1
|
Al Hikmani H, van Oosterhout C, Birley T, Labisko J, Jackson HA, Spalton A, Tollington S, Groombridge JJ. Can genetic rescue help save Arabia's last big cat? Evol Appl 2024; 17:e13701. [PMID: 38784837 PMCID: PMC11113348 DOI: 10.1111/eva.13701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/01/2024] [Accepted: 04/10/2024] [Indexed: 05/25/2024] Open
Abstract
Genetic diversity underpins evolutionary potential that is essential for the long-term viability of wildlife populations. Captive populations harbor genetic diversity potentially lost in the wild, which could be valuable for release programs and genetic rescue. The Critically Endangered Arabian leopard (Panthera pardus nimr) has disappeared from most of its former range across the Arabian Peninsula, with fewer than 120 individuals left in the wild, and an additional 64 leopards in captivity. We (i) examine genetic diversity in the wild and captive populations to identify global patterns of genetic diversity and structure; (ii) estimate the size of the remaining leopard population across the Dhofar mountains of Oman using spatially explicit capture-recapture models on DNA and camera trap data, and (iii) explore the impact of genetic rescue using three complementary computer modeling approaches. We estimated a population size of 51 (95% CI 32-79) in the Dhofar mountains and found that 8 out of 25 microsatellite alleles present in eight loci in captive leopards were undetected in the wild. This includes two alleles present only in captive founders known to have been wild-sourced from Yemen, which suggests that this captive population represents an important source for genetic rescue. We then assessed the benefits of reintroducing novel genetic diversity into the wild population as well as the risks of elevating the genetic load through the release of captive-bred individuals. Simulations indicate that genetic rescue can improve the long-term viability of the wild population by reducing its genetic load and realized load. The model also suggests that the genetic load has been partly purged in the captive population, potentially making it a valuable source population for genetic rescue. However, the greater loss of its genetic diversity could exacerbate genomic erosion of the wild population during a rescue program, and these risks and benefits should be carefully evaluated. An important next step in the recovery of the Arabian leopard is to empirically validate these conclusions, implement and monitor a genomics-informed management plan, and optimize a strategy for genetic rescue as a tool to recover Arabia's last big cat.
Collapse
Affiliation(s)
- Hadi Al Hikmani
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
- Office for Conservation of the EnvironmentDiwan of Royal CourtMuscatOman
- The Royal Commission for AlUlaAlUlaSaudi Arabia
| | - Cock van Oosterhout
- School of Environmental SciencesUniversity of East Anglia, Norwich Research ParkNorwichUK
| | - Thomas Birley
- School of Environmental SciencesUniversity of East Anglia, Norwich Research ParkNorwichUK
| | - Jim Labisko
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
- Centre for Biodiversity and Environment Research, Research Department of Genetics, Evolution and EnvironmentUniversity College LondonLondonUK
- Island Biodiversity and Conservation CentreUniversity of SeychellesVictoriaSeychelles
- Department of Life SciencesThe Natural History MuseumLondonUK
| | - Hazel A. Jackson
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
| | | | - Simon Tollington
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
- School of Animal Rural and Environmental SciencesNottingham Trent UniversityNottinghamUK
| | - Jim J. Groombridge
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
| |
Collapse
|
2
|
Kyriazis CC, Serieys LE, Bishop JM, Drouilly M, Viljoen S, Wayne RK, Lohmueller KE. The influence of gene flow on population viability in an isolated urban caracal population. Mol Ecol 2024; 33:e17346. [PMID: 38581173 PMCID: PMC11035096 DOI: 10.1111/mec.17346] [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: 07/20/2023] [Revised: 01/23/2024] [Accepted: 03/26/2024] [Indexed: 04/08/2024]
Abstract
Wildlife populations are becoming increasingly fragmented by anthropogenic development. Small and isolated populations often face an elevated risk of extinction, in part due to inbreeding depression. Here, we examine the genomic consequences of urbanization in a caracal (Caracal caracal) population that has become isolated in the Cape Peninsula region of the City of Cape Town, South Africa, and is thought to number ~50 individuals. We document low levels of migration into the population over the past ~75 years, with an estimated rate of 1.3 effective migrants per generation. As a consequence of this isolation and small population size, levels of inbreeding are elevated in the contemporary Cape Peninsula population (mean FROH = 0.20). Inbreeding primarily manifests as long runs of homozygosity >10 Mb, consistent with the effects of isolation due to the rapid recent growth of Cape Town. To explore how reduced migration and elevated inbreeding may impact future population dynamics, we parameterized an eco-evolutionary simulation model. We find that if migration rates do not change in the future, the population is expected to decline, though with a low projected risk of extinction. However, if migration rates decline or anthropogenic mortality rates increase, the potential risk of extinction is greatly elevated. To avert a population decline, we suggest that translocating migrants into the Cape Peninsula to initiate a genetic rescue may be warranted in the near future. Our analysis highlights the utility of genomic datasets coupled with computational simulation models for investigating the influence of gene flow on population viability.
Collapse
Affiliation(s)
- Christopher C. Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Laurel E.K. Serieys
- Panthera, 8 W 40th St, 18th Floor, New York, NY 10018, USA
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Jacqueline M. Bishop
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Marine Drouilly
- Panthera, 8 W 40th St, 18th Floor, New York, NY 10018, USA
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
- Centre for Social Science Research, University of Cape Town, Rondebosch, 7701, South Africa
| | - Storme Viljoen
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| |
Collapse
|
3
|
Sutherland BJG, Rycroft C, Duguid A, Beacham TD, Tucker S. Population genomics of harbour seal Phoca vitulina from northern British Columbia through California and comparison to the Atlantic subspecies. Mol Ecol 2024; 33:e17293. [PMID: 38419064 DOI: 10.1111/mec.17293] [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: 05/15/2023] [Revised: 01/29/2024] [Accepted: 02/01/2024] [Indexed: 03/02/2024]
Abstract
The harbour seal Phoca vitulina is a ubiquitous pinniped species found throughout coastal waters of the Northern Hemisphere. Harbour seal impacts on ecosystem dynamics may be significant due to their high abundance and food web position. Two subspecies exist in North America, P. v. richardii in the Pacific Ocean and P. v. vitulina in the Atlantic. Strong natal philopatry of harbour seals can result in fine-scale genetic structure and isolation by distance. Management of harbour seals is expected to benefit from improved resolution of seal population structure and dynamics. Here, we use genotyping-by-sequencing to genotype 146 harbour seals from the eastern Pacific Ocean (i.e. British Columbia (BC), Oregon and California) and the western Atlantic Ocean (i.e. Québec, Newfoundland and Labrador). Using 12,742 identified variants, we confirm the recently identified elevated genetic diversity in the eastern Pacific relative to the western Atlantic and greatest differentiation between the subspecies. Further, we demonstrate that this is independent of reference genome bias or other potential technical artefacts. Coast-specific analyses with 8933 and 3828 variants in Pacific and Atlantic subspecies, respectively, identify divergence between BC and Oregon-California, and between Québec and Newfoundland-Labrador. Unexpected PCA outlier clusters were observed in two populations due to cryptic relatedness of individuals; subsequently, closely related samples were removed. Admixture analysis indicates an isolation-by-distance signature where Oregon seals contained some of the BC signature, whereas California did not. Additional sampling is needed in the central and north coast of BC to determine whether a discrete separation of populations exists within the region.
Collapse
Affiliation(s)
- Ben J G Sutherland
- Sutherland Bioinformatics, Lantzville, British Columbia, Canada
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Claire Rycroft
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Ashtin Duguid
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Terry D Beacham
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Strahan Tucker
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia, Canada
| |
Collapse
|
4
|
Schmidt TL, Thia JA, Hoffmann AA. How Can Genomics Help or Hinder Wildlife Conservation? Annu Rev Anim Biosci 2024; 12:45-68. [PMID: 37788416 DOI: 10.1146/annurev-animal-021022-051810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Genomic data are becoming increasingly affordable and easy to collect, and new tools for their analysis are appearing rapidly. Conservation biologists are interested in using this information to assist in management and planning but are typically limited financially and by the lack of genomic resources available for non-model taxa. It is therefore important to be aware of the pitfalls as well as the benefits of applying genomic approaches. Here, we highlight recent methods aimed at standardizing population assessments of genetic variation, inbreeding, and forms of genetic load and methods that help identify past and ongoing patterns of genetic interchange between populations, including those subjected to recent disturbance. We emphasize challenges in applying some of these methods and the need for adequate bioinformatic support. We also consider the promises and challenges of applying genomic approaches to understand adaptive changes in natural populations to predict their future adaptive capacity.
Collapse
Affiliation(s)
- Thomas L Schmidt
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
| | - Joshua A Thia
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
| |
Collapse
|
5
|
Rieseberg L, Warschefsky E, Burton J, Huang K, Sibbett B. Editorial 2024. Mol Ecol 2024; 33:e17239. [PMID: 38146175 DOI: 10.1111/mec.17239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Affiliation(s)
- Loren Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Emily Warschefsky
- William L. Brown Center, Missouri Botanical Garden, Saint Louis, MO, USA
| | - Jade Burton
- John Wiley & Sons, Atrium Southern Gate, Chichester, West Sussex, UK
| | - Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Benjamin Sibbett
- John Wiley & Sons, Atrium Southern Gate, Chichester, West Sussex, UK
| |
Collapse
|
6
|
Kyriazis CC, Robinson JA, Lohmueller KE. Using Computational Simulations to Model Deleterious Variation and Genetic Load in Natural Populations. Am Nat 2023; 202:737-752. [PMID: 38033186 PMCID: PMC10897732 DOI: 10.1086/726736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
AbstractDeleterious genetic variation is abundant in wild populations, and understanding the ecological and conservation implications of such variation is an area of active research. Genomic methods are increasingly used to quantify the impacts of deleterious variation in natural populations; however, these approaches remain limited by an inability to accurately predict the selective and dominance effects of mutations. Computational simulations of deleterious variation offer a complementary tool that can help overcome these limitations, although such approaches have yet to be widely employed. In this perspective article, we aim to encourage ecological and conservation genomics researchers to adopt greater use of computational simulations to aid in deepening our understanding of deleterious variation in natural populations. We first provide an overview of the components of a simulation of deleterious variation, describing the key parameters involved in such models. Next, we discuss several approaches for validating simulation models. Finally, we compare and validate several recently proposed deleterious mutation models, demonstrating that models based on estimates of selection parameters from experimental systems are biased toward highly deleterious mutations. We describe a new model that is supported by multiple orthogonal lines of evidence and provide example scripts for implementing this model (https://github.com/ckyriazis/simulations_review).
Collapse
|
7
|
Nigenda-Morales SF, Lin M, Nuñez-Valencia PG, Kyriazis CC, Beichman AC, Robinson JA, Ragsdale AP, Urbán R J, Archer FI, Viloria-Gómora L, Pérez-Álvarez MJ, Poulin E, Lohmueller KE, Moreno-Estrada A, Wayne RK. The genomic footprint of whaling and isolation in fin whale populations. Nat Commun 2023; 14:5465. [PMID: 37699896 PMCID: PMC10497599 DOI: 10.1038/s41467-023-40052-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/10/2023] [Indexed: 09/14/2023] Open
Abstract
Twentieth century industrial whaling pushed several species to the brink of extinction, with fin whales being the most impacted. However, a small, resident population in the Gulf of California was not targeted by whaling. Here, we analyzed 50 whole-genomes from the Eastern North Pacific (ENP) and Gulf of California (GOC) fin whale populations to investigate their demographic history and the genomic effects of natural and human-induced bottlenecks. We show that the two populations diverged ~16,000 years ago, after which the ENP population expanded and then suffered a 99% reduction in effective size during the whaling period. In contrast, the GOC population remained small and isolated, receiving less than one migrant per generation. However, this low level of migration has been crucial for maintaining its viability. Our study exposes the severity of whaling, emphasizes the importance of migration, and demonstrates the use of genome-based analyses and simulations to inform conservation strategies.
Collapse
Affiliation(s)
- Sergio F Nigenda-Morales
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, 36824, Mexico.
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA, 92096, USA.
| | - Meixi Lin
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.
| | - Paulina G Nuñez-Valencia
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, 36824, Mexico
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Annabel C Beichman
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Jacqueline A Robinson
- Institute for Human Genetics, University of California, San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Aaron P Ragsdale
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, 36824, Mexico
- Department of Integrative Biology, University of Wisconsin, Madison, WI, 53706, USA
| | - Jorge Urbán R
- Departamento de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur (UABCS), La Paz, Baja California Sur, Mexico
| | - Frederick I Archer
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, La Jolla, CA, 92037, USA
| | - Lorena Viloria-Gómora
- Departamento de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur (UABCS), La Paz, Baja California Sur, Mexico
| | - María José Pérez-Álvarez
- Escuela de Medicina Veterinaria, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Universidad de Chile, Santiago, Chile
| | - Elie Poulin
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Universidad de Chile, Santiago, Chile
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA, 90095, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
| | - Andrés Moreno-Estrada
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, 36824, Mexico.
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| |
Collapse
|
8
|
Ishibashi Y. Preservation of genetic diversity in a highly fragmented population of the gray-sided vole Myodes rufocanus in an intensive farming region. Ecol Evol 2023; 13:e10472. [PMID: 37736279 PMCID: PMC10509600 DOI: 10.1002/ece3.10472] [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: 01/23/2023] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 09/23/2023] Open
Abstract
Individual dispersal plays an important role in preserving genetic diversity in density-fluctuating populations of arvicoline rodents. When habitats are fragmented and dispersal between habitats is severely constrained, genetic diversity can be lost. Here, I investigated whether genetic diversity in the gray-sided vole Myodes rufocanus was preserved in an intensive farming region in Japan, where voles inhabited isolated windbreak forests along the borders of plowed lands. Genetic structure was examined in 673 vole samples (330 in spring and 343 in fall) collected at 34 windbreak forests located 0.35-20 km apart. A part of the control region (425 bp) of mitochondrial DNA (mtDNA) was sequenced in 673 voles, yielding 76 haplotypes. Genetic differentiation of maternally inherited mtDNA among trapping sites was markedly lower in males than in females in both seasons, indicating strong male-biased dispersal. Genotypes at six microsatellite DNA loci were determined in 494 voles (245 in spring and 249 in fall) from 18 trapping sites, and loci harbored 16-24 alleles. The mean number of alleles per locus (allelic diversity) at trapping sites was positively correlated with the number of examined individuals (density) in both seasons, and the relationship was very similar to that of a previous study performed in much less fragmented populations. The genetic differentiation of microsatellite DNA among trapping sites decreased considerably from spring to fall. In a STRUCTURE analysis with a most probable cluster number of two, closer trapping sites showed more similar mean values of cluster admixture proportions. The present findings indicate that gene flow among isolated windbreak forests, which occurred mainly by dispersal of males, was not restrained in this intensive farming region. Furthermore, the results suggest that genetic diversity in the study population was preserved as well as in less fragmented populations.
Collapse
Affiliation(s)
- Yasuyuki Ishibashi
- Hokkaido Research CenterForestry and Forest Products Research InstituteSapporoJapan
| |
Collapse
|