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Zecherle LJ, Nichols HJ, Bar‐David S, Brown RP, Hipperson H, Horsburgh GJ, Templeton AR. Subspecies hybridization as a potential conservation tool in species reintroductions. Evol Appl 2021; 14:1216-1224. [PMID: 34025762 PMCID: PMC8127701 DOI: 10.1111/eva.13191] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/11/2020] [Accepted: 12/27/2020] [Indexed: 11/30/2022] Open
Abstract
Reintroductions are a powerful tool for the recovery of endangered species. However, their long-term success is strongly influenced by the genetic diversity of the reintroduced population. The chances of population persistence can be improved by enhancing the population's adaptive ability through the mixing of individuals from different sources. However, where source populations are too diverse the reintroduced population could also suffer from outbreeding depression or unsuccessful admixture due to behavioural or genetic barriers. For the reintroduction of Asiatic wild ass Equus hemionus ssp. in Israel, a breeding core was created from individuals of two different subspecies (E. h. onager & E. h. kulan). Today the population comprises approximately 300 individuals and displays no signs of outbreeding depression. The aim of this study was a population genomic evaluation of this conservation reintroduction protocol. We used maximum likelihood methods and genetic clustering analyses to investigate subspecies admixture and test for spatial autocorrelation based on subspecies ancestry. Further, we analysed heterozygosity and effective population sizes in the breeding core prior to release and the current wild population. We discovered high levels of subspecies admixture in the breeding core and wild population, consistent with a significant heterozygote excess in the breeding core. Furthermore, we found no signs of spatial autocorrelation associated with subspecies ancestry in the wild population. Inbreeding and variance effective population size estimates were low. Our results indicate no genetic or behavioural barriers to admixture between the subspecies and suggest that their hybridization has led to greater genetic diversity in the reintroduced population. The study provides rare empirical evidence of the successful application of subspecies hybridization in a reintroduction. It supports use of intraspecific hybridization as a tool to increase genetic diversity in conservation translocations.
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Affiliation(s)
- Lilith J. Zecherle
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
- Mitrani Department of Desert EcologyJacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevMidreshet Ben‐GurionIsrael
- NERC Biomolecular Analysis FacilityDepartment of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | | | - Shirli Bar‐David
- Mitrani Department of Desert EcologyJacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevMidreshet Ben‐GurionIsrael
| | - Richard P. Brown
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Helen Hipperson
- NERC Biomolecular Analysis FacilityDepartment of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Gavin J. Horsburgh
- NERC Biomolecular Analysis FacilityDepartment of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
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Braga RT, Rodrigues JFM, Diniz-Filho JAF, Rangel TF. Genetic Population Structure and Allele Surfing During Range Expansion in Dynamic Habitats. AN ACAD BRAS CIENC 2019; 91:e20180179. [PMID: 31038531 DOI: 10.1590/0001-3765201920180179] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 09/10/2018] [Indexed: 12/24/2022] Open
Abstract
Expanding populations may loss genetic diversity because sequential founder events throughout a wave of demographic expansion may cause "allele surfing", as the alleles of founder individuals may propagate rapidly through space. The spatial components of allele surfing have been studied by geneticists, but have never been investigate on dynamic and shifting habitats. Here we used an individual-based-model (IBM) to study how interactions between different habitat restoration scenarios and biological characteristics (dispersal capacity) affect the spatial patterns of the genetic structure of a population during demographic expansion. We found that both habitat dynamics and dispersal capacity, as well as their interaction, were the drivers of emergent pattern of genetic diversity and allele surfing. Specifically, allele surfing is more common when a species with low dispersal capacity colonizes a large geographic area with slow restoration (low carrying capacity). Despite this, we showed that allele surfing can be reduced, or even avoided, by dispersal management through suitable habitat restoration. Thus, investigating how colonization generates a spatial variation in genetic diversity, and which parameters control the emergent genetic pattern, are essential steps to planning assisted gene flow, which is fundamental for an effective planning of habitat restoration.
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Affiliation(s)
- Rosana T Braga
- Programa de Pós-Graduação em Ecologia e Evolução, Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Avenida Esperança, s/n, 74001-970 Goiânia, GO, Brazil
| | - João F M Rodrigues
- Programa de Pós-Graduação em Ecologia e Evolução, Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Avenida Esperança, s/n, 74001-970 Goiânia, GO, Brazil
| | - José A F Diniz-Filho
- Programa de Pós-Graduação em Ecologia e Evolução, Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Avenida Esperança, s/n, 74001-970 Goiânia, GO, Brazil
| | - Thiago F Rangel
- Programa de Pós-Graduação em Ecologia e Evolução, Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Avenida Esperança, s/n, 74001-970 Goiânia, GO, Brazil
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Greenbaum G, Renan S, Templeton AR, Bouskila A, Saltz D, Rubenstein DI, Bar-David S. Revealing life-history traits by contrasting genetic estimations with predictions of effective population size. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2018; 32:817-827. [PMID: 29270998 PMCID: PMC7208180 DOI: 10.1111/cobi.13068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 12/01/2017] [Accepted: 12/08/2017] [Indexed: 06/07/2023]
Abstract
Effective population size, a central concept in conservation biology, is now routinely estimated from genetic surveys and can also be theoretically predicted from demographic, life-history, and mating-system data. By evaluating the consistency of theoretical predictions with empirically estimated effective size, insights can be gained regarding life-history characteristics and the relative impact of different life-history traits on genetic drift. These insights can be used to design and inform management strategies aimed at increasing effective population size. We demonstrated this approach by addressing the conservation of a reintroduced population of Asiatic wild ass (Equus hemionus). We estimated the variance effective size (Nev ) from genetic data (N ev =24.3) and formulated predictions for the impacts on Nev of demography, polygyny, female variance in lifetime reproductive success (RS), and heritability of female RS. By contrasting the genetic estimation with theoretical predictions, we found that polygyny was the strongest factor affecting genetic drift because only when accounting for polygyny were predictions consistent with the genetically measured Nev . The comparison of effective-size estimation and predictions indicated that 10.6% of the males mated per generation when heritability of female RS was unaccounted for (polygyny responsible for 81% decrease in Nev ) and 19.5% mated when female RS was accounted for (polygyny responsible for 67% decrease in Nev ). Heritability of female RS also affected Nev ; hf2=0.91 (heritability responsible for 41% decrease in Nev ). The low effective size is of concern, and we suggest that management actions focus on factors identified as strongly affecting Nev, namely, increasing the availability of artificial water sources to increase number of dominant males contributing to the gene pool. This approach, evaluating life-history hypotheses in light of their impact on effective population size, and contrasting predictions with genetic measurements, is a general, applicable strategy that can be used to inform conservation practice.
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Affiliation(s)
- Gili Greenbaum
- Department of Solar Energy and Environmental Physics, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus 8499000, Israel
- Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus 8499000, Israel
| | - Sharon Renan
- Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus 8499000, Israel
| | - Alan R. Templeton
- Department of Biology, Washington University, St. Louis, MO 63130, U.S.A
- Department of Evolutionary and Environmental Ecology, University of Haifa, Haifa 31905, Israel
| | - Amos Bouskila
- Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus 8499000, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - David Saltz
- Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus 8499000, Israel
| | - Daniel I. Rubenstein
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, U.S.A
| | - Shirli Bar-David
- Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus 8499000, Israel
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Kaczensky P, Kovtun E, Habibrakhmanov R, Hemami MR, Khaleghi A, Linnell JDC, Rustamov E, Sklyarenko S, Walzer C, Zuther S, Kuehn R. Genetic characterization of free-ranging Asiatic wild ass in Central Asia as a basis for future conservation strategies. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1086-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Bennett EA, Champlot S, Peters J, Arbuckle BS, Guimaraes S, Pruvost M, Bar-David S, Davis SJM, Gautier M, Kaczensky P, Kuehn R, Mashkour M, Morales-Muñiz A, Pucher E, Tournepiche JF, Uerpmann HP, Bălăşescu A, Germonpré M, Gündem CY, Hemami MR, Moullé PE, Ötzan A, Uerpmann M, Walzer C, Grange T, Geigl EM. Taming the late Quaternary phylogeography of the Eurasiatic wild ass through ancient and modern DNA. PLoS One 2017; 12:e0174216. [PMID: 28422966 PMCID: PMC5396879 DOI: 10.1371/journal.pone.0174216] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/06/2017] [Indexed: 11/24/2022] Open
Abstract
Taxonomic over-splitting of extinct or endangered taxa, due to an incomplete knowledge of both skeletal morphological variability and the geographical ranges of past populations, continues to confuse the link between isolated extant populations and their ancestors. This is particularly problematic with the genus Equus. To more reliably determine the evolution and phylogeographic history of the endangered Asiatic wild ass, we studied the genetic diversity and inter-relationships of both extinct and extant populations over the last 100,000 years, including samples throughout its previous range from Western Europe to Southwest and East Asia. Using 229 bp of the mitochondrial hypervariable region, an approach which allowed the inclusion of information from extremely poorly preserved ancient samples, we classify all non-African wild asses into eleven clades that show a clear phylogeographic structure revealing their phylogenetic history. This study places the extinct European wild ass, E. hydruntinus, the phylogeny of which has been debated since the end of the 19th century, into its phylogenetic context within the Asiatic wild asses and reveals recent mitochondrial introgression between populations currently regarded as separate species. The phylogeographic organization of clades resulting from these efforts can be used not only to improve future taxonomic determination of a poorly characterized group of equids, but also to identify historic ranges, interbreeding events between various populations, and the impact of ancient climatic changes. In addition, appropriately placing extant relict populations into a broader phylogeographic and genetic context can better inform ongoing conservation strategies for this highly-endangered species.
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Affiliation(s)
- E. Andrew Bennett
- Institut Jacques Monod, UMR7592, CNRS-Université Paris Diderot, Paris, France
| | - Sophie Champlot
- Institut Jacques Monod, UMR7592, CNRS-Université Paris Diderot, Paris, France
| | - Joris Peters
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilian University, Munich, Germany
- SNSB, Bavarian State Collection of Anthropology and Palaeoanatomy, München, Germany
| | - Benjamin S. Arbuckle
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Silvia Guimaraes
- Institut Jacques Monod, UMR7592, CNRS-Université Paris Diderot, Paris, France
| | - Mélanie Pruvost
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilian University, Munich, Germany
| | - Shirli Bar-David
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | | | - Mathieu Gautier
- Centre de Biologie pour la Gestion des Populations CBGP, Montferrier-sur-Lez, France
| | - Petra Kaczensky
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Ralph Kuehn
- Technische Universität München, AG Molekulare Zoologie/Lehrstuhl für Zoologie, Freising, Germany
| | - Marjan Mashkour
- CNRS and Muséum national d'Histoire naturelle, UMR 7209, Archéozoologie, archéobotanique: sociétés, pratiques et environnements, Département Ecologie et Gestion de la Biodiversité, Paris, France
| | - Arturo Morales-Muñiz
- Laboratory of Archaeozoology, Dept. Biologia, Universidad Autonoma de Madrid, Madrid, Spain
| | | | | | - Hans-Peter Uerpmann
- Eberhard-Karls-Universität Tübingen, Institut für Ur- und Frühgeschichte und Archäologie des Mittelalters, Abteilung Ältere Urgeschichte und Quartärökologie, Zentrum für Naturwissenschaftliche Archäologie, Tübingen, Germany
| | - Adrian Bălăşescu
- National History Museum of Romania, National Centre of Pluridisciplinary Research, Bucureşti, Romania
| | - Mietje Germonpré
- Royal Belgian Institute of Natural Sciences, Earth and History of Life, Brussels, Belgium
| | - Can Y. Gündem
- Eberhard-Karls-Universität Tübingen, Institut für Ur- und Frühgeschichte und Archäologie des Mittelalters, Abteilung Ältere Urgeschichte und Quartärökologie, Zentrum für Naturwissenschaftliche Archäologie, Tübingen, Germany
| | - Mahmoud-Reza Hemami
- Department of Natural Resources, Isfahan University of Technology, Isfahan, Iran
| | | | - Aliye Ötzan
- Ankara Üniversitesi Dil ve Tarih-Coğrafya Fakültesi, Ankara, Turkey
| | - Margarete Uerpmann
- Eberhard-Karls-Universität Tübingen, Institut für Ur- und Frühgeschichte und Archäologie des Mittelalters, Abteilung Ältere Urgeschichte und Quartärökologie, Zentrum für Naturwissenschaftliche Archäologie, Tübingen, Germany
| | - Chris Walzer
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Thierry Grange
- Institut Jacques Monod, UMR7592, CNRS-Université Paris Diderot, Paris, France
- * E-mail: (EMG); (TG)
| | - Eva-Maria Geigl
- Institut Jacques Monod, UMR7592, CNRS-Université Paris Diderot, Paris, France
- * E-mail: (EMG); (TG)
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Giotto N, Gerard JF, Ziv A, Bouskila A, Bar-David S. Space-Use Patterns of the Asiatic Wild Ass (Equus hemionus): Complementary Insights from Displacement, Recursion Movement and Habitat Selection Analyses. PLoS One 2015; 10:e0143279. [PMID: 26630393 PMCID: PMC4667895 DOI: 10.1371/journal.pone.0143279] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 11/03/2015] [Indexed: 11/18/2022] Open
Abstract
The way in which animals move and use the landscape is influenced by the spatial distribution of resources, and is of importance when considering species conservation. We aimed at exploring how landscape-related factors affect a large herbivore's space-use patterns by using a combined approach, integrating movement (displacement and recursions) and habitat selection analyses. We studied the endangered Asiatic wild ass (Equus hemionus) in the Negev Desert, Israel, using GPS monitoring and direct observation. We found that the main landscape-related factors affecting the species' space-use patterns, on a daily and seasonal basis, were vegetation cover, water sources and topography. Two main habitat types were selected: high-elevation sites during the day (specific microclimate: windy on warm summer days) and streambed surroundings during the night (coupled with high vegetation when the animals were active in summer). Distribution of recursion times (duration between visits) revealed a 24-hour periodicity, a pattern that could be widespread among large herbivores. Characterizing frequently revisited sites suggested that recursion movements were mainly driven by a few landscape features (water sources, vegetation patches, high-elevation points), but also by social factors, such as territoriality, which should be further explored. This study provided complementary insights into the space-use patterns of E. hemionus. Understanding of the species' space-use patterns, at both large and fine spatial scale, is required for developing appropriate conservation protocols. Our approach could be further applied for studying the space-use patterns of other species in heterogeneous landscapes.
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Affiliation(s)
- Nina Giotto
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Jean-François Gerard
- Comportement et Ecologie de la Faune Sauvage, Institut National de la Recherche Agronomique, Castanet-Tolosan Cedex, France
| | - Alon Ziv
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Amos Bouskila
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Shirli Bar-David
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
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Renan S, Greenbaum G, Shahar N, Templeton AR, Bouskila A, Bar-David S. Stochastic modelling of shifts in allele frequencies reveals a strongly polygynous mating system in the re-introduced Asiatic wild ass. Mol Ecol 2015; 24:1433-46. [PMID: 25728575 DOI: 10.1111/mec.13131] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/16/2015] [Indexed: 11/27/2022]
Abstract
Small populations are prone to loss of genetic variation and hence to a reduction in their evolutionary potential. Therefore, studying the mating system of small populations and its potential effects on genetic drift and genetic diversity is of high importance for their viability assessments. The traditional method for studying genetic mating systems is paternity analysis. Yet, as small populations are often rare and elusive, the genetic data required for paternity analysis are frequently unavailable. The endangered Asiatic wild ass (Equus hemionus), like all equids, displays a behaviourally polygynous mating system; however, the level of polygyny has never been measured genetically in wild equids. Combining noninvasive genetic data with stochastic modelling of shifts in allele frequencies, we developed an alternative approach to paternity analysis for studying the genetic mating system of the re-introduced Asiatic wild ass in the Negev Desert, Israel. We compared the shifts in allele frequencies (as a measure of genetic drift) that have occurred in the wild ass population since re-introduction onset to simulated scenarios under different proportions of mating males. We revealed a strongly polygynous mating system in which less than 25% of all males participate in the mating process each generation. This strongly polygynous mating system and its potential effect on the re-introduced population's genetic diversity could have significant consequences for the long-term persistence of the population in the Negev. The stochastic modelling approach and the use of allele-frequency shifts can be further applied to systems that are affected by genetic drift and for which genetic data are limited.
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Affiliation(s)
- Sharon Renan
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 85104, Israel; Mitrani Department of Desert Ecology, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, 84990, Israel
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