1
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GuibingaMickala A, Weber A, Ntie S, Gahlot P, Lehmann D, Mickala P, Abernethy K, Anthony N. Estimation of the census (Nc) and effective (Ne) population size of a wild mandrill (Mandrillus sphinx) horde in the Lopé National Park, Gabon using a non-invasive genetic approach. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01458-2] [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]
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2
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Gauffre B, Boissinot A, Quiquempois V, Leblois R, Grillet P, Morin S, Picard D, Ribout C, Lourdais O. Agricultural intensification alters marbled newt genetic diversity and gene flow through density and dispersal reduction. Mol Ecol 2021; 31:119-133. [PMID: 34674328 DOI: 10.1111/mec.16236] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/08/2021] [Accepted: 10/18/2021] [Indexed: 11/30/2022]
Abstract
Recent agricultural intensification threatens global biodiversity with amphibians being one of the most impacted groups. Because of their biphasic life cycle, amphibians are particularly vulnerable to habitat loss and fragmentation that often result in small, isolated populations and loss of genetic diversity. Here, we studied how landscape heterogeneity affects genetic diversity, gene flow and demographic parameters in the marbled newt, Triturus marmoratus, over a hedgerow network landscape in Western France. While the northern part of the study area consists of preserved hedged farmland, the southern part was more profoundly converted for intensive arable crops production after WWII. Based on 67 sampled ponds and 10 microsatellite loci, we characterized regional population genetic structure and evaluated the correlation between landscape variables and (i) local genetic diversity using mixed models and (ii) genetic distance using multiple regression methods and commonality analysis. We identified a single genetic population characterized by a spatially heterogeneous isolation-by-distance pattern. Pond density in the surrounding landscape positively affected local genetic diversity while arable crop land cover negatively affected gene flow and connectivity. We used demographic inferences to quantitatively assess differences in effective population density and dispersal between the contrasted landscapes characterizing the northern and southern parts of the study area. Altogether, results suggest recent land conversion affected T. marmoratus through reduction in both effective population density and dispersal due to habitat loss and reduced connectivity.
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Affiliation(s)
- Bertrand Gauffre
- INRAE, UR 1115 PSH, Plantes et Systèmes de culture Horticoles, Avignon, France.,School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - Alexandre Boissinot
- CNRS, UMR 7372 CEBC - Université de La Rochelle, Villiers-en-Bois, France.,Réserve Naturelle Régionale du Bocage des Antonins - Deux-Sèvres Nature Environnement, Niort, France
| | | | - Raphael Leblois
- CBGP UMR 1062, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, Montpellier, France.,Institut de Biologie Computationnelle, Univ. Montpellier, Montpelier, France
| | - Pierre Grillet
- CNRS, UMR 7372 CEBC - Université de La Rochelle, Villiers-en-Bois, France
| | - Sophie Morin
- Office Français de la Biodiversité, Villiers-en-Bois, France
| | - Damien Picard
- Département de Biologie, UFR Sciences, Angers, France
| | - Cécile Ribout
- CNRS, UMR 7372 CEBC - Université de La Rochelle, Villiers-en-Bois, France
| | - Olivier Lourdais
- CNRS, UMR 7372 CEBC - Université de La Rochelle, Villiers-en-Bois, France.,School of Life Sciences, Arizona State University, Tempe, AZ, USA
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3
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Covarrubias S, González C, Gutiérrez‐Rodríguez C. Effects of natural and anthropogenic features on functional connectivity of anurans: a review of landscape genetics studies in temperate, subtropical and tropical species. J Zool (1987) 2020. [DOI: 10.1111/jzo.12851] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- S. Covarrubias
- Instituto de Investigaciones sobre los Recursos Naturales Universidad Michoacana de San Nicolás de Hidalgo Morelia Michoacán México
| | - C. González
- Instituto de Investigaciones sobre los Recursos Naturales Universidad Michoacana de San Nicolás de Hidalgo Morelia Michoacán México
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4
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Olarte Ó, SÁnchez-Montes G, MartÍnez-Solano Í. Integrative demographic study of the Iberian painted frog (Discoglossus galganoi): inter-annual variation in the effective to census population size ratio, with insights on mating system and breeding success. Integr Zool 2020; 15:498-510. [PMID: 32333629 DOI: 10.1111/1749-4877.12452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In the face of worldwide amphibian declines, integrative studies combining individual-based information and genetic data represent a powerful approach to produce robust, reliable, and comparable assessments of demographic dynamics. The Iberian painted frog (Discoglossus galganoi) is endemic to Spain and Portugal and shows decreasing population trends across its range, but few studies have attempted to estimate census sizes or assess genetic diversity in wild populations, and little is known about their reproductive biology. We applied an integrative approach based on the combination of capture-mark-recapture data and multilocus genotypes to monitor a breeding population of D. galganoi in central Spain during two consecutive breeding seasons, focusing on the estimation of demographic parameters and their temporal variation. Specifically, we estimated the number of adults (Na ), the effective population size (Ne ), and the effective number of breeders (Nb ), as well as survival and migration rates. We documented a >50% decrease in the estimated number of adults of both sexes between the breeding seasons of 2018 and 2019, probably associated with reduced rainfall in the latter. Estimates of Nb and the Nb /Na ratio were low in both seasons, with a 20-30% decrease in Nb and a 47% increase in the Nb /Na ratio in 2019. Based on the reconstruction of pedigrees from larval and adult genotypes, we provide the first genetic evidence of polygamy in males and females of D. galganoi and the first estimates of breeding success in the species.
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Affiliation(s)
- Óscar Olarte
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), c/ José Gutiérrez Abascal 2, Madrid, 28006, Spain
| | - Gregorio SÁnchez-Montes
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), c/ José Gutiérrez Abascal 2, Madrid, 28006, Spain
| | - Íñigo MartÍnez-Solano
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), c/ José Gutiérrez Abascal 2, Madrid, 28006, Spain
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5
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Pabijan M, Palomar G, Antunes B, Antoł W, Zieliński P, Babik W. Evolutionary principles guiding amphibian conservation. Evol Appl 2020; 13:857-878. [PMID: 32431739 PMCID: PMC7232768 DOI: 10.1111/eva.12940] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/05/2020] [Accepted: 02/18/2020] [Indexed: 12/18/2022] Open
Abstract
The Anthropocene has witnessed catastrophic amphibian declines across the globe. A multitude of new, primarily human-induced drivers of decline may lead to extinction, but can also push species onto novel evolutionary trajectories. If these are recognized by amphibian biologists, they can be engaged in conservation actions. Here, we summarize how principles stemming from evolutionary concepts have been applied for conservation purposes, and address emerging ideas at the vanguard of amphibian conservation science. In particular, we examine the consequences of increased drift and inbreeding in small populations and their implications for practical conservation. We then review studies of connectivity between populations at the landscape level, which have emphasized the limiting influence of anthropogenic structures and degraded habitat on genetic cohesion. The rapid pace of environmental changes leads to the central question of whether amphibian populations can cope either by adapting to new conditions or by shifting their ranges. We gloomily conclude that extinction seems far more likely than adaptation or range shifts for most species. That said, conservation strategies employing evolutionary principles, such as selective breeding, introduction of adaptive variants through translocations, ecosystem interventions aimed at decreasing phenotype-environment mismatch, or genetic engineering, may effectively counter amphibian decline in some areas or for some species. The spread of invasive species and infectious diseases has often had disastrous consequences, but has also provided some premier examples of rapid evolution with conservation implications. Much can be done in terms of setting aside valuable amphibian habitat that should encompass both natural and agricultural areas, as well as designing protected areas to maximize the phylogenetic and functional diversity of the amphibian community. We conclude that an explicit consideration and application of evolutionary principles, although certainly not a silver bullet, should increase effectiveness of amphibian conservation in both the short and long term.
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Affiliation(s)
- Maciej Pabijan
- Institute of Zoology and Biomedical ResearchFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Gemma Palomar
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Bernardo Antunes
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Weronika Antoł
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Piotr Zieliński
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Wiesław Babik
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
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6
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Bachmann JC, Jansen van Rensburg A, Cortazar-Chinarro M, Laurila A, Van Buskirk J. Gene Flow Limits Adaptation along Steep Environmental Gradients. Am Nat 2020; 195:E67-E86. [DOI: 10.1086/707209] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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7
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Windig JJ, Verweij MJW, Oldenbroek JK. Reducing inbreeding rates with a breeding circle: Theory and practice in Veluws Heideschaap. J Anim Breed Genet 2018; 136:51-62. [PMID: 30548349 PMCID: PMC7379314 DOI: 10.1111/jbg.12371] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 11/30/2022]
Abstract
Breeding circles allow genetic management in closed populations without pedigrees. In a breeding circle, breeding is split over sub‐populations. Each sub‐population receives breeding males from a single sub‐population and supplies breeding males to one other sub‐population. Donor‐recipient combinations of sub‐populations remain the same over time. Here, we derive inbreeding levels both mathematically and by computer simulation and compare them to actual inbreeding rates derived from DNA information in a real sheep population. In Veluws Heideschaap, a breeding circle has been in operation for over 30 years. Mathematically, starting with inbreeding levels and kinships set to zero, inbreeding rates per generation (ΔF) initially were 0.29%–0.47% within flocks but later converged to 0.18% in all flocks. When, more realistically, inbreeding levels at the start were high and kinship between flocks low, inbreeding levels immediately dropped to the kinship levels between flocks and rates more gradually converged to 0.18%. In computer simulations with overlapping generations, inbreeding levels and rates followed the same pattern, but converged to a lower ΔF of 0.12%. ΔF was determined in the real population with a 12 K SNP chip in recent generations. ΔF in the real population was 0.29%, based on markers to 0.41% per generation based on heterozygosity levels. This is two to three times the theoretically derived values. These increased rates in the real population are probably due to selection and/or the presence of dominant rams siring a disproportionate number of offspring. When these were simulated, ΔF agreed better: 0.35% for selection, 0.38% for dominant rams and 0.67% for both together. The realized inbreeding rates are a warning that in a real population inbreeding rates in a breeding circle can be higher than theoretically expected due to selection and dominant rams. Without a breeding circle, however, inbreeding rates would have been even higher.
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Affiliation(s)
- Jack J Windig
- Livestock Research, Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Marjolein J W Verweij
- Livestock Research, Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - J Kor Oldenbroek
- Livestock Research, Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
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8
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Marchesini A, Vernesi C, Battisti A, Ficetola GF. Deciphering the drivers of negative species-genetic diversity correlation in Alpine amphibians. Mol Ecol 2018; 27:4916-4930. [PMID: 30346071 DOI: 10.1111/mec.14902] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 09/26/2018] [Accepted: 10/01/2018] [Indexed: 01/08/2023]
Abstract
The evolutionary and ecological importance of neutral and adaptive genetic diversity is widely recognized. Nevertheless, genetic diversity is rarely assessed for conservation planning, which often implicitly assumes a positive correlation between species and genetic diversity. Multiple drivers can cause the co-variation between the genetic diversity of one species and the richness of the whole communities, and explicit tests are needed to identify the processes that can determine species-genetic diversity correlations (SGDCs). Here, we tested whether intrapopulation genetic diversity (at neutral loci) and species richness co-vary in the amphibian communities of a southern Alpine region (Trentino, Italy), using the common frog (Rana temporaria) as focal species for the study of genetic diversity. We also analysed ecological similarity, niche overlap and interspecific interactions between the species, to unravel the processes determining SGDC. The neutral genetic diversity of common frogs was negatively related to species richness. The negative SGDC was probably due to an opposite influence of environmental gradients on the two levels of biodiversity, since the focal species and the other amphibians differ in ecological preferences, particularly in terms of thermal optimum. Conversely, we did not find evidence for a role of interspecific interactions in the negative SGDC. Our findings stress that species richness cannot be used as a universal proxy for genetic diversity, and only combining SGDC with analyses on the determinants of biodiversity can allow to identify the processes determining the relationships between genetic and species diversity.
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Affiliation(s)
- Alexis Marchesini
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy.,Department of Agronomy, Food, Natural Resources, Animals, & Environment (DAFNAE), University of Padua, Legnaro (PD), Italy
| | - Cristiano Vernesi
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Andrea Battisti
- Department of Agronomy, Food, Natural Resources, Animals, & Environment (DAFNAE), University of Padua, Legnaro (PD), Italy
| | - Gentile Francesco Ficetola
- Departement of Environmental Science and Policy, Università degli Studi di Milano, Milano, Italy.,Univ. Grenoble Alpes, CNRS, Laboratoire d'Ecologie Alpine (LECA), Université Grenoble-Alpes, Grenoble, France
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9
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McCartney-Melstad E, Vu JK, Shaffer HB. Genomic data recover previously undetectable fragmentation effects in an endangered amphibian. Mol Ecol 2018; 27:4430-4443. [PMID: 30307076 DOI: 10.1111/mec.14892] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/17/2018] [Accepted: 10/01/2018] [Indexed: 12/30/2022]
Abstract
A critical consideration when using molecular ecological methods to detect trends and parameterize models at very fine spatial and temporal scales has always been the technical limits of resolution. Key landscape features, including most anthropogenic modifications, can cause biologically important, but very recent changes in gene flow that require substantial statistical power to detect. The problem is one of temporal scale: Human change is rapid and recent, while genetic changes accumulate slowly. We generated SNPs from thousands of nuclear loci to characterize the population structure of New York-endangered eastern tiger salamanders (Ambystoma tigrinum) on Long Island and quantify the impacts of roads on population fragmentation. In stark contrast to a recent microsatellite study, we uncovered highly structured populations over an extremely small spatial scale (approximately 40 km2 ) in an increasingly human-modified landscape. Geographic distance and the presence of roads between ponds were both strong predictors of genetic divergence, suggesting that both natural and anthropogenic factors contribute to the observed patterns of genetic variation. All ponds supported small to modest effective breeding populations, and pond surface area showed a strong positive correlation with population size. None of these patterns emerged in an earlier study of the same system using microsatellite loci, and we determined that at least 300-400 SNPs were needed to recover the fine-scale population structure present in this system. Conservation assessments using earlier genetic techniques in other species may similarly lack the statistical power for small-scale inferences and benefit from reassessments using genomic tools.
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Affiliation(s)
- Evan McCartney-Melstad
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability,, University of California, Los Angeles, Los Angeles, California
| | - Jannet K Vu
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability,, University of California, Los Angeles, Los Angeles, California.,Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability,, University of California, Los Angeles, Los Angeles, California
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10
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Valbuena-Ureña E, Oromi N, Soler-Membrives A, Carranza S, Amat F, Camarasa S, Denoël M, Guillaume O, Sanuy D, Loyau A, Schmeller DS, Steinfartz S. Jailed in the mountains: Genetic diversity and structure of an endemic newt species across the Pyrenees. PLoS One 2018; 13:e0200214. [PMID: 30071027 PMCID: PMC6071966 DOI: 10.1371/journal.pone.0200214] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 06/21/2018] [Indexed: 11/30/2022] Open
Abstract
The Pyrenees represent a natural laboratory for biogeographic, evolutionary and ecological research of mountain fauna as a result of the high variety of habitats and the profound effect of the glacial and interglacial periods. There is a paucity of studies providing a detailed insight into genetic processes and better knowledge on the patterns of genetic diversity and how they are maintained under high altitude conditions. This is of particular interest when considering the course of past climate conditions and glaciations in a species which is considered site tenacious, with long generation times. Here we analyzed the genetic patterns of diversity and structure of the endemic Pyrenean brook newt (Calotriton asper) along its distribution range, with special emphasis on the distinct habitat types (caves, streams, and lakes), and the altitudinal and geographical ranges, using a total set of 900 individuals from 44 different localities across the Pyrenean mountain range genotyped for 19 microsatellite loci. We found evidence for a negative longitudinal and positive altitudinal gradient of genetic diversity in C. asper populations. The fact that genetic diversity was markedly higher westwards is in accordance with other Pyrenean species. However, the impact of altitudinal gradient on the genetic diversity seems to differ from other species, and mostly from other amphibians. We found that lower altitudes can act as a barrier probably because the lowlands do not provide a suitable habitat for C. asper. Regarding the distinct habitat types, caves had significantly lower values of genetic diversity compared to streams or lakes. The mean FST value was relatively high (0.304) with maximum values as high as 0.771, suggesting a highly structured total population. Indeed, populations were grouped into five subclusters, the eastern populations (cluster 1) remained grouped into two subclusters and the central-western Pyrenees (cluster 2) into three subclusters. The increase of isolation with geographical distance is consistent with the population structure detected. In conclusion, C. asper seems to be adapted to high altitude mountain habitats, and its genetic diversity is higher in the western Pyrenees. In terms of conservation priority, we consider more relevant the populations that represent a reservoir of genetic diversity.
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Affiliation(s)
- Emilio Valbuena-Ureña
- Unitat de Zoologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès (Barcelona), Catalonia, Spain
- Centre de Fauna Salvatge de Torreferrussa (Catalan Wildlife Service–Forestal Catalana), Barcelona, Catalonia, Spain
| | - Neus Oromi
- Departament de Ciència Animal (Fauna Silvestre), Universitat de Lleida, Lleida, Catalonia, Spain
| | - Anna Soler-Membrives
- Unitat de Zoologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès (Barcelona), Catalonia, Spain
- * E-mail: (ASM); (SS)
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Fèlix Amat
- Àrea d’Herpetologia, Museu de Granollers, Ciències Naturals, Granollers, Catalonia, Spain
| | - Sebastià Camarasa
- Departament de Ciència Animal (Fauna Silvestre), Universitat de Lleida, Lleida, Catalonia, Spain
| | - Mathieu Denoël
- Laboratory of Fish and Amphibian Ethology, Behavioural Biology Group, Freshwater and OCeanic science Unit of reSearch (FOCUS), University of Liège, Liège, Belgium
| | - Olivier Guillaume
- Station d'Ecologie Théorique et Expérimentale CNRS-Université de Toulouse, Moulis, France
| | - Delfí Sanuy
- Departament de Ciència Animal (Fauna Silvestre), Universitat de Lleida, Lleida, Catalonia, Spain
| | - Adeline Loyau
- Helmholtz Centre for Environmental Research–UFZ, Department of Conservation Biology, Leipzig, Germany
- EcoLab, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Dirk S. Schmeller
- Helmholtz Centre for Environmental Research–UFZ, Department of Conservation Biology, Leipzig, Germany
- EcoLab, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Sebastian Steinfartz
- Zoological Institute, Department of Evolutionary Biology, Unit of Molecular Ecology, Technische Universität Braunschweig, Braunschweig, Germany
- * E-mail: (ASM); (SS)
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11
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Perl RGB, Geffen E, Malka Y, Barocas A, Renan S, Vences M, Gafny S. Population genetic analysis of the recently rediscovered Hula painted frog (Latonia nigriventer) reveals high genetic diversity and low inbreeding. Sci Rep 2018; 8:5588. [PMID: 29615810 PMCID: PMC5882862 DOI: 10.1038/s41598-018-23587-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 03/15/2018] [Indexed: 11/09/2022] Open
Abstract
After its recent rediscovery, the Hula painted frog (Latonia nigriventer) has remained one of the world's rarest and least understood amphibian species. Together with its apparently low dispersal capability and highly disturbed niche, the low abundance of this living fossil calls for urgent conservation measures. We used 18 newly developed microsatellite loci and four different models to calculate the effective population size (Ne) of a total of 125 Hula painted frog individuals sampled at a single location. We compare the Ne estimates to the estimates of potentially reproducing adults in this population (Nad) determined through a capture-recapture study on 118 adult Hula painted frogs captured at the same site. Surprisingly, our data suggests that, despite Nad estimates of only ~234-244 and Ne estimates of ~16.6-35.8, the species appears to maintain a very high genetic diversity (HO = 0.771) and low inbreeding coefficient (FIS = -0.018). This puzzling outcome could perhaps be explained by the hypotheses of either genetic rescue from one or more unknown Hula painted frog populations nearby or by recent admixture of genetically divergent subpopulations. Independent of which scenario is correct, the original locations of these populations still remain to be determined.
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Affiliation(s)
- R G Bina Perl
- Division of Evolutionary Biology, Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106, Braunschweig, Germany. .,School of Marine Sciences, Ruppin Academic Center, Michmoret 40297, Israel.
| | - Eli Geffen
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yoram Malka
- Israel Nature and Parks Authority, 3 Am Ve'Olamo Street, Jerusalem 95463, Israel
| | - Adi Barocas
- San Diego Zoo's Institute for Conservation Research, 15600 San Pasqual Valley Road, Escondido, CA 92027, USA.,Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Oxfordshire OX13 5QL, UK
| | - Sharon Renan
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Miguel Vences
- Division of Evolutionary Biology, Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106, Braunschweig, Germany
| | - Sarig Gafny
- School of Marine Sciences, Ruppin Academic Center, Michmoret 40297, Israel
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12
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Sánchez‐Montes G, Wang J, Ariño AH, Vizmanos JL, Martínez‐Solano I. Reliable effective number of breeders/adult census size ratios in seasonal-breeding species: Opportunity for integrative demographic inferences based on capture-mark-recapture data and multilocus genotypes. Ecol Evol 2017; 7:10301-10314. [PMID: 29238556 PMCID: PMC5723585 DOI: 10.1002/ece3.3387] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 07/20/2017] [Accepted: 08/03/2017] [Indexed: 01/18/2023] Open
Abstract
The ratio of the effective number of breeders (Nb) to the adult census size (Na), Nb/Na, approximates the departure from the standard capacity of a population to maintain genetic diversity in one reproductive season. This information is relevant for assessing population status, understanding evolutionary processes operating at local scales, and unraveling how life-history traits affect these processes. However, our knowledge on Nb/Na ratios in nature is limited because estimation of both parameters is challenging. The sibship frequency (SF) method is adequate for reliable Nb estimation because it is based on sibship and parentage reconstruction from genetic marker data, thereby providing demographic inferences that can be compared with field-based information. In addition, capture-mark-recapture (CMR) robust design methods are well suited for Na estimation in seasonal-breeding species. We used tadpole genotypes of three pond-breeding amphibian species (Epidalea calamita, Hyla molleri, and Pelophylax perezi, n = 73-96 single-cohort tadpoles/species genotyped at 15-17 microsatellite loci) and candidate parental genotypes (n = 94-300 adults/species) to estimate Nb by the SF method. To assess the reliability of Nb estimates, we compared sibship and parentage inferences with field-based information and checked for the convergence of results in replicated subsampled analyses. Finally, we used CMR data from a 6-year monitoring program to estimate annual Na in the three species and calculate the Nb/Na ratio. Reliable ratios were obtained for E. calamita (Nb/Na = 0.18-0.28) and P. perezi (0.5), but in H. molleri, Na could not be estimated and genetic information proved insufficient for reliable Nb estimation. Integrative demographic studies taking full advantage of SF and CMR methods can provide accurate estimates of the Nb/Na ratio in seasonal-breeding species. Importantly, the SF method provides results that can be readily evaluated for reliability. This represents a good opportunity for obtaining robust demographic inferences with wide applications for evolutionary and conservation research.
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Affiliation(s)
- Gregorio Sánchez‐Montes
- Department of Environmental BiologyUniversidad de NavarraPamplonaSpain
- Museo Nacional de Ciencias Naturales, CSICMadridSpain
- Institute of ZoologyZoological Society of LondonLondonUK
- Ecology, Evolution, and Development GroupDepartment of Wetland EcologyDoñana Biological Station, CSICSevilleSpain
| | - Jinliang Wang
- Institute of ZoologyZoological Society of LondonLondonUK
| | - Arturo H. Ariño
- Department of Environmental BiologyUniversidad de NavarraPamplonaSpain
| | - José Luis Vizmanos
- Department of Biochemistry and GeneticsUniversidad de NavarraPamplonaSpain
| | - Iñigo Martínez‐Solano
- Museo Nacional de Ciencias Naturales, CSICMadridSpain
- Ecology, Evolution, and Development GroupDepartment of Wetland EcologyDoñana Biological Station, CSICSevilleSpain
- Instituto de Investigación en Recursos Cinegéticos (IREC‐CSIC‐UCLM‐JCCM)Ciudad RealSpain
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13
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Robertson JM, Fitzpatrick SW, Rothermel BB, Chan LM. Fire Does Not Strongly Affect Genetic Diversity or Structure of a Common Treefrog in the Endangered Florida Scrub. J Hered 2017; 109:243-252. [DOI: 10.1093/jhered/esx088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 10/06/2017] [Indexed: 11/15/2022] Open
Affiliation(s)
- Jeanne M Robertson
- Department of Biology, California State University, Northridge, Northridge, CA
| | - Sarah W Fitzpatrick
- W.K. Kellogg Biological Station, Department of Integrative Biology, Michigan State University, Hickory Corners, MI
| | | | - Lauren M Chan
- Department of Biology, Pacific University, Forest Grove, OR
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14
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15
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Wang IJ, Shaffer HB. Population genetic and field-ecological analyses return similar estimates of dispersal over space and time in an endangered amphibian. Evol Appl 2017; 10:630-639. [PMID: 28616069 PMCID: PMC5469172 DOI: 10.1111/eva.12479] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 02/13/2017] [Indexed: 01/05/2023] Open
Abstract
The explosive growth of empirical population genetics has seen a proliferation of analytical methods leading to a steady increase in our ability to accurately measure key population parameters, including genetic isolation, effective population size, and gene flow, in natural systems. Assuming they yield similar results, population genetic methods offer an attractive complement to, or replacement of, traditional field‐ecological studies. However, empirical assessments of the concordance between direct field‐ecological and indirect population genetic studies of the same populations are uncommon in the literature. In this study, we investigate genetic isolation, rates of dispersal, and population sizes for the endangered California tiger salamander, Ambystoma californiense, across multiple breeding seasons in an intact vernal pool network. We then compare our molecular results to a previously published study based on multiyear, mark–recapture data from the same breeding sites. We found that field and genetic estimates of population size were only weakly correlated, but dispersal rates were remarkably congruent across studies and methods. In fact, dispersal probability functions derived from genetic data and traditional field‐ecological data were a significant match, suggesting that either method can be used effectively to assess population connectivity. These results provide one of the first explicit tests of the correspondence between landscape genetic and field‐ecological approaches to measuring functional population connectivity and suggest that even single‐year genetic samples can return biologically meaningful estimates of natural dispersal and gene flow.
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Affiliation(s)
- Ian J Wang
- Department of Environmental Science, Policy, and Management University of California Berkeley CA USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaLos AngelesCAUSA.,La Kretz Center for California Conservation Science Institute of the Environment and Sustainability University of California Los Angeles CA USA
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16
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Schmeller DS, Weatherdon LV, Loyau A, Bondeau A, Brotons L, Brummitt N, Geijzendorffer IR, Haase P, Kuemmerlen M, Martin CS, Mihoub JB, Rocchini D, Saarenmaa H, Stoll S, Regan EC. A suite of essential biodiversity variables for detecting critical biodiversity change. Biol Rev Camb Philos Soc 2017; 93:55-71. [DOI: 10.1111/brv.12332] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 03/11/2017] [Accepted: 03/16/2017] [Indexed: 01/13/2023]
Affiliation(s)
- Dirk S. Schmeller
- Department of Conservation Biology; Helmholtz Center for Environmental Research - UFZ; 04318 Leipzig Germany
- ECOLAB; Université de Toulouse, CNRS, INPT, UPS; Toulouse France
| | - Lauren V. Weatherdon
- United Nations Environment World Conservation Monitoring Centre; Cambridge CB3 0DL U.K
| | - Adeline Loyau
- ECOLAB; Université de Toulouse, CNRS, INPT, UPS; Toulouse France
- Department of System Ecotoxicology; Helmholtz Center for Environmental Research - UFZ; 04318 Leipzig Germany
| | - Alberte Bondeau
- Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE); Aix Marseille Université, CNRS, IRD, Avignon Université, Technopôle Arbois-Méditerranée Bât; F-13545 Aix-en-Provence cedex 04 France
| | - Lluis Brotons
- Forest Sciences Centre of Catalonia (CEMFOR-CTFC); Catalonia Spain
- CREAF, Centre for Ecological Research and Forestry Applications; Autonomous University of Barcelona; Catalonia Spain
- CSIC, Cerdanyola del Vallés; Catalonia Spain
| | - Neil Brummitt
- Department of Life Sciences; Natural History Museum; London SW7 5BD U.K
| | - Ilse R. Geijzendorffer
- Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE); Aix Marseille Université, CNRS, IRD, Avignon Université, Technopôle Arbois-Méditerranée Bât; F-13545 Aix-en-Provence cedex 04 France
- Tour du Valat, Institut de recherche pour la conservation des zones humides méditerranéennes, Le Sambuc; Arles 13200 France
| | - Peter Haase
- Department of River Ecology and Conservation; Senckenberg Research Institute and Natural History Museum Frankfurt; D-63571 Gelnhausen Germany
- Faculty of Biology; University of Duisburg-Essen; 45141 Essen Germany
| | - Mathias Kuemmerlen
- Department of River Ecology and Conservation; Senckenberg Research Institute and Natural History Museum Frankfurt; D-63571 Gelnhausen Germany
- Department of Systems Analysis; Integrated Assessment and Modelling, Swiss Federal Institute of Aquatic Science and Technology - Eawag; Überlandstrasse 133 8600 Dübendorf Switzerland
| | - Corinne S. Martin
- United Nations Environment World Conservation Monitoring Centre; Cambridge CB3 0DL U.K
| | - Jean-Baptiste Mihoub
- Department of Conservation Biology; Helmholtz Center for Environmental Research - UFZ; 04318 Leipzig Germany
- Sorbonne Universités; UPMC Univ Paris 06, Muséum National d'Histoire Naturelle, CNRS, CESCO; UMR 7204, 75005 Paris France
| | - Duccio Rocchini
- Department of Biodiversity and Molecular Ecology; Fondazione Edmund Mach, Research and Innovation Centre; 38010 S. Micehle all'Adige (TN) Italy
| | | | - Stefan Stoll
- Department of River Ecology and Conservation; Senckenberg Research Institute and Natural History Museum Frankfurt; D-63571 Gelnhausen Germany
- Ecosystem Research Facility Eußerthal, Institute of Environmental Science; University of Koblenz-Landau; Koblenz-Landau Germany
| | - Eugenie C. Regan
- United Nations Environment World Conservation Monitoring Centre; Cambridge CB3 0DL U.K
- The Biodiversity Consultancy; Cambridge CB2 1SJ U.K
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17
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Stubberud MW, Myhre AM, Holand H, Kvalnes T, Ringsby TH, Saether BE, Jensen H. Sensitivity analysis of effective population size to demographic parameters in house sparrow populations. Mol Ecol 2017; 26:2449-2465. [DOI: 10.1111/mec.14057] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/18/2016] [Accepted: 01/27/2017] [Indexed: 01/20/2023]
Affiliation(s)
- Marlene Waege Stubberud
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; NO-7491 Trondheim Norway
| | - Ane Marlene Myhre
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; NO-7491 Trondheim Norway
| | - Håkon Holand
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; NO-7491 Trondheim Norway
| | - Thomas Kvalnes
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; NO-7491 Trondheim Norway
| | - Thor Harald Ringsby
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; NO-7491 Trondheim Norway
| | - Bernt-Erik Saether
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; NO-7491 Trondheim Norway
| | - Henrik Jensen
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; NO-7491 Trondheim Norway
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18
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Murphy SM, Cox JJ, Augustine BC, Hast JT, Guthrie JM, Wright J, McDermott J, Maehr SC, Plaxico JH. Characterizing recolonization by a reintroduced bear population using genetic spatial capture-recapture. J Wildl Manage 2016. [DOI: 10.1002/jwmg.21144] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sean M. Murphy
- Department of Forestry; University of Kentucky; 214 Thomas Poe Cooper Building Lexington KY 40546 USA
| | - John J. Cox
- Department of Forestry; University of Kentucky; 214 Thomas Poe Cooper Building Lexington KY 40546 USA
| | - Ben C. Augustine
- Department of Forestry; University of Kentucky; 214 Thomas Poe Cooper Building Lexington KY 40546 USA
| | - John T. Hast
- Department of Forestry; University of Kentucky; 214 Thomas Poe Cooper Building Lexington KY 40546 USA
| | - Joseph M. Guthrie
- Kentucky Department of Fish and Wildlife Resources; #1 Sportsman's Lane Frankfort KY 40601 USA
| | - John Wright
- Department of Forestry; University of Kentucky; 214 Thomas Poe Cooper Building Lexington KY 40546 USA
| | - Joseph McDermott
- Department of Forestry; University of Kentucky; 214 Thomas Poe Cooper Building Lexington KY 40546 USA
| | - Sutton C. Maehr
- Department of Forestry; University of Kentucky; 214 Thomas Poe Cooper Building Lexington KY 40546 USA
| | - Jayson H. Plaxico
- Kentucky Department of Fish and Wildlife Resources; #1 Sportsman's Lane Frankfort KY 40601 USA
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19
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Trochet A, Courtois EA, Stevens VM, Baguette M, Chaine A, Schmeller DS, Clobert J, Wiens JJ. Evolution of Sex-Biased Dispersal. QUARTERLY REVIEW OF BIOLOGY 2016; 91:297-30. [DOI: 10.1086/688097] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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20
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McCartney-Melstad E, Shaffer HB. Amphibian molecular ecology and how it has informed conservation. Mol Ecol 2015; 24:5084-109. [PMID: 26437125 DOI: 10.1111/mec.13391] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 09/15/2015] [Accepted: 09/16/2015] [Indexed: 02/02/2023]
Abstract
Molecular ecology has become one of the key tools in the modern conservationist's kit. Here we review three areas where molecular ecology has been applied to amphibian conservation: genes on landscapes, within-population processes, and genes that matter. We summarize relevant analytical methods, recent important studies from the amphibian literature, and conservation implications for each section. Finally, we include five in-depth examples of how molecular ecology has been successfully applied to specific amphibian systems.
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Affiliation(s)
- Evan McCartney-Melstad
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, 610 Charles E Young Drive South, Los Angeles, CA, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, 610 Charles E Young Drive South, Los Angeles, CA, USA
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21
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Estimating effective population size of guanacos in Patagonia: an integrative approach for wildlife conservation. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0730-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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22
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Mangold A, Trenkwalder K, Ringler M, Hödl W, Ringler E. Low reproductive skew despite high male-biased operational sex ratio in a glass frog with paternal care. BMC Evol Biol 2015; 15:181. [PMID: 26334630 PMCID: PMC4558732 DOI: 10.1186/s12862-015-0469-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/27/2015] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Reproductive skew, the uneven distribution of reproductive success among individuals, is a common feature of many animal populations. Several scenarios have been proposed to favour either high or low levels of reproductive skew. Particularly a male-biased operational sex ratio and the asynchronous arrival of females is expected to cause high variation in reproductive success among males. Recently it has been suggested that the type of benefits provided by males (fixed vs. dilutable) could also strongly impact individual mating patterns, and thereby affecting reproductive skew. We tested this hypothesis in Hyalinobatrachium valerioi, a Neotropical glass frog with prolonged breeding and paternal care. RESULTS We monitored and genetically sampled a natural population in southwestern Costa Rica during the breeding season in 2012 and performed parentage analysis of adult frogs and tadpoles to investigate individual mating frequencies, possible mating preferences, and estimate reproductive skew in males and females. We identified a polygamous mating system, where high proportions of males (69 %) and females (94 %) reproduced successfully. The variance in male mating success could largely be attributed to differences in time spent calling at the reproductive site, but not to body size or relatedness. Female H. valerioi were not choosy and mated indiscriminately with available males. CONCLUSIONS Our findings support the hypothesis that dilutable male benefits - such as parental care - can favour female polyandry and maintain low levels of reproductive skew among males within a population, even in the presence of direct male-male competition and a highly male-biased operational sex ratio. We hypothesize that low male reproductive skew might be a general characteristic in prolonged breeders with paternal care.
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Affiliation(s)
- Alexandra Mangold
- Department of Integrative Zoology, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria.
| | - Katharina Trenkwalder
- Department of Integrative Zoology, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria.
| | - Max Ringler
- Department of Integrative Zoology, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria.
| | - Walter Hödl
- Department of Integrative Zoology, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria.
| | - Eva Ringler
- Messerli Research Institute, University of Veterinary Medicine Vienna, Veterinärplatz 1, A- 1210, Vienna, Austria.
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23
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Álvarez D, Lourenço A, Oro D, Velo-Antón G. Assessment of census (N) and effective population size (N e ) reveals consistency of N e single-sample estimators and a high N e /N ratio in an urban and isolated population of fire salamanders. CONSERV GENET RESOUR 2015. [DOI: 10.1007/s12686-015-0480-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Temporal genetic and demographic monitoring of pond-breeding amphibians in three contrasting population systems. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0743-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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25
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Waples RS, Luikart G, Faulkner JR, Tallmon DA. Simple life-history traits explain key effective population size ratios across diverse taxa. Proc Biol Sci 2013; 280:20131339. [PMID: 23926150 PMCID: PMC3757969 DOI: 10.1098/rspb.2013.1339] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 06/26/2013] [Indexed: 11/12/2022] Open
Abstract
Effective population size (Ne) controls both the rate of random genetic drift and the effectiveness of selection and migration, but it is difficult to estimate in nature. In particular, for species with overlapping generations, it is easier to estimate the effective number of breeders in one reproductive cycle (Nb) than Ne per generation. We empirically evaluated the relationship between life history and ratios of Ne, Nb and adult census size (N) using a recently developed model (agene) and published vital rates for 63 iteroparous animals and plants. Nb/Ne varied a surprising sixfold across species and, contrary to expectations, Nb was larger than Ne in over half the species. Up to two-thirds of the variance in Nb/Ne and up to half the variance in Ne/N was explained by just two life-history traits (age at maturity and adult lifespan) that have long interested both ecologists and evolutionary biologists. These results provide novel insights into, and demonstrate a close general linkage between, demographic and evolutionary processes across diverse taxa. For the first time, our results also make it possible to interpret rapidly accumulating estimates of Nb in the context of the rich body of evolutionary theory based on Ne per generation.
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Affiliation(s)
- Robin S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98112, USA.
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26
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Drechsler A, Geller D, Freund K, Schmeller DS, Künzel S, Rupp O, Loyau A, Denoël M, Valbuena-Ureña E, Steinfartz S. What remains from a 454 run: estimation of success rates of microsatellite loci development in selected newt species (Calotriton asper, Lissotriton helveticus, and Triturus cristatus) and comparison with Illumina-based approaches. Ecol Evol 2013; 3:3947-57. [PMID: 24198952 PMCID: PMC3810887 DOI: 10.1002/ece3.764] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 08/07/2013] [Accepted: 08/12/2013] [Indexed: 11/24/2022] Open
Abstract
The development of microsatellite loci has become more efficient using next-generation sequencing (NGS) approaches, and many studies imply that the amount of applicable loci is large. However, few studies have sought to quantify the number of loci that are retained for use out of the thousands of sequence reads initially obtained. We analyzed the success rate of microsatellite loci development for three amphibian species using a 454 NGS approach on tetra-nucleotide motif-enriched species-specific libraries. The number of sequence reads obtained differed strongly between species and ranged from 19,562 for Triturus cristatus to 55,626 for Lissotriton helveticus, with 52,075 reads obtained for Calotriton asper. PHOBOS was used to identify sequences with tetra-nucleotide repeat motifs with a minimum repeat number of ten and high quality primer binding sites. Of 107 sequences for T. cristatus, 316 for C. asper and 319 for L. helveticus, we tested the amplification success, polymorphism, and degree of heterozygosity for 41 primer combinations each for C. asper and T. cristatus, and 22 for L. helveticus. We found 11 polymorphic loci for T. cristatus, 20 loci for C. asper, and 15 loci for L. helveticus. Extrapolated, the number of potentially amplifiable loci (PALs) resulted in estimated species-specific success rates of 0.15% (T. cristatus), 0.30% (C. asper), and 0.39% (L. helveticus). Compared with representative Illumina NGS approaches, our applied 454-sequencing approach on specifically enriched sublibraries proved to be quite competitive in terms of success rates and number of finally applicable loci.
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Affiliation(s)
- Axel Drechsler
- Department of Behavioral Biology, Unit of Molecular Ecology and Behavior, University of Bielefeld Morgenbreede 45, D-33619, Bielefeld, Germany
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27
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Vences M, Hauswaldt JS, Steinfartz S, Rupp O, Goesmann A, Künzel S, Orozco-terWengel P, Vieites DR, Nieto-Roman S, Haas S, Laugsch C, Gehara M, Bruchmann S, Pabijan M, Ludewig AK, Rudert D, Angelini C, Borkin LJ, Crochet PA, Crottini A, Dubois A, Ficetola GF, Galán P, Geniez P, Hachtel M, Jovanovic O, Litvinchuk SN, Lymberakis P, Ohler A, Smirnov NA. Radically different phylogeographies and patterns of genetic variation in two European brown frogs, genus Rana. Mol Phylogenet Evol 2013; 68:657-70. [PMID: 23632031 DOI: 10.1016/j.ympev.2013.04.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 04/10/2013] [Accepted: 04/16/2013] [Indexed: 11/26/2022]
Abstract
We reconstruct range-wide phylogeographies of two widespread and largely co-occurring Western Palearctic frogs, Rana temporaria and R. dalmatina. Based on tissue or saliva samples of over 1000 individuals, we compare a variety of genetic marker systems, including mitochondrial DNA, single-copy protein-coding nuclear genes, microsatellite loci, and single nucleotide polymorphisms (SNPs) of transcriptomes of both species. The two focal species differ radically in their phylogeographic structure, with R. temporaria being strongly variable among and within populations, and R. dalmatina homogeneous across Europe with a single strongly differentiated population in southern Italy. These differences were observed across the various markers studied, including microsatellites and SNP density, but especially in protein-coding nuclear genes where R. dalmatina had extremely low heterozygosity values across its range, including potential refugial areas. On the contrary, R. temporaria had comparably high range-wide values, including many areas of probable postglacial colonization. A phylogeny of R. temporaria based on various concatenated mtDNA genes revealed that two haplotype clades endemic to Iberia form a paraphyletic group at the base of the cladogram, and all other haplotypes form a monophyletic group, in agreement with an Iberian origin of the species. Demographic analysis suggests that R. temporaria and R. dalmatina have genealogies of roughly the same time to coalescence (TMRCA ~3.5 mya for both species), but R. temporaria might have been characterized by larger ancestral and current effective population sizes than R. dalmatina. The high genetic variation in R. temporaria can therefore be explained by its early range expansion out of Iberia, with subsequent cycles of differentiation in cryptic glacial refugial areas followed by admixture, while the range expansion of R. dalmatina into central Europe is a probably more recent event.
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Affiliation(s)
- Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany.
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Richmond JQ, Barr KR, Backlin AR, Vandergast AG, Fisher RN. Evolutionary dynamics of a rapidly receding southern range boundary in the threatened California Red-Legged Frog ( Rana draytonii). Evol Appl 2013; 6:808-822. [PMID: 29387167 PMCID: PMC5779129 DOI: 10.1111/eva.12067] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 02/25/2013] [Indexed: 12/01/2022] Open
Abstract
Populations forming the edge of a species range are often imperiled by isolation and low genetic diversity, with proximity to human population centers being a major determinant of edge stability in modern landscapes. Since the 1960s, the California red‐legged frog (Rana draytonii) has undergone extensive declines in heavily urbanized southern California, where the range edge has rapidly contracted northward while shifting its cardinal orientation to an east‐west trending axis. We studied the genetic structure and diversity of these frontline populations, tested for signatures of contemporary disturbance, specifically fire, and attempted to disentangle these signals from demographic events extending deeper into the past. Consistent with the genetic expectations of the ‘abundant‐center’ model, we found that diversity, admixture, and opportunity for random mating increases in populations sampled successively further away from the range boundary. Demographic simulations indicate that bottlenecks in peripheral isolates are associated with processes extending tens to a few hundred generations in the past, despite the demographic collapse of some due to recent fire‐flood events. While the effects of recent disturbance have left little genetic imprint on these populations, they likely contribute to an extinction debt that will lead to continued range contraction unless management intervenes to stall or reverse the process.
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Affiliation(s)
| | - Kelly R Barr
- U. S. Geological Survey Western Ecological Research Center San Diego CA USA
| | - Adam R Backlin
- U. S. Geological Survey Western Ecological Research Center San Diego CA USA
| | - Amy G Vandergast
- U. S. Geological Survey Western Ecological Research Center San Diego CA USA
| | - Robert N Fisher
- U. S. Geological Survey Western Ecological Research Center San Diego CA USA
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29
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Hoehn M, Gruber B, Sarre SD, Lange R, Henle K. Can genetic estimators provide robust estimates of the effective number of breeders in small populations? PLoS One 2012; 7:e48464. [PMID: 23139784 PMCID: PMC3491051 DOI: 10.1371/journal.pone.0048464] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 09/26/2012] [Indexed: 11/18/2022] Open
Abstract
The effective population size (N(e)) is proportional to the loss of genetic diversity and the rate of inbreeding, and its accurate estimation is crucial for the monitoring of small populations. Here, we integrate temporal studies of the gecko Oedura reticulata, to compare genetic and demographic estimators of N(e). Because geckos have overlapping generations, our goal was to demographically estimate N(bI), the inbreeding effective number of breeders and to calculate the N(bI)/N(a) ratio (N(a) =number of adults) for four populations. Demographically estimated N(bI) ranged from 1 to 65 individuals. The mean reduction in the effective number of breeders relative to census size (N(bI)/N(a)) was 0.1 to 1.1. We identified the variance in reproductive success as the most important variable contributing to reduction of this ratio. We used four methods to estimate the genetic based inbreeding effective number of breeders N(bI(gen)) and the variance effective populations size N(eV(gen)) estimates from the genotype data. Two of these methods - a temporal moment-based (MBT) and a likelihood-based approach (TM3) require at least two samples in time, while the other two were single-sample estimators - the linkage disequilibrium method with bias correction LDNe and the program ONeSAMP. The genetic based estimates were fairly similar across methods and also similar to the demographic estimates excluding those estimates, in which upper confidence interval boundaries were uninformative. For example, LDNe and ONeSAMP estimates ranged from 14-55 and 24-48 individuals, respectively. However, temporal methods suffered from a large variation in confidence intervals and concerns about the prior information. We conclude that the single-sample estimators are an acceptable short-cut to estimate N(bI) for species such as geckos and will be of great importance for the monitoring of species in fragmented landscapes.
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Affiliation(s)
- Marion Hoehn
- UFZ - Helmholtz Centre for Environmental Research, Department of Conservation Biology, Leipzig, Germany.
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30
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Gruenthal KM, Drawbridge MA. Toward responsible stock enhancement: broadcast spawning dynamics and adaptive genetic management in white seabass aquaculture. Evol Appl 2012; 5:405-17. [PMID: 25568060 PMCID: PMC3353362 DOI: 10.1111/j.1752-4571.2011.00234.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 12/09/2011] [Indexed: 11/27/2022] Open
Abstract
The evolutionary effects captive-bred individuals that can have on wild conspecifics are necessary considerations for stock enhancement programs, but breeding protocols are often developed without the knowledge of realized reproductive behavior. To help fill that gap, parentage was assigned to offspring produced by a freely mating group of 50 white seabass (Atractoscion nobilis), a representative broadcast spawning marine finfish cultured for conservation. Similar to the well-known and closely related red drum (Sciaenops ocellatus), A. nobilis exhibited large variation in reproductive success. More males contributed and contributed more equally than females within and among spawns in a mating system best described as lottery polygyny. Two females produced 27% of the seasonal offspring pool and female breeding effective size averaged 1.85 per spawn and 12.38 seasonally, whereas male breeding effective size was higher (6.42 and 20.87, respectively), with every male contributing 1-7% of offspring. Further, females batch spawned every 1-5 weeks, while males displayed continuous reproductive readiness. Sex-specific mating strategies resulted in multiple successful mate pairings and a breeding effective to census size ratio of ≥0.62. Understanding a depleted species' mating system allowed management to more effectively utilize parental genetic variability for culture, but the fitness consequences of long-term stocking can be difficult to address.
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Veith M, Baumgart A, Dubois A, Ohler A, Galán P, Vieites DR, Nieto-Román S, Vences M. Discordant patterns of nuclear and mitochondrial introgression in Iberian populations of the European common frog (Rana temporaria). ACTA ACUST UNITED AC 2012; 103:240-9. [PMID: 22319097 DOI: 10.1093/jhered/esr136] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Amphibians often show complex histories of intraspecific and interspecific genetic introgression, which might differ in mitochondrial and nuclear genes. In our study of the genetic differentiation of the European common frog, Rana temporaria (159 specimens from 23 populations were analyzed for 24 presumptive allozyme loci; 82 specimens were sequenced for a 540-bp fragment of the mitochondrial 16S rRNA gene), multilocus correspondence analysis (CA) and Bayesian assignment tests of the nuclear data were concordant in identifying 2 population groups corresponding to 1) the Pyrenees in the east and 2) the Galicia and Asturias regions in the west, the latter corresponding to the subspecies R. temporaria parvipalmata. Geographically intermediate populations were genetically intermediate in the allozyme CA and, less clearly in the Bayesian assignment, with mitochondrial haplotypes exclusively belonging to the parvipalmata group. This indicates different degrees of introgression in the mitochondrial and nuclear genomes. Although Pyrenean high-altitude populations are morphologically distinct from low-altitude populations, these 2 groups were not separate clusters in any analysis. This suggests that the morphological differences may be due to fast adaptation to elevational gradients, likely under maintenance of gene flow, and that the underlying genetic changes are not detectable by the analyzed markers. We argue that a parsimonious explanation for the observed pattern along the east-west axis in northern Spain may be competition between invading and resident populations, with no need to invoke selection. However, in order to conclusively rule out selective processes, additional and finer scale data are required to test for asymmetric mating preference/behaviour, sex-biased gene flow, or sex-biased survival of potential hybrids.
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Affiliation(s)
- Michael Veith
- Department of Biogeography, Trier University, 54286 Trier, Germany.
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Conte M, Zucchi MI, Andrade GV, Souza AP, Recco-Pimentel SM. Study of closely related species within the Physalaemus cuvieri group (Anura): contribution of microsatellite markers. GENETICS AND MOLECULAR RESEARCH 2012; 10:1434-44. [PMID: 21823093 DOI: 10.4238/vol10-3gmr1136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Various species of the Physalaemus cuvieri group of frogs are difficult to distinguish morphologically, making molecular analysis an attractive alternative for indentifying members of this group, which is considered to be at risk because of loss of habitat. The genetic structure of natural populations of P. ephippifer and P. albonotatus species was investigated and analyzed, together with that of five previously studied populations of P. cuvieri. Nine microsatellite loci were used in the analyses. The overall G(ST) value (0.46) revealed high genetic variation among the populations, as expected for different species. Bayesian analysis implemented by the STRUCTURE software clustered the seven populations into seven groups (K = 7). All the P. albonotatus and P. ephippifer specimens were grouped into a single cluster, both species showing clear differentiation from P. cuvieri. The different grouping based on these microsatellites of some P. cuvieri individuals from Porto Nacional and from Passo Fundo suggests that they could be a new species, indicating a necessity for taxonomic reevaluation. Despite the intrinsic difficulties in analyzing closely related species, the nine microsatellite loci were found to be adequate for distinguishing these three species of the P. cuvieri group and their populations.
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Affiliation(s)
- M Conte
- Departamento de Anatomia, Biologia Celular e Fisiologia e Biofísica, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil
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Jourdan-Pineau H, David P, Crochet PA. Phenotypic plasticity allows the Mediterranean parsley frog Pelodytes punctatus to exploit two temporal niches under continuous gene flow. Mol Ecol 2012; 21:876-86. [PMID: 22221487 DOI: 10.1111/j.1365-294x.2011.05420.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Environmental changes, such as climate change, lead to the opening of new niches. In such situations, species that adapt to new niches can survive and/or expand their ranges. However, gene flow can hamper genetic adaptation to new environments. Alternatively, recent models have highlighted the importance of phenotypic plasticity in tracking environmental change. Here, we investigate whether phenotypic plasticity or genetic evolution (or both) allows an amphibian species to exploit two divergent climatic niches. In the Mediterranean region, the parsley frog Pelodytes punctatus breeds both in spring, as do most other species, and in autumn, a temporal niche not exploited by most other species, but which may become increasingly important with global warming. Conditions of development are dramatically different between the two seasons and deeply impact tadpole life-history traits. To determine whether these temporal niches are exploited by two genetically differentiated subpopulations, or whether the bimodal phenology arises in a panmictic population displaying plastic life-history traits, we use two complementary approaches. We measure both molecular genetic differentiation and quantitative-trait differentiation between spring and autumn cohorts, using microsatellites and common garden experiments, respectively. Seasonal cohorts were not genetically differentiated and differences in tadpole life history between cohorts were not maintained in laboratory conditions. We conclude that phenotypic plasticity, rather than genetic adaptation, allows Parsley frog to exploit two contrasting temporal niches.
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Affiliation(s)
- Helene Jourdan-Pineau
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 CNRS, 1919 route de Mende, 34293 Montpellier Cedex 5, France.
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Phillipsen IC, Funk WC, Hoffman EA, Monsen KJ, Blouin MS. Comparative analyses of effective population size within and among species: ranid frogs as a case study. Evolution 2011; 65:2927-45. [PMID: 21967433 DOI: 10.1111/j.1558-5646.2011.01356.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
It has recently become practicable to estimate the effective sizes (N(e) ) of multiple populations within species. Such efforts are valuable for estimating N(e) in evolutionary modeling and conservation planning. We used microsatellite loci to estimate N(e) of 90 populations of four ranid frog species (20-26 populations per species, mean n per population = 29). Our objectives were to determine typical values of N(e) for populations of each species, compare N(e) estimates among the species, and test for correlations between several geographic variables and N(e) within species. We used single-sample linkage disequilibrium (LD), approximate Bayesian computation (ABC), and sibship assignment (SA) methods to estimate contemporary N(e) for each population. Three of the species-Rana pretiosa, R. luteiventris, and R. cascadae- have consistently small effective population sizes (<50). N(e) in Lithobates pipiens spans a wider range, with some values in the hundreds or thousands. There is a strong east-to-west trend of decreasing N(e) in L. pipiens. The smaller effective sizes of western populations of this species may be related to habitat fragmentation and population bottlenecking.
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Affiliation(s)
- Ivan C Phillipsen
- Department of Zoology, Oregon State University, 3029 Cordley Hall, Corvallis, Oregon 97331-2914, USA.
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Cooper IA, Gilman RT, Boughman JW. SEXUAL DIMORPHISM AND SPECIATION ON TWO ECOLOGICAL COINS: PATTERNS FROM NATURE AND THEORETICAL PREDICTIONS. Evolution 2011; 65:2553-71. [DOI: 10.1111/j.1558-5646.2011.01332.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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URSPRUNG EVA, RINGLER MAX, JEHLE ROBERT, HÖDL WALTER. Strong male/male competition allows for nonchoosy females: high levels of polygynandry in a territorial frog with paternal care. Mol Ecol 2011; 20:1759-71. [DOI: 10.1111/j.1365-294x.2011.05056.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Ficetola GF, Padoa-Schioppa E, Wang J, Garner TWJ. Polygyny, census and effective population size in the threatened frog, Rana latastei. Anim Conserv 2010. [DOI: 10.1111/j.1469-1795.2009.00306.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Global Amphibian Declines, Loss of Genetic Diversity and Fitness: A Review. DIVERSITY-BASEL 2010. [DOI: 10.3390/d2010047] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Wu XB, Hu YL. Genetic diversity and molecular differentiation of Chinese toad based on microsatellite markers. Mol Biol Rep 2009; 37:2379-86. [PMID: 19693692 DOI: 10.1007/s11033-009-9745-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Accepted: 08/05/2009] [Indexed: 11/24/2022]
Abstract
Genetic diversity and population structure of 9 populations of Bufo gargarizans with total 111 samples in China were assessed using seven microsatellite loci. The analysed microsatellite markers produced 161 alleles, varied from 9 to 38 alleles each locus. The number of alleles per population per locus ranged from 4.43 to 10.29. Polymorphic information content showed that all seven loci were highly informative (mean = 0.810 + or - 0.071). The average observed heterozygosity was less than the expected (0.353 + or - 0.051 and 0.828 + or - 0.067, respectively). All tested populations gave significant departures from Hardy-Weinberg equilibrium. Genetic differentiation among the populations was considerably high with the overall and pairwise F (ST) values (mean = 0.160 + or - 0.039), and showed fairly high level of inbreeding (indicated by a mean F (IS) value of 0.504 + or - 0.051) and global heterozygote deficit. In comparison to other amphibian studies; however, our results suggested that the level of genetic structuring in B. gargarizans was relatively low in the geographical scale of the study area. Interestingly, the speculated population bottleneck was found to be absent and the analyses provide only weak evidence for a recent contraction in size even though there was severe inbreeding (indicated by the F (IS) value) in the Chinese toad populations.
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Affiliation(s)
- Xiao-Bing Wu
- College of Life Sciences, and Key Laboratory for Conservation and Exploitation of Biological Resource in Anhui Province, Anhui Normal University, 241000 Wuhu, China.
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Broquet T, Jaquiéry J, Perrin N. Opportunity for sexual selection and effective population size in the lek-breeding European treefrog (Hyla arborea). Evolution 2009; 63:674-83. [PMID: 19087183 DOI: 10.1111/j.1558-5646.2008.00586.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Sexual selection in lek-breeding species might drastically lower male effective population size, with potentially important consequences for evolutionary and conservation biology. Using field-monitoring and parental-assignment methods, we analyzed sex-specific variances in breeding success in a population of European treefrogs, to (1) help understanding the dynamics of genetic variance at sex-specific loci, and (2) better quantify the risk posed by genetic drift in this species locally endangered by habitat fragmentation. The variance in male mating success turned out to be markedly lower than values obtained from other amphibian species with polygamous mating systems. The ratio of effective breeding size to census breeding size was only slightly lower in males (0.44) than in females (0.57), in line with the patterns of genetic diversity previously reported from H. arborea sex chromosomes. Combining our results with data on age at maturity and adult survival, we show that the negative effect of the mating system is furthermore compensated by the effect of delayed maturity, so that the estimated instantaneous effective size broadly corresponded to census breeding size. We conclude that the lek-breeding system of treefrogs impacts only weakly the patterns of genetic diversity on sex-linked genes and the ability of natural populations to resist genetic drift.
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Affiliation(s)
- Thomas Broquet
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland.
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Effective number of breeding adults in Oregon spotted frogs (Rana pretiosa): genetic estimates at two life stages. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9862-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Palstra FP, Ruzzante DE. Genetic estimates of contemporary effective population size: what can they tell us about the importance of genetic stochasticity for wild population persistence? Mol Ecol 2008; 17:3428-47. [PMID: 19160474 DOI: 10.1111/j.1365-294x.2008.03842.x] [Citation(s) in RCA: 357] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Friso P Palstra
- Biology Department, Dalhousie University, 1355 Oxford Street, Halifax, Canada B3H 4J1.
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