1
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By Bits and Pieces: The Contributions of Zoos and Aquariums to Science and Society via Biomaterials. JOURNAL OF ZOOLOGICAL AND BOTANICAL GARDENS 2023. [DOI: 10.3390/jzbg4010023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
Scientific research has long been recognized as one of the four pillars of the zoo or aquarium mission, alongside recreation, conservation, and education. This study sought to quantify a sample of zoos’ participation in scientific research via the provision of biomaterials from animals to outside scientists and the associated training of undergraduate and graduate students that resulted from these projects. A convenience sample of zoos provided data on their participation in biomaterials-related projects and a focused analysis of biomaterials-related research facilitated by the Saint Louis Zoo was conducted. In addition, the Association of Zoos & Aquariums’ conservation & science database was queried to uncover what research projects AZA members engaged in over the last five years that likely involved biomaterials research and training of students. Results demonstrate that zoos are making significant contributions to science by agreeing to participate in large numbers of biomaterials-related projects across different areas of focus involving a variety of animal species annually, with results applicable to human and non-human animals. Support of such research often involves student thesis projects, thus contributing to the education of future scientists.
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2
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Lyu D, Sun S, Shan X, Wang W. Inbreeding evaluation using microsatellite confirmed inbreeding depression in growth in the Fenneropenaeus chinensis natural population. Front Genet 2023; 14:1077814. [PMID: 36845375 PMCID: PMC9947229 DOI: 10.3389/fgene.2023.1077814] [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: 10/23/2022] [Accepted: 01/27/2023] [Indexed: 02/11/2023] Open
Abstract
Understanding inbreeding depressions (IBDs), the effect on the phenotypic performance of inbreeding, is of major importance for evolution and conservation genetics. Inbreeding depressions in aquatic animals were well documented in a domestic or captive population, while there is less evidence of inbreeding depression in natural populations. Chinese shrimp, Fenneropenaeus chinensis, is an important species in both aquaculture and fishery activities in China. To investigate inbreeding depression in natural populations, four Fenneropenaeus chinensis natural populations (Huanghua, Qinhuangdao, Qingdao, and Haiyang) were collected from the Bohai and Yellow seas. Microsatellite markers were used to evaluate individual inbreeding coefficients (F) of all samples. Furthermore, the effects of inbreeding on growth traits were investigated. The results showed marker-based F was continuous and ranged from 0 to 0.585, with an average of 0.191 ± 0.127, and there was no significant difference among the average F of the four populations. Regression analysis using the four populations showed inbreeding had a very significant (p < 0.01) effect on body weight. When analyzing a single population, regression coefficients were also all negative and those in Huanghua and in Qingdao were significant at the level of p < 0.05 and < 0.01, respectively. Inbreeding depressions, expressed as the percent change in body weight per 10% increase in F, were 2.75% in Huanghua, 2.22% in Qingdao, and 3.69% in all samples. This study provided a piece of rare evidence of inbreeding depression in natural populations and also guidance toward the conservation of wild Fenneropenaeus chinensis resources.
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Affiliation(s)
- Ding Lyu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China,Function Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Song Sun
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China,Function Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiujuan Shan
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China,Function Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Weiji Wang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China,Function Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China,*Correspondence: Weiji Wang,
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3
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Gray R, Fusco N, Miller JM, Tapia W, Mariani C, Caccone A, Jensen EL. Temporal Monitoring of the Floreana Island Galapagos Giant Tortoise Captive Breeding Program. Integr Comp Biol 2022; 62:1864-1871. [PMID: 35906184 DOI: 10.1093/icb/icac129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/22/2022] [Accepted: 07/22/2022] [Indexed: 01/05/2023] Open
Abstract
Captive breeding programs benefit from genetic analyses that identify relatedness between individuals, assign parentage to offspring, and track levels of genetic diversity. Monitoring these parameters across breeding cycles is critical to the success of a captive breeding program as it allows conservation managers to iteratively evaluate and adjust program structure. However, in practice, genetic tracking of breeding outcomes is rarely conducted. Here, we examined the first three offspring cohorts (2017-2020) of the genetically informed captive breeding program for the Floreana Island Galapagos giant tortoise, Chelonoidis niger. This captive breeding program is unique as the Floreana tortoise has been extinct since the 1800s, but its genome persists, in part, in the form of living hybrids with the extant Volcano Wolf tortoise, C. becki. Breeding over the study period took place at the Galapagos National Park Directorate breeding facility in four corrals, each containing three females and two males. Using 17 microsatellite markers, we were able to assign parentage to 94 of the 98 offspring produced over the study period. We observe that despite the addition of more founders since the pilot breeding program, the effective population size remains low, and changes to the arrangements of breeding corrals may be necessary to encourage more equal reproductive output from the males. This study demonstrates the value of hybrids for species restoration and the importance of continually reassessing the outcomes of captive breeding.
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Affiliation(s)
- Rachel Gray
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Nicole Fusco
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Joshua M Miller
- Department of Biological Sciences, MacEwan University, Edmonton, AB T5J 4S2, Canada
| | - Washington Tapia
- Galapagos Conservancy, Fairfax, VA 22030, USA.,University of Málaga, Campus Teatinos, Apdo. 59. 29080 Málaga, Spain
| | - Carol Mariani
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Evelyn L Jensen
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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4
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Escoda L, Hawlitschek O, González-Esteban J, Castresana J. Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity. Sci Rep 2022; 12:21390. [PMID: 36496459 PMCID: PMC9741620 DOI: 10.1038/s41598-022-25619-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/01/2022] [Indexed: 12/13/2022] Open
Abstract
Recently, populations of various species with very low genetic diversity have been discovered. Some of these persist in the long term, but others could face extinction due to accelerated loss of fitness. In this work, we characterize 45 individuals of one of these populations, belonging to the Iberian desman (Galemys pyrenaicus). For this, we used the ddRADseq technique, which generated 1421 SNPs. The heterozygosity values of the analyzed individuals were among the lowest recorded for mammals, ranging from 26 to 91 SNPs/Mb. Furthermore, the individuals from one of the localities, highly isolated due to strong barriers, presented extremely high inbreeding coefficients, with values above 0.7. Under this scenario of low genetic diversity and elevated inbreeding levels, some individuals appeared to be almost genetically identical. We used different methods and simulations to determine if genetic identification and parentage analysis were possible in this population. Only one of the methods, which does not assume population homogeneity, was able to identify all individuals correctly. Therefore, genetically impoverished populations pose a great methodological challenge for their genetic study. However, these populations are of primary scientific and conservation interest, so it is essential to characterize them genetically and improve genomic methodologies for their research.
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Affiliation(s)
- Lídia Escoda
- grid.507636.10000 0004 0424 5398Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, 08003 Barcelona, Spain
| | - Oliver Hawlitschek
- grid.507636.10000 0004 0424 5398Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, 08003 Barcelona, Spain ,grid.517093.90000 0005 0294 9006Leibniz Institute for the Analysis of Biodiversity Change, Centre for Molecular Biodiversity Research, Zoological Museum, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | | | - Jose Castresana
- grid.507636.10000 0004 0424 5398Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, 08003 Barcelona, Spain
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5
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Rabier R, Erlichman A, Lesobre L, Robert A. The necessity of considering founder kinships in conservation breeding programs. Anim Conserv 2022. [DOI: 10.1111/acv.12779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. Rabier
- Reneco International Wildlife Consultants LLC Abu Dhabi United Arab Emirates
- Centre d'Ecologie et des Sciences de la Conservation (CESCO) Muséum national d'Histoire naturelle, Centre National de la Recherche Scientifique, Sorbonne Université Paris France
- Emirates Center for Wildlife Propagation Missour Morocco
| | - A. Erlichman
- Reneco International Wildlife Consultants LLC Abu Dhabi United Arab Emirates
- Centre d'Ecologie et des Sciences de la Conservation (CESCO) Muséum national d'Histoire naturelle, Centre National de la Recherche Scientifique, Sorbonne Université Paris France
| | - L. Lesobre
- Reneco International Wildlife Consultants LLC Abu Dhabi United Arab Emirates
- Emirates Center for Wildlife Propagation Missour Morocco
| | - A. Robert
- Centre d'Ecologie et des Sciences de la Conservation (CESCO) Muséum national d'Histoire naturelle, Centre National de la Recherche Scientifique, Sorbonne Université Paris France
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6
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Investigating inbreeding in the turkey (Meleagris gallopavo) genome. Poult Sci 2021; 100:101366. [PMID: 34525446 PMCID: PMC8445901 DOI: 10.1016/j.psj.2021.101366] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 06/02/2021] [Accepted: 06/24/2021] [Indexed: 02/06/2023] Open
Abstract
The detrimental effects of increased homozygosity due to inbreeding have prompted the development of methods to reduce inbreeding. The detection of runs of homozygosity (ROH), or contiguous stretches of homozygous marker genotypes, can be used to describe and quantify the level of inbreeding in an individual. The estimation of inbreeding coefficients can be calculated based on pedigree information, ROH, or the genomic relationship matrix. The aim of this study was to detect and describe ROH in the turkey genome and compare estimates of pedigree-based inbreeding coefficients (FPED) with genomic-based inbreeding coefficients estimated from ROH (FROH) and the genomic relationship matrix (FGRM). A total of 2,616,890 pedigree records were available. Of these records, 6,371 genotyped animals from three purebred turkey (Meleagris gallopavo) lines between 2013 and 2019 were available, and these were obtained using a dense single nucleotide polymorphism array (56,452 SNPs). The overall mean length of detected ROH was 2.87 ± 0.29 Mb with a mean number of 84.87 ± 8.79 ROH per animal. Short ROH with lengths of 1 to 2 Mb long were the most abundant throughout the genome. Mean ROH coverage differed greatly between chromosomes and lines. Considering inbreeding coefficient means across all lines, genomic derived inbreeding coefficients (FROH = 0.27; FGRM = 0.32) were higher than coefficients estimated from pedigree records (FPED = 0.14). Correlations between FROH and FPED, FROH and FGRM, and FPED and FGRM ranged between 0.19 to 0.31, 0.68 to 0.73, and 0.17 to 0.30, respectively. Additionally, correlations between FROH from different lengths and FPED substantially increased with ROH length from -0.06 to 0.33. Results of the current research, including the distribution of ROH throughout the genome and ROH-derived inbreeding estimates, can provide a more comprehensive description of inbreeding in the turkey genome. This knowledge can be used to evaluate genetic diversity, a requirement for genetic improvement, and develop methods to minimize inbreeding in turkey breeding programs.
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7
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Minias P, Drzewińska-Chańko J, Włodarczyk R. Evolution of innate and adaptive immune genes in a non-model waterbird, the common tern. INFECTION GENETICS AND EVOLUTION 2021; 95:105069. [PMID: 34487864 DOI: 10.1016/j.meegid.2021.105069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/28/2021] [Accepted: 09/01/2021] [Indexed: 11/25/2022]
Abstract
Toll-like receptors (TLRs) and the Major Histocompatibility Complex (MHC) are the key pathogen-recognition genes of vertebrate immune system and they have a crucial role in the initiation of innate and adaptive immune response, respectively. Recent advancements in sequencing technology sparked research on highly duplicated MHC genes in non-model species, but TLR variation in natural vertebrate populations has remained little studied and comparisons of polymorphism across both TLRs and MHC are scarce. Here, we aimed to compare variation across innate (four TLR loci) and adaptive (MHC class I and class II) immune genes in a non-model avian species, the common tern Sterna hirundo. We detected relatively high allelic richness at TLR genes (9-48 alleles per locus), which was similar to or even higher than the estimated per locus allelic richness at the MHC (24-30 alleles at class I and 13-16 alleles at class II under uniform sample sizes). Despite this, the total number of MHC alleles across all duplicated loci (four class I and three class II) was much higher and MHC alleles showed greater sequence divergence than TLRs. Positive selection targeted relatively more sites at the MHC than TLRs, but the strength of selection (dN/dS ratios) at TLRs was higher when compared to MHC class I. There were also differences in the signature of positive selection and recombination (gene conversion) between MHC class I and II (stronger signature at class II), suggesting that mechanisms maintaining variation at the MHC may vary between both classes. Our study indicates that allelic richness of both innate and adaptive immune receptors may be maintained at relatively high levels in viable avian populations and we recommend a transition from the traditional gene-specific to multi-gene approach in studying molecular evolution of vertebrate immune system.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237 Łódź, Poland.
| | - Joanna Drzewińska-Chańko
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237 Łódź, Poland
| | - Radosław Włodarczyk
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237 Łódź, Poland
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8
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Wold J, Koepfli KP, Galla SJ, Eccles D, Hogg CJ, Le Lec MF, Guhlin J, Santure AW, Steeves TE. Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern. Mol Ecol 2021; 30:5949-5965. [PMID: 34424587 PMCID: PMC9290615 DOI: 10.1111/mec.16141] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 07/28/2021] [Accepted: 08/18/2021] [Indexed: 12/28/2022]
Abstract
Structural variants (SVs) are large rearrangements (>50 bp) within the genome that impact gene function and the content and structure of chromosomes. As a result, SVs are a significant source of functional genomic variation, that is, variation at genomic regions underpinning phenotype differences, that can have large effects on individual and population fitness. While there are increasing opportunities to investigate functional genomic variation in threatened species via single nucleotide polymorphism (SNP) data sets, SVs remain understudied despite their potential influence on fitness traits of conservation interest. In this future-focused Opinion, we contend that characterizing SVs offers the conservation genomics community an exciting opportunity to complement SNP-based approaches to enhance species recovery. We also leverage the existing literature-predominantly in human health, agriculture and ecoevolutionary biology-to identify approaches for readily characterizing SVs and consider how integrating these into the conservation genomics toolbox may transform the way we manage some of the world's most threatened species.
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Affiliation(s)
- Jana Wold
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, Front Royal, Virginia, USA.,Centre for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA.,Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russia
| | - Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biological Sciences, Boise State University, Boise, Idaho, USA
| | - David Eccles
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Marissa F Le Lec
- Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand
| | - Joseph Guhlin
- Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand.,Genomics Aotearoa, Dunedin, Otago, New Zealand
| | - Anna W Santure
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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9
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Rabier R, Robert A, Lacroix F, Lesobre L. Genetic assessment of a conservation breeding program of the houbara bustard (Chlamydotis undulata undulata) in Morocco, based on pedigree and molecular analyses. Zoo Biol 2020; 39:422-435. [PMID: 32956518 DOI: 10.1002/zoo.21569] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 08/20/2020] [Accepted: 09/04/2020] [Indexed: 12/29/2022]
Abstract
Protection and restoration of species in the wild may require conservation breeding programs under genetic management to minimize deleterious effects of genetic changes that occur in captivity, while preserving populations' genetic diversity and evolutionary resilience. Here, through interannual pedigree analyses, we first assessed the efficiency of a 21-year genetic management, including minimization of mean kinship, inbreeding avoidance, and regular addition of founders, of a conservation breeding program targeting on Houbara bustard (Chlamydotis undulata undulata) in Morocco. Secondly, we compared pedigree analyses, the classical way of assessing and managing genetic diversity in captivity, to molecular analyses based on seven microsatellites. Pedigree-based results indicated an efficient maintenance of the genetic diversity (99% of the initial genetic diversity retained) while molecular-based results indicated an increase in allelic richness and an increase in unbiased expected heterozygosity across time. The pedigree-based average inbreeding coefficient F remained low (between 0.0004 and 0.003 in 2017) while the proportion of highly inbred individuals (F > .1) decreased over time and reached 0.2% in 2017. Furthermore, pedigree-based F and molecular-based individual multilocus heterozygosity were weakly negatively correlated, (Pearson's r = -.061 when considering all genotyped individuals), suggesting that they cannot be considered as alternatives, but rather as complementary sources of information. These findings suggest that a strict genetic monitoring and management, based on both pedigree and molecular tools can help mitigate genetic changes and allow to preserve genetic diversity and evolutionary resilience in conservation breeding programs.
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Affiliation(s)
- Robin Rabier
- Reneco International Wildlife Consultant LLC, Abu Dhabi, United Arab Emirates.,Centre d'Ecologie et des Sciences de la Conservation (CESCO), Muséum national d'Histoire naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, Paris, France.,Emirates Center for Wildlife Propagation, Missour, Morocco
| | - Alexandre Robert
- Centre d'Ecologie et des Sciences de la Conservation (CESCO), Muséum national d'Histoire naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, Paris, France
| | - Frédéric Lacroix
- Reneco International Wildlife Consultant LLC, Abu Dhabi, United Arab Emirates.,Emirates Center for Wildlife Propagation, Missour, Morocco
| | - Loïc Lesobre
- Reneco International Wildlife Consultant LLC, Abu Dhabi, United Arab Emirates.,Emirates Center for Wildlife Propagation, Missour, Morocco
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10
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Santana ML. Quantitative genetic analyses provide parameters for selection and conservation of captive Great-billed Seed-finches (Sporophila maximiliani). PLoS One 2020; 15:e0236647. [PMID: 32730350 PMCID: PMC7392336 DOI: 10.1371/journal.pone.0236647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 07/09/2020] [Indexed: 11/18/2022] Open
Abstract
The Great-billed Seed-finch (Sporophila maximiliani) is an endangered South American bird that has suffered from trafficking and the destruction of its natural habitat. In contrast, there are over 180,000 Great-billed Seed-finches legally raised in captivity in Brazil. The interest as a pet for Great-billed Seed-finches is due to their exceptional ability to sing. In the present research, the unknown genetic structure of the Great-billed Seed-finch captive population was investigated by quantitative analysis of 6,226 pedigree records. Additionally, 7,671 phenotypic records were available to estimate genetic parameters such as heritability and evolvability of a song-related trait of these birds for competitions. The captive Great-billed Seed-Finch population faces many of the problems commonly encountered in domestic animal populations such as a high level of inbreeding (average of 8.26%, 70.47% of birds were inbred), pedigree bottlenecks, unbalanced contribution of breeding animals and structuring (equivalent number of subpopulations of 2.91). Despite this, most genetic diversity remains preserved within aviaries. The high generation interval (5.74 years) found for this population should help to prevent a rapid increase in inbreeding and genetic drift. These results should serve as strong motivation and support for urgent actions to manage the genetic diversity of captive Great-billed Seed-Finches. From the viewpoint of genetic improvement for singing time in tournaments (STT), this trait presents sufficient variability to allow response to artificial selection given the heritability of 18.7% and evolvability of 2,447%. In contrast, inbreeding and high generation interval appear to be the most considerable barriers that may limit the genetic gain for STT. Widespread adoption of techniques such as optimal genetic contribution selection and implementation of routine genetic diversity monitoring via pedigree analysis and molecular tools can be crucial both in terms of breeding and conservation of genetic diversity of captive Great-billed Seed-Finches.
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Affiliation(s)
- Mário L. Santana
- Grupo de Melhoramento Animal de Mato Grosso (GMAT), Instituto de Ciências Agrárias e Tecnológicas, Universidade Federal de Rondonópolis, Rondonópolis, Mato Grosso, Brazil
- * E-mail:
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11
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12
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Galla SJ, Moraga R, Brown L, Cleland S, Hoeppner MP, Maloney RF, Richardson A, Slater L, Santure AW, Steeves TE. A comparison of pedigree, genetic and genomic estimates of relatedness for informing pairing decisions in two critically endangered birds: Implications for conservation breeding programmes worldwide. Evol Appl 2020; 13:991-1008. [PMID: 32431748 PMCID: PMC7232769 DOI: 10.1111/eva.12916] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 12/27/2019] [Accepted: 01/02/2020] [Indexed: 12/18/2022] Open
Abstract
Conservation management strategies for many highly threatened species include conservation breeding to prevent extinction and enhance recovery. Pairing decisions for these conservation breeding programmes can be informed by pedigree data to minimize relatedness between individuals in an effort to avoid inbreeding, maximize diversity and maintain evolutionary potential. However, conservation breeding programmes struggle to use this approach when pedigrees are shallow or incomplete. While genetic data (i.e., microsatellites) can be used to estimate relatedness to inform pairing decisions, emerging evidence indicates this approach may lack precision in genetically depauperate species, and more effective estimates will likely be obtained from genomic data (i.e., thousands of genome-wide single nucleotide polymorphisms, or SNPs). Here, we compare relatedness estimates and subsequent pairing decisions using pedigrees, microsatellites and SNPs from whole-genome resequencing approaches in two critically endangered birds endemic to New Zealand: kakī/black stilt (Himantopus novaezelandiae) and kākāriki karaka/orange-fronted parakeet (Cyanoramphus malherbi). Our findings indicate that SNPs provide more precise estimates of relatedness than microsatellites when assessing empirical parent-offspring and full sibling relationships. Further, our results show that relatedness estimates and subsequent pairing recommendations using PMx are most similar between pedigree- and SNP-based approaches. These combined results indicate that in lieu of robust pedigrees, SNPs are an effective tool for informing pairing decisions, which has important implications for many poorly pedigreed conservation breeding programmes worldwide.
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Affiliation(s)
- Stephanie J. Galla
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | - Roger Moraga
- Tea Break Bioinformatics, LtdPalmerston NorthNew Zealand
| | - Liz Brown
- New Zealand Department of ConservationTwizelNew Zealand
| | | | - Marc P. Hoeppner
- Institute for Clinical Molecular BiologyChristian‐Albrechts‐University KielKielGermany
| | | | - Anne Richardson
- The Isaac Conservation and Wildlife TrustChristchurchNew Zealand
| | - Lyndon Slater
- New Zealand Department of ConservationRangioraNew Zealand
| | - Anna W. Santure
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Tammy E. Steeves
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
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13
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Waters CD, Hard JJ, Fast DE, Knudsen CM, Bosch WJ, Naish KA. Genomic and phenotypic effects of inbreeding across two different hatchery management regimes in Chinook salmon. Mol Ecol 2020; 29:658-672. [PMID: 31957935 DOI: 10.1111/mec.15356] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 12/09/2019] [Accepted: 01/13/2020] [Indexed: 01/14/2023]
Abstract
Genomic approaches permit direct estimation of inbreeding and its effect on fitness. We used genomic-based estimates of inbreeding to investigate their relationship with eight adult traits in a captive-reared Pacific salmonid that is released into the wild. Estimates were also used to determine whether alternative broodstock management approaches reduced risks of inbreeding. Specifically, 1,100 unlinked restriction-site associated (RAD) loci were used to compare pairwise relatedness, derived from a relationship matrix, and individual inbreeding, estimated by comparing observed and expected homozygosity, across four generations in two hatchery lines of Chinook salmon that were derived from the same source. The lines are managed as "integrated" with the founding wild stock, with ongoing gene flow, and as "segregated" with no gene flow. While relatedness and inbreeding increased in the first generation of both lines, possibly due to population subdivision caused by hatchery initiation, the integrated line had significantly lower levels in some subsequent generations (relatedness: F2 -F4 ; inbreeding F2 ). Generally, inbreeding was similar between the lines despite large differences in effective numbers of breeders. Inbreeding did not affect fecundity, reproductive effort, return timing, fork length, weight, condition factor, and daily growth coefficient. However, it delayed spawn timing by 1.75 days per one standard deviation increase in F (~0.16). The results indicate that integrated management may reduce inbreeding but also suggest that it is relatively low in a small, segregated hatchery population that maximized number of breeders. Our findings demonstrate the utility of genomics to monitor inbreeding under alternative management strategies in captive breeding programs.
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Affiliation(s)
- Charles D Waters
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Jeffrey J Hard
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | | | | | | | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
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14
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Hogg CJ, Wright B, Morris KM, Lee AV, Ivy JA, Grueber CE, Belov K. Founder relationships and conservation management: empirical kinships reveal the effect on breeding programmes when founders are assumed to be unrelated. Anim Conserv 2018. [DOI: 10.1111/acv.12463] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- C. J. Hogg
- School of Life and Environmental Sciences The University of Sydney Sydney NSW Australia
- Zoo and Aquarium Association Australasia Mosman NSW Australia
| | - B. Wright
- School of Life and Environmental Sciences The University of Sydney Sydney NSW Australia
| | - K. M. Morris
- School of Life and Environmental Sciences The University of Sydney Sydney NSW Australia
| | - A. V. Lee
- Save the Tasmanian Devil Program DPIPWE Hobart TAS Australia
| | - J. A. Ivy
- San Diego Zoo Global San Diego CA USA
| | - C. E. Grueber
- School of Life and Environmental Sciences The University of Sydney Sydney NSW Australia
- San Diego Zoo Global San Diego CA USA
| | - K. Belov
- School of Life and Environmental Sciences The University of Sydney Sydney NSW Australia
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15
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Athrey G, Faust N, Hieke ASC, Brisbin IL. Effective population sizes and adaptive genetic variation in a captive bird population. PeerJ 2018; 6:e5803. [PMID: 30356989 PMCID: PMC6196071 DOI: 10.7717/peerj.5803] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 09/21/2018] [Indexed: 12/31/2022] Open
Abstract
Captive populations are considered a key component of ex situ conservation programs. Research on multiple taxa has shown the differential success of maintaining demographic versus genetic stability and viability in captive populations. In typical captive populations, usually founded by few or related individuals, genetic diversity can be lost and inbreeding can accumulate rapidly, calling into question their ultimate utility for release into the wild. Furthermore, domestication selection for survival in captive conditions is another concern. Therefore, it is crucial to understand the dynamics of population sizes, particularly the effective population size, and genetic diversity at non-neutral and adaptive loci in captive populations. In this study, we assessed effective population sizes and genetic variation at both neutral microsatellite markers, as well as SNP variants from the MHC-B locus of a captive Red Junglefowl population. This population represents a rare instance of a population with a well-documented history in captivity, following a realistic scenario of chain-of-custody, unlike many captive lab populations. Our analyses, which included 27 individuals comprising the entirety of one captive population show very low neutral and adaptive genetic variation, as well as low effective sizes, which correspond with the known demographic history. Finally, our study also shows the divergent impacts of small effective size and inbreeding in captive populations on microsatellite versus adaptive genetic variation in the MHC-B locus. Our study provides insights into the difficulties of maintaining adaptive genetic variation in small captive populations.
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Affiliation(s)
- Giridhar Athrey
- Department of Poultry Science, Texas A&M University, College Station, TX, United States of America.,Faculty of Ecology and Evolutionary Biology, Texas A&M University, College Station, TX, United States of America
| | - Nikolas Faust
- Department of Poultry Science, Texas A&M University, College Station, TX, United States of America
| | | | - I Lehr Brisbin
- Savannah River Ecology Lab, Aiken, SC, United States of America
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16
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REVIEW OF MORTALITY AND EFFECTIVENESS OF NEONATAL TREATMENT IN CAPTIVE ATTWATER'S PRAIRIE CHICKENS ( TYMPANUCHUS CUPIDO ATTWATERI). J Zoo Wildl Med 2018; 49:671-679. [PMID: 30212352 DOI: 10.1638/2016-0297.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A retrospective study of mortality and neonatal treatment for 975 Attwater's prairie chickens ( Tympanuchus cupido attwateri) was conducted from 2009-2015. Gross necropsy, histopathology, and medical records for chicks less than 8 wk of age at the Houston Zoo were reviewed and summarized. The total mortality rate was 36% ( n = 352). Yolk sac infection was the most common cause of death (21%; n = 73) followed by maladaptation (19%; n = 68), musculoskeletal abnormalities (19%; n = 66), necrotic enteritis (13%; n = 44), and mucoid enteritis (11%; n = 39). Gavage feeding of a highly digestible formula was associated with a higher proportion of necrotic enteritis and a reduced occurrence of both mucoid enteritis and maladaptation. Meloxicam administration had a significantly reduced incidence of mucoid enteritis. Survival past 10 days of age, prevention of neonatal bacterial infection, and supportive treatment with meloxicam are important factors to increase chick survival and improve captive breeding success for Attwater's prairie chickens. Gavage feeding of a diet low in digestible carbohydrates has the potential for reducing disease due to necrotic enteritis in this species.
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17
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Sutton JT, Helmkampf M, Steiner CC, Bellinger MR, Korlach J, Hall R, Baybayan P, Muehling J, Gu J, Kingan S, Masuda BM, Ryder OA. A High-Quality, Long-Read De Novo Genome Assembly to Aid Conservation of Hawaii's Last Remaining Crow Species. Genes (Basel) 2018; 9:genes9080393. [PMID: 30071683 PMCID: PMC6115840 DOI: 10.3390/genes9080393] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/23/2018] [Accepted: 07/27/2018] [Indexed: 11/16/2022] Open
Abstract
Genome-level data can provide researchers with unprecedented precision to examine the causes and genetic consequences of population declines, which can inform conservation management. Here, we present a high-quality, long-read, de novo genome assembly for one of the world’s most endangered bird species, the ʻAlalā (Corvus hawaiiensis; Hawaiian crow). As the only remaining native crow species in Hawaiʻi, the ʻAlalā survived solely in a captive-breeding program from 2002 until 2016, at which point a long-term reintroduction program was initiated. The high-quality genome assembly was generated to lay the foundation for both comparative genomics studies and the development of population-level genomic tools that will aid conservation and recovery efforts. We illustrate how the quality of this assembly places it amongst the very best avian genomes assembled to date, comparable to intensively studied model systems. We describe the genome architecture in terms of repetitive elements and runs of homozygosity, and we show that compared with more outbred species, the ʻAlalā genome is substantially more homozygous. We also provide annotations for a subset of immunity genes that are likely to be important in conservation management, and we discuss how this genome is currently being used as a roadmap for downstream conservation applications.
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Affiliation(s)
- Jolene T Sutton
- Department of Biology, University of Hawaii at Hilo, Hilo, HI 96720, USA.
| | - Martin Helmkampf
- Department of Biology, University of Hawaii at Hilo, Hilo, HI 96720, USA.
| | - Cynthia C Steiner
- Institute for Conservation Research, San Diego Zoo, Escondido, CA 92027, USA.
| | - M Renee Bellinger
- Department of Biology, University of Hawaii at Hilo, Hilo, HI 96720, USA.
| | | | | | | | | | - Jenny Gu
- Pacific Biosciences, Menlo Park, CA 94025, USA.
| | | | - Bryce M Masuda
- Institute for Conservation Research, San Diego Zoo Global, Volcano, HI 96785, USA.
| | - Oliver A Ryder
- Institute for Conservation Research, San Diego Zoo, Escondido, CA 92027, USA.
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18
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Wells DA, Cant MA, Nichols HJ, Hoffman JI. A high-quality pedigree and genetic markers both reveal inbreeding depression for quality but not survival in a cooperative mammal. Mol Ecol 2018; 27:2271-2288. [PMID: 29603504 DOI: 10.1111/mec.14570] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 03/05/2018] [Accepted: 03/12/2018] [Indexed: 01/07/2023]
Abstract
Inbreeding depression, the reduced fitness of offspring of closely related parents, is commonplace in both captive and wild populations and has important consequences for conservation and mating system evolution. However, because of the difficulty of collecting pedigree and life-history data from wild populations, relatively few studies have been able to compare inbreeding depression for traits at different points in the life cycle. Moreover, pedigrees give the expected proportion of the genome that is identical by descent (IBDg ) whereas in theory with enough molecular markers realized IBDg can be quantified directly. We therefore investigated inbreeding depression for multiple life-history traits in a wild population of banded mongooses using pedigree-based inbreeding coefficients (fped ) and standardized multilocus heterozygosity (sMLH) measured at 35-43 microsatellites. Within an information theoretic framework, we evaluated support for either fped or sMLH as inbreeding terms and used sequential regression to determine whether the residuals of sMLH on fped explain fitness variation above and beyond fped . We found no evidence of inbreeding depression for survival, either before or after nutritional independence. By contrast, inbreeding was negatively associated with two quality-related traits, yearling body mass and annual male reproductive success. Yearling body mass was associated with fped but not sMLH, while male annual reproductive success was best explained by both fped and residual sMLH. Thus, our study not only uncovers variation in the extent to which different traits show inbreeding depression, but also reveals trait-specific differences in the ability of pedigrees and molecular markers to explain fitness variation and suggests that for certain traits, genetic markers may capture variation in realized IBDg above and beyond the pedigree expectation.
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Affiliation(s)
- David A Wells
- Department of Animal Behaviour, University of Bielefeld, Bielefeld, Germany.,School of Natural Science and Psychology, Liverpool John Moores University, Liverpool, UK
| | - Michael A Cant
- College of Life and Environmental Sciences, University of Exeter, Penryn, UK
| | - Hazel J Nichols
- School of Natural Science and Psychology, Liverpool John Moores University, Liverpool, UK
| | - Joseph I Hoffman
- Department of Animal Behaviour, University of Bielefeld, Bielefeld, Germany
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19
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Gooley R, Hogg CJ, Belov K, Grueber CE. No evidence of inbreeding depression in a Tasmanian devil insurance population despite significant variation in inbreeding. Sci Rep 2017; 7:1830. [PMID: 28500329 PMCID: PMC5431960 DOI: 10.1038/s41598-017-02000-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 04/06/2017] [Indexed: 01/08/2023] Open
Abstract
Inbreeding depression occurs when inbred individuals experience reduced fitness as a result of reduced genome-wide heterozygosity. The Tasmanian devil faces extinction due to a contagious cancer, devil facial tumour disease (DFTD). An insurance metapopulation was established in 2006 to ensure the survival of the species and to be used as a source population for re-wilding and genetic rescue. The emergence of DFTD and the rapid decline of wild devil populations have rendered the species at risk of inbreeding depression. We used 33 microsatellite loci to (1) reconstruct a pedigree for the insurance population and (2) estimate genome-wide heterozygosity for 200 individuals. Using heterozygosity-fitness correlations, we investigated the effect of heterozygosity on six diverse fitness measures (ulna length, asymmetry, weight-at-weaning, testes volume, reproductive success and survival). Despite statistically significant evidence of variation in individual inbreeding in this population, we found no associations between inbreeding and any of our six fitness measurements. We propose that the benign environment in captivity may decrease the intensity of inbreeding depression, relative to the stressful conditions in the wild. Future work will need to measure fitness of released animals to facilitate translation of this data to the broader conservation management of the species in its native range.
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Affiliation(s)
- Rebecca Gooley
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.,Zoo and Aquarium Association Australasia, Mosman, NSW, 2088, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
| | - Catherine E Grueber
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.,San Diego Zoo Global, PO Box 120551, San Diego, CA, 92112, USA
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20
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Escoda L, González-Esteban J, Gómez A, Castresana J. Using relatedness networks to infer contemporary dispersal: Application to the endangered mammal Galemys pyrenaicus. Mol Ecol 2017; 26:3343-3357. [DOI: 10.1111/mec.14133] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 03/21/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Lídia Escoda
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra); Barcelona Spain
| | | | | | - Jose Castresana
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra); Barcelona Spain
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21
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Steeves TE, Johnson JA, Hale ML. Maximising evolutionary potential in functional proxies for extinct species: a conservation genetic perspective on de‐extinction. Funct Ecol 2017. [DOI: 10.1111/1365-2435.12843] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Tammy E. Steeves
- School of Biological Sciences University of Canterbury Private Bag 4800 Christchurch8140 New Zealand
| | - Jeff A. Johnson
- Department of Biological Sciences and Institute of Applied Science University of North Texas 1155 Union Circle Denton TX76203 USA
| | - Marie L. Hale
- School of Biological Sciences University of Canterbury Private Bag 4800 Christchurch8140 New Zealand
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22
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Bateson ZW, Hammerly SC, Johnson JA, Morrow ME, Whittingham LA, Dunn PO. Specific alleles at immune genes, rather than genome‐wide heterozygosity, are related to immunity and survival in the critically endangered Attwater's prairie‐chicken. Mol Ecol 2016; 25:4730-44. [DOI: 10.1111/mec.13793] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/17/2016] [Accepted: 07/19/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Zachary W. Bateson
- Behavioral and Molecular Ecology Group Department of Biological Sciences University of Wisconsin‐Milwaukee PO Box 413 Milwaukee WI 53201 USA
| | - Susan C. Hammerly
- Department of Biological Sciences Institute of Applied Sciences University of North Texas 1155 Union Circle Denton TX 76203 USA
| | - Jeff A. Johnson
- Department of Biological Sciences Institute of Applied Sciences University of North Texas 1155 Union Circle Denton TX 76203 USA
| | - Michael E. Morrow
- Attwater Prairie Chicken National Wildlife Refuge PO Box 519 Eagle Lake TX 77434 USA
| | - Linda A. Whittingham
- Behavioral and Molecular Ecology Group Department of Biological Sciences University of Wisconsin‐Milwaukee PO Box 413 Milwaukee WI 53201 USA
| | - Peter O. Dunn
- Behavioral and Molecular Ecology Group Department of Biological Sciences University of Wisconsin‐Milwaukee PO Box 413 Milwaukee WI 53201 USA
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23
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Trask AE, Bignal EM, McCracken DI, Monaghan P, Piertney SB, Reid JM. Evidence of the phenotypic expression of a lethal recessive allele under inbreeding in a wild population of conservation concern. J Anim Ecol 2016; 85:879-91. [PMID: 26996516 DOI: 10.1111/1365-2656.12503] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/15/2016] [Indexed: 11/27/2022]
Abstract
Deleterious recessive alleles that are masked in outbred populations are predicted to be expressed in small, inbred populations, reducing both individual fitness and population viability. However, there are few definitive examples of phenotypic expression of lethal recessive alleles under inbreeding conditions in wild populations. Studies that demonstrate the action of such alleles, and infer their distribution and dynamics, are required to understand their potential impact on population viability and inform management responses. The Scottish population of red-billed choughs (Pyrrhocorax pyrrhocorax), which currently totals <60 breeding pairs and is of major conservation concern, has recently been affected by lethal blindness in nestlings. We used family data to show that the pattern of occurrence of blindness within and across affected families that produced blind nestlings was exactly 0·25, matching that expected given a single-locus autosomal lethal recessive allele. Furthermore, the observed distribution of blind nestlings within affected families did not differ from that expected given Mendelian inheritance of such an allele. Relatedness estimates showed that individuals from affected families were not more closely related to each other than they were to individuals from unaffected families that did not produce blind nestlings. Blind individuals tended to be less heterozygous than non-blind individuals, as expected if blindness was caused by the expression of a recessive allele under inbreeding. However, there was no difference in the variance in heterozygosity estimates, suggesting that some blind individuals were relatively outbred. These results suggest carriers of the blindness allele may be widely distributed across contemporary families rather than restricted to a single family lineage, implying that the allele has persisted across multiple generations. Blindness occurred at low frequency (affecting 1·6% of observed nestlings since 1981). However, affected families had larger initial brood sizes than unaffected families. Such high fecundity of carriers of a lethal recessive allele might reflect overdominance, potentially reducing purging and increasing allele persistence probability. We thereby demonstrate the phenotypic expression of a lethal recessive allele in a wild population of conservation concern, and provide a general framework for inferring allele distribution and persistence and informing management responses.
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Affiliation(s)
- Amanda E Trask
- Institute of Biological & Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Eric M Bignal
- Scottish Chough Study Group, Kindrochaid, Bridgend, Isle of Islay, Argyll, PA44 7PT, UK
| | - Davy I McCracken
- Future Farming Systems, Scotland's Rural College, Auchincruive, Ayr, KA6 5HW, UK
| | - Pat Monaghan
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Graham Kerr Building, Glasgow, G12 8QQ, UK
| | - Stuart B Piertney
- Institute of Biological & Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Jane M Reid
- Institute of Biological & Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
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24
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Hammerly SC, Cerda DA, Bailey H, Johnson JA. A pedigree gone bad: increased offspring survival after using DNA‐based relatedness to minimize inbreeding in a captive population. Anim Conserv 2015. [DOI: 10.1111/acv.12247] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- S. C. Hammerly
- Department of Biological Sciences Institute of Applied Sciences University of North Texas Denton TX USA
| | - D. A. Cerda
- Department of Biological Sciences Institute of Applied Sciences University of North Texas Denton TX USA
| | | | - J. A. Johnson
- Department of Biological Sciences Institute of Applied Sciences University of North Texas Denton TX USA
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25
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Williams JL, Hall SJ, Del Corvo M, Ballingall KT, Colli L, Ajmone Marsan P, Biscarini F. Inbreeding and purging at the genomic Level: the Chillingham cattle reveal extensive, non-random SNP heterozygosity. Anim Genet 2015; 47:19-27. [DOI: 10.1111/age.12376] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2015] [Indexed: 11/29/2022]
Affiliation(s)
- J. L. Williams
- PTP Science Park; Via Einstein - Loc. Cascina Codazza 26900 Lodi Italy
| | - S. J.G. Hall
- School of Life Sciences; University of Lincoln; Brayford Pool Lincoln LN6 7TS UK
| | - M. Del Corvo
- PTP Science Park; Via Einstein - Loc. Cascina Codazza 26900 Lodi Italy
| | - K. T. Ballingall
- Moredun Research Institute; Pentlands Science Park; Bush Loan Penicuik Midlothian EH26 0PZ UK
| | - L. Colli
- Università Cattolica del Sacro Cuore; via Emilia Parmense 84 29122 Piacenza Italy
| | - P. Ajmone Marsan
- Università Cattolica del Sacro Cuore; via Emilia Parmense 84 29122 Piacenza Italy
| | - F. Biscarini
- PTP Science Park; Via Einstein - Loc. Cascina Codazza 26900 Lodi Italy
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26
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Development of a SNP-based assay for measuring genetic diversity in the Tasmanian devil insurance population. BMC Genomics 2015; 16:791. [PMID: 26467759 PMCID: PMC4607143 DOI: 10.1186/s12864-015-2020-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 10/07/2015] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The Tasmanian devil (Sarcophilus harrisii) has undergone a recent, drastic population decline due to the highly contagious devil facial tumor disease. The tumor is one of only two naturally occurring transmissible cancers and is almost inevitably fatal. In 2006 a disease-free insurance population was established to ensure that the Tasmanian devil is protected from extinction. The insurance program is dependent upon preserving as much wild genetic diversity as possible to maximize the success of subsequent reintroductions to the wild. Accurate genotypic data is vital to the success of the program to ensure that loss of genetic diversity does not occur in captivity. Until recently, microsatellite markers have been used to study devil population genetics, however as genetic diversity is low in the devil and potentially decreasing in the captive population, a more sensitive genotyping assay is required. METHODS Utilising the devil reference genome and whole genome re-sequencing data, we have identified polymorphic regions for use in a custom genotyping assay. These regions were amplified using PCR and sequenced on the Illumina MiSeq platform to refine a set a markers to genotype the Tasmanian devil insurance population. RESULTS We have developed a set of single nucleotide polymorphic (SNP) markers, assayed by amplicon sequencing, that provide a high-throughput method for monitoring genetic diversity and assessing familial relationships among devils. To date we have used a total of 267 unique SNPs within both putatively neutral and functional loci to genotype 305 individuals in the Tasmanian devil insurance population. We have used these data to assess genetic diversity in the population as well as resolve the parentage of 21 offspring. CONCLUSIONS Our molecular data has been incorporated with studbook management practices to provide more accurate pedigree information and to inform breeding recommendations. The assay will continue to be used to monitor the genetic diversity of the insurance population of Tasmanian devils with the aim of reducing inbreeding and maximizing success of reintroductions to the wild.
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27
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Taylor HR. The use and abuse of genetic marker-based estimates of relatedness and inbreeding. Ecol Evol 2015; 5:3140-50. [PMID: 26357542 PMCID: PMC4559056 DOI: 10.1002/ece3.1541] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 05/05/2015] [Accepted: 05/18/2015] [Indexed: 01/10/2023] Open
Abstract
Genetic marker-based estimators remain a popular tool for measuring relatedness (r xy ) and inbreeding (F) coefficients at both the population and individual level. The performance of these estimators fluctuates with the number and variability of markers available, and the relatedness composition and demographic history of a population. Several methods are available to evaluate the reliability of the estimates of r xy and F, some of which are implemented in the program COANCESTRY. I used the simulation module in COANCESTRY since assess the performance of marker-based estimators of r xy and F in a species with very low genetic diversity, New Zealand's little spotted kiwi (Apteryx owenii). I also conducted a review of published papers that have used COANCESTRY as its release to assess whether and how the reliability of the estimates of r xy and F produced by genetic markers are being measured and reported in published studies. My simulation results show that even when the correlation between true (simulated) and estimated r xy or F is relatively high (Pearson's r = 0.66-0.72 and 0.81-0.85, respectively) the imprecision of the estimates renders them highly unreliable on an individual basis. The literature review demonstrates that the majority of studies do not report the reliability of marker-based estimates of r xy and F. There is currently no standard practice for selecting the best estimator for a given data set or reporting an estimator's performance. This could lead to experimental results being interpreted out of context and render the robustness of conclusions based on measures of r xy and F debatable.
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Affiliation(s)
- Helen R Taylor
- Allan Wilson Centre, School of Biological Sciences, Victoria University of WellingtonKelburn Parade, Wellington, New Zealand
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28
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Ishtiaq F, Prakash V, Green RE, Johnson J. Management implications of genetic studies forex situpopulations of three critically endangered AsianGypsvultures. Anim Conserv 2014. [DOI: 10.1111/acv.12166] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- F. Ishtiaq
- Wildlife Institute of India; Dehradun Uttarakhand India
| | - V. Prakash
- Bombay Natural History Society; Mumbai Maharashtra India
| | - R. E. Green
- Royal Society for the Protection of Birds; Bedfordshire UK
- Conservation Science Group; the Department of Zoology; University of Cambridge; Cambridge UK
| | - J. Johnson
- Department of Biological Sciences; Institute of Applied Sciences; University of North Texas; Denton TX USA
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29
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Miller JM, Coltman DW. Assessment of identity disequilibrium and its relation to empirical heterozygosity fitness correlations: a meta-analysis. Mol Ecol 2014; 23:1899-909. [DOI: 10.1111/mec.12707] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 02/18/2014] [Accepted: 02/21/2014] [Indexed: 01/31/2023]
Affiliation(s)
- Joshua M. Miller
- Department of Biological Sciences; University of Alberta; Edmonton Alberta T6G 2E9 Canada
| | - David W. Coltman
- Department of Biological Sciences; University of Alberta; Edmonton Alberta T6G 2E9 Canada
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30
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de Cara MÁR, Villanueva B, Toro MÁ, Fernández J. Using genomic tools to maintain diversity and fitness in conservation programmes. Mol Ecol 2013; 22:6091-9. [PMID: 24128280 DOI: 10.1111/mec.12560] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 10/01/2013] [Accepted: 10/11/2013] [Indexed: 12/31/2022]
Abstract
Conservation programmes aim at maximizing the survival probability of populations, by minimizing the loss of genetic diversity, which allows populations to adapt to changes, and controlling inbreeding increases. The best known strategy to achieve these goals is optimizing the contributions of the parents to minimize global coancestry in their offspring. Results on neutral scenarios showed that management based on molecular coancestry could maintain more diversity than management based on genealogical coancestry when a large number of markers were available. However, if the population has deleterious mutations, managing using optimal contributions can lead to a decrease in fitness, especially using molecular coancestry, because both beneficial and harmful alleles are maintained, compromising the long-term viability of the population. We introduce here two strategies to avoid this problem: The first one uses molecular coancestry calculated removing markers with low minor allele frequencies, as they could be linked to selected loci. The second one uses a coancestry based on segments of identity by descent, which measures the proportion of genome segments shared by two individuals because of a common ancestor. We compare these strategies under two contrasting mutational models of fitness effects, one assuming many mutations of small effect and another with few mutations of large effect. Using markers at intermediate frequencies maintains a larger fitness than using all markers, but leads to maintaining less diversity. Using the segment-based coancestry provides a compromise solution between maintaining diversity and fitness, especially when the population has some inbreeding load.
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