1
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Unglaub B, Cayuela H, Schmidt BR, Preißler K, Glos J, Steinfartz S. Context-dependent dispersal determines relatedness and genetic structure in a patchy amphibian population. Mol Ecol 2021; 30:5009-5028. [PMID: 34490661 DOI: 10.1111/mec.16114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 07/19/2021] [Accepted: 07/23/2021] [Indexed: 12/26/2022]
Abstract
Dispersal is a central process in ecology and evolution with far reaching consequences for the dynamics and genetics of spatially structured populations (SSPs). Individuals can adjust their decisions to disperse according to local fitness prospects, resulting in context-dependent dispersal. By determining dispersal rate, distance and direction, these individual-level decisions further modulate the demography, relatedness and genetic structure of SSPs. Here, we examined how context-dependent dispersal influences the dynamics and genetics of a great crested newt (Triturus cristatus) SSP. We collected capture-recapture data of 5564 individuals and genetic data of 950 individuals across an SSP in northern Germany. We added genetic data from six sites outside this SSP to assess genetic structure and gene flow at a regional level. Dispersal rates within the SSP were high but dispersal distances were short. Dispersal was context-dependent: individuals preferentially immigrated into high-quality ponds where breeding probabilities were higher. The studied SSP behaved like a patchy population, where subpopulations at each pond were demographically interdependent. High context-dependent dispersal led to weak but significant spatial genetic structure and relatedness within the SSP. At the regional level, a strong hierarchical genetic structure with very few first-generation migrants as well as low effective dispersal rates suggest the presence of independent demographic units. Overall, our study highlights the importance of habitat quality for driving context-dependent dispersal and therefore demography and genetic structure in SSPs. Limited capacity for long-distance dispersal seems to increase genetic structure within a population and leads to demographic isolation in anthropogenic landscapes.
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Affiliation(s)
- Bianca Unglaub
- Institute of Biology, Molecular Evolution and Systematics of Animals, University of Leipzig, Leipzig, Germany.,Department of Animal Ecology and Conservation, Biocentre Grindel, University of Hamburg, Hamburg, Germany
| | - Hugo Cayuela
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Benedikt R Schmidt
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Info Fauna Karch, Neuchâtel, Switzerland
| | - Kathleen Preißler
- Institute of Biology, Molecular Evolution and Systematics of Animals, University of Leipzig, Leipzig, Germany
| | - Julian Glos
- Department of Animal Ecology and Conservation, Biocentre Grindel, University of Hamburg, Hamburg, Germany
| | - Sebastian Steinfartz
- Institute of Biology, Molecular Evolution and Systematics of Animals, University of Leipzig, Leipzig, Germany
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2
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Kanbe T, Yumoto K, Yamakawa U, Nakajima S, Kaneko S, Kitamura K, Saito Y, Tsuda Y. Isolation and characterization of microsatellites from a cicada, Yezoterpnosia nigricosta (Hemiptera: Cicadidae), distributed in subarctic and cool temperate forests. Genes Genet Syst 2021; 95:269-273. [PMID: 33361646 DOI: 10.1266/ggs.20-00023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The cicada Yezoterpnosia nigricosta (Hemiptera: Cicadidae) is distributed in subarctic and cool temperate forests in Japan, China and the Russian Far East. Due to its limited and isolated distribution at higher altitudes in cool temperate forests on the main island of Japan, especially in the central and southern areas, this species is listed as a threatened or near-threatened species on the Red List of 12 prefectures in Japan. Moreover, there are concerns about the impacts of climate change on the species' distribution and population demography. In this study, seventeen microsatellite markers were developed for Y. nigricosta, and marker suitability was evaluated using 32 individuals from two populations in Nagano prefecture (central Japan) and Hokkaido, a northern island of Japan. The number of alleles, expected heterozygosity and fixation index at each locus were 1-15 (mean = 4.294), 0.000-0.914 (mean = 0.519) and -0.225-0.456 (mean = 0.108), respectively. Furthermore, there was moderate genetic differentiation between the two populations (FST = 0.111, F'ST = 0.237). These markers will be useful to evaluate the genetic structure and to infer population demographic history of Y. nigricosta populations, which can contribute to population genetics studies of this species.
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Affiliation(s)
- Takashi Kanbe
- Systematic Entomology, Graduate School of Agriculture, Hokkaido University
| | - Keisuke Yumoto
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba
| | - Uchu Yamakawa
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba
| | - Souta Nakajima
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba
| | - Shingo Kaneko
- Faculty of Symbiotic Systems Science, Fukushima University
| | - Keiko Kitamura
- Hokkaido Research Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization
| | - Yoko Saito
- Department of Ecosystem Studies, Graduate School of Agricultural and Life Sciences, University of Tokyo
| | - Yoshiaki Tsuda
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba
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3
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Lucati F, Poignet M, Miró A, Trochet A, Aubret F, Barthe L, Bertrand R, Buchaca T, Calvez O, Caner J, Darnet E, Denoël M, Guillaume O, Le Chevalier H, Martínez-Silvestre A, Mossoll-Torres M, O'Brien D, Osorio V, Pottier G, Richard M, Sabás I, Souchet J, Tomàs J, Ventura M. Multiple glacial refugia and contemporary dispersal shape the genetic structure of an endemic amphibian from the Pyrenees. Mol Ecol 2020; 29:2904-2921. [PMID: 32563209 DOI: 10.1111/mec.15521] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 05/25/2020] [Accepted: 05/29/2020] [Indexed: 12/31/2022]
Abstract
Historical factors (colonization scenarios, demographic oscillations) and contemporary processes (population connectivity, current population size) largely contribute to shaping species' present-day genetic diversity and structure. In this study, we use a combination of mitochondrial and nuclear DNA markers to understand the role of Quaternary climatic oscillations and present-day gene flow dynamics in determining the genetic diversity and structure of the newt Calotriton asper (Al. Dugès, 1852), endemic to the Pyrenees. Mitochondrial DNA did not show a clear phylogeographic pattern and presented low levels of variation. In contrast, microsatellites revealed five major genetic lineages with admixture patterns at their boundaries. Approximate Bayesian computation analyses and linear models indicated that the five lineages likely underwent separate evolutionary histories and can be tracked back to distinct glacial refugia. Lineage differentiation started around the Last Glacial Maximum at three focal areas (western, central and eastern Pyrenees) and extended through the end of the Last Glacial Period in the central Pyrenees, where it led to the formation of two more lineages. Our data revealed no evidence of recent dispersal between lineages, whereas borders likely represent zones of secondary contact following expansion from multiple refugia. Finally, we did not find genetic evidence of sex-biased dispersal. This work highlights the importance of integrating past evolutionary processes and present-day gene flow and dispersal dynamics, together with multilocus approaches, to gain insights into what shaped the current genetic attributes of amphibians living in montane habitats.
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Affiliation(s)
- Federica Lucati
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculty of Sciences, University of Lisbon, Lisbon, Portugal.,Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Spain
| | - Manon Poignet
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), Université Paul Sabatier, Moulis, France
| | - Alexandre Miró
- Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Spain
| | - Audrey Trochet
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), Université Paul Sabatier, Moulis, France.,Société Herpétologique de France, Muséum National d'Histoire Naturelle, Paris, France
| | - Fabien Aubret
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), Université Paul Sabatier, Moulis, France
| | - Laurent Barthe
- Association Nature En Occitanie, Maison de l'Environnement de Midi-Pyrénées, Toulouse, France
| | - Romain Bertrand
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), Université Paul Sabatier, Moulis, France
| | - Teresa Buchaca
- Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Spain
| | - Olivier Calvez
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), Université Paul Sabatier, Moulis, France
| | - Jenny Caner
- Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Spain
| | - Elodie Darnet
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), Université Paul Sabatier, Moulis, France
| | - Mathieu Denoël
- Laboratory of Ecology and Conservation of Amphibians (LECA), Freshwater and OCeanic science Unit of reSearch (FOCUS), University of Liege, Liege, Belgium
| | - Olivier Guillaume
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), Université Paul Sabatier, Moulis, France
| | - Hugo Le Chevalier
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), Université Paul Sabatier, Moulis, France
| | | | | | | | - Víctor Osorio
- Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Spain
| | - Gilles Pottier
- Association Nature En Occitanie, Maison de l'Environnement de Midi-Pyrénées, Toulouse, France
| | - Murielle Richard
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), Université Paul Sabatier, Moulis, France
| | - Ibor Sabás
- Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Spain
| | - Jérémie Souchet
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), Université Paul Sabatier, Moulis, France
| | - Jan Tomàs
- Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Spain
| | - Marc Ventura
- Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Spain
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4
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Haugen H, Linløkken A, Østbye K, Heggenes J. Landscape genetics of northern crested newt Triturus cristatus populations in a contrasting natural and human-impacted boreal forest. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01266-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
AbstractAmong vertebrates, amphibians currently have the highest proportion of threatened species worldwide, mainly through loss of habitat, leading to increased population isolation. Smaller amphibian populations may lose more genetic diversity, and become more dependent on immigration for survival. Investigations of landscape factors and patterns mediating migration and population genetic differentiation are fundamental for knowledge-based conservation. The pond-breeding northern crested newt (Triturus cristatus) populations are decreasing throughout Europe, and are a conservation concern. Using microsatellites, we studied the genetic structure of the northern crested newt in a boreal forest ecosystem containing two contrasting landscapes, one subject to recent change and habitat loss by clear-cutting and roadbuilding, and one with little anthropogenic disturbance. Newts from 12 breeding ponds were analyzed for 13 microsatellites and 7 landscape and spatial variables. With a Maximum-likelihood population-effects model we investigated important landscape factors potentially explaining genetic patterns. Results indicate that intervening landscape factors between breeding ponds, explain the genetic differentiation in addition to an isolation-by-distance effect. Geographic distance, gravel roads, and south/south-west facing slopes reduced landscape permeability and increased genetic differentiation for these newts. The effect was opposite for streams, presumably being more favorable for newt dispersal. Populations within or bordering on old growth forest had a higher allelic richness than populations in managed forest outside these areas. Old growth forest areas may be important source habitats in the conservation of northern crested newt populations.
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5
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Xia Y, Luo W, Yuan S, Zheng Y, Zeng X. Microsatellite development from genome skimming and transcriptome sequencing: comparison of strategies and lessons from frog species. BMC Genomics 2018; 19:886. [PMID: 30526480 PMCID: PMC6286531 DOI: 10.1186/s12864-018-5329-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 11/28/2018] [Indexed: 11/14/2022] Open
Abstract
Background Even though microsatellite loci frequently have been isolated using recently developed next-generation sequencing (NGS) techniques, this task is still difficult because of the subsequent polymorphism screening requires a substantial amount of time. Selecting appropriate polymorphic microsatellites is a critical issue for ecological and evolutionary studies. However, the extent to which assembly strategy, read length, sequencing depth, and library layout produce a measurable effect on microsatellite marker development remains unclear. Here, we use six frog species for genome skimming and two frog species for transcriptome sequencing to develop microsatellite markers, and investigate the effect of different isolation strategies on the yield of microsatellites. Results The results revealed that the number of isolated microsatellites increases with increased data quantity and read length. Assembly strategy could influence the yield and the polymorphism of microsatellite development. Larger k-mer sizes produced fewer total number of microsatellite loci, but these loci had a longer repeat length, suggesting greater polymorphism. However, the proportion of each type of nucleotide repeats was not affected; dinucleotide repeats were always the dominant type. Finally, the transcriptomic microsatellites displayed lower levels of polymorphisms and were less abundant than genomic microsatellites, but more likely to be functionally linked loci. Conclusions These observations provide deep insight into the evolution and distribution of microsatellites and how different isolation strategies affect microsatellite development using NGS. Electronic supplementary material The online version of this article (10.1186/s12864-018-5329-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yun Xia
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Wei Luo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Siqi Yuan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,College of Bioengineering, Sichuan University of Science & Engineering, Zigong, 643000, China
| | - Yuchi Zheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiaomao Zeng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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6
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Oromi N, Valbuena‐Ureña E, Soler‐Membrives A, Amat F, Camarasa S, Carranza S, Sanuy D, Denoël M. Genetic structure of lake and stream populations in a Pyrenean amphibian (
Calotriton asper
) reveals evolutionary significant units associated with paedomorphosis. J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12250] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Neus Oromi
- Departament de Ciència Animal (Fauna Silvestre) Universitat de Lleida Lleida Catalonia Spain
- Laboratory of Fish and Amphibian Ethology Behavioural Biology Group Freshwater and OCeanic science Unit of reSearch (FOCUS) University of Liège Liège Belgium
| | - Emilio Valbuena‐Ureña
- Unitat de Zoologia Facultat de Biociències Universitat Autònoma de Barcelona Barcelona Catalonia Spain
- Centre de Fauna Salvatge de Torreferrussa (Catalan Wildlife Service – Forestal Catalana) Finca de Torreferrusa Barcelona Catalonia Spain
| | - Anna Soler‐Membrives
- Unitat de Zoologia Facultat de Biociències Universitat Autònoma de Barcelona Barcelona Catalonia Spain
| | - Felix 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
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra) Barcelona Spain
| | - Delfi Sanuy
- 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
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7
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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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8
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Valbuena-Ureña E, Soler-Membrives A, Steinfartz S, Alonso M, Carbonell F, Larios-Martín R, Obon E, Carranza S. Getting off to a good start? Genetic evaluation of the ex situ conservation project of the Critically Endangered Montseny brook newt ( Calotriton arnoldi). PeerJ 2017. [PMID: 28626615 PMCID: PMC5472038 DOI: 10.7717/peerj.3447] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Ex situ management strategies play an important role in the conservation of threatened species when the wild survival of the species cannot be ensured. Molecular markers have become an outstanding tool for the evaluation and management of captive breeding programs. Two main genetic objectives should be prioritized when planning breeding programs: the maintenance of maximum neutral genetic diversity, and to obtain “self-sustaining” captive populations. In this study, we use 24 microsatellite loci to analyze and evaluate the genetic representativity of the initial phases of the captive breeding program of the Montseny brook newt, Calotriton arnoldi, an Iberian endemic listed as Critically Endangered. The results show that the initial captive stock has 74–78% of the alleles present in the wild populations, and captures roughly 93–95% of their total genetic diversity as observed in a previous study on wild newts, although it does not reach the desired 97.5%. Moreover, the percentage of unrelatedness among individuals does not exceed 95%. Therefore, we conclude that the genetic diversity of the captive stock should be improved by incorporating genetic material from unrelated wild newts. In recognition of the previously described significant genetic and morphological differentiation between eastern and western wild populations of C. arnoldi, we suggest maintaining two distinct breeding lines, and we do not recommend outbreeding between these lines. Our comparisons of genetic diversity estimates between real and distinct sample-sized simulated populations corroborated that a minimum of 20 individuals are needed for each captive population, in order to match the level of genetic diversity present in the wild populations. Thus, the current initial stock should be reinforced by adding wild specimens. The captive stock and subsequent cohorts should be monitored in order to preserve genetic variation. In order to avoid genetic adaptation to captivity, occasionally incorporating previously genotyped individuals from the wild into the captive populations is recommended.
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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, Santa Perpètua de la Mogoda, Barcelona, Catalonia, Spain
| | - Anna Soler-Membrives
- Unitat de Zoologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
| | - Sebastian Steinfartz
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Mònica Alonso
- Centre de Fauna Salvatge de Torreferrussa, Catalan Wildlife Service -Forestal Catalana, Santa Perpètua de la Mogoda, Barcelona, Catalonia, Spain
| | - Francesc Carbonell
- Centre de Fauna Salvatge de Torreferrussa, Catalan Wildlife Service -Forestal Catalana, Santa Perpètua de la Mogoda, Barcelona, Catalonia, Spain
| | - Raquel Larios-Martín
- Centre de Fauna Salvatge de Torreferrussa, Catalan Wildlife Service -Forestal Catalana, Santa Perpètua de la Mogoda, Barcelona, Catalonia, Spain
| | - Elena Obon
- Centre de Fauna Salvatge de Torreferrussa, Catalan Wildlife Service -Forestal Catalana, Santa Perpètua de la Mogoda, Barcelona, Catalonia, Spain
| | - Salvador Carranza
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
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9
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Isselin-Nondedeu F, Trochet A, Joubin T, Picard D, Etienne R, Chevalier HL, Legrand D, Ribéron A. Spatial genetic structure of Lissotriton helveticus L. following the restoration of a forest ponds network. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0932-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Ball SE, Bovero S, Sotgiu G, Tessa G, Angelini C, Bielby J, Durrant C, Favelli M, Gazzaniga E, Garner TWJ. Islands within an island: Population genetic structure of the endemic Sardinian newt, Euproctus platycephalus. Ecol Evol 2017; 7:1190-1211. [PMID: 28303189 PMCID: PMC5306002 DOI: 10.1002/ece3.2665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 10/21/2016] [Indexed: 12/04/2022] Open
Abstract
The identification of historic and contemporary barriers to dispersal is central to the conservation of endangered amphibians, but may be hindered by their complex life history and elusive nature. The complementary information generated by mitochondrial (mtDNA) and microsatellite markers generates a valuable tool in elucidating population structure and the impact of habitat fragmentation. We applied this approach to the study of an endangered montane newt, Euproctus platycephalus. Endemic to the Mediterranean island of Sardinia, it is threatened by anthropogenic activity, disease, and climate change. We have demonstrated a clear hierarchy of structure across genetically divergent and spatially distinct subpopulations. Divergence between three main mountain regions dominated genetic partitioning with both markers. Mitochondrial phylogeography revealed a deep division dating to ca. 1 million years ago (Mya), isolating the northern region, and further differentiation between the central and southern regions ca. 0.5 Mya, suggesting an association with Pleistocene severe glacial oscillations. Our findings are consistent with a model of southward range expansion during glacial periods, with postglacial range retraction to montane habitat and subsequent genetic isolation. Microsatellite markers revealed further strong population structure, demonstrating significant divergence within the central region, and partial differentiation within the south. The northern population showed reduced genetic diversity. Discordance between mitochondrial and microsatellite markers at this scale indicated a further complexity of population structure, in keeping with male-biased dispersal and female philopatry. Our study underscores the need to elucidate cryptic population structure in the ecology and conservation strategies for endangered island-restricted amphibians, especially in the context of disease and climate change.
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Affiliation(s)
- Sarah E. Ball
- Institute of ZoologyThe Zoological Society of LondonLondonUK
| | - Stefano Bovero
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Giuseppe Sotgiu
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Giulia Tessa
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
- Dipartimento di Scienze della Vita e Biologia dei SistemiUniversita degli Studi di TorinoTorinoItaly
| | - Claudio Angelini
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Jon Bielby
- Institute of ZoologyThe Zoological Society of LondonLondonUK
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | | | - Marco Favelli
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Enrico Gazzaniga
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Trenton W. J. Garner
- Institute of ZoologyThe Zoological Society of LondonLondonUK
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
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11
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No signs of inbreeding despite long-term isolation and habitat fragmentation in the critically endangered Montseny brook newt (Calotriton arnoldi). Heredity (Edinb) 2017; 118:424-435. [PMID: 28074844 DOI: 10.1038/hdy.2016.123] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 10/14/2016] [Accepted: 10/19/2016] [Indexed: 11/09/2022] Open
Abstract
Endemic species with restricted geographic ranges potentially suffer the highest risk of extinction. If these species are further fragmented into genetically isolated subpopulations, the risk of extinction is elevated. Habitat fragmentation is generally considered to have negative effects on species survival, despite some evidence for neutral or even positive effects. Typically, non-negative effects are ignored by conservation biology. The Montseny brook newt (Calotriton arnoldi) has one of the smallest distribution ranges of any European amphibian (8 km2) and is considered critically endangered by the International Union for Conservation of Nature. Here we apply molecular markers to analyze its population structure and find that habitat fragmentation owing to a natural barrier has resulted in strong genetic division of populations into two sectors, with no detectable migration between sites. Although effective population size estimates suggest low values for all populations, we found low levels of inbreeding and relatedness between individuals within populations. Moreover, C. arnoldi displays similar levels of genetic diversity to its sister species Calotriton asper, from which it separated around 1.5 million years ago and which has a much larger distribution range. Our extensive study shows that natural habitat fragmentation does not result in negative genetic effects, such as the loss of genetic diversity and inbreeding on an evolutionary timescale. We hypothesize that species in such conditions may evolve strategies (for example, special mating preferences) to mitigate the effects of small population sizes. However, it should be stressed that the influence of natural habitat fragmentation on an evolutionary timescale should not be conflated with anthropogenic habitat loss or degradation when considering conservation strategies.
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12
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Oromi N, Michaux J, Denoël M. High gene flow between alternative morphs and the evolutionary persistence of facultative paedomorphosis. Sci Rep 2016; 6:32046. [PMID: 27534370 PMCID: PMC4989185 DOI: 10.1038/srep32046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 08/02/2016] [Indexed: 11/25/2022] Open
Abstract
Paedomorphosis and metamorphosis are two major developmental processes that characterize the evolution of complex life cycles in many lineages. Whereas these processes were fixed in some taxa, they remained facultative in others, with alternative phenotypes expressed in the same populations. From a genetic perspective, it is still unknown whether such phenotypes form a single population or whether they show some patterns of isolation in syntopy. This has deep implications for understanding the evolution of the phenotypes, i.e. towards their persistence or their fixation and speciation. Newts and salamanders are excellent models to test this hypothesis because they exhibit both developmental processes in their populations: the aquatic paedomorphs retain gills, whereas the metamorphs are able to colonize land. Using microsatellite data of coexisting paedomorphic and metamorphic palmate newts (Lissotriton helveticus), we found that they formed a panmictic population, which evidences sexual compatibility between the two phenotypes. The high gene flow could be understood as an adaptation to unstable habitats in which phenotypic plasticity is favored over the fixation of developmental alternatives. This makes then possible the persistence of a polyphenism: only metamorphosis could be maintained in case of occasional drying whereas paedomorphosis could offer specific advantages in organisms remaining in water.
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Affiliation(s)
- Neus Oromi
- Laboratory of Fish and Amphibian Ethology, Behavioural Biology Unit, Freshwater and Oceanic Science Unit of Research (FOCUS), University of Liège, 22 Quai van Beneden, 4020 Liège, Belgium
| | - Johan Michaux
- Conservation Genetics, University of Liège, Institute of Botany (Bat. 22), 2 Chemin de la Vallée, 4000 Liège, Belgium
| | - Mathieu Denoël
- Laboratory of Fish and Amphibian Ethology, Behavioural Biology Unit, Freshwater and Oceanic Science Unit of Research (FOCUS), University of Liège, 22 Quai van Beneden, 4020 Liège, Belgium
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13
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Adamson EAS, Saha A, Maddock ST, Nussbaum RA, Gower DJ, Streicher JW. Microsatellite discovery in an insular amphibian (Grandisonia alternans) with comments on cross-species utility and the accuracy of locus identification from unassembled Illumina data. CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0580-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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14
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Vera M, Bello X, Álvarez-Dios JA, Pardo BG, Sánchez L, Carlsson J, Carlsson JE, Bartolomé C, Maside X, Martinez P. Screening of repetitive motifs inside the genome of the flat oyster (Ostrea edulis): Transposable elements and short tandem repeats. Mar Genomics 2015; 24 Pt 3:335-41. [DOI: 10.1016/j.margen.2015.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/03/2015] [Accepted: 08/25/2015] [Indexed: 10/23/2022]
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15
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Denoël M, Ficetola GF. Using kernels and ecological niche modeling to delineate conservation areas in an endangered patch-breeding phenotype. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2015; 25:1922-1931. [PMID: 26591457 DOI: 10.1890/14-1041.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Efficient delineation of conservation areas is a great challenge in maintaining biodiversity. Kernel density estimators (KDEs) are a powerful tool in this perspective, but they have not been applied at the population level on patch-distributed organisms. This would be particularly worthy for species that need broad habitats beyond those where they can be sampled; such as terrestrial lands for pond-breeding amphibians. The aim of this study was to compare different approaches for the identification of suitable areas for conservation: KDE, ecological niche modelling, and a combination of KDE and niche models. Paedomorphosis was chosen as a model system because this is an important form of intraspecific variation that is present in numerous taxa, but geographically localized within species and globally endangered. 277 ponds were sampled in one of the hotspots of paedomorphosis to determine the abundance and distribution of paedomorphs (i.e., individuals retaining gills at the adult stage) of the palmate newt (Lissotriton helveticus), with emphasis on the connections between the most valuable populations. KDEs gave insights into the surface areas required to balance the maintenance of certain number of connected ponds and the respective number of disjoint areas in which the whole population is divided. The inclusion of barriers in the models helped in accurately designing the limits of the areas to protect. Alone, habitat models were not able to successfully delineate the area to protect, but the integration between terrestrial suitable areas or barriers and KDE allowed an objective identification of areas required for conservation. Overall, the best performance was observed by the KDE integrating ecological barriers, and by the combination between KDE and niche modelling. In a broader perspective, KDEs are thus a pertinent tool in providing quantitative spatial measurements to delineate conservation areas based on patch-abundance data with a specific focus to connectivity.
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16
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Amavet PS, Rueda EC, Siroski PA, Larriera A, Saidman BO. Isolation and characterization of new microsatellite markers for application in population genetic studies of Caiman latirostris and related species. AMPHIBIA-REPTILIA 2015. [DOI: 10.1163/15685381-00002987] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Wild populations ofCaiman latirostrisare subject to sustainable use programs in Argentina, becoming a species with important impact in the regional economy, based in their skin and meat. Genetic studies are fundamental to acquire information on important parameters for conservation and management, which may be obtained from analysis of molecular markers. Some microsatellites have been previously isolated in this species, but due to some difficulties in using them, we obtained new ones using Next Generation Sequencing approach. This study reports eight new microsatellites forC. latirostrisand tests their utility in a related species,Caiman yacare, with successful application in population genetics and mating systems studies. In addition, we shared data about a novel and fast bioinformatics tool to find microsatellites and to design their corresponding primers.
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Affiliation(s)
- Patricia Susana Amavet
- Laboratorio de Genética, Departamento de Ciencias Naturales, Facultad de Humanidades y Ciencias, UNL, Ciudad Universitaria, 3000 Santa Fe, Argentina
- Proyecto Yacaré – Laboratorio de Zoología Aplicada: Anexo Vertebrados (FHUC – UNL/MASPyMA), A. del Valle 8700, 3000 Santa Fe, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Rivadavia 1917, C1033AAJ Buenos Aires, Argentina
| | - Eva Carolina Rueda
- Laboratorio de Genética, Departamento de Ciencias Naturales, Facultad de Humanidades y Ciencias, UNL, Ciudad Universitaria, 3000 Santa Fe, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Rivadavia 1917, C1033AAJ Buenos Aires, Argentina
| | - Pablo Ariel Siroski
- Proyecto Yacaré – Laboratorio de Zoología Aplicada: Anexo Vertebrados (FHUC – UNL/MASPyMA), A. del Valle 8700, 3000 Santa Fe, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Rivadavia 1917, C1033AAJ Buenos Aires, Argentina
- Instituto de Ciencias Veterinarias del Litoral (ICiVet-UNL-CONICET), Kreder 2805, S3080HOF Esperanza, Argentina
| | - Alejandro Larriera
- Proyecto Yacaré – Laboratorio de Zoología Aplicada: Anexo Vertebrados (FHUC – UNL/MASPyMA), A. del Valle 8700, 3000 Santa Fe, Argentina
| | - Beatriz Ofelia Saidman
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Rivadavia 1917, C1033AAJ Buenos Aires, Argentina
- Departamento Ecología, Genética y Evolución, IEGEBA, CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina
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17
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Drechsler A, Helling T, Steinfartz S. Genetic fingerprinting proves cross-correlated automatic photo-identification of individuals as highly efficient in large capture-mark-recapture studies. Ecol Evol 2014; 5:141-51. [PMID: 25628871 PMCID: PMC4298441 DOI: 10.1002/ece3.1340] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 10/09/2014] [Accepted: 10/10/2014] [Indexed: 11/06/2022] Open
Abstract
Capture-mark-recapture (CMR) approaches are the backbone of many studies in population ecology to gain insight on the life cycle, migration, habitat use, and demography of target species. The reliable and repeatable recognition of an individual throughout its lifetime is the basic requirement of a CMR study. Although invasive techniques are available to mark individuals permanently, noninvasive methods for individual recognition mainly rest on photographic identification of external body markings, which are unique at the individual level. The re-identification of an individual based on comparing shape patterns of photographs by eye is commonly used. Automated processes for photographic re-identification have been recently established, but their performance in large datasets (i.e., > 1000 individuals) has rarely been tested thoroughly. Here, we evaluated the performance of the program AMPHIDENT, an automatic algorithm to identify individuals on the basis of ventral spot patterns in the great crested newt (Triturus cristatus) versus the genotypic fingerprint of individuals based on highly polymorphic microsatellite loci using GENECAP. Between 2008 and 2010, we captured, sampled and photographed adult newts and calculated for 1648 samples/photographs recapture rates for both approaches. Recapture rates differed slightly with 8.34% for GENECAP and 9.83% for AMPHIDENT. With an estimated rate of 2% false rejections (FRR) and 0.00% false acceptances (FAR), AMPHIDENT proved to be a highly reliable algorithm for CMR studies of large datasets. We conclude that the application of automatic recognition software of individual photographs can be a rather powerful and reliable tool in noninvasive CMR studies for a large number of individuals. Because the cross-correlation of standardized shape patterns is generally applicable to any pattern that provides enough information, this algorithm is capable of becoming a single application with broad use in CMR studies for many species.
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Affiliation(s)
- Axel Drechsler
- Department of Behavioural Biology, Unit of Molecular Ecology and Behaviour, University of Bielefeld Morgenbreede 45, D-33619, Bielefeld, Germany
| | - Tobias Helling
- Department of Behavioural Biology, Unit of Molecular Ecology and Behaviour, University of Bielefeld Morgenbreede 45, D-33619, Bielefeld, Germany
| | - Sebastian Steinfartz
- Department of Behavioural Biology, Unit of Molecular Ecology and Behaviour, University of Bielefeld Morgenbreede 45, D-33619, Bielefeld, Germany ; Zoological Institute, Department of Evolutionary Biology, Unit Molecular Ecology, Technische Universität Braunschweig, Mendelssohnstr. 4 38106, Braunschweig, Germany
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18
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Development of 12 novel polymorphic microsatellite markers using a next generation sequencing approach for Spiculopteragia spiculoptera, a nematode parasite of deer. Mol Biochem Parasitol 2014; 196:122-5. [DOI: 10.1016/j.molbiopara.2014.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/08/2014] [Accepted: 09/15/2014] [Indexed: 02/04/2023]
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19
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Dufresnes C, Brelsford A, Béziers P, Perrin N. Stronger transferability but lower variability in transcriptomic- than in anonymous microsatellites: evidence from Hylid frogs. Mol Ecol Resour 2014; 14:716-25. [PMID: 24345298 DOI: 10.1111/1755-0998.12215] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 12/03/2013] [Accepted: 12/11/2013] [Indexed: 11/28/2022]
Abstract
A simple way to quickly optimize microsatellites in nonmodel organisms is to reuse loci available in closely related taxa; however, this approach can be limited by the stochastic and low cross-amplification success experienced in some groups (e.g. amphibians). An efficient alternative is to develop loci from transcriptome sequences. Transcriptomic microsatellites have been found to vary in their levels of cross-species amplification and variability, but this has to date never been tested in amphibians. Here, we compare the patterns of cross-amplification and levels of polymorphism of 18 published anonymous microsatellites isolated from genomic DNA vs. 17 loci derived from a transcriptome, across nine species of tree frogs (Hyla arborea and Hyla cinerea group). We established a clear negative relationship between divergence time and amplification success, which was much steeper for anonymous than transcriptomic markers, with half-lives (time at which 50% of the markers still amplify) of 1.1 and 37 My, respectively. Transcriptomic markers are significantly less polymorphic than anonymous loci, but remain variable across diverged taxa. We conclude that the exploitation of amphibian transcriptomes for developing microsatellites seems an optimal approach for multispecies surveys (e.g. analyses of hybrid zones, comparative linkage mapping), whereas anonymous microsatellites may be more informative for fine-scale analyses of intraspecific variation. Moreover, our results confirm the pattern that microsatellite cross-amplification is greatly variable among amphibians and should be assessed independently within target lineages. Finally, we provide a bank of microsatellites for Palaearctic tree frogs (so far only available for H. arborea), which will be useful for conservation and evolutionary studies in this radiation.
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Affiliation(s)
- Christophe Dufresnes
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne , 1015, Switzerland
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20
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Valbuena-Ureña E, Steinfartz S, Carranza S. Characterization of microsatellite loci markers for the critically endangered Montseny brook newt (Calotriton arnoldi). CONSERV GENET RESOUR 2013. [DOI: 10.1007/s12686-013-0082-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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