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Brereton JE, Rose PE. The Zone Overlap Index: A new measure of shared resource use in the zoo. Zoo Biol 2023; 42:811-817. [PMID: 37283070 DOI: 10.1002/zoo.21786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 04/26/2023] [Accepted: 05/24/2023] [Indexed: 06/08/2023]
Abstract
It is important that the environment provided in the zoo is relevant to the species being housed and its suitability be easily assessed by personnel. As shared space and resources can overlap in a zoo's enclosure a tool is required to measure the effects of such overlap between individual animals in a shared enclosure. This paper outlines the Pianka Index (PI), a tool used in ecology to quantify niche overlap, that has value in quantifying the amount of time that animals spend in shared enclosure zones. One limitation to this method, however, is that the established method of determining the PI requires division of the enclosure into equally sized zones, something that is not always relevant to a zoo enclosure. To combat this, we created a modified index, entitled the Zone Overlap Index (ZOI). This modified index is the exact mathematical equivalent of the original index when zone sizes are equal. When zone sizes are unequal, the ZOI generates higher values when animals share smaller, as opposed to larger, zones. This is because animals are more likely to share larger enclosure zones simply by chance, and shared use of smaller zones brings individuals into closer proximity with the potential for competition. To illustrate the application of the ZOI, a series of hypothetical situations were generated to reflect real-world scenarios, demonstrating how this index could be used to better understand zone occupancy overlap in the zoo.
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Affiliation(s)
- James E Brereton
- Higher Education, University Centre Sparsholt, Hampshire, UK
- Animal, Rural and Environmental Sciences, Nottingham Trent University, Southwell, UK
| | - Paul E Rose
- Centre for Research in Animal Behaviour, University of Exeter, Exeter, UK
- WWT, Slimbridge Wetland Centre, Slimbridge, UK
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Menor-Flores M, Vega-Rodríguez MA, Molina F. Iterative Level-0: A new and fast algorithm to traverse mating networks calculating the inbreeding and relationship coefficients. Comput Biol Med 2023; 164:107296. [PMID: 37566933 DOI: 10.1016/j.compbiomed.2023.107296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 06/24/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023]
Abstract
In population medical genetics, the study of autosomal recessive disorders in highly endogamous populations is a major topic where calculating the inbreeding and relationship coefficients on mating networks is crucial. However, a challenge arises when dealing with large and complex mating networks, making their traversal difficult during the calculation process. For this calculation, we propose using Iterative Level-0 (IL0) as a new and faster algorithm that traverses mating networks more efficiently. The purpose of this work is to explain in detail the IL0 algorithm and prove its superiority by comparing it with two algorithms based on the best-known algorithms in the area: Depth First Search (DFS) and Breadth First Search (BFS). A Cytoscape application has been developed to calculate the inbreeding and relationship coefficients of individuals composing any mating network. In this application, the IL0 proposal together with DFS-based and BFS-based algorithms have been implemented. Any user can access this freely available Cytoscape application (https://apps.cytoscape.org/apps/inbreeding) that allows the comparison between the IL0 proposal and the best-known algorithms (based on DFS and BFS). In addition, a diverse set of mating networks has been collected in terms of complexity (number of edges) and species (humans, primates, and dogs) for the experiments. The runtime obtained by the IL0, DFS-based, and BFS-based algorithms when calculating the inbreeding and relationship coefficients proved the improvement of IL0. In fact, a speedup study reflected that the IL0 algorithm is 7.60 to 127.50 times faster than DFS-based and BFS-based algorithms. Moreover, a scalability study found that the growth of the IL0 runtime has a linear dependence on the number of edges of the mating network, while the DFS-based and BFS-based runtimes have a quadratic dependence. Therefore, the IL0 algorithm can solve the problem of calculating the inbreeding and relationship coefficients many times faster (up to 127.50) than the two algorithms based on the famous DFS and BFS. Furthermore, our results demonstrate that IL0 scales much better as the complexity of mating networks increases.
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Affiliation(s)
- Manuel Menor-Flores
- Escuela Politécnica, Universidad de Extremadura(1), Campus Universitario s/n, 10003 Cáceres, Spain.
| | - Miguel A Vega-Rodríguez
- Escuela Politécnica, Universidad de Extremadura(1), Campus Universitario s/n, 10003 Cáceres, Spain.
| | - Felipe Molina
- Facultad de Ciencias, Universidad de Extremadura (1), Avda. de Elvas s/n, 06006 Badajoz, Spain.
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Aliaga-Samanez GG, Bulhões Javarotti N, Orecife G, Chávez-Congrains K, Pissinatti A, Monticelli C, Cristina Marques M, Galbusera P, Galetti PM, Domingues de Freitas P. Genetic diversity in ex situ populations of the endangered Leontopithecus chrysomelas and implications for its conservation. PLoS One 2023; 18:e0288097. [PMID: 37531319 PMCID: PMC10395972 DOI: 10.1371/journal.pone.0288097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/19/2023] [Indexed: 08/04/2023] Open
Abstract
Leontopithecus chrysomelas, the Golden-headed Lion Tamarin (GHLT), is an endangered and endemic Neotropical primate from the Atlantic Forest of Brazil that has suffered a reduction of its habitat and population size in the wild. Ex situ populations have been established as a relevant alternative to safeguard the species and retain its genetic diversity and evolutionary potential. This study evaluated the genetic diversity and structure of the two main Brazilian captive populations of GHLT, which have been under human care at the Primatology Center of Rio de Janeiro (CPRJ) and the Zoological Park Foundation of São Paulo (FPZSP). Our results revealed levels of genetic diversity overall comparable to those observed for other Leontopithecus species and for ex situ and in situ populations of GHLT previously studied. Bayesian and principal coordinate analyses showed a moderate differentiation between CPRJ and FPZSP populations. Both populations presented observed heterozygosity values higher than expected heterozygosity values for most of the microsatellites used in this study, suggesting that the management has been efficient in avoiding an increase in homozygosity. However, simulations point to a significant loss of genetic diversity in the next 100 years, mainly in the FPZSP population. Such data are relevant for further decision-making on the metapopulation management of L. chrysomelas in captive conditions and for integrating in situ and ex situ conservation plans.
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Affiliation(s)
| | | | - Gisele Orecife
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Karla Chávez-Congrains
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Alcides Pissinatti
- Centro de Primatologia do Rio de Janeiro, Guapimirim, Rio de Janeiro, Brazil
| | - Cauê Monticelli
- Departamento de Conservação e Pesquisas Aplicadas, Coordenadoria de Fauna Silvestre, Secretaria de Meio Ambiente, Infraestrutura e Logística do Estado de São Paulo, São Paulo, São Paulo, Brazil
| | | | - Peter Galbusera
- Antwerp Zoo Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Pedro Manoel Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
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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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Barrett KG, Amaral G, Elphinstone M, McAdie ML, Davis CS, Janes JK, Carnio J, Moehrenschlager A, Gorrell JC. Genetic management on the brink of extinction: sequencing microsatellites does not improve estimates of inbreeding in wild and captive Vancouver Island marmots ( Marmota vancouverensis). CONSERV GENET 2022; 23:417-428. [PMID: 35401067 PMCID: PMC8948115 DOI: 10.1007/s10592-022-01429-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/04/2022] [Indexed: 11/27/2022]
Abstract
Captive breeding is often a last resort management option in the conservation of endangered species which can in turn lead to increased risk of inbreeding depression and loss of genetic diversity. Thus, recording breeding events via studbook for the purpose of estimating relatedness, and facilitating mating pair selection to minimize inbreeding, is common practice. However, as founder relatedness is often unknown, loss of genetic variation and inbreeding cannot be entirely avoided. Molecular genotyping is slowly being adopted in captive breeding programs, however achieving sufficient resolution can be challenging in small, low diversity, populations. Here, we evaluate the success of the Vancouver Island marmot (Marmota vancouverensis; VIM; among the worlds most endangered mammals) captive breeding program in preventing inbreeding and maintaining genetic diversity. We explored the use of high-throughput amplicon sequencing of microsatellite regions to assay greater genetic variation in both captive and wild populations than traditional length-based fragment analysis. Contrary to other studies, this method did not considerably increase diversity estimates, suggesting: (1) that the technique does not universally improve resolution, and (2) VIM have exceedingly low diversity. Studbook estimates of pairwise relatedness and inbreeding in the current population were weakly, but positively, correlated to molecular estimates. Thus, current studbooks are moderately effective at predicting genetic similarity when founder relatedness is known. Finally, we found that captive and wild populations did not differ in allelic frequencies, and conservation efforts to maintain diversity have been successful with no significant decrease in diversity over the last three generations. Supplementary Information The online version contains supplementary material available at 10.1007/s10592-022-01429-7.
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Affiliation(s)
- Kimberley G. Barrett
- Biology Department, Vancouver Island University, Nanaimo, BC V9R 5S5 Canada
- Present Address: Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2R3 Canada
| | - Geneviève Amaral
- Biology Department, Vancouver Island University, Nanaimo, BC V9R 5S5 Canada
- Present Address: Island Medical Program, University of Victoria, 3800 Finnerty Road, Victoria, BC V8P 5C2 Canada
| | | | | | - Corey S. Davis
- Present Address: Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2R3 Canada
| | - Jasmine K. Janes
- Biology Department, Vancouver Island University, Nanaimo, BC V9R 5S5 Canada
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351 Australia
| | - John Carnio
- Marmot Recovery Foundation, Nanaimo, BC V9R 6X9 Canada
| | - Axel Moehrenschlager
- Wilder Institute Calgary Zoo, Calgary, AB T2E 7V6 Canada
- IUCN Species Survival Commission, Conservation Translocation Specialist Group, Calgary, AB Canada
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Miller-Butterworth CM, Vacco K, Russell AL, Gaspard JC. Genetic Diversity and Relatedness among Captive African Painted Dogs in North America. Genes (Basel) 2021; 12:genes12101463. [PMID: 34680858 PMCID: PMC8535225 DOI: 10.3390/genes12101463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 11/24/2022] Open
Abstract
African painted dogs (Lycaon pictus, APD) are highly endangered, with fewer than 7000 remaining in nature. Captive breeding programs can preserve a genetically diverse population and provide a source of individuals for reintroductions. However, most programs are initiated from few founders and suffer from low genetic diversity and inbreeding. The aims of this study were to use molecular markers to assess genetic variation, inbreeding, and relatedness among APDs in the North American captive population, to use these data to realign studbook records, and to compare these data to wild populations and to the European captive population to facilitate the development of a global management plan. We sequenced mitochondrial and major histocompatibility (MHC) class II loci and genotyped 14 microsatellite loci from 109 APDs from 34 institutions in North America. We identified three likely studbook errors and resolved ten cases of uncertain paternity. Overall, microsatellite heterozygosity was higher than reported in Europe, but effective population size estimates were lower. Mitochondrial sequence variation was extremely limited, and there were fewer MHC haplotypes than in Europe or the wild. Although the population did not show evidence of significant inbreeding overall, several individuals shared high relatedness values, which should be incorporated into future breeding programs.
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Affiliation(s)
| | - Karen Vacco
- Pittsburgh Zoo & PPG Aquarium, Pittsburgh, PA 15206, USA; (K.V.); (J.C.G.III)
| | - Amy L. Russell
- Biology Department, Grand Valley State University, Allendale, MI 49401, USA;
| | - Joseph C. Gaspard
- Pittsburgh Zoo & PPG Aquarium, Pittsburgh, PA 15206, USA; (K.V.); (J.C.G.III)
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Iglesias Pastrana C, Navas González FJ, Ruiz Aguilera MJ, Dávila García JA, Delgado Bermejo JV, Abelló MT. White-naped mangabeys' viable insurance population within European Zoo Network. Sci Rep 2021; 11:674. [PMID: 33436901 PMCID: PMC7804940 DOI: 10.1038/s41598-020-80281-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 12/18/2020] [Indexed: 01/29/2023] Open
Abstract
The success and viability of an ex-situ conservation program lie in the establishment and potential maintenance of a demographically and genetically viable insurance population. Such population reserve may support reintroduction and reinforcement activities of wild populations. White-naped mangabeys are endangered restricted-range African primates which have experienced a dramatic population decrease in their natural habitats over the last few decades. Since 2001, some European zoos singularly monitor an ex-situ population aiming to seek the recovery of the current wild population. The aim of the present paper is to evaluate the genetic status and population demographics of European zoo-captive white-naped mangabeys based on pedigree data. The captive population is gradually growing and preserves specific reproductive and demographic parameters linked to the species. The intensive management program that is implemented has brought about the minimization of inbreeding and average relatedness levels, thus maintaining high levels of genetic diversity despite the existence of fragmented populations. This finding suggests white-naped mangabey ex-situ preservation actions may be a good example of multifaceted conservation throughout studbook management which could be used as a model for other ex-situ live-animal populations.
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Affiliation(s)
| | | | | | | | | | - María Teresa Abelló
- White-naped mangabey EEP Coordination (EAZA: European Association of Zoos & Aquariums), Parc Zoològic de Barcelona, Barcelona, Spain
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