Conservation management strategy impacts inbreeding and genetic load 1 in scimitar-horned oryx 2

Abstract

[1]  N. Galtier,et al.  Purging of deleterious burden in the endangered Iberian lynx , 2022, Proceedings of the National Academy of Sciences of the United States of America.

[2]  G. Bertorelle,et al.  Genetic load: genomic estimates and applications in non-model animals , 2022, Nature Reviews Genetics.

[3]  J. Novembre,et al.  Parental relatedness through time revealed by runs of homozygosity in ancient DNA , 2021, Nature Communications.

[4]  Fergal J. Martin,et al.  Population genomics of the critically endangered kākāpō , 2021, Cell genomics.

[5]  Nina Overgaard Therkildsen,et al.  Batch effects in population genomic studies with low-coverage whole genome sequencing data: causes, detection, and mitigation. , 2021, Molecular ecology resources.

[6]  P. Hedrick,et al.  The crucial role of genome-wide genetic variation in conservation , 2021, Proceedings of the National Academy of Sciences.

[7]  J. DeWoody,et al.  The long‐standing significance of genetic diversity in conservation , 2021, Molecular ecology.

[8]  U. Ramakrishnan,et al.  Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers , 2021, Proceedings of the National Academy of Sciences.

[9]  B. Goossens,et al.  Genomic insights into the conservation status of the world’s last remaining Sumatran rhinoceros populations , 2021, Nature Communications.

[10]  J. DeWoody,et al.  Genetic load has potential in large populations but is realized in small inbred populations , 2021, Evolutionary applications.

[11]  J. Pemberton,et al.  Mutation load decreases with haplotype age in wild Soay sheep , 2021, bioRxiv.

[12]  R. Frankham,et al.  Genetic rescue: A critique of the evidence supports maximizing genetic diversity rather than minimizing the introduction of putatively harmful genetic variation , 2020 .

[13]  J. C. Teixeira,et al.  The inflated significance of neutral genetic diversity in conservation genetics , 2020, Proceedings of the National Academy of Sciences.

[14]  J. Pemberton,et al.  Genetic architecture and lifetime dynamics of inbreeding depression in a wild mammal , 2020, Nature Communications.

[15]  B. Pukazhenthi,et al.  Comparison of genomic diversity and structure of sable antelope (Hippotragus niger) in zoos, conservation centers, and private ranches in North America , 2020, Evolutionary applications.

[16]  L. Keller,et al.  Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex , 2020, Nature Communications.

[17]  K. Gharbi,et al.  Benefits and pitfalls of captive conservation genetic management: Evaluating diversity in scimitar-horned oryx to support reintroduction planning , 2020, Biological Conservation.

[18]  Erez Lieberman Aiden,et al.  Chromosomal-level genome assembly of the scimitar-horned oryx: insights into diversity and demography of a species extinct in the wild , 2019, bioRxiv.

[19]  J. Piedrafita,et al.  Mapping Recombination Rate on the Autosomal Chromosomes Based on the Persistency of Linkage Disequilibrium Phase Among Autochthonous Beef Cattle Populations in Spain , 2019, Front. Genet..

[20]  B. Pukazhenthi,et al.  Breeding Centers, Private Ranches, and Genomics for Creating Sustainable Wildlife Populations , 2019, Bioscience.

[21]  A. Ives,et al.  Inbreeding reduces long-term growth of Alpine ibex populations , 2019, Nature Ecology & Evolution.

[22]  Christopher C. Kyriazis,et al.  Strongly deleterious mutations are a primary determinant of extinction risk due to inbreeding depression , 2019, bioRxiv.

[23]  K. Nielsen,et al.  Genomic variation predicts adaptive evolutionary responses better than population bottleneck history , 2019, PLoS genetics.

[24]  D. Spielman Genetic Management of Fragmented Animal and Plant Populations , 2019 .

[25]  T. Marquès-Bonet,et al.  Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas , 2019, Current Biology.

[26]  Bernard Y. Kim,et al.  Purging of Strongly Deleterious Mutations Explains Long-Term Persistence and Absence of Inbreeding Depression in Island Foxes , 2018, Current Biology.

[27]  M. Kardos,et al.  The Peril of Gene-Targeted Conservation. , 2018, Trends in ecology & evolution.

[28]  R. Wayne,et al.  Genomic signatures of extensive inbreeding in Isle Royale wolves, a population on the threshold of extinction , 2018, Science Advances.

[29]  J. Flowers,et al.  Origins and geographic diversification of African rice (Oryza glaberrima) , 2018, bioRxiv.

[30]  A. Albrechtsen,et al.  Inferring Population Structure and Admixture Proportions in Low-Depth NGS Data , 2018, Genetics.

[31]  B. Charlesworth Mutational load, inbreeding depression and heterosis in subdivided populations , 2018, bioRxiv.

[32]  C. Grueber,et al.  The effects of group versus intensive housing on the retention of genetic diversity in insurance populations , 2018 .

[33]  L. Rockwood,et al.  Integrating In-Situ and Ex-Situ Data Management Processes for Biodiversity Conservation , 2017, Front. Ecol. Evol..

[34]  K. Traylor‐Holzer,et al.  IUCN Guidelines for Determining When and How Ex Situ Management Should Be Used in Species Conservation , 2017 .

[35]  H. Ellegren,et al.  Inferring Individual Inbreeding and Demographic History from Segments of Identity by Descent in Ficedula Flycatcher Genome Sequences , 2017, Genetics.

[36]  T. Woodfine,et al.  The Fall and Rise of the Scimitar‐Horned Oryx , 2016 .

[37]  F. Cunningham,et al.  The Ensembl Variant Effect Predictor , 2016, bioRxiv.

[38]  R. Frankham Genetic rescue benefits persist to at least the F3 generation, based on a meta-analysis , 2016 .

[39]  Brian L Browning,et al.  Accurate Non-parametric Estimation of Recent Effective Population Size from Segments of Identity by Descent. , 2015, American journal of human genetics.

[40]  R. Frankham Genetic rescue of small inbred populations: meta-analysis reveals large and consistent benefits of gene flow. , 2015, Molecular ecology.

[41]  Peter H. Sudmant,et al.  Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding , 2015, Science.

[42]  G. Luikart,et al.  Measuring individual inbreeding in the age of genomics: marker-based measures are better than pedigrees , 2015, Heredity.

[43]  D. Reich,et al.  No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans , 2014, Nature Genetics.

[44]  Anders Albrechtsen,et al.  ANGSD: Analysis of Next Generation Sequencing Data , 2014, BMC Bioinformatics.

[45]  T. Korneliussen,et al.  Estimating Individual Admixture Proportions from Next Generation Sequencing Data , 2013, Genetics.

[46]  J. Kirkwood Guidelines for reintroductions and other conservation translocations , 2013, Animal Welfare.

[47]  Mauricio O. Carneiro,et al.  From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline , 2013, Current protocols in bioinformatics.

[48]  M. Goddard,et al.  Inferring Demography from Runs of Homozygosity in Whole-Genome Sequence, with Correction for Sequence Errors , 2013, Molecular biology and evolution.

[49]  E. Thompson Identity by Descent: Variation in Meiosis, Across Genomes, and in Populations , 2013, Genetics.

[50]  Heng Li Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.

[51]  D. Field,et al.  Source population characteristics affect heterosis following genetic rescue of fragmented plant populations , 2013, Proceedings of the Royal Society B: Biological Sciences.

[52]  K. Redford,et al.  Integrating the Captive and the Wild , 2012, Science.

[53]  Richard M Myers,et al.  Genomic patterns of homozygosity in worldwide human populations. , 2012, American journal of human genetics.

[54]  A. García-Dorado Understanding and Predicting the Fitness Decline of Shrunk Populations: Inbreeding, Purging, Mutation, and Standard Selection , 2012, Genetics.

[55]  S. Oldfield,et al.  Bring the captive closer to the wild: redefining the role of ex situ conservation , 2011, Oryx.

[56]  Heng Li,et al.  A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data , 2011, Bioinform..

[57]  I. Jamieson,et al.  Preserving genetic diversity in threatened species reintroductions: how many individuals should be released? , 2011 .

[58]  R. Frankham,et al.  Assessing the benefits and risks of translocations in changing environments: a genetic perspective , 2011, Evolutionary applications.

[59]  Gonçalo R. Abecasis,et al.  The variant call format and VCFtools , 2011, Bioinform..

[60]  Marcel Martin Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[61]  Harry Campbell,et al.  Genomic Runs of Homozygosity Record Population History and Consanguinity , 2010, PloS one.

[62]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[63]  Igor Rudan,et al.  Runs of homozygosity in European populations. , 2008, American journal of human genetics.

[64]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[65]  Joan Kimmelman Royal (Dick) School of Veterinary Studies , 2007, Veterinary Record.

[66]  S. Edmands Between a rock and a hard place: evaluating the relative risks of inbreeding and outbreeding for conservation and management , 2006, Molecular ecology.

[67]  G. Evanno,et al.  Detecting the number of clusters of individuals using the software structure: a simulation study , 2005, Molecular ecology.

[68]  R. Frankham,et al.  Most species are not driven to extinction before genetic factors impact them. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[69]  A. Caballero,et al.  Managing Individuals' Contributions to Maximize the Allelic Diversity Maintained in Small, Conserved Populations , 2004 .

[70]  D. H. Reed,et al.  Correlation between Fitness and Genetic Diversity , 2003 .

[71]  M. Whitlock Selection, load and inbreeding depression in a large metapopulation. , 2002, Genetics.

[72]  R. Frankham,et al.  Inbreeding and extinction: Effects of purging , 2001, Conservation Genetics.

[73]  P. Donnelly,et al.  Inference of population structure using multilocus genotype data. , 2000, Genetics.

[74]  W. G. Hill,et al.  Effect of selection against deleterious mutations on the decline in heterozygosity at neutral loci in closely inbreeding populations. , 1999, Genetics.

[75]  R. Lacy,et al.  EFFECTIVENESS OF SELECTION IN REDUCING THE GENETIC LOAD IN POPULATIONS OF PEROMYSCUS POLIONOTUS DURING GENERATIONS OF INBREEDING , 1998, Evolution; international journal of organic evolution.

[76]  I. Hanski,et al.  Inbreeding and extinction in a butterfly metapopulation , 1998, Nature.

[77]  R. Lande,et al.  THE ROLE OF GENETIC VARIATION IN ADAPTATION AND POPULATION PERSISTENCE IN A CHANGING ENVIRONMENT , 1996, Evolution; international journal of organic evolution.

[78]  M. Lynch,et al.  Mutation Accumulation and the Extinction of Small Populations , 1995, The American Naturalist.

[79]  R. Lande RISK OF POPULATION EXTINCTION FROM FIXATION OF NEW DELETERIOUS MUTATIONS , 1994, Evolution; international journal of organic evolution.

[80]  R. Lacy Loss of Genetic Diversity from Managed Populations: Interacting Effects of Drift, Mutation, Immigration, Selection, and Population Subdivision , 1987 .

[81]  C. Grueber,et al.  Preserving the demographic and genetic integrity of a single source population during multiple translocations , 2020 .

[82]  Rebecca N. Johnson,et al.  Genetic Management of Captive and Reintroduced Bilby Populations , 2019, The Journal of Wildlife Management.

[83]  M. Songer,et al.  Management Background and Release Conditions Structure Post-release Movements in Reintroduced Ungulates , 2019, Front. Ecol. Evol..

[84]  D. Tallmon,et al.  Genetic rescue to the rescue. , 2015, Trends in ecology & evolution.

[85]  J. DeWoody,et al.  Using molecular methods to improve the genetic management of captive breeding programs for threatened species , 2010 .

[86]  R. Frankham,et al.  Minimizing kinship in captive breeding programs , 1997 .

[87]  T. Foose,et al.  Demographic and genetic management of captive populations , 1996 .

[88]  Deborah Charlesworth,et al.  INBREEDING DEPRESSION AND ITS EVOLUTIONARY CONSEQUENCES , 1987 .

[89]  F. THE MUTATION LOAD IN SMALL POPULATIONS , 2022 .