1
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Coleman JL, Wyffels JT, Penfold LM, Richardson D, Maddox JD. Development of genetic markers for reproductive management of toucans. Zoo Biol 2023; 42:825-833. [PMID: 37338091 DOI: 10.1002/zoo.21792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 04/26/2023] [Accepted: 06/08/2023] [Indexed: 06/21/2023]
Abstract
Retention of genetic diversity in successive generations is key to successful ex situ programs and will become increasingly important to restore wild populations of threatened animals. When animal genealogy is partly unknown or gaps exist in studbook records, the application of molecular resources facilitates informed breeding. Here, we apply molecular resources to an ex situ breeding population of toucans (Ramphastidae), a bird family zoos commonly maintain. Toucans face population declines from illegal poaching and habitat degradation. We developed novel microsatellite markers using blood samples from 15 Keel-billed Toucans (Ramphastos sulfuratus Lesson 1830). Parentage of two individuals was known a priori, but possible sibship among 13 putative founders-including the parents-was unknown. We compared available avian heterologous and novel microsatellite markers to recover known relationships and reconstruct sibship. Eight of 61 heterologous markers amplified consistently and were polymorphic, but less so than the 18 novel markers. Known sibship (and three sibling pairs whose relatedness was unknown a priori) and paternity-though not maternity except in one case-were well-recovered using both likelihood and pairwise relatedness methods, when incorporating novel but not heterologous markers. Zoo researchers seeking microsatellite primer sets for their breeding toucan populations will likely benefit from our heterologous markers, which can be leveraged both to assess relatedness and select breeding pairs. We recommend that zoo biologists rely on species-specific primers and not optimize heterologous primers for toucan species without molecular resources. We conclude with a brief discussion of modern genotyping methods of interest to zoo researchers.
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Affiliation(s)
- Jeffrey L Coleman
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Jennifer T Wyffels
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, Delaware, USA
- Ripley's Aquariums, Orlando, Florida, USA
| | - Linda M Penfold
- South-East Zoo Alliance for Reproduction & Conservation, Yulee, Florida, USA
| | | | - J Dylan Maddox
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
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2
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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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3
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Klütsch CFC, Maduna SN, Polikarpova N, Forfang K, Beddari B, Gjelland KØ, Aspholm PE, Amundsen PA, Hagen SB. Temporal analysis shows relaxed genetic erosion following improved stocking practices in a subarctic transnational brown trout population. Sci Rep 2021; 11:17396. [PMID: 34462480 PMCID: PMC8405680 DOI: 10.1038/s41598-021-96681-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/03/2021] [Indexed: 11/10/2022] Open
Abstract
Maintaining standing genetic variation is a challenge in human-dominated landscapes. We used genetic (i.e., 16 short tandem repeats) and morphological (i.e., length and weight) measurements of 593 contemporary and historical brown trout (Salmo trutta) samples to study fine-scale and short-term impacts of different management practices. These had changed from traditional breeding practices, using the same broodstock for several years, to modern breeding practices, including annual broodstock replacement, in the transnational subarctic Pasvik River. Using population genetic structure analyses (i.e., Bayesian assignment tests, DAPCs, and PCAs), four historical genetic clusters (E2001A-D), likely representing family lineages resulting from different crosses, were found in zone E. These groups were characterized by consistently lower genetic diversity, higher within-group relatedness, lower effective population size, and significantly smaller body size than contemporary stocked (E2001E) and wild fish (E2001F). However, even current breeding practices are insufficient to prevent genetic diversity loss and morphological changes as demonstrated by on average smaller body sizes and recent genetic bottleneck signatures in the modern breeding stock compared to wild fish. Conservation management must evaluate breeding protocols for stocking programs and assess if these can preserve remaining natural genetic diversity and morphology in brown trout for long-term preservation of freshwater fauna.
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Affiliation(s)
- Cornelya F C Klütsch
- Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research (NIBIO), Svanhovd, Norway.
| | - Simo N Maduna
- Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research (NIBIO), Svanhovd, Norway
| | | | - Kristin Forfang
- Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research (NIBIO), Svanhovd, Norway
| | - Benedicte Beddari
- Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research (NIBIO), Svanhovd, Norway
| | | | - Paul Eric Aspholm
- Division of Forest and Forest Resources, Norwegian Institute of Bioeconomy Research (NIBIO), Svanhovd, Norway
| | - Per-Arne Amundsen
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
| | - Snorre B Hagen
- Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research (NIBIO), Svanhovd, Norway.
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4
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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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5
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Furlan EM, Gruber B, Attard CRM, Wager RNE, Kerezsy A, Faulks LK, Beheregaray LB, Unmack PJ. Assessing the benefits and risks of translocations in depauperate species: A theoretical framework with an empirical validation. J Appl Ecol 2020. [DOI: 10.1111/1365-2664.13581] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Elise M. Furlan
- Institute for Applied Ecology University of Canberra Canberra ACT Australia
| | - Bernd Gruber
- Institute for Applied Ecology University of Canberra Canberra ACT Australia
| | - Catherine R. M. Attard
- Molecular Ecology Laboratory College of Science and Engineering Flinders University Adelaide SA Australia
| | - Robert N. E. Wager
- Bush Heritage Australia Melbourne Vic. Australia
- “Rockatoo” Esk Qld Australia
| | - Adam Kerezsy
- Bush Heritage Australia Melbourne Vic. Australia
- DrFishContracting Lake Cargelligo NSW Australia
| | - Leanne K. Faulks
- Sugadaira Research Station Mountain Science Center University of Tsukuba Tsukuba Japan
| | - Luciano B. Beheregaray
- Molecular Ecology Laboratory College of Science and Engineering Flinders University Adelaide SA Australia
| | - Peter J. Unmack
- Institute for Applied Ecology University of Canberra Canberra ACT Australia
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6
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Quinzin MC, Sandoval-Castillo J, Miller JM, Beheregaray LB, Russello MA, Hunter EA, Gibbs JP, Tapia W, Villalva F, Caccone A. Genetically informed captive breeding of hybrids of an extinct species of Galapagos tortoise. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2019; 33:1404-1414. [PMID: 30901116 DOI: 10.1111/cobi.13319] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 03/08/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Hybridization poses a major challenge for species conservation because it threatens both genetic integrity and adaptive potential. Yet, hybridization can occasionally offer unprecedented opportunity for species recovery if the genome of an extinct taxon is present among living hybrids such that selective breeding could recapture it. We explored the design elements for establishing a captive-breeding program for Galapagos tortoises (Chelonoidis spp.) built around individuals with admixed ancestry involving an extinct species. The target individuals were hybrids between the extinct species from Floreana Island, C. niger, and an extant species, C. becki, which were recently found in the endemic range of C. becki, from Wolf Volcano on Isabela Island. We combined genotypic data from 35 tortoises with high ancestry from C. niger with forward-in-time simulations to explore captive breeding strategies that maximized overall genetic diversity and ancestry from C. niger while accommodating resource constraints, species biology, and the urgency to return tortoises to Floreana Island for facilitating ecosystem restoration. Overall genetic diversity was maximized when in the simulation tortoises were organized in relatively small breeding groups. Substantial amounts of the C. niger genome were captured despite limited resources available for selectively breeding tortoises in captivity. Genetic diversity was maximized when captive-bred offspring were released to the wild rather than being used as additional breeders. Our results provide genetic-based and practical guidance on the inclusion of hybrids with genomic representation from extinct taxa into species restoration programs and informs the ongoing debate on the value of hybrids in biodiversity conservation.
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Affiliation(s)
- Maud C Quinzin
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT, 06520, U.S.A
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Lab, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Joshua M Miller
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT, 06520, U.S.A
| | - Luciano B Beheregaray
- Molecular Ecology Lab, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, BC, V1V 1V7, Canada
| | - Elizabeth A Hunter
- Department of Biology, Georgia Southern University, Statesboro, GA, 30460, U.S.A
| | - James P Gibbs
- Department of Environmental and Forest Biology, College of Environmental Science and Forestry, State University of New York, 247 Illick Hall, Syracuse, NY, 13210, U.S.A
| | - Washington Tapia
- Giant Tortoise Restoration Initiative, Galapagos Conservancy, Fairfax, VA, 22030, U.S.A
| | - Freddy Villalva
- Galapagos National Park Directorate, Puerto Ayora, Galapagos, Ecuador
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT, 06520, U.S.A
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7
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Mandimbihasina AR, Frasier CL, Hagenson RA, Robertson BAD, Engberg SE, Lewis RE, Woolaver LG, Razafimahatratra E, Rabetafika LL, Louis EE. Conservation genetics of Madagascar’s critically endangered ploughshare tortoise (Astrochelys yniphora). CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01236-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Çilingir FG, Seah A, Horne BD, Som S, Bickford DP, Rheindt FE. Last exit before the brink: Conservation genomics of the Cambodian population of the critically endangered southern river terrapin. Ecol Evol 2019; 9:9500-9510. [PMID: 31534671 PMCID: PMC6745661 DOI: 10.1002/ece3.5434] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 05/04/2019] [Accepted: 06/11/2019] [Indexed: 11/14/2022] Open
Abstract
The southern river terrapin, Batagur affinis is one of the world's 25 most endangered freshwater turtle species. The major portion of the global population is currently found in peninsular Malaysia, with the only remnant Indochinese population in southern Cambodia. For more than a decade, wild nests in this remnant Cambodian population have been fenced and hatchlings reared in captivity. Here we amplified 10 microsatellite markers from all 136 captive individuals, obtained 2,658 presumably unlinked and neutral single nucleotide polymorphisms from 72 samples with ddRAD-seq, and amplified 784 bp of mtDNA from 50 samples. Our results reveal that the last Indochinese population comprised only four kinship groups as of 2012, with all offspring sired from <10 individuals in the wild. We demonstrate an obvious decrease in genetic contributions of breeders in the wild from 2006-2012 and identify high-value breeders instrumental for ex-situ management of the contemporary genetic stock of the species.
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Affiliation(s)
- F. Gözde Çilingir
- Department of Biological SciencesNational University of SingaporeSingapore CitySingapore
| | - Adeline Seah
- Department of Biological SciencesNational University of SingaporeSingapore CitySingapore
- Wildlife Conservation Society, Bronx ZooBronxNew YorkUSA
| | - Brian D. Horne
- Wildlife Conservation Society, Bronx ZooBronxNew YorkUSA
| | - Sitha Som
- Wildlife Conservation SocietyPhnom PenhCambodia
| | - David P. Bickford
- Department of Biological SciencesNational University of SingaporeSingapore CitySingapore
- Present address:
Department of BiologyUniversity of La VerneLa VerneCaliforniaUSA
| | - Frank E. Rheindt
- Department of Biological SciencesNational University of SingaporeSingapore CitySingapore
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9
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Reference Genomes from Distantly Related Species Can Be Used for Discovery of Single Nucleotide Polymorphisms to Inform Conservation Management. Genes (Basel) 2018; 10:genes10010009. [PMID: 30583569 PMCID: PMC6356778 DOI: 10.3390/genes10010009] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/16/2018] [Accepted: 12/19/2018] [Indexed: 11/21/2022] Open
Abstract
Threatened species recovery programmes benefit from incorporating genomic data into conservation management strategies to enhance species recovery. However, a lack of readily available genomic resources, including conspecific reference genomes, often limits the inclusion of genomic data. Here, we investigate the utility of closely related high-quality reference genomes for single nucleotide polymorphism (SNP) discovery using the critically endangered kakī/black stilt (Himantopus novaezelandiae) and four Charadriiform reference genomes as proof of concept. We compare diversity estimates (i.e., nucleotide diversity, individual heterozygosity, and relatedness) based on kakī SNPs discovered from genotyping-by-sequencing and whole genome resequencing reads mapped to conordinal (killdeer, Charadrius vociferus), confamilial (pied avocet, Recurvirostra avosetta), congeneric (pied stilt, Himantopus himantopus) and conspecific reference genomes. Results indicate that diversity estimates calculated from SNPs discovered using closely related reference genomes correlate significantly with estimates calculated from SNPs discovered using a conspecific genome. Congeneric and confamilial references provide higher correlations and more similar measures of nucleotide diversity, individual heterozygosity, and relatedness. While conspecific genomes may be necessary to address other questions in conservation, SNP discovery using high-quality reference genomes of closely related species is a cost-effective approach for estimating diversity measures in threatened species.
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10
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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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11
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Miller JM, Quinzin MC, Scheibe EH, Ciofi C, Villalva F, Tapia W, Caccone A. Genetic Pedigree Analysis of the Pilot Breeding Program for the Rediscovered Galapagos Giant Tortoise from Floreana Island. J Hered 2018; 109:620-630. [DOI: 10.1093/jhered/esy010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/25/2018] [Indexed: 12/16/2022] Open
Affiliation(s)
- Joshua M Miller
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
| | - Maud C Quinzin
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
| | - Elizabeth H Scheibe
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
| | - Claudio Ciofi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Fredy Villalva
- Galapagos Galapagos National Park Directorate, Puerto Ayora, Ecuador
| | - Washington Tapia
- Galapagos Galapagos National Park Directorate, Puerto Ayora, Ecuador
- Galapagos Conservancy, Fairfax, VA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
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12
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