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Wolfenson LI, Pereira JA, Ruzzante DE, Solé-Cava AM, McCracken GR, Gómez-Fernández MJ, Pereyra MD, Mirol PM. Southern marsh deer (Blastocerus dichotomus) populations assessed using Amplicon Sequencing on fecal samples. Sci Rep 2024; 14:16169. [PMID: 39003391 PMCID: PMC11246461 DOI: 10.1038/s41598-024-67062-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 07/08/2024] [Indexed: 07/15/2024] Open
Abstract
Populations in isolated and small fragments lose genetic variability very fast and are usually of conservation concern because they are at greater risk of local extinction. The largest native deer in South America, Blastocerus dichotomus (Illiger, 1815), is a Vulnerable species according to the IUCN categorization, which inhabits tropical and subtropical swampy areas. In Argentina, its presence has been restricted to four isolated fragments. Here we examine the genetic diversity and differentiation among three of them, including the three different patches that form the southernmost population, using 18 microsatellite markers genotyped by Amplicon Sequencing of DNA extracted from fecal samples. Genetic diversity was low (HE < 0.45) in all three populations studied. We found three genetic clusters compatible with the geographic location of the samples. We also found a metapopulation dynamics that involves the patches that make up the southernmost population, with evidence of a barrier to gene flow between two of them. Our results point to the creation of a corridor as a necessary and urgent management action. This is the first study, at the population level, employing microsatellite genotyping by Amplicon Sequencing with non-invasive samples in an endangered species.
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Affiliation(s)
- Laura I Wolfenson
- División de Mastozoología, Museo Argentino de Ciencias Naturales, "Bernardino Rivadavia", Av. Ángel Gallardo 470, Ciudad Autónoma de Buenos Aires, CP 1405, Buenos Airesss, Argentina.
| | - Javier A Pereira
- División de Mastozoología, Museo Argentino de Ciencias Naturales, "Bernardino Rivadavia", Av. Ángel Gallardo 470, Ciudad Autónoma de Buenos Aires, CP 1405, Buenos Airesss, Argentina
| | | | - Antonio M Solé-Cava
- Departamento de Genetica, Centro Nacional Para a Identificação Molecular do Pescado (CENIMP), Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - María J Gómez-Fernández
- División de Mastozoología, Museo Argentino de Ciencias Naturales, "Bernardino Rivadavia", Av. Ángel Gallardo 470, Ciudad Autónoma de Buenos Aires, CP 1405, Buenos Airesss, Argentina
| | - María D Pereyra
- División de Mastozoología, Museo Argentino de Ciencias Naturales, "Bernardino Rivadavia", Av. Ángel Gallardo 470, Ciudad Autónoma de Buenos Aires, CP 1405, Buenos Airesss, Argentina
| | - Patricia M Mirol
- División de Mastozoología, Museo Argentino de Ciencias Naturales, "Bernardino Rivadavia", Av. Ángel Gallardo 470, Ciudad Autónoma de Buenos Aires, CP 1405, Buenos Airesss, Argentina
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2
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Mitani JC, Abwe E, Campbell G, Giles-Vernick T, Goldberg T, McLennan MR, Preuschoft S, Supriatna J, Marshall AJ. Future coexistence with great apes will require major changes to policy and practice. Nat Hum Behav 2024; 8:632-643. [PMID: 38374442 DOI: 10.1038/s41562-024-01830-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 12/21/2023] [Indexed: 02/21/2024]
Abstract
The great apes-bonobos, chimpanzees, gorillas and orangutans-are critically threatened by human activities. We have destroyed their habitats, hunted them and transmitted fatal diseases to them. Yet we also conduct research on them, try to protect them and live alongside them. They are endangered, and time is running out. Here we outline what must be done to ensure that future generations continue to share this planet with great apes. We urge dialogue with those who live with great apes and interact with them often. We advocate conservation plans that acknowledge the realities of climate change, economic drivers and population growth. We encourage researchers to use technology to minimize risks to great apes. Our proposals will require substantial investment, and we identify ways to generate these funds. We conclude with a discussion of how field researchers might alter their work to protect our closest living relatives more effectively.
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Affiliation(s)
- John C Mitani
- Department of Anthropology, University of Michigan, Ann Arbor, MI, USA.
- Ngogo Chimpanzee Project, Phoenix, AZ, USA.
| | - Ekwoge Abwe
- San Diego Zoo Wildlife Alliance, Escondido, CA, USA
- Cameroon Biodiversity Association, Douala, Cameroon
| | | | - Tamara Giles-Vernick
- Anthropology and Ecology of Disease Emergence Unit, Institut Pasteur/Université Paris Cité, Paris, France
| | - Tony Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Matthew R McLennan
- Bulindi Chimpanzee and Community Project, Hoima, Uganda
- Faculty of Humanities and Social Sciences, Oxford Brookes University, Oxford, UK
| | | | - Jatna Supriatna
- Department of Biology, Faculty of Mathematics and Sciences, University of Indonesia, Depok, West Java, Indonesia
| | - Andrew J Marshall
- Department of Anthropology, University of Michigan, Ann Arbor, MI, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
- Program in the Environment, University of Michigan, Ann Arbor, MI, USA
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA
- Program in Computing for the Arts and Sciences, University of Michigan, Ann Arbor, MI, USA
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3
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Debetencourt B, Barry MM, Arandjelovic M, Stephens C, Maldonado N, Boesch C. Camera traps unveil demography, social structure, and home range of six unhabituated Western chimpanzee groups in the Moyen Bafing National Park, Guinea. Am J Primatol 2024; 86:e23578. [PMID: 37985945 DOI: 10.1002/ajp.23578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 11/02/2023] [Accepted: 11/05/2023] [Indexed: 11/22/2023]
Abstract
Precise estimates of population dynamics and social grouping patterns are required for effective conservation of wild animal populations. It is difficult to obtain such information on non-human great apes as they have slow reproductive rates. To gain a better understanding of demography in these populations, previous research has typically involved habituation\, a process that requires years. Here, we collected data continuously over year-long periods to monitor an unhabituated population of critically endangered Western chimpanzees (Pan troglodytes verus) in the Moyen Bafing National Park, Guinea. We used two arrays of 100 camera traps that were placed opportunistically in two distinct 100 km2 sites, named Bakoun and Koukoutamba. We identified 227 individuals in Bakoun and 207 in Koukoutamba through their unique facial features. Our camera trap data make clear that these individuals belong to six and seven closed groups, respectively. Six of those groups were near-completely sampled with an average minimum size of 46.8 individuals (range: 37-58), and a mean adult sex ratio of 1.32 (range: 0.93-2.10). We described the demographic composition of these groups and use Bayesian social network analysis to understand population structure. The network analyses suggested that the social bonds within the two populations were structured by sex homophily, with male chimpanzees being more or equally likely to be observed together than other adult associations. Through estimation of minimum convex polygons, we described the minimum home range for those groups. Compared to other chimpanzee groups living in a similar environment (mosaic savanna-forest), the Moyen Bafing region seems to host a high-density of chimpanzees with small home ranges for their group size. Our research highlights the potential of camera traps for studying the demographic composition of chimpanzee populations with high resolution and obtaining crucial information on several groups in a time-efficient and cost-effective way.
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Affiliation(s)
- Benjamin Debetencourt
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
- Wild Chimpanzee Foundation, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mamadou Moussa Barry
- Wild Chimpanzee Foundation, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mimi Arandjelovic
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - Colleen Stephens
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
| | - Nuria Maldonado
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
| | - Christophe Boesch
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
- Wild Chimpanzee Foundation, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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4
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Rosenblatt E, Creel S, Gieder K, Murdoch J, Donovan T. Advances in wildlife abundance estimation using pedigree reconstruction. Ecol Evol 2023; 13:e10650. [PMID: 37869434 PMCID: PMC10585057 DOI: 10.1002/ece3.10650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 10/24/2023] Open
Abstract
The conservation and management of wildlife populations, particularly for threatened and endangered species are greatly aided with abundance, growth rate, and density measures. Traditional methods of estimating abundance and related metrics represent trade-offs in effort and precision of estimates. Pedigree reconstruction is an emerging, attractive alternate approach because its use of one-time, noninvasive sampling of individuals to infer the existence of unsampled individuals. However, advances in pedigree reconstruction could improve its utility, including forming a measure of precision for the method, establishing required spatial sampling effort for accurate estimates, ascertaining the spatial extent of abundance estimates derived from pedigree reconstruction, and assessing how population density affects the estimator's performance. Using established relationships for a stochastic, spatially explicit simulated moose (Alces americanus) population, pedigree reconstruction provided accurate estimates of the adult moose population size and trend. Novel bootstrapped confidence intervals performed as expected with intensive sampling but underperformed with moderate sampling efforts that could produce abundance estimates with low bias. Adult population estimates more closely reflected the total number of adults in the extant population, rather than number of adults inhabiting the area where sampling occurred. Increasing sampling effort, measured as the proportion of individuals sampled and as the proportion of a hypothetical study area, yielded similar asymptotic patterns over time. Simulations indicated a positive relationship between animal density and sampling effort required for unbiased estimates. These results indicate that pedigree reconstruction can produce accurate abundance estimates and may be particularly valuable for surveying smaller areas and low-density populations.
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Affiliation(s)
- Elias Rosenblatt
- Vermont Cooperative Fish and Wildlife Research Unit, Rubenstein School of Environment and Natural ResourcesUniversity of VermontBurlingtonVermontUSA
| | - Scott Creel
- Department of EcologyMontana State UniversityBozemanMontanaUSA
| | | | - James Murdoch
- Wildlife and Fisheries Biology Program, Rubenstein School of Environment and Natural ResourcesUniversity of VermontBurlingtonVermontUSA
| | - Therese Donovan
- U.S. Geological Survey, Vermont Cooperative Fish and Wildlife Research Unit, Rubenstein School of Environment and Natural ResourcesUniversity of VermontBurlingtonVermontUSA
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5
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Robbins MM. Reflections on connections. Primates 2023; 64:191-197. [PMID: 36867278 PMCID: PMC9982802 DOI: 10.1007/s10329-023-01059-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 02/18/2023] [Indexed: 03/04/2023]
Affiliation(s)
- Martha M Robbins
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leizpig, Germany.
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6
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Howe EJ, Potter D, Beauclerc KB, Jackson KE, Northrup JM. Estimating animal abundance at multiple scales by spatially explicit capture-recapture. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e2638. [PMID: 35441452 PMCID: PMC9788300 DOI: 10.1002/eap.2638] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Information about how animal abundance varies across landscapes is needed to inform management action but is costly and time-consuming to obtain; surveys of a single population distributed over a large area can take years to complete. Surveys employing small, spatially replicated sampling units improve efficiency, but statistical estimators rely on assumptions that constrain survey design or become less reasonable as larger areas are sampled. Efficient methods that avoid assumptions about similarity of detectability or density among replicates are therefore appealing. Using simulations and data from >3500 black bears sampled on 73 independent study areas in Ontario, Canada, we (1) quantified bias induced by unmodeled spatial heterogeneity in detectability and density; (2) evaluated novel, design-based estimators of average density across replicate study areas; and (3) evaluated two estimators of the variance of average density across study areas: an analytic estimator that assumed an underlying homogeneous spatial Poisson point process for the distribution of animals' activity centers, and an empirical estimator of variance across study areas. In simulations where detectability varied in space, assuming spatially constant detectability yielded density estimates that were negatively biased by 20% to 30%; estimating local detectability and density from local data and treating study areas as independent, equal replicates when estimating average density across study areas using the design-based estimator yielded unbiased estimates at local and landscape scales. Similarly, detectability of black bears varied among study areas and estimates of bear density at landscape scales were higher when no information was shared across study areas when estimating detectability. This approach also maximized precision (relative SEs of estimates of average black bear density ranged from 7% to 18%) and computational efficiency. In simulations, the analytic variance estimator was robust to threefold variation in local densities but the empirical estimator performed poorly. Conducting multiple, similar SECR surveys and treating them as independent replicates during analyses allowed us to efficiently estimate density at multiple scales and extents while avoiding biases caused by pooling spatially heterogeneous data. This approach enables researchers to address a wide range of ecological or management-related questions and is applicable with most types of SECR data.
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Affiliation(s)
- Eric J. Howe
- Wildlife Research and Monitoring SectionOntario Ministry of Northern Development, Mines, Natural Resources and ForestryPeterboroughOntarioCanada
| | - Derek Potter
- Wildlife Research and Monitoring SectionOntario Ministry of Northern Development, Mines, Natural Resources and ForestryPeterboroughOntarioCanada
| | - Kaela B. Beauclerc
- Wildlife Research and Monitoring SectionOntario Ministry of Northern Development, Mines, Natural Resources and ForestryPeterboroughOntarioCanada
| | - Katelyn E. Jackson
- Wildlife Research and Monitoring SectionOntario Ministry of Northern Development, Mines, Natural Resources and ForestryPeterboroughOntarioCanada
| | - Joseph M. Northrup
- Wildlife Research and Monitoring SectionOntario Ministry of Northern Development, Mines, Natural Resources and ForestryPeterboroughOntarioCanada
- Environmental and Life Sciences Graduate ProgramTrent UniversityPeterboroughOntarioCanada
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7
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Faecal DNA-based genetic survey of a relict Eurasian otter (Lutra lutra) population (Sila Massif, S Italy). CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01286-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractFaecal DNA-based genetic analysis is a suitable tool for assessing both population size and genetic diversity of threatened and elusive species. We applied microsatellite analysis and mtDNA sequencing for investigating the southernmost Italian (Sila Massif, Calabria Region) population of the Eurasian otter (Lutra lutra). This relict population, filed as extinct in the mid-1980s, is currently expanding but still quite isolated. On the two main rivers hosting otters permanently since 2014, we collected 47 spraints, out of which 24 (51.1%) were successfully genotyped (on average 2.0 alleles per locus). Thirteen individuals were identified: seven females and three males (sex identification success of 76.9%). Population size was assessed as 16 individuals (13–22), corresponding to a density of 0.15 (0.13–0.21) ind/km. Successfully amplified mtDNA samples (N = 16) confirmed the occurrence of a haplotype—H10—which had been previously reported only for Southern Italy, bringing new evidence of the unicity of the Italian otter population. Although density values complied with those reported for the core area of otter Italian range, the small size and genetic isolation of this population require special attention. To assist the ongoing re-colonisation of the Sila Massif, habitat management should aim to enhance fish availability and connectivity with the core area.
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8
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Marrotte RR, Howe EJ, Beauclerc KB, Potter D, Northrup JM. Explaining detection heterogeneity with finite mixture and non-Euclidean movement in spatially explicit capture-recapture models. PeerJ 2022; 10:e13490. [PMID: 35694380 PMCID: PMC9186326 DOI: 10.7717/peerj.13490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/03/2022] [Indexed: 01/17/2023] Open
Abstract
Landscape structure affects animal movement. Differences between landscapes may induce heterogeneity in home range size and movement rates among individuals within a population. These types of heterogeneity can cause bias when estimating population size or density and are seldom considered during analyses. Individual heterogeneity, attributable to unknown or unobserved covariates, is often modelled using latent mixture distributions, but these are demanding of data, and abundance estimates are sensitive to the parameters of the mixture distribution. A recent extension of spatially explicit capture-recapture models allows landscape structure to be modelled explicitly by incorporating landscape connectivity using non-Euclidean least-cost paths, improving inference, especially in highly structured (riparian & mountainous) landscapes. Our objective was to investigate whether these novel models could improve inference about black bear (Ursus americanus) density. We fit spatially explicit capture-recapture models with standard and complex structures to black bear data from 51 separate study areas. We found that non-Euclidean models were supported in over half of our study areas. Associated density estimates were higher and less precise than those from simple models and only slightly more precise than those from finite mixture models. Estimates were sensitive to the scale (pixel resolution) at which least-cost paths were calculated, but there was no consistent pattern across covariates or resolutions. Our results indicate that negative bias associated with ignoring heterogeneity is potentially severe. However, the most popular method for dealing with this heterogeneity (finite mixtures) yielded potentially unreliable point estimates of abundance that may not be comparable across surveys, even in data sets with 136-350 total detections, 3-5 detections per individual, 97-283 recaptures, and 80-254 spatial recaptures. In these same study areas with high sample sizes, we expected that landscape features would not severely constrain animal movements and modelling non-Euclidian distance would not consistently improve inference. Our results suggest caution in applying non-Euclidean SCR models when there is no clear landscape covariate that is known to strongly influence the movement of the focal species, and in applying finite mixture models except when abundant data are available.
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Affiliation(s)
- Robby R. Marrotte
- Wildlife Research & Monitoring Section, Ministry of Northern Development, Mines, Natural Resources and Forestry, Peterborough, Ontario, Canada
| | - Eric J. Howe
- Wildlife Research & Monitoring Section, Ministry of Northern Development, Mines, Natural Resources and Forestry, Peterborough, Ontario, Canada
| | - Kaela B. Beauclerc
- Wildlife Research & Monitoring Section, Ministry of Northern Development, Mines, Natural Resources and Forestry, Peterborough, Ontario, Canada
| | - Derek Potter
- Wildlife Research & Monitoring Section, Ministry of Northern Development, Mines, Natural Resources and Forestry, Peterborough, Ontario, Canada
| | - Joseph M. Northrup
- Wildlife Research & Monitoring Section, Ministry of Northern Development, Mines, Natural Resources and Forestry, Peterborough, Ontario, Canada,Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
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9
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Janiak MC, Silva FE, Beck RMD, de Vries D, Kuderna LFK, Torosin NS, Melin AD, Marquès-Bonet T, Goodhead IB, Messias M, da Silva MNF, Sampaio I, Farias IP, Rossi R, de Melo FR, Valsecchi J, Hrbek T, Boubli JP. 205 newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates. Mol Ecol 2022; 31:3888-3902. [PMID: 35638312 PMCID: PMC9546496 DOI: 10.1111/mec.16554] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/06/2022] [Accepted: 05/20/2022] [Indexed: 12/02/2022]
Abstract
Mitochondrial DNA remains a cornerstone for molecular ecology, especially for study species from which high‐quality tissue samples cannot be easily obtained. Methods using mitochondrial markers are usually reliant on reference databases, but these are often incomplete. Furthermore, available mitochondrial genomes often lack crucial metadata, such as sampling location, limiting their utility for many analyses. Here, we assembled 205 new mitochondrial genomes for platyrrhine primates, most from the Amazon and with known sampling locations. We present a dated mitogenomic phylogeny based on these samples along with additional published platyrrhine mitogenomes, and use this to assess support for the long‐standing riverine barrier hypothesis (RBH), which proposes that river formation was a major driver of speciation in Amazonian primates. Along the Amazon, Negro, and Madeira rivers, we found mixed support for the RBH. While we identified divergences that coincide with a river barrier, only some occur synchronously and also overlap with the proposed dates of river formation. The most compelling evidence is for the Amazon river potentially driving speciation within bearded saki monkeys (Chiropotes spp.) and within the smallest extant platyrrhines, the marmosets and tamarins. However, we also found that even large rivers do not appear to be barriers for some primates, including howler monkeys (Alouatta spp.), uakaris (Cacajao spp.), sakis (Pithecia spp.), and robust capuchins (Sapajus spp.). Our results support a more nuanced, clade‐specific effect of riverine barriers and suggest that other evolutionary mechanisms, besides the RBH and allopatric speciation, may have played an important role in the diversification of platyrrhines.
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Affiliation(s)
- Mareike C Janiak
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom
| | - Felipe E Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Brazil.,Department of Evolutionary Biology and Ecology, Université Libre de Bruxelles, Belgium
| | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom
| | - Lukas F K Kuderna
- Ilumina Inc., Hayward, CA, USA.,Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
| | - Nicole S Torosin
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Amanda D Melin
- Department of Anthropology & Archaeology and Department of Medical Genetics, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute, Calgary, AB, Canada
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), 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, Edifici ICTA-ICP, Cerdanyola del Vallès, Barcelona, Spain
| | - Ian B Goodhead
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom
| | - Mariluce Messias
- Department of Biology, Universidade Federal de Rondônia, Porto Velho, Brazil
| | - Maria N F da Silva
- Coleção de Mamíferos, Instituto Nacional de Pesquisas da Amazônia, Brazil
| | | | - Izeni P Farias
- Laboratory of Evolution and Animal Genetics, Universidade Federal do Amazonas, Brazil
| | - Rogerio Rossi
- Instituto de Biociências, Universidade Federal do Mato Grosso, Brazil
| | - Fabiano R de Melo
- Department of Forestry Engineering, Universidade Federal de Viçosa, Brazil
| | - João Valsecchi
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Brazil
| | - Tomas Hrbek
- Department of Biology, Trinity University, San Antonio, TX, USA
| | - Jean P Boubli
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom.,Coleção de Mamíferos, Instituto Nacional de Pesquisas da Amazônia, Brazil
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10
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Städele V, Arandjelovic M, Nixon S, Bergl RA, Bradley BJ, Breuer T, Cameron KN, Guschanski K, Head J, Kyungu JC, Masi S, Morgan DB, Reed P, Robbins MM, Sanz C, Smith V, Stokes EJ, Thalmann O, Todd A, Vigilant L. The complex Y-chromosomal history of gorillas. Am J Primatol 2022; 84:e23363. [PMID: 35041228 DOI: 10.1002/ajp.23363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 12/27/2021] [Accepted: 01/08/2022] [Indexed: 11/10/2022]
Abstract
Studies of the evolutionary relationships among gorilla populations using autosomal and mitochondrial sequences suggest that male-mediated gene flow may have been important in the past, but data on the Y-chromosomal relationships among the gorilla subspecies are limited. Here, we genotyped blood and noninvasively collected fecal samples from 12 captives and 257 wild male gorillas of known origin representing all four subspecies (Gorilla gorilla gorilla, G. g. diehli, G. beringei beringei, and G. b. graueri) at 10 Y-linked microsatellite loci resulting in 102 unique Y-haplotypes for 224 individuals. We found that western lowland gorilla (G. g. gorilla) haplotypes were consistently more diverse than any other subspecies for all measures of diversity and comprised several genetically distinct groups. However, these did not correspond to geographical proximity and some closely related haplotypes were found several hundred kilometers apart. Similarly, our broad sampling of eastern gorillas revealed that mountain (G. b. beringei) and Grauer's (G. b. graueri) gorilla Y-chromosomal haplotypes did not form distinct clusters. These observations suggest structure in the ancestral population with subsequent mixing of differentiated haplotypes by male dispersal for western lowland gorillas, and postisolation migration or incomplete lineage sorting due to short divergence times for eastern gorillas.
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Affiliation(s)
- Veronika Städele
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA.,Institute of Human Origins, Arizona State University, Tempe, Arizona, USA.,Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mimi Arandjelovic
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Evolutionary and Anthropocene Ecology, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Stuart Nixon
- Field Programmes and Conservation Science, Chester Zoo, North of England Zoological Society, Chester, UK
| | | | - Brenda J Bradley
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, District of Columbia, USA
| | - Thomas Breuer
- WWF Germany, Berlin, Germany.,Mbeli Bai Study, Wildlife Conservation Society, Congo Program, Brazzaville, Republic of the Congo
| | | | - Katerina Guschanski
- Department of Ecology and Genetics/Animal Ecology, Uppsala University, Uppsala, Sweden.,Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Josephine Head
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Shelly Masi
- Eco-Anthropologie, Muséum National d'Histoire Naturelle, CNRS, Musée de l'Homme, Université de Paris, Paris, France
| | - David B Morgan
- Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, Chicago, Illinois, USA
| | | | - Martha M Robbins
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Crickette Sanz
- Department of Anthropology, Washington University in Saint Louis, Saint Louis, Missouri, USA.,Wildlife Conservation Society, Congo Program, Brazzaville, Republic of the Congo
| | | | - Emma J Stokes
- Wildlife Conservation Society, Global Conservation Program, New York City, New York, USA
| | - Olaf Thalmann
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Linda Vigilant
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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11
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Vigués J, Menci S, Wilkinson C, Le Vaillant M, Angerbjörn A, Norén K. A beacon of dung: using lemming (Lemmus lemmus) winter nests and DNA analysis of faeces to further understand predator–prey dynamics in Northern Sweden. Polar Biol 2021. [DOI: 10.1007/s00300-021-02958-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Abstract The hypothesis that predation is the cause of the regular small rodent population oscillations observed in boreal and Arctic regions has long been debated. Within this hypothesis, it is proposed that the most likely predators to cause these destabilizing effects are sedentary specialists, with small mustelids being possible candidates. One such case would be the highly specialized least weasel (Mustela nivalis) driving the Norwegian lemming (Lemmus lemmus) cycle in Fennoscandia. These predators are often elusive and therefore distribution data can only be based on field signs, which is problematic when various mustelid species are sympatric, such as weasels and stoats (Mustela erminea). Here we present the results of using mustelid faeces in predated winter lemming nests to correctly identify the predator and thus discern which species exerts the strongest predation pressure on lemming winter populations. Samples were obtained during different phases in the lemming cycle, spanning 6 years, to account for different prey densities. Faecal mitochondrial DNA extraction and amplification of a 400-bp fragment was successful in 92/114 samples (81%); the sequencing of these samples proved that most predation occurrences (83%) could be attributed to the least weasel. These findings support the hypothesis that weasels in particular show high specificity in predation and could therefore be candidates to driving the lemming cycle in this area. We conclude that DNA analysis of faecal remains around predated nests can be a useful tool for further investigations concerning predator–prey interactions in the tundra.
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Abstract
AbstractObserving and quantifying primate behavior in the wild is challenging. Human presence affects primate behavior and habituation of new, especially terrestrial, individuals is a time-intensive process that carries with it ethical and health concerns, especially during the recent pandemic when primates are at even greater risk than usual. As a result, wildlife researchers, including primatologists, have increasingly turned to new technologies to answer questions and provide important data related to primate conservation. Tools and methods should be chosen carefully to maximize and improve the data that will be used to answer the research questions. We review here the role of four indirect methods—camera traps, acoustic monitoring, drones, and portable field labs—and improvements in machine learning that offer rapid, reliable means of combing through large datasets that these methods generate. We describe key applications and limitations of each tool in primate conservation, and where we anticipate primate conservation technology moving forward in the coming years.
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FISH and Chimps: Insights into Frequency and Distribution of Sperm Aneuploidy in Chimpanzees ( Pan troglodytes). Int J Mol Sci 2021; 22:ijms221910383. [PMID: 34638739 PMCID: PMC8509033 DOI: 10.3390/ijms221910383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 12/03/2022] Open
Abstract
Numerical chromosomal aberrations in sperm are considered to be a major factor in infertility, early pregnancy loss and syndromes with developmental and cognitive disabilities in mammals, including primates. Despite numerous studies in human and farm animals, the incidence and importance of sperm aneuploidies in non-human primate remains mostly undetermined. Here we investigated the incidence and distribution of sperm aneuploidy in chimpanzees (Pan troglodytes), the species closest to human. We identify evolutionary conserved DNA sequences in human and chimpanzee and selected homologous sub-telomeric regions for all chromosomes to build custom probes and perform sperm-FISH analysis on more than 10,000 sperm nuclei per chromosome. Chimpanzee mean autosomal disomy rate was 0.057 ± 0.02%, gonosomes disomy rate was 0.198% and the total disomy rate was 1.497%. The proportion of X or Y gametes was respectively 49.94% and 50.06% for a ratio of 1.002 and diploidy rate was 0.053%. Our data provide for the first time an overview of aneuploidy in non-human primate sperm and shed new insights into the issues of aneuploidy origins and mechanisms.
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Martínez-Íñigo L, Baas P, Klein H, Pika S, Deschner T. Home range size in central chimpanzees (Pan troglodytes troglodytes) from Loango National Park, Gabon. Primates 2021; 62:723-734. [PMID: 34218403 PMCID: PMC8410711 DOI: 10.1007/s10329-021-00927-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 06/21/2021] [Indexed: 11/25/2022]
Abstract
Ranging behavior has been studied extensively in eastern (Pan troglodytes schweinfurthii) and western (P. t. verus) chimpanzees, but relatively little is known regarding home ranges of the other two subspecies (P. t. ellioti; P. t. troglodytes). In this study, we determined the home range size and space use of a habituated community (Rekambo) of central chimpanzees living in a habitat mosaic in Loango National Park, Gabon. Data on travel routes were collected during follows between January 2017 and April 2019 (N = 670,616 relocations, collected over 640 days and 5690 h of observation). We used three methods for calculating home range size (minimum convex polygon, kernel density estimation, and biased random bridges). We compare our estimates to those obtained from prior genetic and camera trap studies of the Rekambo community and contrast them with estimates from other chimpanzee communities of the four chimpanzee subspecies. Depending on the methodology used, the home range size of the Rekambo community ranged between 27.64 and 59.03 km2. The location of the center of the home range remained relatively stable over the last decade, while the overall size decreased. The Rekambo home range is, therefore, one of the largest documented so far for chimpanzees outside savannah-woodland habitats. We discuss several explanations, including the presence of savannah, interspecies competition, and intercommunity interactions.
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Affiliation(s)
- Laura Martínez-Íñigo
- Interim Group Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany. .,Wild Chimpanzee Foundation - Guinean Representation, Commune de Dixinn, BP1487P, Conakry, Guinea.
| | - Pauline Baas
- Interim Group Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Harmonie Klein
- Interim Group Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Simone Pika
- Institute of Cognitive Science, Comparative BioCognition, Osnabrück University, Artilleriestrasse 34, 49076, Osnabrück, Germany
| | - Tobias Deschner
- Interim Group Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
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15
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Ibouroi MT, Arnal V, Cheha A, Dhurham SAO, Montgelard C, Besnard A. Noninvasive genetic sampling for flying foxes: a valuable method for monitoring demographic parameters. Ecosphere 2021. [DOI: 10.1002/ecs2.3327] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Mohamed Thani Ibouroi
- Centre for Functional and Evolutionary Ecology (CEFE UMR 5175) EPHE PSL Research University, CNRS University of Montpellier, SupAgro, IRD, INRA Montpellier F‐34293 France
- Sustainable Development Task Force (GIDD) Moroni Hamramba Comores
| | - Véronique Arnal
- Centre for Functional and Evolutionary Ecology (CEFE UMR 5175) EPHE PSL Research University, CNRS University of Montpellier, SupAgro, IRD, INRA Montpellier F‐34293 France
| | - Ali Cheha
- Sustainable Development Task Force (GIDD) Moroni Hamramba Comores
| | | | - Claudine Montgelard
- Centre for Functional and Evolutionary Ecology (CEFE UMR 5175) EPHE PSL Research University, CNRS University of Montpellier, SupAgro, IRD, INRA Montpellier F‐34293 France
| | - Aurélien Besnard
- Centre for Functional and Evolutionary Ecology (CEFE UMR 5175) EPHE PSL Research University, CNRS University of Montpellier, SupAgro, IRD, INRA Montpellier F‐34293 France
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16
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García NC, Robinson WD. Current and Forthcoming Approaches for Benchmarking Genetic and Genomic Diversity. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.622603] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The current attrition of biodiversity extends beyond loss of species and unique populations to steady loss of a vast genomic diversity that remains largely undescribed. Yet the accelerating development of new techniques allows us to survey entire genomes ever faster and cheaper, to obtain robust samples from a diversity of sources including degraded DNA and residual DNA in the environment, and to address conservation efforts in new and innovative ways. Here we review recent studies that highlight the importance of carefully considering where to prioritize collection of genetic samples (e.g., organisms in rapidly changing landscapes or along edges of geographic ranges) and what samples to collect and archive (e.g., from individuals of little-known subspecies or populations, even of species not currently considered endangered). Those decisions will provide the sample infrastructure to detect the disappearance of certain genotypes or gene complexes, increases in inbreeding levels, and loss of genomic diversity as environmental conditions change. Obtaining samples from currently endangered, protected, and rare species can be particularly difficult, thus we also focus on studies that use new, non-invasive ways of obtaining genomic samples and analyzing them in these cases where other sampling options are highly constrained. Finally, biological collections archiving such samples face an inherent contradiction: their main goal is to preserve biological material in good shape so it can be used for scientific research for centuries to come, yet the technologies that can make use of such materials are advancing faster than collections can change their standardized practices. Thus, we also discuss current and potential new practices in biological collections that might bolster their usefulness for future biodiversity conservation research.
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Brandt JR, Saidah SH, Zhao K, Ishida Y, Apriyana I, Ryder OA, Ramono W, Sudoyo H, Suryadi H, Van Coeverden de Groot PJ, Roca AL. Characterization of 29 polymorphic microsatellite markers developed by genomic screening of Sumatran rhinoceros (Dicerorhinus sumatrensis). BMC Res Notes 2021; 14:119. [PMID: 33771210 PMCID: PMC7995689 DOI: 10.1186/s13104-021-05522-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 03/12/2021] [Indexed: 11/23/2022] Open
Abstract
Objective The Sumatran rhinoceros is critically endangered, with fewer than 100 individuals surviving across its current range. Accurate census estimates of the remaining populations are essential for development and implementation of conservation plans. In order to enable molecular censusing, we here develop microsatellite markers with amplicon sizes of short length, appropriate for non-invasive fecal sampling. Results Due to limited sample quantity and potential lack of genome-wide diversity, Illumina sequence reads were generated from two Sumatran rhinoceros samples. Genomic screening identified reads with short tandem repeats and loci that were polymorphic within the dataset. Twenty-nine novel polymorphic microsatellite markers were characterized (A = 2.4; HO = 0.30). These were sufficient to distinguish among individuals (PID < 0.0001), and to distinguish among siblings (PID(sib) < 0.0001). Among rhinos in Indonesia, almost all markers were established as polymorphic and effective for genotyping DNA from fecal samples. Notably, the markers amplified and displayed microsatellite polymorphisms using DNA extracted from 11 fecal samples collected non-invasively from wild Sumatran rhinoceros. These microsatellite markers provide an important resource for a census and genetic studies of wild Sumatran rhinos. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-021-05522-x.
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Affiliation(s)
- Jessica R Brandt
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.,Department of Biology, Marian University, Fond du Lac, WI, 54935, USA
| | - Sinta H Saidah
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jl. Diponegoro No. 69, Jakarta, 10430, Indonesia
| | - Kai Zhao
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yasuko Ishida
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Isabella Apriyana
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jl. Diponegoro No. 69, Jakarta, 10430, Indonesia
| | - Oliver A Ryder
- Institute of Conservation Research, San Diego Zoo Global, Escondido, CA, 92027, USA
| | - Widodo Ramono
- Rhino Foundation of Indonesia, Jl. Bima IV/10, Bogor, 16153, Indonesia
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jl. Diponegoro No. 69, Jakarta, 10430, Indonesia
| | - Helena Suryadi
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jl. Diponegoro No. 69, Jakarta, 10430, Indonesia
| | | | - Alfred L Roca
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA. .,Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
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18
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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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19
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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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20
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Schenker L, Bollmann K, Rehnus M, Brodbeck S, Gugerli F. Hare's affairs: Lessons learnt from a noninvasive genetic monitoring for tracking mountain hare individuals. Ecol Evol 2020; 10:10150-10166. [PMID: 33005371 PMCID: PMC7520196 DOI: 10.1002/ece3.6676] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 06/29/2020] [Accepted: 07/20/2020] [Indexed: 01/31/2023] Open
Abstract
Systematic monitoring of individuals and their abundance over time has become an important tool to provide information for conservation. For genetic monitoring studies, noninvasive sampling has emerged as a valuable approach, particularly so for elusive or rare animals. Here, we present the 5-year results of an ongoing noninvasive genetic monitoring of mountain hares (Lepus timidus) in a protected area in the Swiss Alps. We used nuclear microsatellites and a sex marker to identify individuals and assign species to noninvasively collected feces samples. Through including a marker for sex identification, we were able to assess sex ratio changes and sex-specific demographic parameters over time. Male abundance in the area showed high fluctuations and apparent survival for males was lower than for females. Generally, males and females showed only little temporary migration into and out of the study area. Additionally, using genotyped tissue samples from mountain hares, European hares (Lepus europaeus) and their hybrids, we were able to provide evidence for the first occurrence of a European hare in the study area at an elevation of 2,300 m a.s.l. in spring 2016. For future monitoring studies, we suggest to include complementary analysis methods to reliably infer species identities of the individuals analyzed and, thus, not only monitor mountain hare individual abundance, but also assess the potential threats given through competitive exclusion by and hybridization with the European hare.
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Affiliation(s)
- Laura Schenker
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | - Kurt Bollmann
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | - Maik Rehnus
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | - Sabine Brodbeck
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | - Felix Gugerli
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
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21
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Three decades of Philippine nonhuman primate studies: research gaps and opportunities for Philippine primatology. Primates 2020; 62:233-239. [PMID: 32681352 DOI: 10.1007/s10329-020-00847-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 07/09/2020] [Indexed: 10/23/2022]
Abstract
The Philippines is considered a megadiverse country. However, there are few published studies on its nonhuman primate (NHP) species (Carlito syrichta, Macaca fascicularis, and Nycticebus menagensis). Understanding the nature and extent of existing NHP research in the Philippines would help us to determine research gaps and opportunities. Thus, studies on NHPs of Philippine origin were retrieved from online databases including Google Scholar, ResearchGate, Primate Lit, the Integrated Taxonomic Information System (ITIS), and relevant authors. Of a total of 107 studies on Philippine NHP from 1989 to 2019, most focused on Philippine long-tailed macaque (52.78%), and Philippine tarsier (42.59%), with far fewer on Philippine slow loris (4.63%). Fewer studies were based on fieldwork (26.17%); more were based on research on captive animals or that undertaken in the laboratory (34.58%), or used only existing specimens or data (33.64%). Studies on wild NHPs were mostly conducted in Bohol Island. In terms of the type of research, studies on diseases (38.60%) were the most prevalent for macaques; ecological studies (23.91%) for tarsiers; evolutionary, taxonomic, and systematic studies (40%), and ecological and natural history studies (40%) for lorises. Philippine researchers and collaborations with foreign researchers contributed fewer studies (43.93%) than foreign-only researchers (56.07%). In conclusion, although research on Philippine NHPs is increasing, there is a bias with regards to the species studied, the type of research, and study location. Conservation-driven studies are also lacking. These gaps offer opportunities for further research to identify threats to the survival of NHPs in the Philippines, and for the development of plans and effective strategies for their conservation.
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Brand CM, Johnson MB, Parker LD, Maldonado JE, Korte L, Vanthomme H, Alonso A, Ruiz-Lopez MJ, Wells CP, Ting N. Abundance, density, and social structure of African forest elephants (Loxodonta cyclotis) in a human-modified landscape in southwestern Gabon. PLoS One 2020; 15:e0231832. [PMID: 32348354 PMCID: PMC7190099 DOI: 10.1371/journal.pone.0231832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/01/2020] [Indexed: 11/28/2022] Open
Abstract
Population monitoring is critical to effective conservation, but forest living taxa can be difficult to directly observe. This has been true of African forest elephants (Loxodonta cyclotis), for which we have limited information regarding population size and social behavior despite their threatened conservation status. In this study, we estimated demographic parameters using genetic capture-recapture of forest elephants in the southern Industrial Corridor of the Gamba Complex of Protected Areas in southwestern Gabon, which is considered a global stronghold for forest elephants. Additionally, we examined social networks, predicting that we would find matrilineal structure seen in both savanna and forest elephants. Given 95% confidence intervals, we estimate population size in the sampled area to be between 754 and 1,502 individuals and our best density estimate ranges from 0.47 to 0.80 elephants per km2. When extrapolated across the entire Industrial Corridor, this estimate suggests an elephant population size of 3,033 to 6,043 based on abundance or 1,684 to 2,832 based on density, approximately 40–80% smaller than previously suggested. Our social network analysis revealed approximately half of network components included females with different mitochondrial haplotypes suggesting a wider range of variation in forest elephant sociality than previously thought. This study emphasizes the threatened status of forest elephants and demonstrates the need to further refine baseline estimates of population size and knowledge on social behavior in this taxon, both of which will aid in determining how population dynamics in this keystone species may be changing through time in relation to increasing conservation threats.
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Affiliation(s)
- Colin M. Brand
- Department of Anthropology, University of Oregon, Eugene, OR, United States of America
| | - Mireille B. Johnson
- Gabon Biodiversity Program, Smithsonian Conservation Biology Institute, Gamba, Gabon
| | - Lillian D. Parker
- Department of Biosciences, School of Systems Biology, George Mason University, Fairfax, VA, United States of America
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, United States of America
| | - Jesús E. Maldonado
- Department of Biosciences, School of Systems Biology, George Mason University, Fairfax, VA, United States of America
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, United States of America
| | - Lisa Korte
- Gabon Biodiversity Program, Smithsonian Conservation Biology Institute, Gamba, Gabon
| | - Hadrien Vanthomme
- Center for Conservation and Sustainability, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, United States of America
| | - Alfonso Alonso
- Center for Conservation and Sustainability, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, United States of America
| | | | - Caitlin P. Wells
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO, United States of America
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States of America
| | - Nelson Ting
- Department of Anthropology, University of Oregon, Eugene, OR, United States of America
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States of America
- * E-mail:
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Mitelberg A, Vandergast AG, Nussear KE, Dutcher K, Esque TC. Development of a Genotyping Protocol for Mojave Desert Tortoise Scat. CHELONIAN CONSERVATION AND BIOLOGY 2019. [DOI: 10.2744/ccb-1394.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Anna Mitelberg
- US Geological Survey, Western Ecological Research Center, 3020 State University Drive, Modoc Hall, Room 4004, Sacramento, California 95819 USA [; ; ]
| | - Amy G. Vandergast
- US Geological Survey, Western Ecological Research Center, 3020 State University Drive, Modoc Hall, Room 4004, Sacramento, California 95819 USA [; ; ]
| | - Ken E. Nussear
- University of Nevada, Department of Geography, Mackay Science Hall, 1664 North Virginia Street, Reno, Nevada 89557 USA [; ]
| | - Kirsten Dutcher
- University of Nevada, Department of Geography, Mackay Science Hall, 1664 North Virginia Street, Reno, Nevada 89557 USA [; ]
| | - Todd C. Esque
- US Geological Survey, Western Ecological Research Center, 3020 State University Drive, Modoc Hall, Room 4004, Sacramento, California 95819 USA [; ; ]
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Hagemann L, Arandjelovic M, Robbins MM, Deschner T, Lewis M, Froese G, Boesch C, Vigilant L. Long-term inference of population size and habitat use in a socially dynamic population of wild western lowland gorillas. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01209-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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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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How to spot a black-footed cat? Successful application of cross-species markers to identify captive-bred individuals from non-invasive genetic sampling. MAMMAL RES 2018. [DOI: 10.1007/s13364-018-0407-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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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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Sabino-Marques H, Ferreira CM, Paupério J, Costa P, Barbosa S, Encarnação C, Alpizar-Jara R, Alves PC, Searle JB, Mira A, Beja P, Pita R. Combining genetic non-invasive sampling with spatially explicit capture-recapture models for density estimation of a patchily distributed small mammal. EUR J WILDLIFE RES 2018. [DOI: 10.1007/s10344-018-1206-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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