1
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Aktürk Ş, Mapelli I, Güler MN, Gürün K, Katırcıoğlu B, Vural KB, Sağlıcan E, Çetin M, Yaka R, Sürer E, Atağ G, Çokoğlu SS, Sevkar A, Altınışık NE, Koptekin D, Somel M. Benchmarking kinship estimation tools for ancient genomes using pedigree simulations. Mol Ecol Resour 2024; 24:e13960. [PMID: 38676702 DOI: 10.1111/1755-0998.13960] [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] [Received: 11/25/2023] [Revised: 03/19/2024] [Accepted: 03/28/2024] [Indexed: 04/29/2024]
Abstract
There is growing interest in uncovering genetic kinship patterns in past societies using low-coverage palaeogenomes. Here, we benchmark four tools for kinship estimation with such data: lcMLkin, NgsRelate, KIN, and READ, which differ in their input, IBD estimation methods, and statistical approaches. We used pedigree and ancient genome sequence simulations to evaluate these tools when only a limited number (1 to 50 K, with minor allele frequency ≥0.01) of shared SNPs are available. The performance of all four tools was comparable using ≥20 K SNPs. We found that first-degree related pairs can be accurately classified even with 1 K SNPs, with 85% F1 scores using READ and 96% using NgsRelate or lcMLkin. Distinguishing third-degree relatives from unrelated pairs or second-degree relatives was also possible with high accuracy (F1 > 90%) with 5 K SNPs using NgsRelate and lcMLkin, while READ and KIN showed lower success (69 and 79% respectively). Meanwhile, noise in population allele frequencies and inbreeding (first-cousin mating) led to deviations in kinship coefficients, with different sensitivities across tools. We conclude that using multiple tools in parallel might be an effective approach to achieve robust estimates on ultra-low-coverage genomes.
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Affiliation(s)
- Şevval Aktürk
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Igor Mapelli
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Merve N Güler
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Kanat Gürün
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Büşra Katırcıoğlu
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Ekin Sağlıcan
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Mehmet Çetin
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Reyhan Yaka
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Elif Sürer
- Department of Modeling and Simulation, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Gözde Atağ
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Sevim Seda Çokoğlu
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Arda Sevkar
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - N Ezgi Altınışık
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Dilek Koptekin
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
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2
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Sopniewski J, Catullo RA. Estimates of heterozygosity from single nucleotide polymorphism markers are context-dependent and often wrong. Mol Ecol Resour 2024; 24:e13947. [PMID: 38433491 DOI: 10.1111/1755-0998.13947] [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] [Received: 12/09/2022] [Revised: 02/18/2024] [Accepted: 02/21/2024] [Indexed: 03/05/2024]
Abstract
Genetic diversity is frequently described using heterozygosity, particularly in a conservation context. Often, it is estimated using single nucleotide polymorphisms (SNPs); however, it has been shown that heterozygosity values calculated from SNPs can be biased by both study design and filtering parameters. Though solutions have been proposed to address these issues, our own work has found them to be inadequate in some circumstances. Here, we aimed to improve the reliability and comparability of heterozygosity estimates, specifically by investigating how sample size and missing data thresholds influenced the calculation of autosomal heterozygosity (heterozygosity calculated from across the genome, i.e. fixed and variable sites). We also explored how the standard practice of tri- and tetra-allelic site exclusion could bias heterozygosity estimates and influence eventual conclusions relating to genetic diversity. Across three distinct taxa (a frog, Litoria rubella; a tree, Eucalyptus microcarpa; and a grasshopper, Keyacris scurra), we found heterozygosity estimates to be meaningfully affected by sample size and missing data thresholds, partly due to the exclusion of tri- and tetra-allelic sites. These biases were inconsistent both between species and populations, with more diverse populations tending to have their estimates more severely affected, thus having potential to dramatically alter interpretations of genetic diversity. We propose a modified framework for calculating heterozygosity that reduces bias and improves the utility of heterozygosity as a measure of genetic diversity, whilst also highlighting the need for existing population genetic pipelines to be adjusted such that tri- and tetra-allelic sites be included in calculations.
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Affiliation(s)
- Jarrod Sopniewski
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Renee A Catullo
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, Australia
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3
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Blanchet G, Bellinger MR, Kearns AM, Cortes-Rodriguez N, Masuda B, Campana MG, Rutz C, Fleischer RC, Sutton JT. Reduction of genetic diversity in 'Alalā (Hawaiian crow; Corvus hawaiiensis) between the late 1800s and the late 1900s. J Hered 2024; 115:32-44. [PMID: 37846510 DOI: 10.1093/jhered/esad063] [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: 06/18/2023] [Revised: 09/26/2023] [Accepted: 10/12/2023] [Indexed: 10/18/2023] Open
Abstract
Genetic and genomic data are increasingly used to aid conservation management of endangered species by providing insights into evolutionary histories, factors associated with extinction risks, and potential for future adaptation. For the 'Alalā, or Hawaiian crow (Corvus hawaiiensis), genetic concerns include negative correlations between inbreeding and hatching success. However, it is unclear if low genetic diversity and inbreeding depression are consequences of a historical population bottleneck, or if 'Alalā had historically low genetic diversity that predated human influence, perhaps as a result of earlier declines or founding events. In this study, we applied a hybridization-based sequence capture to generate a genome-wide single nucleotide polymorphism (SNP) dataset for comparing historical specimens collected in the 1890s, when 'Alalā were more numerous, to samples taken between 1973 and 1998, when 'Alalā population densities were near the lowest documented levels in the wild, prior to all individuals being collected for captive rearing. We found low genome-wide diversity in both sample groups, however, the modern sample group (1973 to 1998 cohort) exhibited relatively fewer polymorphic alleles, a lower proportion of polymorphic loci, and lower observed heterozygosity, consistent with a population decline and potential bottleneck effects. These results combined with a current low population size highlight the importance of continued efforts by conservation managers to mitigate inbreeding and maintain founder representation to preserve what genetic diversity remains.
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Affiliation(s)
- Geneviève Blanchet
- Department of Biology, University of Hawai'i at Hilo, 200 W Kāwili St, Hilo, Hawai'i 96720, United States
| | - M Renee Bellinger
- Department of Biology, University of Hawai'i at Hilo, 200 W Kāwili St, Hilo, Hawai'i 96720, United States
- U.S. Geological Survey, Pacific Island Ecosystems Research Center, PO Box 44, Hawai'i National Park, Hawai'i 96718, United States
| | - Anna M Kearns
- Center for Conservation Genomics, National Zoo and Conservation Biology Institute, Smithsonian Institution, Washington DC 20008, United States
| | - Nandadevi Cortes-Rodriguez
- Center for Conservation Genomics, National Zoo and Conservation Biology Institute, Smithsonian Institution, Washington DC 20008, United States
| | - Bryce Masuda
- San Diego Zoo Wildlife Alliance, P.O. Box 39, Volcano, HI 96785, United States
| | - Michael G Campana
- Center for Conservation Genomics, National Zoo and Conservation Biology Institute, Smithsonian Institution, Washington DC 20008, United States
| | - Christian Rutz
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews KY16 9TH, United Kingdom
| | - Robert C Fleischer
- Center for Conservation Genomics, National Zoo and Conservation Biology Institute, Smithsonian Institution, Washington DC 20008, United States
| | - Jolene T Sutton
- Department of Biology, University of Hawai'i at Hilo, 200 W Kāwili St, Hilo, Hawai'i 96720, United States
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4
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Domínguez S, Cervantes I, Gutiérrez JP, Moreno E. Pedigree analysis in the mhorr gazelle ( Nanger dama mhorr): Genetic variability evolution of the captive population. Ecol Evol 2024; 14:e10876. [PMID: 38371855 PMCID: PMC10873689 DOI: 10.1002/ece3.10876] [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: 07/11/2023] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 02/20/2024] Open
Abstract
Breeding programs have an essential role in the recovery of threatened populations through optimal genetic management and mating strategies. The dama gazelle (Nanger dama) is a North African ungulate listed as critically endangered. The mhorr subspecies is extinct in the wild and currently survives thanks to the creation in 1971 of an ex situ breeding program. The aim of the present study was to assess the evolution of genetic variability in this mhorr gazelle captive population, as well as the mating strategy used in two reference populations studied (Almeria and Europe). The entire pedigree, with 2739 animals, was analyzed to measure demographic characters, pedigree completeness level, probability of gene origin, level of relatedness and genetic structure of the population. The population size has been progressively increasing, with up to 264 individuals alive in Europe at the time of the study. The average number of equivalent complete generations was 5.55. The effective number of founders and ancestors was both 3, and the founder genome equivalent was 1.99. The genetic contributions of the four main ancestors were unbalanced. The average values of inbreeding and average relatedness for the whole pedigree were, respectively, 28.34% and 50.14%. The effective population size was 8.7 by individual increase in inbreeding and 9.8 by individual increase in coancestry. F-statistics evidenced a very small level of population subdivision (F ST = 0.033370). The mating strategy used, based on the minimum coancestry of the individuals, has minimized the losses of genetic variability and helped to balance the genetic contributions between ancestors. The strategy also avoided large subdivisions within the population and the appearance of new bottlenecks. This study shows how pedigree analysis can both be used to determine the genetic variability of the population and to assess the influence of the mating strategy used in the breeding program on such variability.
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Affiliation(s)
| | - Isabel Cervantes
- Departamento de Producción Animal, Facultad de VeterinariaUCMMadridSpain
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5
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White LC, Städele V, Ramirez Amaya S, Langergraber K, Vigilant L. Female chimpanzees avoid inbreeding even in the presence of substantial bisexual philopatry. ROYAL SOCIETY OPEN SCIENCE 2024; 11:230967. [PMID: 38234436 PMCID: PMC10791533 DOI: 10.1098/rsos.230967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 12/13/2023] [Indexed: 01/19/2024]
Abstract
Inbreeding (reproduction between relatives) often decreases the fitness of offspring and is thus expected to lead to the evolution of inbreeding avoidance strategies. Chimpanzees (Pan troglodytes) are expected to avoid inbreeding as they are long-lived, invest heavily in offspring and may encounter adult, opposite sex kin frequently, especially in populations where both males and females commonly remain in the group in which they were born (bisexual philopatry). However, it is unclear whether substantial bisexual philopatry has been a feature of chimpanzees' evolutionary history or whether it is a result of recent anthropogenic interference, as the only groups for which it has been documented are significantly impacted by human encroachment and experience notable rates of potentially unsustainable inbreeding. Here we use 14 years of observational data and a large genomic dataset of 256 481 loci sequenced from 459 individuals to document dispersal and inbreeding dynamics in an eastern chimpanzee (P. t. schweinfurthii) community with low levels of anthropogenic disturbance. We document the first case of substantial bisexual philopatry in a relatively undisturbed chimpanzee community and show that, despite an increased inbreeding risk incurred by females who do not disperse before reaching reproductive age, natal females were still able to avoid producing inbred offspring.
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Affiliation(s)
- Lauren C. White
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Arthur Rylah Institute for Environmental Research, Department of Energy, Environment and Climate Action, Melbourne, Australia
| | - Veronika Städele
- Institute of Human Origins, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Sebastian Ramirez Amaya
- Institute of Human Origins, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Kevin Langergraber
- Institute of Human Origins, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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6
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Beninde J, Wittische J, Frantz AC. Quantifying uncertainty in inferences of landscape genetic resistance due to choice of individual-based genetic distance metric. Mol Ecol Resour 2024; 24:e13831. [PMID: 37475166 DOI: 10.1111/1755-0998.13831] [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: 03/15/2021] [Revised: 05/12/2023] [Accepted: 06/22/2023] [Indexed: 07/22/2023]
Abstract
Estimates of gene flow resulting from landscape resistance inferences frequently inform conservation management decision-making processes. Therefore, results must be robust across approaches and reflect real-world gene flow instead of methodological artefacts. Here, we tested the impact of 32 individual-based genetic distance metrics on the robustness and accuracy of landscape resistance modelling results. We analysed three empirical microsatellite datasets and 36 simulated datasets that varied in landscape resistance and genetic spatial autocorrelation. We used ResistanceGA to generate optimised multi-feature resistance surfaces for each of these datasets using 32 different genetic distance metrics. Results of the empirical dataset demonstrated that the choice of genetic distance metric can have strong impacts on inferred optimised resistance surfaces. Simulations showed accurate parametrisation of resistance surfaces across most genetic distance metrics only when a small number of environmental features was impacting gene flow. Landscape scenarios with many features impacting gene flow led to a generally poor recovery of true resistance surfaces. Simulation results also emphasise that choosing a genetic distance metric should not be based on marginal R2 -based model fit. Until more robust methods are available, resistance surfaces can be optimised with different genetic distance metrics and the convergence of results needs to be assessed via pairwise matrix correlations. Based on the results presented here, high correlation coefficients across different genetic distance categories likely indicate accurate inference of true landscape resistance. Most importantly, empirical results should be interpreted with great caution, especially when they appear counter-intuitive in light of the ecology of a species.
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Affiliation(s)
- Joscha Beninde
- LA Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, California, USA
- IUCN WCPA Connectivity Conservation Specialist Group, Gland, Switzerland
- Amsterdam Institute for Life and Environment (A-LIFE), Section Ecology and Evolution, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Julian Wittische
- Musée National d'Histoire Naturelle, Luxembourg City, Luxembourg
- The Fondation Faune-Flore, Luxembourg City, Luxembourg
| | - Alain C Frantz
- Musée National d'Histoire Naturelle, Luxembourg City, Luxembourg
- The Fondation Faune-Flore, Luxembourg City, Luxembourg
- The University of Sheffield, Sheffield, UK
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7
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Bossu CM, Rodriguez M, Rayne C, Chromczak DA, Higgins PG, Trulio LA, Ruegg KC. Genomic approaches to mitigating genetic diversity loss in declining populations. Mol Ecol 2023; 32:5228-5240. [PMID: 37610278 DOI: 10.1111/mec.17109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/17/2023] [Accepted: 08/04/2023] [Indexed: 08/24/2023]
Abstract
The accelerating pace of global biodiversity loss is exacerbated by habitat fragmentation and subsequent inbreeding in small populations. To address this problem, conservation practitioners often turn to assisted breeding programmes with the aim of enhancing genetic diversity in declining populations. Although genomic information is infrequently included in these efforts, it has the potential to significantly enhance the success of such programmes. In this study, we showcase the value of genomic approaches for increasing genetic diversity in assisted breeding efforts, specifically focusing on a highly inbred population of Western burrowing owls. To maximize genetic diversity in the resulting offspring, we begin by creating an optimal pairing decision tree based on sex, kinship and patterns of homozygosity across the genome. To evaluate the effectiveness of our strategy, we compare genetic diversity, brood size and nestling success rates between optimized and non-optimized pairs. Additionally, we leverage recently discovered correlations between telomere length and fitness across species to investigate whether genomic optimization could have long-term fitness benefits. Our results indicate that pairing individuals with contrasting patterns of homozygosity across the genome is an effective way to increase genetic diversity in offspring. Although short-term field-based metrics of success did not differ significantly between optimized and non-optimized pairs, offspring from optimized pairs had significantly longer telomeres, suggesting that genetic optimization can help reduce the risk of inbreeding depression. These findings underscore the importance of genomic tools for informing efforts to preserve the adaptive potential of small, inbred populations at risk of further decline.
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Affiliation(s)
- Christen M Bossu
- Department of Biology, Colorado State University, Colorado, Fort Collins, USA
| | - Marina Rodriguez
- Department of Biology, Colorado State University, Colorado, Fort Collins, USA
| | - Christine Rayne
- Department of Biology, Colorado State University, Colorado, Fort Collins, USA
| | - Debra A Chromczak
- Burrowing Owl Researcher & Consultant, Riegelsville, Pennsylvania, USA
| | | | - Lynne A Trulio
- Department of Environmental Studies, San José State University, San Jose, California, USA
| | - Kristen C Ruegg
- Department of Biology, Colorado State University, Colorado, Fort Collins, USA
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8
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Taylor RS. New tools for the recovery of the kākāpō. Nat Ecol Evol 2023; 7:1589-1590. [PMID: 37640764 DOI: 10.1038/s41559-023-02112-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Affiliation(s)
- Rebecca S Taylor
- Landscape Science and Technology Division, Environment and Climate Change Canada, Ottawa, Ontario, Canada.
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9
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Guhlin J, Le Lec MF, Wold J, Koot E, Winter D, Biggs PJ, Galla SJ, Urban L, Foster Y, Cox MP, Digby A, Uddstrom LR, Eason D, Vercoe D, Davis T, Howard JT, Jarvis ED, Robertson FE, Robertson BC, Gemmell NJ, Steeves TE, Santure AW, Dearden PK. Species-wide genomics of kākāpō provides tools to accelerate recovery. Nat Ecol Evol 2023; 7:1693-1705. [PMID: 37640765 DOI: 10.1038/s41559-023-02165-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 07/11/2023] [Indexed: 08/31/2023]
Abstract
The kākāpō is a critically endangered, intensively managed, long-lived nocturnal parrot endemic to Aotearoa New Zealand. We generated and analysed whole-genome sequence data for nearly all individuals living in early 2018 (169 individuals) to generate a high-quality species-wide genetic variant callset. We leverage extensive long-term metadata to quantify genome-wide diversity of the species over time and present new approaches using probabilistic programming, combined with a phenotype dataset spanning five decades, to disentangle phenotypic variance into environmental and genetic effects while quantifying uncertainty in small populations. We find associations for growth, disease susceptibility, clutch size and egg fertility within genic regions previously shown to influence these traits in other species. Finally, we generate breeding values to predict phenotype and illustrate that active management over the past 45 years has maintained both genome-wide diversity and diversity in breeding values and, hence, evolutionary potential. We provide new pathways for informing future conservation management decisions for kākāpō, including prioritizing individuals for translocation and monitoring individuals with poor growth or high disease risk. Overall, by explicitly addressing the challenge of the small sample size, we provide a template for the inclusion of genomic data that will be transformational for species recovery efforts around the globe.
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Affiliation(s)
- Joseph Guhlin
- Genomics Aotearoa, Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand
| | - Marissa F Le Lec
- Genomics Aotearoa, Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand
| | - Jana Wold
- School of Biological Sciences, University of Canterbury, Christchurch, Aotearoa New Zealand
| | - Emily Koot
- The New Zealand Institute for Plant and Food Research Ltd, Palmerston North, Aotearoa New Zealand
| | - David Winter
- School of Natural Sciences, Massey University, Palmerston North, Aotearoa New Zealand
| | - Patrick J Biggs
- School of Natural Sciences, Massey University, Palmerston North, Aotearoa New Zealand
- School of Veterinary Science, Massey University, Palmerston North, Aotearoa New Zealand
| | - Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Christchurch, Aotearoa New Zealand
- Department of Biological Sciences, Boise State University, Boise, ID, USA
| | - Lara Urban
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand
- Helmholtz Pioneer Campus, Helmholtz Zentrum Muenchen, Neuherberg, Germany
- Helmholtz AI, Helmholtz Zentrum Muenchen, Neuherberg, Germany
- School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Yasmin Foster
- Department of Zoology, University of Otago, Dunedin, Aotearoa New Zealand
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North, Aotearoa New Zealand
- Department of Statistics, University of Auckland, Auckland, Aotearoa New Zealand
| | - Andrew Digby
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand
| | - Lydia R Uddstrom
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand
| | - Daryl Eason
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand
| | - Deidre Vercoe
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand
| | - Tāne Davis
- Rakiura Tītī Islands Administering Body, Invercargill, Aotearoa New Zealand
| | - Jason T Howard
- Neurogenetics of Language Lab, The Rockefeller University, New York, NY, USA
- Mirxes, Cambridge, MA, USA
| | - Erich D Jarvis
- The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Fiona E Robertson
- Department of Zoology, University of Otago, Dunedin, Aotearoa New Zealand
| | - Bruce C Robertson
- Department of Zoology, University of Otago, Dunedin, Aotearoa New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, Aotearoa New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa New Zealand
| | - Peter K Dearden
- Genomics Aotearoa, Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand.
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10
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Smith KJ, Evans MJ, Gordon IJ, Pierson JC, Newport J, Manning AD. Analyzing captive breeding outcomes to inform reintroduction practice: lessons from the pookila ( Pseudomys novaehollandiae). J Mammal 2023; 104:1047-1061. [PMID: 37800101 PMCID: PMC10550247 DOI: 10.1093/jmammal/gyad056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 05/04/2023] [Indexed: 10/07/2023] Open
Abstract
Captive breeding is often used to produce individuals for reintroduction programs in order to reestablish a species in an area where it has become locally extinct. To maximize the likelihood of establishing a self-sustaining population in the wild, an analysis of data from captive breeding programs is commonly undertaken to (1) increase the quantity of individuals and rate at which they can be released, and (2) maintain or improve the genetic and phenotypic quality of individuals. Here we demonstrate how the knowledge gained from these analyses can also be applied to decision-making during the design of subsequent reintroductions to further advance a reintroduction program toward success. We conducted an analysis of data from a captive breeding program for the threatened pookila (Pseudomys novaehollandiae, New Holland mouse) spanning 6 years. We found evidence for relationships between the reproductive output of pookila and behavioral, demographic, experiential, health, and physiological predictors. Based on a biological interpretation of these results, and with reference to a checklist of all known translocation tactics, we recommend 11 specific design elements to maximize the probability of pookila reproduction postrelease (thereby improving the likelihood of reintroduction success). These recommendations should be interpreted as hypotheses to be evaluated and refined in future reintroduction trials for the pookila. The uncertainty around the postrelease survival and reproduction of a species that is common in reintroduction practice warrants the creative use of existing data to inform adaptive management. Indeed, there is a wealth information in well-kept captive breeding records that is currently underused by reintroduction practitioners. The direct integration of knowledge derived from captive breeding (where available) with decision-making for reintroductions, as described here, will help navigate these uncertainties, which would benefit the conservation of both understudied and well-known species around the world.
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Affiliation(s)
- Kiarrah J Smith
- Fenner School of Environment and Society, The Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Maldwyn J Evans
- Fenner School of Environment and Society, The Australian National University, Acton, Australian Capital Territory 2601, Australia
- Department of Ecosystem Studies, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Iain J Gordon
- Fenner School of Environment and Society, The Australian National University, Acton, Australian Capital Territory 2601, Australia
- The James Hutton Institute, Dundee DD2 5DA, United Kingdom
- Central Queensland University, Townsville, Queensland 4810, Australia
- Land and Water, CSIRO, Townsville, Queensland 4810, Australia
- Lead, Protected Places Mission, National Environmental Science Program, Reef and Rainforest Research Centre, Cairns, Queensland 4870, Australia
| | - Jennifer C Pierson
- Fenner School of Environment and Society, The Australian National University, Acton, Australian Capital Territory 2601, Australia
- Australian Wildlife Conservancy, Subiaco East, Western Australia 6008, Australia
- Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Jenny Newport
- Fenner School of Environment and Society, The Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Adrian D Manning
- Fenner School of Environment and Society, The Australian National University, Acton, Australian Capital Territory 2601, Australia
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11
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Wylie MJ, Kitson J, Russell K, Yoshizaki G, Yazawa R, Steeves TE, Wellenreuther M. Fish germ cell cryobanking and transplanting for conservation. Mol Ecol Resour 2023. [PMID: 37712134 DOI: 10.1111/1755-0998.13868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 05/26/2023] [Accepted: 07/18/2023] [Indexed: 09/16/2023]
Abstract
The unprecedented loss of global biodiversity is linked to multiple anthropogenic stressors. New conservation technologies are urgently needed to mitigate this loss. The rights, knowledge and perspectives of Indigenous peoples in biodiversity conservation-including the development and application of new technologies-are increasingly recognised. Advances in germplasm cryopreservation and germ cell transplantation (termed 'broodstock surrogacy') techniques offer exciting tools to preserve biodiversity, but their application has been underappreciated. Here, we use teleost fishes as an exemplar group to outline (1) the power of these techniques to preserve genome-wide genetic diversity, (2) the need to apply a conservation genomic lens when selecting individuals for germplasm cryobanking and broodstock surrogacy and (3) the value of considering the cultural significance of these genomic resources. We conclude by discussing the opportunities and challenges of these techniques for conserving biodiversity in threatened teleost fish and beyond.
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Affiliation(s)
- Matthew J Wylie
- The New Zealand Institute for Plant & Food Research Limited, Nelson, New Zealand
| | - Jane Kitson
- Kitson Consulting Ltd, Invercargill, New Zealand
| | - Khyla Russell
- Kāti Huirapa Rūnaka ki Puketeraki, Karitane, New Zealand
| | - Goro Yoshizaki
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ryosuke Yazawa
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Maren Wellenreuther
- The New Zealand Institute for Plant & Food Research Limited, Nelson, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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12
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Cavedon M, Neufeld L, Finnegan L, Hervieux D, Michalak A, Pelletier A, Polfus J, Schwantje H, Skinner G, Steenweg R, Thacker C, Poissant J, Musiani M. Genomics of founders for conservation breeding: the Jasper caribou case. CONSERV GENET 2023; 24:855-867. [PMID: 37969360 PMCID: PMC10638200 DOI: 10.1007/s10592-023-01540-3] [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: 12/05/2022] [Accepted: 06/07/2023] [Indexed: 11/17/2023]
Abstract
Conservation breeding programs are increasingly used as recovery actions for wild animals; bringing founders into captivity to rear captive populations for future reintroduction into the wild. The International Union for the Conservation of Nature recommends that founders should come from genetically close populations and should have sufficient genetic diversity to avoid mating among relatives. Genomic data are highly informative for evaluating founders due to their high resolution and ability to capture adaptive divergence, yet, their application in that context remains limited. Woodland caribou are federally listed as a Species at Risk in Canada, with several populations facing extirpation, such as those in the Rocky Mountains of Alberta and British Columbia (BC). To prevent local extirpation, Jasper National Park (JNP) is proposing a conservation breeding program. We examined single nucleotide polymorphisms for 144 caribou from 11 populations encompassing a 200,0002 km area surrounding JNP to provide information useful for identifying appropriate founders for this program. We found that this area likely hosts a caribou metapopulation historically characterized by high levels of gene flow, which indicates that multiple sources of founders would be appropriate for initiating a breeding program. However, population structure and adaptive divergence analyses indicate that JNP caribou are closest to populations in the BC Columbia range, which also have suitable genetic diversity for conservation breeding. We suggest that collaboration among jurisdictions would be beneficial to implement the program to promote recovery of JNP caribou and possibly other caribou populations in the surrounding area, which is strategically at the periphery of the distribution of this endangered species. Supplementary Information The online version contains supplementary material available at 10.1007/s10592-023-01540-3.
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Affiliation(s)
- Maria Cavedon
- Deparment of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Lalenia Neufeld
- Jasper National Park of Canada, Parks Canada, Jasper, Canada
| | - Laura Finnegan
- fRI Research, 1176 Switzer Drive, Hinton, AB T7V 1V3 Canada
| | - Dave Hervieux
- Fish and Wildlife Stewardship Branch, Alberta Environment and Protected Areas, Grande Prairie, AB T8V 6J4 Canada
| | - Anita Michalak
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Agnes Pelletier
- Ministry of Land, Water and Resource Stewardship Northeast Region, 400-10003-110Th Avenue, Fort St. John, BC V1J 6M7 Canada
| | - Jean Polfus
- Canadian Wildlife Service – Pacific Region, Environment and Climate Change Canada, 1238 Discovery Ave, Kelowna, BC V1V 1V9 Canada
| | - Helen Schwantje
- Wildlife and Habitat Branch, Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Government of British Columbia, 2080 Labieux Road, Nanaimo, BC V9T 6J 9 Canada
| | - Geoff Skinner
- Jasper National Park of Canada, Parks Canada, Jasper, Canada
| | - Robin Steenweg
- Canadian Wildlife Service – Pacific Region, Environment and Climate Change Canada, 1238 Discovery Ave, Kelowna, BC V1V 1V9 Canada
| | - Caeley Thacker
- Wildlife and Habitat Branch, Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Government of British Columbia, 2080 Labieux Road, Nanaimo, BC V9T 6J 9 Canada
| | - Jocelyn Poissant
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Marco Musiani
- Dipartimento Scienze Biologiche Geologiche Ambientali, Università Di Bologna, Via Zamboni, 33 - 40126 Bologna, Italia
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13
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Digby A, Eason D, Catalina A, Lierz M, Galla S, Urban L, Le Lec MF, Guhlin J, Steeves TE, Dearden PK, Joustra T, Lees C, Davis T, Vercoe D. Hidden impacts of conservation management on fertility of the critically endangered kākāpō. PeerJ 2023; 11:e14675. [PMID: 36755872 PMCID: PMC9901309 DOI: 10.7717/peerj.14675] [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: 11/19/2021] [Accepted: 12/11/2022] [Indexed: 02/05/2023] Open
Abstract
Background Animal conservation often requires intensive management actions to improve reproductive output, yet any adverse effects of these may not be immediately apparent, particularly in threatened species with small populations and long lifespans. Hand-rearing is an example of a conservation management strategy which, while boosting populations, can cause long-term demographic and behavioural problems. It is used in the recovery of the critically endangered kākāpō (Strigops habroptilus), a flightless parrot endemic to New Zealand, to improve the slow population growth that is due to infrequent breeding, low fertility and low hatching success. Methods We applied Bayesian mixed models to examine whether hand-rearing and other factors were associated with clutch fertility in kākāpō. We used projection predictive variable selection to compare the relative contributions to fertility from the parents' rearing environment, their age and previous copulation experience, the parental kinship, and the number of mates and copulations for each clutch. We also explored how the incidence of repeated copulations and multiple mates varied with kākāpō density. Results The rearing status of the clutch father and the number of mates and copulations of the clutch mother were the dominant factors in predicting fertility. Clutches were less likely to be fertile if the father was hand-reared compared to wild-reared, but there was no similar effect for mothers. Clutches produced by females copulating with different males were more likely to be fertile than those from repeated copulations with one male, which in turn had a higher probability of fertility than those from a single copulation. The likelihood of multiple copulations and mates increased with female:male adult sex ratio, perhaps as a result of mate guarding by females. Parental kinship, copulation experience and age all had negligible associations with clutch fertility. Conclusions These results provide a rare assessment of factors affecting fertility in a wild threatened bird species, with implications for conservation management. The increased fertility due to multiple mates and copulations, combined with the evidence for mate guarding and previous results of kākāpō sperm morphology, suggests that an evolutionary mechanism exists to optimise fertility through sperm competition in kākāpō. The high frequency of clutches produced from single copulations in the contemporary population may therefore represent an unnatural state, perhaps due to too few females. This suggests that opportunity for sperm competition should be maximised by increasing population densities, optimising sex ratios, and using artificial insemination. The lower fertility of hand-reared males may result from behavioural defects due to lack of exposure to conspecifics at critical development stages, as seen in other taxa. This potential negative impact of hand-rearing must be balanced against the short-term benefits it provides.
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Affiliation(s)
- Andrew Digby
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, New Zealand
| | - Daryl Eason
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, New Zealand
| | | | - Michael Lierz
- Clinic for Birds, Reptiles, Amphibians and Fish, Justus-Liebig University Giessen, Giessen, Germany
| | - Stephanie Galla
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand,Department of Biological Sciences, Boise State University, Boise, ID, United States of America
| | - Lara Urban
- Genomics Aotearoa, Dunedin, New Zealand,Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Marissa F. Le Lec
- Genomics Aotearoa, Dunedin, New Zealand,Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Joseph Guhlin
- Genomics Aotearoa, Dunedin, New Zealand,Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Tammy E. Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand,Genomics Aotearoa, Christchurch, New Zealand
| | - Peter K. Dearden
- Genomics Aotearoa, Dunedin, New Zealand,Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | - Caroline Lees
- IUCN SSC Conservation Planning Specialist Group, Auckland, New Zealand
| | - Tane Davis
- Te Rūnanga o Ngāi Tahu, Christchurch, New Zealand
| | - Deidre Vercoe
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, New Zealand
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14
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Davidović S, Marinković S, Hribšek I, Patenković A, Stamenković-Radak M, Tanasković M. Sex ratio and relatedness in the Griffon vulture ( Gyps fulvus) population of Serbia. PeerJ 2022; 10:e14477. [PMID: 36523455 PMCID: PMC9745909 DOI: 10.7717/peerj.14477] [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: 07/13/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
Background Once a widespread species across the region of Southeast Europe, the Griffon vulture is now confined to small and isolated populations across the Balkan Peninsula. The population from Serbia represents its biggest and most viable population that can serve as an important reservoir of genetic diversity from which the birds can be used for the region's reintroduction programmes. The available genetic data for this valuable population are scarce and as a protected species that belongs to the highly endangered vulture group, it needs to be well described so that it can be properly managed and used as a restocking population. Considering the serious recent bottleneck event that the Griffon vulture population from Serbia experienced we estimated the overall relatedness among the birds from this population. Sex ratio, another important parameter that shows the vitality and strength of the population was evaluated as well. Methods During the annual monitoring that was performed in the period from 2013-2021, we collected blood samples from individual birds that were marked in the nests. In total, 169 samples were collected and each was used for molecular sexing while 58 presumably unrelated birds from different nests were used for inbreeding and relatedness analyses. The relatedness was estimated using both biparentally (10 microsatellite loci) and uniparentally (Cytb and D-loop I of mitochondrial DNA) inherited markers. Results The level of inbreeding was relatively high and on average it was 8.3% while the mean number of relatives for each bird was close to three. The sex ratio was close to 1:1 and for the analysed period of 9 years, it didn't demonstrate a statistically significant deviation from the expected ratio of 1:1, suggesting that this is a stable and healthy population. Our data suggest that, even though a relatively high level of inbreeding can be detected among the individual birds, the Griffon vulture population from Serbia can be used as a source population for restocking and reintroduction programmes in the region. These data combined with previously observed genetic differentiation between the populations from the Iberian and Balkan Peninsulas suggest that the introduction of foreign birds should be avoided and that local birds should be used instead.
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Affiliation(s)
- Slobodan Davidović
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia,Birds of Prey Protection Foundation, Belgrade, Serbia
| | - Saša Marinković
- Birds of Prey Protection Foundation, Belgrade, Serbia,Department of Ecology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Irena Hribšek
- Birds of Prey Protection Foundation, Belgrade, Serbia,Natural History Museum Belgrade, Belgrade, Serbia
| | - Aleksandra Patenković
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Marina Stamenković-Radak
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia,Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Marija Tanasković
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
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15
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Srinivas Y, Yumnam B, Dutta S, Jhala Y. Assessing genetic diversity and population structure for prioritizing conservation of the critically endangered Great Indian Bustard (Aredotis nigriceps). Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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16
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Magid M, Wold JR, Moraga R, Cubrinovska I, Houston DM, Gartrell BD, Steeves TE. Leveraging an existing whole genome resequencing population dataset to characterize toll‐like receptor gene diversity in a threatened bird. Mol Ecol Resour 2022; 22:2810-2825. [PMID: 35635119 PMCID: PMC9543821 DOI: 10.1111/1755-0998.13656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/29/2022] [Accepted: 05/26/2022] [Indexed: 11/27/2022]
Abstract
Species recovery programs are increasingly using genomic data to measure neutral genetic diversity and calculate metrics like relatedness. While these measures can inform conservation management, determining the mechanisms underlying inbreeding depression requires information about functional genes associated with adaptive or maladaptive traits. Toll‐like receptors (TLRs) are one family of functional genes, which play a crucial role in recognition of pathogens and activation of the immune system. Previously, these genes have been analysed using species‐specific primers and PCR. Here, we leverage an existing short‐read reference genome, whole‐genome resequencing population data set, and bioinformatic tools to characterize TLR gene diversity in captive and wild tchūriwat’/tūturuatu/shore plover (Thinornis novaeseelandiae), a threatened bird endemic to Aotearoa New Zealand. Our results show that TLR gene diversity in tchūriwat’/tūturuatu is low, and forms two distinct captive and wild genetic clusters. The bioinformatic approach presented here has broad applicability to other threatened species with existing genomic resources in Aotearoa New Zealand and beyond.
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Affiliation(s)
- Molly Magid
- University of Canterbury School of Biological Sciences Christchurch NZ
| | - Jana R. Wold
- University of Canterbury School of Biological Sciences Christchurch NZ
| | - Roger Moraga
- Tea Break Bioinformatics, Ltd Palmerston North NZ
| | - Ilina Cubrinovska
- University of Canterbury School of Biological Sciences Christchurch NZ
| | | | - Brett D. Gartrell
- Wildbase Massey University Institute of Veterinary, Animal, and Biomedical Sciences, Palmerston North, Manawatu NZ
| | - Tammy E. Steeves
- University of Canterbury School of Biological Sciences Christchurch NZ
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17
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Undin M, Castro I. Predicting breeding systems to guide conservation strategies: A kiwi example. Ethology 2022. [DOI: 10.1111/eth.13286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Malin Undin
- Department of Natural Sciences Mid Sweden University Sundsvall Sweden
- Wildlife and Ecology Group, School of Agriculture and Environment Massey University Palmerston North New Zealand
| | - Isabel Castro
- Wildlife and Ecology Group, School of Agriculture and Environment Massey University Palmerston North New Zealand
- Wildbase Research Massey University Palmerston North New Zealand
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18
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Hauser S, Galla SJ, Putnam AS, Steeves TE, Latch EK. Comparing genome-based estimates of relatedness for use in pedigree-based conservation management. Mol Ecol Resour 2022; 22:2546-2558. [PMID: 35510790 DOI: 10.1111/1755-0998.13630] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 02/28/2022] [Accepted: 03/30/2022] [Indexed: 12/01/2022]
Abstract
Researchers have long debated which estimator of relatedness best captures the degree of relationship between two individuals. In the genomics era, this debate continues, with relatedness estimates being sensitive to the methods used to generate markers, marker quality, and levels of diversity in sampled individuals. Here, we compare six commonly used genome-based relatedness estimators (kinship genetic distance (KGD), Wang Maximum Likelihood (TrioML), Queller and Goodnight (Rxy ), Kinship INference for Genome-wide association studies (KING-robust), and Pairwise Relatedness (RAB ), allele-sharing co-ancestry (AS)) across five species bred in captivity-including three birds and two mammals-with varying degrees of reliable pedigree data, using reduced-representation and whole genome resequencing data. Genome-based relatedness estimates varied widely across estimators, sequencing methods, and species, yet the most consistent results for known first order relationships were found using Rxy , RAB , and AS. However, AS was found to be less consistently correlated with known pedigree relatedness than either Rxy or RAB . Our combined results indicate there is not a single genome-based estimator that is ideal across different species and data types. To determine the most appropriate genome-based relatedness estimator for each new dataset, we recommend assessing the relative: (1) correlation of candidate estimators with known relationships in the pedigree and (2) precision of candidate estimators with known first-order relationships. These recommendations are broadly applicable to conservation breeding programs, particularly where genome-based estimates of relatedness can complement and complete poorly pedigreed populations. Given a growing interest in the application of wild pedigrees, our results are also applicable to in-situ wildlife management.
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Affiliation(s)
- Samantha Hauser
- Department of Biological Sciences, University of Wisconsin, Milwaukee, Wisconsin, USA.,Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Stephanie J Galla
- School of Biological Sciences, University of Canterbury, New Zealand.,Department of Biological Sciences, Boise State University, Boise, Idaho, USA
| | - Andrea S Putnam
- Department of Exhibit-Curators, San Diego Zoo Wildlife Alliance, San Diego, California, USA
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, New Zealand
| | - Emily K Latch
- Department of Biological Sciences, University of Wisconsin, Milwaukee, Wisconsin, USA
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19
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Barrett KG, Amaral G, Elphinstone M, McAdie ML, Davis CS, Janes JK, Carnio J, Moehrenschlager A, Gorrell JC. Genetic management on the brink of extinction: sequencing microsatellites does not improve estimates of inbreeding in wild and captive Vancouver Island marmots (Marmota vancouverensis). CONSERV GENET 2022; 23:417-428. [PMID: 35401067 PMCID: PMC8948115 DOI: 10.1007/s10592-022-01429-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/04/2022] [Indexed: 11/27/2022]
Abstract
Captive breeding is often a last resort management option in the conservation of endangered species which can in turn lead to increased risk of inbreeding depression and loss of genetic diversity. Thus, recording breeding events via studbook for the purpose of estimating relatedness, and facilitating mating pair selection to minimize inbreeding, is common practice. However, as founder relatedness is often unknown, loss of genetic variation and inbreeding cannot be entirely avoided. Molecular genotyping is slowly being adopted in captive breeding programs, however achieving sufficient resolution can be challenging in small, low diversity, populations. Here, we evaluate the success of the Vancouver Island marmot (Marmota vancouverensis; VIM; among the worlds most endangered mammals) captive breeding program in preventing inbreeding and maintaining genetic diversity. We explored the use of high-throughput amplicon sequencing of microsatellite regions to assay greater genetic variation in both captive and wild populations than traditional length-based fragment analysis. Contrary to other studies, this method did not considerably increase diversity estimates, suggesting: (1) that the technique does not universally improve resolution, and (2) VIM have exceedingly low diversity. Studbook estimates of pairwise relatedness and inbreeding in the current population were weakly, but positively, correlated to molecular estimates. Thus, current studbooks are moderately effective at predicting genetic similarity when founder relatedness is known. Finally, we found that captive and wild populations did not differ in allelic frequencies, and conservation efforts to maintain diversity have been successful with no significant decrease in diversity over the last three generations.
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Affiliation(s)
- Kimberley G. Barrett
- Biology Department, Vancouver Island University, Nanaimo, BC V9R 5S5 Canada
- Present Address: Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2R3 Canada
| | - Geneviève Amaral
- Biology Department, Vancouver Island University, Nanaimo, BC V9R 5S5 Canada
- Present Address: Island Medical Program, University of Victoria, 3800 Finnerty Road, Victoria, BC V8P 5C2 Canada
| | | | | | - Corey S. Davis
- Present Address: Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2R3 Canada
| | - Jasmine K. Janes
- Biology Department, Vancouver Island University, Nanaimo, BC V9R 5S5 Canada
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351 Australia
| | - John Carnio
- Marmot Recovery Foundation, Nanaimo, BC V9R 6X9 Canada
| | - Axel Moehrenschlager
- Wilder Institute Calgary Zoo, Calgary, AB T2E 7V6 Canada
- IUCN Species Survival Commission, Conservation Translocation Specialist Group, Calgary, AB Canada
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20
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Genetic approaches for increasing fitness in endangered species. Trends Ecol Evol 2022; 37:332-345. [PMID: 35027225 DOI: 10.1016/j.tree.2021.12.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 12/02/2021] [Accepted: 12/06/2021] [Indexed: 12/17/2022]
Abstract
The global rate of wildlife extinctions is accelerating, and the persistence of many species requires conservation breeding programs. A central paradigm of these programs is to preserve the genetic diversity of the founder populations. However, this may preserve original characteristics that make them vulnerable to extinction. We introduce targeted genetic intervention (TGI) as an alternative approach that promotes traits that enable species to persist in the face of threats by changing the incidence of alleles that impact on fitness. The TGI toolkit includes methods with established efficacy in model organisms and agriculture but are largely untried for conservation, such as synthetic biology and artificial selection. We explore TGI approaches as a species-restoration tool for intractable threats including infectious disease and climate change.
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21
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Alvarez‐Estape M, Fontsere C, Serres‐Armero A, Kuderna LF, Dobrynin P, Guidara H, Pukazhenthi BS, Koepfli K, Marques‐Bonet T, Moreno E, Lizano E. Insights from the rescue and breeding management of Cuvier’s gazelle (
Gazella cuvieri
) through whole genome sequencing. Evol Appl 2021; 15:351-364. [PMID: 35386395 PMCID: PMC8965372 DOI: 10.1111/eva.13336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 12/03/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
- Marina Alvarez‐Estape
- Institute of Evolutionary Biology UPF‐CSIC PRBB, Dr. Aiguader 88 08003 Barcelona Spain
| | - Claudia Fontsere
- Institute of Evolutionary Biology UPF‐CSIC PRBB, Dr. Aiguader 88 08003 Barcelona Spain
| | - Aitor Serres‐Armero
- Institute of Evolutionary Biology UPF‐CSIC PRBB, Dr. Aiguader 88 08003 Barcelona Spain
| | - Lukas F.K. Kuderna
- Institute of Evolutionary Biology UPF‐CSIC PRBB, Dr. Aiguader 88 08003 Barcelona Spain
| | - Pavel Dobrynin
- ITMO University Computer Technologies Laboratory St. Petersburg Russian Federation
- Smithsonian Conservation Biology Institute Center for Species Survival National Zoological Park Front Royal, VA and Washington DC USA
| | - Héla Guidara
- Direction Générale des Forêts 30 rue Alain Savary 1002 Tunis Tunisia
| | - Budhan S. Pukazhenthi
- Smithsonian Conservation Biology Institute Center for Species Survival National Zoological Park Front Royal, VA and Washington DC USA
| | - Klaus‐Peter Koepfli
- ITMO University Computer Technologies Laboratory St. Petersburg Russian Federation
- Smithsonian Conservation Biology Institute Center for Species Survival National Zoological Park Front Royal, VA and Washington DC USA
- Smithsonian‐Mason School of Conservation Front Royal VA USA
| | - Tomas Marques‐Bonet
- Institute of Evolutionary Biology UPF‐CSIC PRBB, Dr. Aiguader 88 08003 Barcelona Spain
- CNAG‐CRG Centre for Genomic Regulation (CRG) Barcelona Institute of Science and Technology (BIST) Baldiri I Reixac 408028 Barcelona Spain
- Institut Català de Paleontologia Miquel Crusafont Universitat Autònoma de Barcelona (UAB) Edifici ICTA‐ICP, c/ Columnes s/n Cerdanyola del Vallès 08193 Barcelona Spain
- Catalan Institution of Research and Advanced Studies (ICREA) Passeig de Lluís Companys 23 08010 Barcelona Spain
| | - Eulalia Moreno
- Dept Ecología Funcional y Evolutiva Estación Experimental de Zonas Áridas‐CSIC E‐04120 La Cañada de San Urbano Almería Spain
| | - Esther Lizano
- Institute of Evolutionary Biology UPF‐CSIC PRBB, Dr. Aiguader 88 08003 Barcelona Spain
- Institut Català de Paleontologia Miquel Crusafont Universitat Autònoma de Barcelona (UAB) Edifici ICTA‐ICP, c/ Columnes s/n Cerdanyola del Vallès 08193 Barcelona Spain
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22
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Duntsch L, Brekke P, Ewen JG, Santure AW. Who are you? A framework to identify and report genetic sample mix-ups. Mol Ecol Resour 2021; 22:1855-1867. [PMID: 34907643 DOI: 10.1111/1755-0998.13575] [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: 02/25/2021] [Revised: 12/01/2021] [Accepted: 12/07/2021] [Indexed: 11/28/2022]
Abstract
Sample mix-ups occur when samples have accidentally been duplicated, mislabelled or swapped. When samples are subsequently genotyped or sequenced, this can lead to individual IDs being incorrectly linked to genetic data, resulting in incorrect or biased research results, or reduced power to detect true biological patterns. We surveyed the community and found that almost 80% of responding researchers have encountered sample mix-ups. However, many recent studies in the field of molecular ecology do not appear to systematically report individual assignment checks as part of their publications. Although checks may be done, lack of consistent reporting means that it is difficult to assess whether sample mix-ups have occurred or been detected. Here, we present an easy-to-follow sample verification framework that can utilise existing metadata, including species, population structure, sex and pedigree information. We demonstrate its application to a dataset representing individuals of a threatened Aotearoa New Zealand bird species, the hihi, genotyped on a 50K SNP array. We detected numerous incorrect genotype-ID associations when comparing observed and genetic sex or comparing to relationships in a verified microsatellite pedigree. The framework proposed here helped to confirm 488 individuals (39%), correct another 20 bird-genotype links, and detect hundreds of incorrect sample IDs, emphasizing the value of routinely checking genetic and genomic datasets for their accuracy. We therefore promote the implementation and reporting of this simple yet effective sample verification framework as a standardized quality control step for studies in the field of molecular ecology.
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Affiliation(s)
- Laura Duntsch
- Centre for Biodiversity and Biosecurity, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - John G Ewen
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - Anna W Santure
- Centre for Biodiversity and Biosecurity, School of Biological Sciences, University of Auckland, Auckland, New Zealand
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23
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Dolman PM, Burnside RJ, Scotland KM, Collar NJ. Captive breeding and the conservation of the threatened houbara bustards. ENDANGER SPECIES RES 2021. [DOI: 10.3354/esr01151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Translocation of captive-bred individuals to reinforce wild populations may be an important conservation approach for some species, but can be detrimental when employed to boost exploited wild populations, particularly where repeated long-term reinforcement aims to compensate for repeated unregulated offtake. We review evidence that captive breeding alters multiple physiological, life-history and temperamental traits through founder effects, genetic drift and unintended adaption to captivity; degrades learnt behaviours; and compromises biogeography, population structure and viability through introgression. We highlight these risks for the globally threatened African houbara Chlamydotis undulata and Asian houbara C. macqueenii, 2 bustard species hunted throughout much of their ranges and now subject to multiple large-scale captive-breeding programmes and translocations. In eastern Morocco, annual releases of captive-bred African houbara are 2‒3 times higher than original wild numbers, but no investigation of their potentially deleterious effects has, to our knowledge, been published, although most wild populations may now have been replaced by captive-bred domestic stock, which are reportedly not self-sustaining. Despite multiple decades of reinforcement, we are not aware of any analysis of the contribution of captive breeding to African houbara population dynamics, or of the genomic consequences. Asian houbara release programmes may also be promoting rather than preventing declines, and need to contextualise themselves through rigorous analyses of wild population numbers, demographic rates and threats, maintenance of phylogeographic concordance of released with supplemented populations, profiling of traits crucial to survival and the measurement and modelling of the impacts of reinforcement on physiological and behavioural fitness of wild populations.
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Affiliation(s)
- PM Dolman
- School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - RJ Burnside
- School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - KM Scotland
- Emirates Bird Breeding Centre for Conservation, Al Ain, Abu Dhabi, United Arab Emirates
| | - NJ Collar
- BirdLife International, Cambridge CB2 3QZ, UK
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24
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New developments in the field of genomic technologies and their relevance to conservation management. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01415-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
AbstractRecent technological advances in the field of genomics offer conservation managers and practitioners new tools to explore for conservation applications. Many of these tools are well developed and used by other life science fields, while others are still in development. Considering these technological possibilities, choosing the right tool(s) from the toolbox is crucial and can pose a challenging task. With this in mind, we strive to inspire, inform and illuminate managers and practitioners on how conservation efforts can benefit from the current genomic and biotechnological revolution. With inspirational case studies we show how new technologies can help resolve some of the main conservation challenges, while also informing how implementable the different technologies are. We here focus specifically on small population management, highlight the potential for genetic rescue, and discuss the opportunities in the field of gene editing to help with adaptation to changing environments. In addition, we delineate potential applications of gene drives for controlling invasive species. We illuminate that the genomic toolbox offers added benefit to conservation efforts, but also comes with limitations for the use of these novel emerging techniques.
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25
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Galla SJ, Brown L, Couch-Lewis Ngāi Tahu Te Hapū O Ngāti Wheke Ngāti Waewae Y, Cubrinovska I, Eason D, Gooley RM, Hamilton JA, Heath JA, Hauser SS, Latch EK, Matocq MD, Richardson A, Wold JR, Hogg CJ, Santure AW, Steeves TE. The relevance of pedigrees in the conservation genomics era. Mol Ecol 2021; 31:41-54. [PMID: 34553796 PMCID: PMC9298073 DOI: 10.1111/mec.16192] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/12/2021] [Accepted: 09/17/2021] [Indexed: 01/21/2023]
Abstract
Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long‐standing tools available to manage genetics—the pedigree—has been widely used to characterize diversity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput sequencing to estimate relatedness, inbreeding, and genome‐wide functional diversity, some have asked whether it is warranted for conservation biologists to continue collecting and collating pedigrees for species management. In this perspective, we argue that pedigrees remain a relevant tool, and when combined with genomic data, create an invaluable resource for conservation genomic management. Genomic data can address pedigree pitfalls (e.g., founder relatedness, missing data, uncertainty), and in return robust pedigrees allow for more nuanced research design, including well‐informed sampling strategies and quantitative analyses (e.g., heritability, linkage) to better inform genomic inquiry. We further contend that building and maintaining pedigrees provides an opportunity to strengthen trusted relationships among conservation researchers, practitioners, Indigenous Peoples, and Local Communities.
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Affiliation(s)
- Stephanie J Galla
- Department of Biological Sciences, Boise State University, Boise, Idaho, USA.,School of Biological Sciences, University of Canterbury, Christchurch, Canterbury, New Zealand
| | - Liz Brown
- New Zealand Department of Conservation, Twizel, Canterbury, New Zealand
| | | | - Ilina Cubrinovska
- School of Biological Sciences, University of Canterbury, Christchurch, Canterbury, New Zealand
| | - Daryl Eason
- New Zealand Department of Conservation, Invercargill, Southland, New Zealand
| | - Rebecca M Gooley
- Smithsonian-Mason School of Conservation, Front Royal, Maryland, USA.,Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA
| | - Jill A Hamilton
- Department of Biological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Julie A Heath
- Department of Biological Sciences, Boise State University, Boise, Idaho, USA
| | - Samantha S Hauser
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Emily K Latch
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Marjorie D Matocq
- Department of Natural Resources and Environmental Science, Program in Ecology, Evolution and Conservation Biology, University of Nevada Reno, Reno, Nevada, USA
| | - Anne Richardson
- The Isaac Conservation and Wildlife Trust, Christchurch, Canterbury, New Zealand
| | - Jana R Wold
- School of Biological Sciences, University of Canterbury, Christchurch, Canterbury, New Zealand
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, Auckland, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, Canterbury, New Zealand
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26
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Dickel L, Arcese P, Nietlisbach P, Keller LF, Jensen H, Reid JM. Are immigrants outbred and unrelated? Testing standard assumptions in a wild metapopulation. Mol Ecol 2021; 30:5674-5686. [PMID: 34516687 DOI: 10.1111/mec.16173] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 11/30/2022]
Abstract
Immigration into small recipient populations is expected to alleviate inbreeding and increase genetic variation, and hence facilitate population persistence through genetic and/or evolutionary rescue. Such expectations depend on three standard assumptions: that immigrants are outbred, unrelated to existing natives at arrival, and unrelated to each other. These assumptions are rarely explicitly verified, including in key field systems in evolutionary ecology. Yet, they could be violated due to non-random or repeated immigration from adjacent small populations. We combined molecular genetic marker data for 150-160 microsatellite loci with comprehensive pedigree data to test the three assumptions for a song sparrow (Melospiza melodia) population that is a model system for quantifying effects of inbreeding and immigration in the wild. Immigrants were less homozygous than existing natives on average, with mean homozygosity that closely resembled outbred natives. Immigrants can therefore be considered outbred on the focal population scale. Comparisons of homozygosity of real or hypothetical offspring of immigrant-native, native-native and immigrant-immigrant pairings implied that immigrants were typically unrelated to existing natives and to each other. Indeed, immigrants' offspring would be even less homozygous than outbred individuals on the focal population scale. The three standard assumptions of population genetic and evolutionary theory were consequently largely validated. Yet, our analyses revealed some deviations that should be accounted for in future analyses of heterosis and inbreeding depression, implying that the three assumptions should be verified in other systems to probe patterns of non-random or repeated dispersal and facilitate precise and unbiased estimation of key evolutionary parameters.
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Affiliation(s)
- Lisa Dickel
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Peter Arcese
- Department of Forest & Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pirmin Nietlisbach
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Lukas F Keller
- Department of Evolutionary Biology & Environmental Studies, University of Zurich, Zurich, Switzerland.,Zoological Museum, University of Zurich, Zurich, Switzerland
| | - Henrik Jensen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jane M Reid
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway.,School of Biological Sciences, University of Aberdeen, Aberdeen, UK
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27
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Samaha G, Wade CM, Mazrier H, Grueber CE, Haase B. Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management. BMC Genomics 2021; 22:601. [PMID: 34362297 PMCID: PMC8348863 DOI: 10.1186/s12864-021-07899-2] [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: 09/30/2020] [Accepted: 07/14/2021] [Indexed: 11/10/2022] Open
Abstract
Background While recent advances in genomics has enabled vast improvements in the quantification of genome-wide diversity and the identification of adaptive and deleterious alleles in model species, wildlife and non-model species have largely not reaped the same benefits. This has been attributed to the resources and infrastructure required to develop essential genomic datasets such as reference genomes. In the absence of a high-quality reference genome, cross-species alignments can provide reliable, cost-effective methods for single nucleotide variant (SNV) discovery. Here, we demonstrated the utility of cross-species genome alignment methods in gaining insights into population structure and functional genomic features in cheetah (Acinonyx jubatas), snow leopard (Panthera uncia) and Sumatran tiger (Panthera tigris sumatrae), relative to the domestic cat (Felis catus). Results Alignment of big cats to the domestic cat reference assembly yielded nearly complete sequence coverage of the reference genome. From this, 38,839,061 variants in cheetah, 15,504,143 in snow leopard and 13,414,953 in Sumatran tiger were discovered and annotated. This method was able to delineate population structure but limited in its ability to adequately detect rare variants. Enrichment analysis of fixed and species-specific SNVs revealed insights into adaptive traits, evolutionary history and the pathogenesis of heritable diseases. Conclusions The high degree of synteny among felid genomes enabled the successful application of the domestic cat reference in high-quality SNV detection. The datasets presented here provide a useful resource for future studies into population dynamics, evolutionary history and genetic and disease management of big cats. This cross-species method of variant discovery provides genomic context for identifying annotated gene regions essential to understanding adaptive and deleterious variants that can improve conservation outcomes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07899-2.
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Affiliation(s)
- Georgina Samaha
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW, Australia.
| | - Claire M Wade
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Hamutal Mazrier
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Catherine E Grueber
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Bianca Haase
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
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28
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Flanagan AM, Masuda B, Grueber CE, Sutton JT. Moving from trends to benchmarks by using regression tree analysis to find inbreeding thresholds in a critically endangered bird. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2021; 35:1278-1287. [PMID: 33025666 DOI: 10.1111/cobi.13650] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/03/2020] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Abstract
Understanding how inbreeding affects endangered species in conservation breeding programs is essential for their recovery. The Hawaiian Crow ('Alalā) (Corvus hawaiiensis) is one of the world's most endangered birds. It went extinct in the wild in 2002, and, until recent release efforts starting in 2016, nearly all of the population remained under human care for conservation breeding. Using pedigree inbreeding coefficients (F), we evaluated the effects of inbreeding on Hawaiian Crow offspring survival and reproductive success. We used regression tree analysis to identify the level of inbreeding (i.e., inbreeding threshold) that explains a substantial decrease in 'Alalā offspring survival to recruitment. Similar to a previous study of inbreeding in 'Alalā, we found that inbreeding had a negative impact on offspring survival but that parental (vs. artificial) egg incubation improved offspring survival to recruitment. Furthermore, we found that inbreeding did not substantially affect offspring reproductive success, based on the assumption that offspring that survive to adulthood breed with distantly related mates. Our novel application of regression tree analysis showed that offspring with inbreeding levels exceeding F = 0.098 were 69% less likely to survive to recruitment than more outbred offspring, providing a specific threshold value for ongoing population management. Our results emphasize the importance of assessing inbreeding depression across all life history stages, confirm the importance of prioritizing parental over artificial egg incubation in avian conservation breeding programs, and demonstrate the utility of regression tree analysis as a tool for identifying inbreeding thresholds, if present, in any pedigree-managed population.
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Affiliation(s)
- Alison M Flanagan
- Hawaii Endangered Bird Conservation Program, Institute for Conservation Research, San Diego Zoo Global, P.O. Box 39, Volcano, HI, 96785, U.S.A
| | - Bryce Masuda
- Hawaii Endangered Bird Conservation Program, Institute for Conservation Research, San Diego Zoo Global, P.O. Box 39, Volcano, HI, 96785, U.S.A
| | - Catherine E Grueber
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jolene T Sutton
- Department of Biology, University of Hawaii at Hilo, Hilo, HI, 96720, U.S.A
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29
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Forsdick NJ, Martini D, Brown L, Cross HB, Maloney RF, Steeves TE, Knapp M. Genomic sequencing confirms absence of introgression despite past hybridisation between a critically endangered bird and its common congener. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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30
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Robledo-Ruiz DA, Pavlova A, Clarke RH, Magrath MJL, Quin B, Harrisson KA, Gan HM, Low GW, Sunnucks P. A novel framework for evaluating in situ breeding management strategies in endangered populations. Mol Ecol Resour 2021; 22:239-253. [PMID: 34288508 DOI: 10.1111/1755-0998.13476] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 06/29/2021] [Accepted: 07/15/2021] [Indexed: 11/30/2022]
Abstract
Conservation breeding management aims to reduce inbreeding and maximize the retention of genetic diversity in endangered populations. However, breeding management of wild populations is still rare, and there is a need for approaches that provide data-driven evidence of the likelihood of success of alternative in situ strategies. Here, we provide an analytical framework that uses in silico simulations to evaluate, for real wild populations, (i) the degree of population-level inbreeding avoidance, (ii) the genetic quality of mating pairs, and (iii) the potential genetic benefits of implementing two breeding management strategies. The proposed strategies aim to improve the genetic quality of breeding pairs by splitting detrimental pairs and allowing the members to re-pair in different ways. We apply the framework to the wild population of the Critically Endangered helmeted honeyeater by combining genomic data and field observations to estimate the inbreeding (i.e., pair-kinship) and genetic quality (i.e., Mate Suitability Index) of all mating pairs for seven consecutive breeding seasons. We found no evidence of population-level inbreeding avoidance and that ~91.6% of breeding pairs were detrimental to the genetic health of the population. Furthermore, the framework revealed that neither proposed management strategy would significantly improve the genetic quality or reduce inbreeding of the mating pairs in this population. Our results demonstrate the usefulness of our analytical framework for testing the efficacy of different in situ breeding management strategies and for making evidence-based management decisions.
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Affiliation(s)
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - Rohan H Clarke
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - Michael J L Magrath
- Department of Wildlife Conservation and Science, Zoos Victoria, Parkville, Vic., Australia.,School of BioSciences, University of Melbourne, Parkville, Vic., Australia
| | - Bruce Quin
- Department of Environment, Land, Water and Planning, Woori Yallock, Vic., Australia
| | - Katherine A Harrisson
- Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Vic., Australia.,Department of Environment, Land, Water and Planning, Arthur Rylah Institute for Environmental Research, Heidelberg, Vic., Australia
| | - Han Ming Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Vic., Australia.,Deakin Genomics Centre, Deakin University, Geelong, Vic., Australia
| | - Gabriel W Low
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
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31
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Meta-analytic evidence that animals rarely avoid inbreeding. Nat Ecol Evol 2021; 5:949-964. [PMID: 33941905 DOI: 10.1038/s41559-021-01453-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 03/24/2021] [Indexed: 02/02/2023]
Abstract
Animals are usually expected to avoid mating with relatives (kin avoidance) as incestuous mating can lead to the expression of inbreeding depression. Yet, theoretical models predict that unbiased mating with regards to kinship should be common, and that under some conditions, the inclusive fitness benefits associated with inbreeding can even lead to a preference for mating with kin. This mismatch between empirical and theoretical expectations generates uncertainty as to the prevalence of inbreeding avoidance in animals. Here, we synthesized 677 effect sizes from 139 experimental studies of mate choice for kin versus non-kin in diploid animals, representing 40 years of research, using a meta-analytical approach. Our meta-analysis revealed little support for the widely held view that animals avoid mating with kin, despite clear evidence of publication bias. Instead, unbiased mating with regards to kinship appears widespread across animals and experimental conditions. The significance of a variety of moderators was explored using meta-regressions, revealing that the degree of relatedness and prior experience with kin explained some variation in the effect sizes. Yet, we found no difference in kin avoidance between males and females, choice and no-choice experiments, mated and virgin animals or between humans and animals. Our findings highlight the need to rethink the widely held view that inbreeding avoidance is a given in experimental studies.
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32
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Genetic structure and population history in two critically endangered Kaua‘i honeycreepers. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01382-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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33
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Seaborn T, Andrews KR, Applestein CV, Breech TM, Garrett MJ, Zaiats A, Caughlin TT. Integrating genomics in population models to forecast translocation success. Restor Ecol 2021. [DOI: 10.1111/rec.13395] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Travis Seaborn
- Department of Fish and Wildlife Sciences University of Idaho Moscow ID U.S.A
| | - Kimberly R. Andrews
- Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow ID U.S.A
| | | | - Tyler M. Breech
- Department of Biological Sciences Idaho State University Pocatello ID U.S.A
| | - Molly J. Garrett
- Department of Fish and Wildlife Sciences University of Idaho Moscow ID U.S.A
| | - Andrii Zaiats
- Biological Sciences Boise State University Boise ID U.S.A
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34
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Baveja P, Garg KM, Chattopadhyay B, Sadanandan KR, Prawiradilaga DM, Yuda P, Lee JGH, Rheindt FE. Using historical genome-wide DNA to unravel the confused taxonomy in a songbird lineage that is extinct in the wild. Evol Appl 2021; 14:698-709. [PMID: 33767745 PMCID: PMC7980273 DOI: 10.1111/eva.13149] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/13/2020] [Indexed: 11/29/2022] Open
Abstract
Urgent conservation action for terminally endangered species is sometimes hampered by taxonomic uncertainty, especially in illegally traded animals that are often cross-bred in captivity. To overcome these problems, we used a genomic approach to analyze historical DNA from museum samples across the Asian Pied Starling (Gracupica contra) complex in tropical Asia, a popular victim of the ongoing songbird crisis whose distinct Javan population ("Javan Pied Starling") is extinct in the wild and subject to admixture in captivity. Comparing genomic profiles across the entire distribution, we detected three deeply diverged lineages at the species level characterized by a lack of genomic intermediacy near areas of contact. Our study demonstrates that the use of historical DNA can be instrumental in delimiting species in situations of taxonomic uncertainty, especially when modern admixture may obfuscate species boundaries. Results of our research will enable conservationists to commence a dedicated ex situ breeding program for the Javan Pied Starling, and serve as a blueprint for similar conservation problems involving terminally endangered species subject to allelic infiltration from close congeners.
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Affiliation(s)
- Pratibha Baveja
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Kritika M. Garg
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
- Institute of Bioinformatics and Applied BiotechnologyBangaloreIndia
| | - Balaji Chattopadhyay
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Keren R. Sadanandan
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
- Max Planck Institute for OrnithologySeewiesenGermany
| | | | - Pramana Yuda
- Fakultas TeknobiologiUniversitas Atma Jaya YogyakartaYogyakartaIndonesia
| | - Jessica G. H. Lee
- Department of Conservation and ResearchWildlife Reserves SingaporeSingaporeSingapore
| | - Frank E. Rheindt
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
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35
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Undin M, Lockhart PJ, Hills SFK, Castro I. Genetic Rescue and the Plight of Ponui Hybrids. FRONTIERS IN CONSERVATION SCIENCE 2021. [DOI: 10.3389/fcosc.2020.622191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Long-term sustainable and resilient populations is a key goal of conservation. How to best achieve this is controversial. There are, for instance, polarized views concerning the fitness and conservation value of hybrid populations founded through multi-origin translocations. A classic example concerns Apteryx (kiwi) in New Zealand. The A. mantelli of Ponui Island constitute a hybrid population where the birds are highly successful in their island habitat. A key dilemma for managers is understanding the reason for this success. Are the hybrid birds of Ponui Island of “no future conservation value” as recently asserted, or do they represent an outstanding example of genetic rescue and an important resource for future translocations? There has been a paradigm shift in scientific thinking concerning hybrids, but the ecological significance of admixed genomes remains difficult to assess. This limits what we can currently predict in conservation science. New understanding from genome science challenges the sufficiency of population genetic models to inform decision making and suggests instead that the contrasting outcomes of hybridization, “outbreeding depression” and “heterosis,” require understanding additional factors that modulate gene and protein expression and how these factors are influenced by the environment. We discuss these findings and the investigations that might help us to better understand the birds of Ponui, inform conservation management of kiwi and provide insight relevant for the future survival of Apteryx.
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36
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Iglesias Pastrana C, Navas González FJ, Ruiz Aguilera MJ, Dávila García JA, Delgado Bermejo JV, Abelló MT. White-naped mangabeys' viable insurance population within European Zoo Network. Sci Rep 2021; 11:674. [PMID: 33436901 PMCID: PMC7804940 DOI: 10.1038/s41598-020-80281-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 12/18/2020] [Indexed: 01/29/2023] Open
Abstract
The success and viability of an ex-situ conservation program lie in the establishment and potential maintenance of a demographically and genetically viable insurance population. Such population reserve may support reintroduction and reinforcement activities of wild populations. White-naped mangabeys are endangered restricted-range African primates which have experienced a dramatic population decrease in their natural habitats over the last few decades. Since 2001, some European zoos singularly monitor an ex-situ population aiming to seek the recovery of the current wild population. The aim of the present paper is to evaluate the genetic status and population demographics of European zoo-captive white-naped mangabeys based on pedigree data. The captive population is gradually growing and preserves specific reproductive and demographic parameters linked to the species. The intensive management program that is implemented has brought about the minimization of inbreeding and average relatedness levels, thus maintaining high levels of genetic diversity despite the existence of fragmented populations. This finding suggests white-naped mangabey ex-situ preservation actions may be a good example of multifaceted conservation throughout studbook management which could be used as a model for other ex-situ live-animal populations.
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Affiliation(s)
| | | | | | | | | | - María Teresa Abelló
- White-naped mangabey EEP Coordination (EAZA: European Association of Zoos & Aquariums), Parc Zoològic de Barcelona, Barcelona, Spain
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Duntsch L, Tomotani BM, de Villemereuil P, Brekke P, Lee KD, Ewen JG, Santure AW. Polygenic basis for adaptive morphological variation in a threatened Aotearoa | New Zealand bird, the hihi ( Notiomystis cincta). Proc Biol Sci 2020; 287:20200948. [PMID: 32842928 PMCID: PMC7482260 DOI: 10.1098/rspb.2020.0948] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 07/30/2020] [Indexed: 12/26/2022] Open
Abstract
To predict if a threatened species can adapt to changing selective pressures, it is crucial to understand the genetic basis of adaptive traits, especially in species historically affected by severe bottlenecks. We estimated the heritability of three hihi (Notiomystis cincta) morphological traits known to be under selection (nestling tarsus length, body mass and head-bill length) using 523 individuals and 39 699 single nucleotide polymorphisms (SNPs) from a 50 K Affymetrix SNP chip. We then examined the genetic architecture of the traits via chromosome partitioning analyses and genome-wide association scans (GWAS). Heritabilities estimated using pedigree relatedness or genomic relatedness were low. For tarsus length, the proportion of genetic variance explained by each chromosome was positively correlated with its size, and more than one chromosome explained significant variation for body mass and head-bill length. Finally, GWAS analyses suggested many loci of small effect contributing to trait variation for all three traits, although one locus (an SNP within an intron of the transcription factor HEY2) was tentatively associated with tarsus length. Our findings suggest a polygenic nature for the morphological traits, with many small effect size loci contributing to the majority of the variation, similar to results from many other wild populations. However, the small effective population size, polygenic architecture and already low heritabilities suggest that both the total response and rate of response to selection are likely to be limited in hihi.
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Affiliation(s)
- Laura Duntsch
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Pierre de Villemereuil
- Institut de Systématique, Évolution, Biodiversité (ISYEB), École Pratique des Hautes Études PSL, MNHN, CNRS, Sorbonne Université, Université des Antilles, Paris, France
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - Kate D. Lee
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - John G. Ewen
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - Anna W. Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony. G3-GENES GENOMES GENETICS 2020; 10:2787-2799. [PMID: 32540866 PMCID: PMC7407454 DOI: 10.1534/g3.120.401268] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
High density single nucleotide polymorphism (SNP) arrays allow large numbers of individuals to be rapidly and cost-effectively genotyped at large numbers of genetic markers. However, despite being widely used in studies of humans and domesticated plants and animals, SNP arrays are lacking for most wild organisms. We developed a custom 85K Affymetrix Axiom array for an intensively studied pinniped, the Antarctic fur seal (Arctocephalus gazella). SNPs were discovered from a combination of genomic and transcriptomic resources and filtered according to strict criteria. Out of a total of 85,359 SNPs tiled on the array, 75,601 (88.6%) successfully converted and were polymorphic in 270 animals from a breeding colony at Bird Island in South Georgia. Evidence was found for inbreeding, with three genomic inbreeding coefficients being strongly intercorrelated and the proportion of the genome in runs of homozygosity being non-zero in all individuals. Furthermore, analysis of genomic relatedness coefficients identified previously unknown first-degree relatives and multiple second-degree relatives among a sample of ostensibly unrelated individuals. Such “cryptic relatedness” within fur seal breeding colonies may increase the likelihood of consanguineous matings and could therefore have implications for understanding fitness variation and mate choice. Finally, we demonstrate the cross-amplification potential of the array in three related pinniped species. Overall, our SNP array will facilitate future studies of Antarctic fur seals and has the potential to serve as a more general resource for the wider pinniped research community.
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Rayne A, Byrnes G, Collier‐Robinson L, Hollows J, McIntosh A, Ramsden M, Rupene M, Tamati‐Elliffe P, Thoms C, Steeves TE. Centring Indigenous knowledge systems to re‐imagine conservation translocations. PEOPLE AND NATURE 2020. [DOI: 10.1002/pan3.10126] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Aisling Rayne
- School of Biological Sciences University of Canterbury Christchurch New Zealand
| | - Greg Byrnes
- Te Kōhaka o Tūhaitara Trust Christchurch New Zealand
| | | | | | - Angus McIntosh
- School of Biological Sciences University of Canterbury Christchurch New Zealand
| | | | - Makarini Rupene
- Environment Canterbury Christchurch New Zealand
- Ngāi Tahu Research Centre University of Canterbury Christchurch New Zealand
| | | | - Channell Thoms
- School of Biological Sciences University of Canterbury Christchurch New Zealand
| | - Tammy E. Steeves
- School of Biological Sciences University of Canterbury Christchurch New Zealand
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