Niehoff PP, Ngobobo-As-Ibungu U, Nishuli Pekeyake R, Stoinski T, Caillaud D. Behavioral responses around conspecific corpses in adult eastern gorillas ( Gorilla beringei spp.). PeerJ 2019; 7:e6655. [PMID: 30972250 PMCID: PMC6450378 DOI: 10.7717/peerj.6655] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 02/20/2019] [Indexed: 11/20/2022] Open
Abstract
Humans were once considered unique in having a concept of death but a growing number of observations of animal responses to dying and dead conspecifics suggests otherwise. Complex arrays of behaviors have been described ranging from corpse removal and burial among social insects to quiet attendance and caregiving among elephants and primates. Less frequently described, however, are behavioral responses of individuals from different age/sex classes or social position toward the death of conspecifics. We describe behavioral responses of mountain gorillas (Gorilla beringei beringei) to the deaths of a dominant silverback and a dominant adult female from the same social group in Volcanoes National Park in Rwanda and the responses of Grauer’s gorillas (Gorilla b. graueri) to the corpse of an extra-group silverback in Kahuzi-Biega National Park, Democratic Republic of Congo. In gorillas, interactions between groups or with a lone silverback often result in avoidance or aggression. We predicted that: (i) more individuals should interact with the corpses of same-group members than with the corpse of the extra-group silverback; (ii) adult females with infants should avoid the corpse of the extra-group silverback; and (iii) in the mountain gorilla cases, individuals that shared close social relationships with the dead individual should spend more time with the corpse than other individuals in the group. We used a combination of detailed qualitative reports, photos, and videos to describe all occurrences of affiliative/investigative and agonistic behaviors observed at the corpses. We observed similar responses toward the corpses of group and extra-group individuals. Animals in all three cases showed a variety of affiliative/investigative and agonistic behaviors directed to the corpses. Animals of all age/sex classes interacted with the corpses in affiliative/investigative ways but there was a notable absence of all adult females at the corpse of the extra-group silverback. In all three cases, we observed only silverbacks and blackbacks being agonistic around and/or toward the corpses. In the mountain gorilla cases, the individuals who spent the most time with the corpses were animals who shared close social relationships with the deceased. We emphasize the similarity in the behavioral responses around the corpses of group and extra-group individuals, and suggest that the behavioral responses were influenced in part by close social relationships between the deceased and certain group members and by a general curiosity about death. We further discuss the implications close interactions with corpses have for disease transmission within and between gorilla social groups.
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Affiliation(s)
- Amy Porter
- The Dian Fossey Gorilla Fund International, Atlanta, GA, United States of America
| | - Winnie Eckardt
- The Dian Fossey Gorilla Fund International, Atlanta, GA, United States of America
| | - Veronica Vecellio
- The Dian Fossey Gorilla Fund International, Atlanta, GA, United States of America
| | - Katerina Guschanski
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala Universitet, Uppsala, Sweden
| | - Peter Philip Niehoff
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala Universitet, Uppsala, Sweden
| | | | - Radar Nishuli Pekeyake
- Institut Congolais pour la Conservation de la Nature, Kinshasa, Democratic Republic of Congo
| | - Tara Stoinski
- The Dian Fossey Gorilla Fund International, Atlanta, GA, United States of America
| | - Damien Caillaud
- The Dian Fossey Gorilla Fund International, Atlanta, GA, United States of America.,Department of Anthropology, University of California, Davis, Davis, CA, United States of America
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27
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Bourgeois S, Kaden J, Senn H, Bunnefeld N, Jeffery KJ, Akomo-Okoue EF, Ogden R, McEwing R. Improving cost-efficiency of faecal genotyping: New tools for elephant species. PLoS One 2019; 14:e0210811. [PMID: 30699177 PMCID: PMC6353156 DOI: 10.1371/journal.pone.0210811] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 01/02/2019] [Indexed: 11/18/2022] Open
Abstract
Despite the critical need for non-invasive tools to improve monitoring of wildlife populations, especially for endangered and elusive species, faecal genetic sampling has not been adopted as regular practice, largely because of the associated technical challenges and cost. Substantial work needs to be undertaken to refine sample collection and preparation methods in order to improve sample set quality and provide cost-efficient tools that can effectively support wildlife management. In this study, we collected an extensive set of forest elephant (Loxodonta cyclotis) faecal samples throughout Gabon, Central Africa, and prepared them for genotyping using 107 single-nucleotide polymorphism assays. We developed a new quantitative polymerase chain reaction (PCR) assay targeting a 130-bp nuclear DNA fragment and demonstrated its suitability for degraded samples in all three elephant species. Using this assay to compare the efficacy of two sampling methods for faecal DNA recovery, we found that sampling the whole surface of a dung pile with a swab stored in a small tube of lysis buffer was a convenient method producing high extraction success and DNA yield. We modelled the influence of faecal quality and storage time on DNA concentration in order to provide recommendations for optimized collection and storage. The maximum storage time to ensure 75% success was two months for samples collected within 24 hours after defecation and extended to four months for samples collected within one hour. Lastly, the real-time quantitative PCR assay allowed us to predict genotyping success and pre-screen DNA samples, thus further increasing the cost-efficiency of our approach. We recommend combining the validation of an efficient sampling method, the build of in-country DNA extraction capacity for reduced storage time and the development of species-specific quantitative PCR assays in order to increase the cost-efficiency of routine non-invasive DNA analyses and expand the use of next-generation markers to non-invasive samples.
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Affiliation(s)
- Stéphanie Bourgeois
- Agence Nationale des Parcs Nationaux, Libreville, Gabon
- WildGenes Laboratory, The Royal Zoological Society of Scotland, RZSS Edinburgh Zoo, Edinburgh, United Kingdom
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
- * E-mail:
| | - Jenny Kaden
- WildGenes Laboratory, The Royal Zoological Society of Scotland, RZSS Edinburgh Zoo, Edinburgh, United Kingdom
| | - Helen Senn
- WildGenes Laboratory, The Royal Zoological Society of Scotland, RZSS Edinburgh Zoo, Edinburgh, United Kingdom
| | - Nils Bunnefeld
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - Kathryn J. Jeffery
- Agence Nationale des Parcs Nationaux, Libreville, Gabon
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
- Institut de Recherche en Écologie Tropicale, Libreville, Gabon
| | | | - Rob Ogden
- TRACE Wildlife Forensics Network, Edinburgh, United Kingdom
| | - Ross McEwing
- TRACE Wildlife Forensics Network, Edinburgh, United Kingdom
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28
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Sacks BN, Milburn PJ. Genetic characterization of kit foxes at their northern range extent and monitoring recommendations. WILDLIFE SOC B 2018. [DOI: 10.1002/wsb.933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Benjamin N. Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory and Department of Population Health and Reproduction; School of Veterinary Medicine, University of California, Davis, One Shields Avenue/Old Davis Road; Davis CA 95616 USA
| | - Philip J. Milburn
- Oregon Department of Fish and Wildlife; 3814 Clark Boulevard Ontario OR 97914 USA
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29
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Ishizuka S, Kawamoto Y, Toda K, Furuichi T. Bonobos’ saliva remaining on the pith of terrestrial herbaceous vegetation can serve as non-invasive wild genetic resources. Primates 2018; 60:7-13. [DOI: 10.1007/s10329-018-00704-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 11/29/2018] [Indexed: 11/24/2022]
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30
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Rosenbaum S, Vigilant L, Kuzawa CW, Stoinski TS. Caring for infants is associated with increased reproductive success for male mountain gorillas. Sci Rep 2018; 8:15223. [PMID: 30323256 PMCID: PMC6189178 DOI: 10.1038/s41598-018-33380-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/27/2018] [Indexed: 11/09/2022] Open
Abstract
Socioecological theory predicts that male parenting among mammals should be rare due to the large payoffs of prioritizing mating effort over parenting. Although these predictions are generally met, in some promiscuous primate species males overcome this by identifying their offspring, and providing benefits such as protection and resource access. Mountain gorillas, which often organize into multi-male groups, are an intriguing exception. Males frequently affiliate with infants despite not discriminating their own from other males' offspring, raising questions about the function of this behavior. Here we demonstrate that, independent of multiple controls for rank, age, and siring opportunities, male gorillas who affiliated more with all infants, not only their own, sired more offspring than males who affiliated less with young. Predictive margins indicate males in the top affiliation tertile can expect to sire approximately five times more infants than males in the bottom tertile, across the course of their reproductive careers. These findings establish a link between males' fitness and their associations with infants in the absence of kin discrimination or high paternity certainty, and suggest a strategy by which selection could generate more involved male parenting among non-monogamous species.
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Affiliation(s)
- Stacy Rosenbaum
- Department of Anthropology, Northwestern University, Evanston, IL, USA.
- Davee Center for Epidemiology and Endocrinology, Lincoln Park Zoo, Chicago, IL, USA.
| | - Linda Vigilant
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Christopher W Kuzawa
- Department of Anthropology, Northwestern University, Evanston, IL, USA
- Institute for Policy Research, Northwestern University, Evanston, IL, USA
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31
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Barbian HJ, Connell AJ, Avitto AN, Russell RM, Smith AG, Gundlapally MS, Shazad AL, Li Y, Bibollet‐Ruche F, Wroblewski EE, Mjungu D, Lonsdorf EV, Stewart FA, Piel AK, Pusey AE, Sharp PM, Hahn BH. CHIIMP: An automated high-throughput microsatellite genotyping platform reveals greater allelic diversity in wild chimpanzees. Ecol Evol 2018; 8:7946-7963. [PMID: 30250675 PMCID: PMC6145012 DOI: 10.1002/ece3.4302] [Citation(s) in RCA: 15] [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: 05/01/2018] [Revised: 05/14/2018] [Accepted: 05/29/2018] [Indexed: 12/29/2022] Open
Abstract
Short tandem repeats (STRs), also known as microsatellites, are commonly used to noninvasively genotype wild-living endangered species, including African apes. Until recently, capillary electrophoresis has been the method of choice to determine the length of polymorphic STR loci. However, this technique is labor intensive, difficult to compare across platforms, and notoriously imprecise. Here we developed a MiSeq-based approach and tested its performance using previously genotyped fecal samples from long-term studied chimpanzees in Gombe National Park, Tanzania. Using data from eight microsatellite loci as a reference, we designed a bioinformatics platform that converts raw MiSeq reads into locus-specific files and automatically calls alleles after filtering stutter sequences and other PCR artifacts. Applying this method to the entire Gombe population, we confirmed previously reported genotypes, but also identified 31 new alleles that had been missed due to sequence differences and size homoplasy. The new genotypes, which increased the allelic diversity and heterozygosity in Gombe by 61% and 8%, respectively, were validated by replicate amplification and pedigree analyses. This demonstrated inheritance and resolved one case of an ambiguous paternity. Using both singleplex and multiplex locus amplification, we also genotyped fecal samples from chimpanzees in the Greater Mahale Ecosystem in Tanzania, demonstrating the utility of the MiSeq-based approach for genotyping nonhabituated populations and performing comparative analyses across field sites. The new automated high-throughput analysis platform (available at https://github.com/ShawHahnLab/chiimp) will allow biologists to more accurately and effectively determine wildlife population size and structure, and thus obtain information critical for conservation efforts.
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Affiliation(s)
- Hannah J. Barbian
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Andrew Jesse Connell
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Alexa N. Avitto
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Ronnie M. Russell
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Andrew G. Smith
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Madhurima S. Gundlapally
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Alexander L. Shazad
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Yingying Li
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Frederic Bibollet‐Ruche
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Emily E. Wroblewski
- Department of AnthropologyWashington University in St. LouisSt. LouisMissouri
| | | | | | - Fiona A. Stewart
- School of Natural Sciences and PsychologyLiverpool John Moores UniversityLiverpoolUK
| | - Alexander K. Piel
- School of Natural Sciences and PsychologyLiverpool John Moores UniversityLiverpoolUK
| | - Anne E. Pusey
- Department of Evolutionary AnthropologyDuke UniversityDurhamNorth Carolina
| | - Paul M. Sharp
- Institute of Evolutionary Biology and Centre for ImmunityInfection and EvolutionUniversity of EdinburghEdinburghUK
| | - Beatrice H. Hahn
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
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Hagemann L, Boesch C, Robbins MM, Arandjelovic M, Deschner T, Lewis M, Froese G, Vigilant L. Long-term group membership and dynamics in a wild western lowland gorilla population (Gorilla gorilla gorilla) inferred using non-invasive genetics. Am J Primatol 2018; 80:e22898. [PMID: 30024040 DOI: 10.1002/ajp.22898] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 06/22/2018] [Accepted: 07/01/2018] [Indexed: 01/07/2023]
Abstract
The social organization of a group-living animal is defined by a balance between group dynamic events such as group formation, group dissolution, and dispersal events and group stability in membership and over time. Understanding these processes, which are relevant for questions ranging from disease transmission patterns to the evolution of polygyny, requires long-term monitoring of multiple social units over time. Because all great ape species are long-lived and elusive, the number of studies on these key aspects of social organization are limited, especially for western lowland gorillas (Gorilla gorilla gorilla). In this study, we used non-invasive genetic samples collected within an approximately 100 km2 area of Loango National Park, Gabon to reconstruct group compositions and changes in composition over more than a decade. We identified 98 gorillas and 11 mixed sex groups sampled during 2014-2017. Using published data from 85 individuals and 12 groups surveyed between 2005 and 2009 at the same locality, we tracked groups and individuals back in time. The identification of 11 silverbacks via parentage analyses and the genetic tracking of 39 individuals across studies allowed us to infer six group formations, five group dissolutions, and 40 dispersal events within 12 years. We also observed four groups persisting across the sampling periods with a maximum inferred existence of nearly 17 years and exhibiting variation in membership stability. Our results highlight the variation in composition and stability among groups of western lowland gorillas and illustrate the power of non-invasive genetic sampling for long-term monitoring.
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Affiliation(s)
- Laura Hagemann
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Christophe Boesch
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Martha M Robbins
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mimi Arandjelovic
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tobias Deschner
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthew Lewis
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Graden Froese
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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33
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Rich AM, Wasserman MD, Deimel C, Breeden SK, Kaestle F, Hunt KD. Is genetic drift to blame for testicular dysgenesis syndrome in Semliki chimpanzees (Pan troglodytes schweinfurthii)? J Med Primatol 2018; 47:257-269. [PMID: 29799118 DOI: 10.1111/jmp.12352] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2018] [Indexed: 11/26/2022]
Abstract
BACKGROUND We present 3 likely cases of testicular dysgenesis syndrome (TDS) within a community of chimpanzees (Pan troglodytes schweinfurthii). We tested whether genetic drift may be the culprit, as a genetic cause has been suspected to account for TDS among other wildlife. METHODS We successfully sequenced a 367-bp segment spanning the first hypervariable region within the D-loop of the mitochondrial genome for 78 DNA samples. RESULTS We found 24 polymorphic sequence sites consisting of 7 singletons and 17 parsimony informative sites. This sample contained 9 haplotypes with a diversity index of 0.78 (SD = 0.03). All tests against the null hypothesis of neutral polymorphisms were non-significant (P > .10). The mismatch distribution of pairwise differences does not fit a Poisson's curve (raggedness index = 0.166; SSD = 0.12; P = 1). CONCLUSIONS Thus, we found no significant signs of genetic isolation, population expansion, or genetic bottleneck. Alternative causes of TDS and how they might pertain to this population are discussed.
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Affiliation(s)
- Alicia M Rich
- Department of Anthropology, Boston University, Boston, MA, USA
- Department of Anthropology, Indiana University, Bloomington, IN, USA
| | | | - Caroline Deimel
- Department of Anthropology, Indiana University, Bloomington, IN, USA
| | - Scott K Breeden
- Marian University College of Osteopathic Medicine, Indianapolis, IN, USA
| | - Frederika Kaestle
- Department of Anthropology, Indiana University, Bloomington, IN, USA
| | - Kevin D Hunt
- Department of Anthropology, Indiana University, Bloomington, IN, USA
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34
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Arandjelovic M, Vigilant L. Non-invasive genetic censusing and monitoring of primate populations. Am J Primatol 2018; 80:e22743. [PMID: 29457631 DOI: 10.1002/ajp.22743] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 12/16/2017] [Accepted: 01/14/2018] [Indexed: 02/06/2023]
Abstract
Knowing the density or abundance of primate populations is essential for their conservation management and contextualizing socio-demographic and behavioral observations. When direct counts of animals are not possible, genetic analysis of non-invasive samples collected from wildlife populations allows estimates of population size with higher accuracy and precision than is possible using indirect signs. Furthermore, in contrast to traditional indirect survey methods, prolonged or periodic genetic sampling across months or years enables inference of group membership, movement, dynamics, and some kin relationships. Data may also be used to estimate sex ratios, sex differences in dispersal distances, and detect gene flow among locations. Recent advances in capture-recapture models have further improved the precision of population estimates derived from non-invasive samples. Simulations using these methods have shown that the confidence interval of point estimates includes the true population size when assumptions of the models are met, and therefore this range of population size minima and maxima should be emphasized in population monitoring studies. Innovations such as the use of sniffer dogs or anti-poaching patrols for sample collection are important to ensure adequate sampling, and the expected development of efficient and cost-effective genotyping by sequencing methods for DNAs derived from non-invasive samples will automate and speed analyses.
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Affiliation(s)
- Mimi Arandjelovic
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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35
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Baas P, van der Valk T, Vigilant L, Ngobobo U, Binyinyi E, Nishuli R, Caillaud D, Guschanski K. Population-level assessment of genetic diversity and habitat fragmentation in critically endangered Grauer's gorillas. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 165:565-575. [PMID: 29313894 DOI: 10.1002/ajpa.23393] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 11/27/2017] [Accepted: 12/13/2017] [Indexed: 11/06/2022]
Abstract
OBJECTIVES The critically endangered Grauer's gorilla (Gorilla beringei graueri) has experienced an estimated 77% population decline within a single generation. Although crucial for informed conservation decisions, there is no clear understanding about population structure and distribution of genetic diversity across the species' highly fragmented range. We fill this gap by studying several core and peripheral Grauer's gorilla populations throughout their distribution range. MATERIALS AND METHODS We generated genetic profiles for a sampling of an unstudied population of Grauer's gorillas from within the species' core range at 13 autosomal microsatellite loci and combined them with previously published and newly generated data from four other Grauer's gorilla populations, two mountain gorilla populations, and one western lowland gorilla population. RESULTS In agreement with previous studies, the genetic diversity of Grauer's gorillas is intermediate, falling between western lowland and mountain gorillas. Among Grauer's gorilla populations, we observe lower genetic diversity and high differentiation in peripheral compared with central populations, indicating a strong effect of genetic drift and limited gene flow among small, isolated forest fragments. DISCUSSION Although genetically less diverse, peripheral populations are frequently essential for the long-term persistence of a species and migration between peripheral and core populations may significantly enrich the overall species genetic diversity. Thus, in addition to central Grauer's gorilla populations from the core of the distribution range that clearly deserve conservation attention, we argue that conservation strategies aiming to ensure long-term species viability should include preserving peripheral populations and enhancing habitat connectivity.
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Affiliation(s)
- Pauline Baas
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Tom van der Valk
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Linda Vigilant
- Primatology Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany
| | - Urbain Ngobobo
- Dian Fossey Gorilla Fund International, 800 Cherokee Avenue, Atlanta, Georgia
| | - Escobar Binyinyi
- Dian Fossey Gorilla Fund International, 800 Cherokee Avenue, Atlanta, Georgia
| | - Radar Nishuli
- Institut Congolais pour la Conservation de la Nature, N4, Réserve de Faune à Okapis, Democratic Republic of Congo
| | - Damien Caillaud
- Dian Fossey Gorilla Fund International, 800 Cherokee Avenue, Atlanta, Georgia.,Department of Anthropology, University of California, Davis, One Shields Ave, Davis, California
| | - Katerina Guschanski
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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36
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Ishizuka S, Kawamoto Y, Sakamaki T, Tokuyama N, Toda K, Okamura H, Furuichi T. Paternity and kin structure among neighbouring groups in wild bonobos at Wamba. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171006. [PMID: 29410812 PMCID: PMC5792889 DOI: 10.1098/rsos.171006] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 01/02/2018] [Indexed: 06/08/2023]
Abstract
Although both bonobos and chimpanzees are male-philopatric species, outcomes of male-male reproductive competition seem to be more closely associated with mating success in chimpanzees. This suggests that the extent of male reproductive skew is lower in bonobos. In addition, between-group male-male reproductive competition is more lethal in chimpanzees. This suggests that between-group differentiation in male kinship is lower in bonobos. We analysed the paternity of 17 offspring in two bonobo groups and estimated the relatedness of individuals among three neighbouring groups by using DNA extracted from non-invasive samples at Wamba, in the Democratic Republic of the Congo. The alpha males sired at least nine of 17 offspring. This supports a previous finding that the male reproductive skew is higher in bonobos than that in chimpanzees. Average relatedness among males within groups was significantly higher than that among males across groups, whereas there was no significant difference among females between within and across groups. These results are consistent with male philopatry, highly skewed reproductive success of males and female dispersal. Higher average relatedness among males within groups suggest that the differences in hostility towards males of different groups between bonobos and chimpanzees may be explained by factors other than kinship.
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Affiliation(s)
- Shintaro Ishizuka
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
- Japan Society for the Promotion of Science, Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Yoshi Kawamoto
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Tetsuya Sakamaki
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Nahoko Tokuyama
- Japan Society for the Promotion of Science, Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan
| | - Kazuya Toda
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
- Japan Society for the Promotion of Science, Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Hiroki Okamura
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Takeshi Furuichi
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
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37
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Hernandez-Rodriguez J, Arandjelovic M, Lester J, de Filippo C, Weihmann A, Meyer M, Angedakin S, Casals F, Navarro A, Vigilant L, Kühl HS, Langergraber K, Boesch C, Hughes D, Marques-Bonet T. The impact of endogenous content, replicates and pooling on genome capture from faecal samples. Mol Ecol Resour 2017; 18:319-333. [PMID: 29058768 PMCID: PMC5900898 DOI: 10.1111/1755-0998.12728] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/06/2017] [Accepted: 10/16/2017] [Indexed: 12/11/2022]
Abstract
Target-capture approach has improved over the past years, proving to be very efficient tool for selectively sequencing genetic regions of interest. These methods have also allowed the use of noninvasive samples such as faeces (characterized by their low quantity and quality of endogenous DNA) to be used in conservation genomic, evolution and population genetic studies. Here we aim to test different protocols and strategies for exome capture using the Roche SeqCap EZ Developer kit (57.5 Mb). First, we captured a complex pool of DNA libraries. Second, we assessed the influence of using more than one faecal sample, extract and/or library from the same individual, to evaluate its effect on the molecular complexity of the experiment. We validated our experiments with 18 chimpanzee faecal samples collected from two field sites as a part of the Pan African Programme: The Cultured Chimpanzee. Those two field sites are in Kibale National Park, Uganda (N = 9) and Loango National Park, Gabon (N = 9). We demonstrate that at least 16 libraries can be pooled, target enriched through hybridization, and sequenced allowing for the genotyping of 951,949 exome markers for population genetic analyses. Further, we observe that molecule richness, and thus, data acquisition, increase when using multiple libraries from the same extract or multiple extracts from the same sample. Finally, repeated captures significantly decrease the proportion of off-target reads from 34.15% after one capture round to 7.83% after two capture rounds, supporting our conclusion that two rounds of target enrichment are advisable when using complex faecal samples.
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Affiliation(s)
- Jessica Hernandez-Rodriguez
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Barcelona, Spain
| | - Mimi Arandjelovic
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jack Lester
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cesare de Filippo
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Antje Weihmann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Samuel Angedakin
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Ferran Casals
- Genomics Core Facility, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Arcadi Navarro
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Barcelona, Spain.,Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Hjalmar S Kühl
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Leipzig-Jena, Leipzig, Germany
| | - Kevin Langergraber
- School of Human Evolution & Social Change, Arizona State University, Tempe, AZ, USA
| | - Christophe Boesch
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - David Hughes
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Barcelona, Spain.,MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Tomas Marques-Bonet
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Barcelona, Spain.,Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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38
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Kistler L, Johnson SM, Irwin MT, Louis EE, Ratan A, Perry GH. A massively parallel strategy for STR marker development, capture, and genotyping. Nucleic Acids Res 2017; 45:e142. [PMID: 28666376 PMCID: PMC5587753 DOI: 10.1093/nar/gkx574] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 06/21/2017] [Indexed: 12/11/2022] Open
Abstract
Short tandem repeat (STR) variants are highly polymorphic markers that facilitate powerful population genetic analyses. STRs are especially valuable in conservation and ecological genetic research, yielding detailed information on population structure and short-term demographic fluctuations. Massively parallel sequencing has not previously been leveraged for scalable, efficient STR recovery. Here, we present a pipeline for developing STR markers directly from high-throughput shotgun sequencing data without a reference genome, and an approach for highly parallel target STR recovery. We employed our approach to capture a panel of 5000 STRs from a test group of diademed sifakas (Propithecus diadema, n = 3), endangered Malagasy rainforest lemurs, and we report extremely efficient recovery of targeted loci—97.3–99.6% of STRs characterized with ≥10x non-redundant sequence coverage. We then tested our STR capture strategy on P. diadema fecal DNA, and report robust initial results and suggestions for future implementations. In addition to STR targets, this approach also generates large, genome-wide single nucleotide polymorphism (SNP) panels from flanking regions. Our method provides a cost-effective and scalable solution for rapid recovery of large STR and SNP datasets in any species without needing a reference genome, and can be used even with suboptimal DNA more easily acquired in conservation and ecological studies.
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Affiliation(s)
- Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.,Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Stephen M Johnson
- Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Mitchell T Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, IL 60115, USA
| | - Edward E Louis
- Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE 68107, USA
| | - Aakrosh Ratan
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - George H Perry
- Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA 16802, USA
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Oklander LI, Miño CI, Fernández G, Caputo M, Corach D. Genetic structure in the southernmost populations of black-and-gold howler monkeys (Alouatta caraya) and its conservation implications. PLoS One 2017; 12:e0185867. [PMID: 28968440 PMCID: PMC5624639 DOI: 10.1371/journal.pone.0185867] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 09/20/2017] [Indexed: 11/19/2022] Open
Abstract
Black-and-gold howler monkeys Alouatta caraya, are arboreal primates, inhabitants of Neotropical forests, highly susceptible to the yellow fever virus, considered early 'sentinels' of outbreaks, and thus, of major epidemiological importance. Currently, anthropogenic habitat loss and modifications threatens their survival. Habitat modification can prevent, reduce or change dispersal behavior, which, in turn, may influence patterns of gene flow. We explored past and contemporary levels of genetic diversity, elucidated genetic structure and identified its possible drivers, in ten populations (n = 138) located in the southernmost distribution range of the species in South America, in Argentina and Paraguay. Overall, genetic variability was moderate (ten microsatellites: 3.16 ± 0.18 alleles per locus, allelic richness of 2.93 ± 0.81, 0.443±0.025 unbiased expected heterozygosity; 22 haplotypes of 491-bp mitochondrial Control Region, haplotypic diversity of 0.930 ± 0.11, and nucleotide diversity of0.01± 0.007). Significant evidence of inbreeding was found in a population that was, later, decimated by yellow fever. Population-based gene flow measures (FST = 0.13; θST = 018), hierarchical analysis of molecular variance and Bayesian clustering methods revealed significant genetic structure, grouping individuals into four clusters. Shared haplotypes and lack of mitochondrial differentiation (non-significant θST) among some populations seem to support the hypothesis of historical dispersal via riparian forests. Current resistance analyses revealed a significant role of landscape features in modeling contemporary gene flow: continuous forest and riparian forests could promote genetic exchange, whereas disturbed forests or crop/grassland fields may restrict it. Estimates of effective population size allow anticipating that the studied populations will lose 75% of heterozygosity in less than 50 generations. Our findings suggest that anthropogenic modifications on native forests, increasingly ongoing in Northeastern Argentina, Southern Paraguay and Southeastern Brazil, might prevent the dispersal of howlers, leading to population isolation. To ensure long-term viability and maintain genetic connectivity of A. caraya remnant populations, we recommend preserving and restoring habitat continuity. To conserve the species genetic pool, as well, the four genetic clusters identified here should be considered separate Management Units and given high conservation priority. In light of our findings and considering complementary non-genetic information, we suggest upgrading the international conservation status of A. caraya to "Vulnerable".
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Affiliation(s)
- Luciana Inés Oklander
- Instituto de Biología Subtropical (IBS), Nodo Iguazú, Universidad Nacional de Misiones (UNaM) – CONICET and Asociación Civil Centro de Investigaciones del Bosque Atlántico (CeIBA), Puerto Iguazú, Misiones, Argentina
- Centro de Bioinvestigaciones – CeBio, Universidad Nacional del Noroeste de la Provincia de Buenos Aires (UNNOBA) – CONICET, Pergamino, Buenos Aires, Argentina
| | - Carolina Isabel Miño
- Instituto de Biología Subtropical (IBS), Nodo Iguazú, Universidad Nacional de Misiones (UNaM) – CONICET and Asociación Civil Centro de Investigaciones del Bosque Atlántico (CeIBA), Puerto Iguazú, Misiones, Argentina
- Centro de Bioinvestigaciones – CeBio, Universidad Nacional del Noroeste de la Provincia de Buenos Aires (UNNOBA) – CONICET, Pergamino, Buenos Aires, Argentina
| | - Gabriela Fernández
- Centro de Bioinvestigaciones – CeBio, Universidad Nacional del Noroeste de la Provincia de Buenos Aires (UNNOBA) – CONICET, Pergamino, Buenos Aires, Argentina
| | - Mariela Caputo
- Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (UBA) – CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Daniel Corach
- Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (UBA) – CONICET, Ciudad Autónoma de Buenos Aires, Argentina
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40
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Pan X, Wang J, Zhang Y, Dong P, Li C, Liang X. Detection of trace amounts of target DNA from massive background of nucleic acids by using the LM-PCR-based preamplification method. Biotechnol Appl Biochem 2017; 64:879-887. [DOI: 10.1002/bab.1545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 11/02/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Xiaoming Pan
- College of Food Science and Engineering; Ocean University of China; Qingdao Peoples’ Republic of China
| | - Jing Wang
- College of Food Science and Engineering; Ocean University of China; Qingdao Peoples’ Republic of China
| | - Yanfang Zhang
- College of Food Science and Engineering; Ocean University of China; Qingdao Peoples’ Republic of China
| | - Ping Dong
- College of Food Science and Engineering; Ocean University of China; Qingdao Peoples’ Republic of China
| | - Chunchuan Li
- College of Food Science and Engineering; Ocean University of China; Qingdao Peoples’ Republic of China
| | - Xingguo Liang
- College of Food Science and Engineering; Ocean University of China; Qingdao Peoples’ Republic of China
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41
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Engelhardt A, Muniz L, Perwitasari-Farajallah D, Widdig A. Highly Polymorphic Microsatellite Markers for the Assessment of Male Reproductive Skew and Genetic Variation in Critically Endangered Crested Macaques ( Macaca nigra). INT J PRIMATOL 2017; 38:672-691. [PMID: 28845069 PMCID: PMC5550527 DOI: 10.1007/s10764-017-9973-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 05/11/2017] [Indexed: 11/24/2022]
Abstract
Genetic analyses based on noninvasively collected samples have become an important tool for evolutionary biology and conservation. Crested macaques (Macaca nigra), endemic to Sulawesi, Indonesia, are important for our understanding of primate evolution as Sulawesi macaques represent an exceptional example of primate adaptive radiation. Crested macaques are also Critically Endangered. However, to date we know very little about their genetics. The aim of our study was to find and validate microsatellite markers useful for evolutionary, conservation, and other genetic studies on wild crested macaques. Using fecal samples of 176 wild macaques living in the Tangkoko Reserve, Sulawesi, we identified 12 polymorphic microsatellite loci through cross-species polymerase chain reaction amplification with later modification of some of these primers. We tested their suitability by investigating and exploring patterns of paternity, observed heterozygosity, and evidence for inbreeding. We assigned paternity to 63 of 65 infants with high confidence. Among cases with solved paternity, we found no evidence of extragroup paternity and natal breeding. We found a relatively steep male reproductive skew B index of 0.330 ± 0.267; mean ± SD) and mean alpha paternity of 65% per year with large variation across groups and years (29–100%). Finally, we detected an excess in observed heterozygosity and no evidence of inbreeding across our three study groups, with an observed heterozygosity of 0.766 ± 0.059 and expected heterozygosity of 0.708 ± 0.059, and an inbreeding coefficient of −0.082 ± 0.035. Our results indicate that the selected markers are useful for genetic studies on wild crested macaques, and possibly also on other Sulawesi and closely related macaques. They further suggest that the Tangkoko population of crested macaques is still genetically variable despite its small size, isolation, and the species’ reproductive patterns. This gives us hope that other endangered primate species living in small, isolated populations may also retain a healthy gene pool, at least in the short term.
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Affiliation(s)
- Antje Engelhardt
- School of Natural Sciences and Psychology, Liverpool John Moores University, L3 3AF, Liverpool, UK.,Junior Research Group of Primate Sexual Selection, German Primate Center, 37077 Göttingen, Germany.,Courant Research Center Evolution of Social Behavior, Georg August University, 37077 Göttingen, Germany
| | - Laura Muniz
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.,Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, 04103 Leipzig, Germany
| | - Dyah Perwitasari-Farajallah
- Primate Research Centre, Bogor Agricultural University, Bogor, Indonesia.,Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Bogor, Indonesia
| | - Anja Widdig
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.,Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, 04103 Leipzig, Germany.,German Center for Integrative Biodiversity Research, 04103 Leipzig, Germany
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42
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LeBlanc NM, Stewart DT, Pálsson S, Elderkin MF, Mittelhauser G, Mockford S, Paquet J, Robertson GJ, Summers RW, Tudor L, Mallory ML. Population structure of Purple Sandpipers ( Calidris maritima) as revealed by mitochondrial DNA and microsatellites. Ecol Evol 2017; 7:3225-3242. [PMID: 28480021 PMCID: PMC5415539 DOI: 10.1002/ece3.2927] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 11/14/2016] [Accepted: 12/21/2016] [Indexed: 11/16/2022] Open
Abstract
The Purple Sandpiper (Calidris maritima) is a medium‐sized shorebird that breeds in the Arctic and winters along northern Atlantic coastlines. Migration routes and affiliations between breeding grounds and wintering grounds are incompletely understood. Some populations appear to be declining, and future management policies for this species will benefit from understanding their migration patterns. This study used two mitochondrial DNA markers and 10 microsatellite loci to analyze current population structure and historical demographic trends. Samples were obtained from breeding locations in Nunavut (Canada), Iceland, and Svalbard (Norway) and from wintering locations along the coast of Maine (USA), Nova Scotia, New Brunswick, and Newfoundland (Canada), and Scotland (UK). Mitochondrial haplotypes displayed low genetic diversity, and a shallow phylogeny indicating recent divergence. With the exception of the two Canadian breeding populations from Nunavut, there was significant genetic differentiation among samples from all breeding locations; however, none of the breeding populations was a monophyletic group. We also found differentiation between both Iceland and Svalbard breeding populations and North American wintering populations. This pattern of divergence is consistent with a previously proposed migratory pathway between Canadian breeding locations and wintering grounds in the United Kingdom, but argues against migration between breeding grounds in Iceland and Svalbard and wintering grounds in North America. Breeding birds from Svalbard also showed a genetic signature intermediate between Canadian breeders and Icelandic breeders. Our results extend current knowledge of Purple Sandpiper population genetic structure and present new information regarding migration routes to wintering grounds in North America.
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Affiliation(s)
| | | | - Snaebjörn Pálsson
- Department of Life and Environmental Sciences University of Iceland Reykjavík Iceland
| | - Mark F Elderkin
- Department of Natural Resources Government of Nova Scotia Kentville NS Canada
| | | | | | - Julie Paquet
- Canadian Wildlife Service, Environment and Climate Change Canada Sackville NB Canada
| | - Gregory J Robertson
- Wildlife Research Division, Environment and Climate Change Canada Mount Pearl NL Canada
| | - Ron W Summers
- Lismore, 7 Mill Crescent North Kessock Ross-shire UK
| | - Lindsay Tudor
- Maine Department of Inland Fisheries and Wildlife Bangor ME USA
| | - Mark L Mallory
- Department of Biology Acadia University Wolfville NS Canada
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43
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Moscovice LR, Douglas PH, Martinez-Iñigo L, Surbeck M, Vigilant L, Hohmann G. Stable and fluctuating social preferences and implications for cooperation among female bonobos at LuiKotale, Salonga National Park, DRC. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 163:158-172. [DOI: 10.1002/ajpa.23197] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 02/08/2017] [Accepted: 02/10/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Liza R. Moscovice
- Department of Primatology; Max Planck Institute for Evolutionary Anthropology; Leipzig 04133 Germany
| | - Pamela Heidi Douglas
- Department of Primatology; Max Planck Institute for Evolutionary Anthropology; Leipzig 04133 Germany
| | - Laura Martinez-Iñigo
- School of Psychology, College of Social Science; University of Lincoln; Lincolnshire United Kingdom
| | - Martin Surbeck
- Department of Primatology; Max Planck Institute for Evolutionary Anthropology; Leipzig 04133 Germany
| | - Linda Vigilant
- Department of Primatology; Max Planck Institute for Evolutionary Anthropology; Leipzig 04133 Germany
| | - Gottfried Hohmann
- Department of Primatology; Max Planck Institute for Evolutionary Anthropology; Leipzig 04133 Germany
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44
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Duboscq J, Neumann C, Agil M, Perwitasari-Farajallah D, Thierry B, Engelhardt A. Degrees of freedom in social bonds of crested macaque females. Anim Behav 2017. [DOI: 10.1016/j.anbehav.2016.11.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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45
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Granjon AC, Rowney C, Vigilant L, Langergraber KE. Evaluating genetic capture-recapture using a chimpanzee population of known size. J Wildl Manage 2016. [DOI: 10.1002/jwmg.21190] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Anne-Céline Granjon
- Department of Primatology; Max Planck Institute for Evolutionary Anthropology; Deutscher Platz 6 04103 Leipzig Germany
| | - Carolyn Rowney
- Department of Primatology; Max Planck Institute for Evolutionary Anthropology; Deutscher Platz 6 04103 Leipzig Germany
| | - Linda Vigilant
- Department of Primatology; Max Planck Institute for Evolutionary Anthropology; Deutscher Platz 6 04103 Leipzig Germany
| | - Kevin E. Langergraber
- School of Human Evolution and Social Change and Institute of Human Origins; Arizona State University; 900 Cady Mall Tempe AZ 85287 USA
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46
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Wittig RM, Crockford C, Weltring A, Langergraber KE, Deschner T, Zuberbühler K. Social support reduces stress hormone levels in wild chimpanzees across stressful events and everyday affiliations. Nat Commun 2016; 7:13361. [PMID: 27802260 PMCID: PMC5097121 DOI: 10.1038/ncomms13361] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 09/27/2016] [Indexed: 11/11/2022] Open
Abstract
Stress is a major cause of poor health and mortality in humans and other social mammals. Close social bonds buffer stress, however much of the underlying physiological mechanism remains unknown. Here, we test two key hypotheses: bond partner effects occur only during stress (social buffering) or generally throughout daily life (main effects). We assess urinary glucocorticoids (uGC) in wild chimpanzees, with or without their bond partners, after a natural stressor, resting or everyday affiliation. Chimpanzees in the presence of, or interacting with, bond partners rather than others have lowered uGC levels across all three contexts. These results support the main effects hypothesis and indicate that hypothalamic-pituitary-adrenocortical (HPA) axis regulation is mediated by daily engagement with bond partners both within and out of stressful contexts. Regular social support with bond partners could lead to better health through daily 'micro-management' of the HPA axis, a finding with potential medical implications for humans.
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Affiliation(s)
- Roman M. Wittig
- Max Planck Institute for Evolutionary Anthropology, Department of Primatology, 04103 Leipzig, Germany
- University of St Andrews, School of Psychology & Neuroscience, St Andrews, KY16 9JP, UK
- Budongo Conservation Field Station, PO Box 362, Masindi, Uganda
| | - Catherine Crockford
- Max Planck Institute for Evolutionary Anthropology, Department of Primatology, 04103 Leipzig, Germany
- University of St Andrews, School of Psychology & Neuroscience, St Andrews, KY16 9JP, UK
- Budongo Conservation Field Station, PO Box 362, Masindi, Uganda
| | - Anja Weltring
- Max Planck Institute for Evolutionary Anthropology, Department of Primatology, 04103 Leipzig, Germany
| | - Kevin E. Langergraber
- Arizona State University, School of Human Evolution & Social Change and Institute of Human Origins, Tempe, Arizona 85281, USA
| | - Tobias Deschner
- Max Planck Institute for Evolutionary Anthropology, Department of Primatology, 04103 Leipzig, Germany
| | - Klaus Zuberbühler
- University of St Andrews, School of Psychology & Neuroscience, St Andrews, KY16 9JP, UK
- Budongo Conservation Field Station, PO Box 362, Masindi, Uganda
- University of Neuchatel, Department of Comparative Cognition, 2000 Neuchatel, Switzerland
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47
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Kumar A, Rai U, Roka B, Jha AK, Reddy PA. Genetic assessment of captive red panda ( Ailurus fulgens) population. SPRINGERPLUS 2016; 5:1750. [PMID: 27795893 PMCID: PMC5055525 DOI: 10.1186/s40064-016-3437-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 09/29/2016] [Indexed: 11/21/2022]
Abstract
Red panda (Ailurus fulgens) is threatened across its range by detrimental human activities and rapid habitat changes necessitating captive breeding programs in various zoos globally to save this flagship species from extinction. One of the ultimate aims of ex situ conservation is reintroduction of endangered animals into their natural habitats while maintaining 90 % of the founder genetic diversity. Advances in molecular genetics and microsatellite genotyping techniques make it possible to accurately estimate genetic diversity of captive animals of unknown ancestry. Here we assess genetic diversity of the red panda population in Padmaja Naidu Himalayan Zoological Park, Darjeeling, which plays a pivotal role in ex situ conservation of red panda in India. We generated microsatellite genotypes of fifteen red pandas with a set of fourteen loci. This population is genetically diverse with 68 % observed heterozygosity (HO) and mean inbreeding (FIS) coefficient of 0.05. However population viability analysis reveals that this population has a very low survival probability (<2 %) and will rapidly loose its genetic diversity to 37 % mainly due to small population size and skewed male-biased sex ratio. Regular supplementation with a pair of adult individuals every five years will increase survival probability and genetic diversity to 99 and 61 % respectively and will also support future harvesting of individuals for reintroduction into the wild and exchange with other zoos.
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Affiliation(s)
- Arun Kumar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007 India
| | - Upashna Rai
- Padmaja Naidu Himalayan Zoological Park, Darjeeling, 734101 India
| | - Bhupen Roka
- Padmaja Naidu Himalayan Zoological Park, Darjeeling, 734101 India
| | - Alankar K Jha
- Padmaja Naidu Himalayan Zoological Park, Darjeeling, 734101 India
| | - P Anuradha Reddy
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007 India
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48
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Walker FM, Williamson CHD, Sanchez DE, Sobek CJ, Chambers CL. Species From Feces: Order-Wide Identification of Chiroptera From Guano and Other Non-Invasive Genetic Samples. PLoS One 2016; 11:e0162342. [PMID: 27654850 PMCID: PMC5031397 DOI: 10.1371/journal.pone.0162342] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 08/22/2016] [Indexed: 11/25/2022] Open
Abstract
Bat guano is a relatively untapped reservoir of information, having great utility as a DNA source because it is often available at roosts even when bats are not and is an easy type of sample to collect from a difficult-to-study mammalian order. Recent advances from microbial community studies in primer design, sequencing, and analysis enable fast, accurate, and cost-effective species identification. Here, we borrow from this discipline to develop an order-wide DNA mini-barcode assay (Species from Feces) based on a segment of the mitochondrial gene cytochrome c oxidase I (COI). The assay works effectively with fecal DNA and is conveniently transferable to low-cost, high-throughput Illumina MiSeq technology that also allows simultaneous pairing with other markers. Our PCR primers target a region of COI that is highly discriminatory among Chiroptera (92% species-level identification of barcoded species), and are sufficiently degenerate to allow hybridization across diverse bat taxa. We successfully validated our system with 54 bat species across both suborders. Despite abundant arthropod prey DNA in guano, our primers were highly specific to bats; no arthropod DNA was detected in thousands of feces run on Sanger and Illumina platforms. The assay is extendable to fecal pellets of unknown age as well as individual and pooled guano, to allow for individual (using singular fecal pellets) and community (using combined pellets collected from across long-term roost sites) analyses. We developed a searchable database (http://nau.edu/CEFNS/Forestry/Research/Bats/Search-Tool/) that allows users to determine the discriminatory capability of our markers for bat species of interest. Our assay has applications worldwide for examining disease impacts on vulnerable species, determining species assemblages within roosts, and assessing the presence of bat species that are vulnerable or facing extinction. The development and analytical pathways are rapid, reliable, and inexpensive, and can be applied to ecology and conservation studies of other taxa.
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Affiliation(s)
- Faith M. Walker
- Bat Ecology & Genetics Laboratory, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Charles H. D. Williamson
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Daniel E. Sanchez
- Bat Ecology & Genetics Laboratory, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Colin J. Sobek
- Bat Ecology & Genetics Laboratory, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Carol L. Chambers
- Bat Ecology & Genetics Laboratory, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
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49
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Godoy I, Vigilant L, Perry SE. Cues to kinship and close relatedness during infancy in white-faced capuchin monkeys, Cebus capucinus. Anim Behav 2016. [DOI: 10.1016/j.anbehav.2016.03.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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50
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Mother-male bond, but not paternity, influences male-infant affiliation in wild crested macaques. Behav Ecol Sociobiol 2016; 70:1117-1130. [PMID: 27478299 PMCID: PMC4954837 DOI: 10.1007/s00265-016-2116-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 03/29/2016] [Accepted: 03/30/2016] [Indexed: 11/16/2022]
Abstract
Abstract In promiscuous primates, interactions between adult males and infants have rarely been investigated. However, recent evidence suggests that male affiliation towards infants has an influence on several aspects of the infants’ life. Furthermore, affiliations may be associated with male reproductive strategy. In this study, we examined which social factors influenced male-infant affiliation initiated by either male or infant, in wild crested macaques (Macaca nigra). We combined behavioral data and genetic paternity analysis from 30 infants living in three wild groups in Tangkoko Reserve, Indonesia. Our results indicate that adult males and infants do not interact at random, but rather form preferential associations. The social factors with the highest influence on infant-initiated interactions were male rank and male association with the infant’s mother. While infants initiated affiliations with males more often in the absence of their mothers, adult males initiated more affiliations with infants when their mothers were present. Furthermore, males initiated affiliations more often when they were in the same group at the time the infant was conceived, when they held a high dominance rank, or when they had a close relationship with the mother. Interestingly, paternity did not affect male-infant affiliation despite being highly skewed in this species. Overall, our results suggest that adult males potentially associate with an infant to secure future mating with the mother. Infants are more likely to associate with a male to receive better support, suggesting a strategy to increase the chance of infant survival in a primate society with high infant mortality. Significance statement We explore social relationships between males and infants in a promiscuous primate, the wild crested macaque. Our novel approach addresses the nature of affiliations both from males’ and infants’ perspectives. The results show that males and infants form preferential associations. Male-female affiliation, but not paternity, was a significant predictor of interactions initiated both by males and infants. Males initiated more interactions towards infants when the mother was in proximity, while infants initiated more interactions in her absence. Finally, high-ranking males were more likely to initiate interactions towards infants. We demonstrated that paternity is not a good predictor of male-infant affiliations, even in a species with a high reproductive skew and a relatively high confidence of paternity. Our paper is one of the first to show that infants are active agents in establishing and maintaining preferential relationships with males. Electronic supplementary material The online version of this article (doi:10.1007/s00265-016-2116-0) contains supplementary material, which is available to authorized users.
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