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      Unsustainable anthropogenic mortality disrupts natal dispersal and promotes inbreeding in leopards

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          Abstract

          Anthropogenic mortality of wildlife is typically inferred from measures of the absolute decline in population numbers. However, increasing evidence suggests that indirect demographic effects including changes to the age, sex, and social structure of populations, as well as the behavior of survivors, can profoundly impact population health and viability. Specifically, anthropogenic mortality of wildlife (especially when unsustainable) and fragmentation of the spatial distribution of individuals (home‐ranges) could disrupt natal dispersal mechanisms, with long‐term consequences to genetic structure, by compromising outbreeding behavior and gene flow. We investigate this threat in African leopards ( Panthera pardus pardus), a polygynous felid with male‐biased natal dispersal. Using a combination of spatial (home‐range) and genetic (21 polymorphic microsatellites) data from 142 adult leopards, we contrast the structure of two South African populations with markedly different histories of anthropogenically linked mortality. Home‐range overlap, parentage assignment, and spatio‐genetic autocorrelation together show that historical exploitation of leopards in a recovering protected area has disrupted and reduced subadult male dispersal, thereby facilitating opportunistic male natal philopatry, with sons establishing territories closer to their mothers and sisters. The resultant kin‐clustering in males of this historically exploited population is comparable to that of females in a well‐protected reserve and has ultimately led to localized inbreeding. Our findings demonstrate novel evidence directly linking unsustainable anthropogenic mortality to inbreeding through disrupted dispersal in a large, solitary felid and expose the genetic consequences underlying this behavioral change. We therefore emphasize the importance of managing and mitigating the effects of unsustainable exploitation on local populations and increasing habitat fragmentation between contiguous protected areas by promoting in situ recovery and providing corridors of suitable habitat that maintain genetic connectivity.

          Abstract

          Unsustainable anthropogenic mortality of wildlife and fragmentation of the spatial distribution of individuals disrupts natal dispersal mechanisms, with long‐term consequences to genetic structure, by compromising outbreeding behavior and gene flow. Our study investigates this threat in African leopards, demonstrating novel evidence directly linking unsustainable anthropogenic mortality to inbreeding through disrupted dispersal in a large, solitary felid and exposes the genetic consequences underlying this behavioral change.

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          ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

          After more than fifteen years of existence, the R package ape has continuously grown its contents, and has been used by a growing community of users. The release of version 5.0 has marked a leap towards a modern software for evolutionary analyses. Efforts have been put to improve efficiency, flexibility, support for 'big data' (R's long vectors), ease of use and quality check before a new release. These changes will hopefully make ape a useful software for the study of biodiversity and evolution in a context of increasing data quantity.
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            adegenet: a R package for the multivariate analysis of genetic markers.

            The package adegenet for the R software is dedicated to the multivariate analysis of genetic markers. It extends the ade4 package of multivariate methods by implementing formal classes and functions to manipulate and analyse genetic markers. Data can be imported from common population genetics software and exported to other software and R packages. adegenet also implements standard population genetics tools along with more original approaches for spatial genetics and hybridization. Stable version is available from CRAN: http://cran.r-project.org/mirrors.html. Development version is available from adegenet website: http://adegenet.r-forge.r-project.org/. Both versions can be installed directly from R. adegenet is distributed under the GNU General Public Licence (v.2).
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              Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment.

              Genotypes are frequently used to identify parentage. Such analysis is notoriously vulnerable to genotyping error, and there is ongoing debate regarding how to solve this problem. Many scientists have used the computer program CERVUS to estimate parentage, and have taken advantage of its option to allow for genotyping error. In this study, we show that the likelihood equations used by versions 1.0 and 2.0 of CERVUS to accommodate genotyping error miscalculate the probability of observing an erroneous genotype. Computer simulation and reanalysis of paternity in Rum red deer show that correcting this error increases success in paternity assignment, and that there is a clear benefit to accommodating genotyping errors when errors are present. A new version of CERVUS (3.0) implementing the corrected likelihood equations is available at http://www.fieldgenetics.com.
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                Author and article information

                Contributors
                vnaude@panthera.org
                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                18 March 2020
                April 2020
                : 10
                : 8 ( doiID: 10.1002/ece3.v10.8 )
                : 3605-3619
                Affiliations
                [ 1 ] Institute for Communities and Wildlife in Africa University of Cape Town Cape Town South Africa
                [ 2 ] Panthera New York NY USA
                [ 3 ] Wildlife Conservation Society Bronx NY USA
                [ 4 ] Centre for Functional Biodiversity School of Life Sciences University of KwaZulu‐Natal Durban South Africa
                [ 5 ] Wyoming Cooperative Fish and Wildlife Research Unit Department of Zoology and Physiology University of Wyoming Laramie WY USA
                Author notes
                [*] [* ] Correspondence

                Vincent Naude, Institute for Communities and Wildlife in Africa, University of Cape Town, Cape Town, Western Cape, South Africa.

                Email: vnaude@ 123456panthera.org

                Author information
                https://orcid.org/0000-0002-0275-1727
                Article
                ECE36089
                10.1002/ece3.6089
                7160178
                32313621
                b3470196-b60d-439f-a373-49692f1ec1ec
                © 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 12 January 2020
                : 16 January 2020
                : 20 January 2020
                Page count
                Figures: 4, Tables: 1, Pages: 15, Words: 11012
                Funding
                Funded by: National Research Foundation South Africa
                Award ID: FA 2004050400038
                Funded by: Timbo Afrika Foundation
                Funded by: National Research Foundation
                Funded by: University of KwaZulu‐Natal
                Funded by: Panthera
                Categories
                Original Research
                Original Research
                Custom metadata
                2.0
                April 2020
                Converter:WILEY_ML3GV2_TO_JATSPMC version:5.8.0 mode:remove_FC converted:15.04.2020

                Evolutionary Biology
                home‐range,kin‐clustering,microsatellites,panthera pardus,philopatry,relatedness

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