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Bartolomé C, Buendía-Abad M, Ornosa C, De la Rúa P, Martín-Hernández R, Higes M, Maside X. Bee Trypanosomatids: First Steps in the Analysis of the Genetic Variation and Population Structure of Lotmaria passim, Crithidia bombi and Crithidia mellificae. MICROBIAL ECOLOGY 2022; 84:856-867. [PMID: 34609533 PMCID: PMC9622509 DOI: 10.1007/s00248-021-01882-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Trypanosomatids are among the most prevalent parasites in bees but, despite the fact that their impact on the colonies can be quite important and that their infectivity may potentially depend on their genotypes, little is known about the population diversity of these pathogens. Here we cloned and sequenced three non-repetitive single copy loci (DNA topoisomerase II, glyceraldehyde-3-phosphate dehydrogenase and RNA polymerase II large subunit, RPB1) to produce new genetic data from Crithidia bombi, C. mellificae and Lotmaria passim isolated from honeybees and bumblebees. These were analysed by applying population genetic tools in order to quantify and compare their variability within and between species, and to obtain information on their demography and population structure. The general pattern for the three species was that (1) they were subject to the action of purifying selection on nonsynonymous variants, (2) the levels of within species diversity were similar irrespective of the host, (3) there was evidence of recombination among haplotypes and (4) they showed no haplotype structuring according to the host. C. bombi exhibited the lowest levels of synonymous variation (πS= 0.06 ± 0.04 %) - and a mutation frequency distribution compatible with a population expansion after a bottleneck - that contrasted with the extensive polymorphism displayed by C. mellificae (πS= 2.24 ± 1.00 %), which likely has a more ancient origin. L. passim showed intermediate values (πS= 0.40 ± 0.28 %) and an excess of variants a low frequencies probably linked to the spread of this species to new geographical areas.
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Affiliation(s)
- Carolina Bartolomé
- Grupo de Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Galicia, Spain.
- Instituto de Investigación Sanitaria de Santiago (IDIS), 15706, Santiago de Compostela, Galicia, Spain.
| | - María Buendía-Abad
- Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal (IRIAF), Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, 19180, Marchamalo, Spain
| | - Concepción Ornosa
- Departamento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Pilar De la Rúa
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, 30100, Murcia, Spain
| | - Raquel Martín-Hernández
- Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal (IRIAF), Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, 19180, Marchamalo, Spain
- Instituto de Recursos Humanos para la Ciencia y la Tecnología, Fundación Parque Científico Tecnológico de Albacete, 02006, Albacete, Spain
| | - Mariano Higes
- Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal (IRIAF), Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, 19180, Marchamalo, Spain
| | - Xulio Maside
- Grupo de Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Galicia, Spain
- Instituto de Investigación Sanitaria de Santiago (IDIS), 15706, Santiago de Compostela, Galicia, Spain
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2
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Souza AT, Argillier C, Blabolil P, Děd V, Jarić I, Monteoliva AP, Reynaud N, Ribeiro F, Ritterbusch D, Sala P, Šmejkal M, Volta P, Kubečka J. Empirical evidence on the effects of climate on the viability of common carp (Cyprinus carpio) populations in European lakes. Biol Invasions 2022. [DOI: 10.1007/s10530-021-02710-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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3
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Herrando‐Pérez S, Tobler R, Huber CD. smartsnp
, an
r
package for fast multivariate analyses of big genomic data. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13684] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Salvador Herrando‐Pérez
- Australian Centre for Ancient DNA School of Biological Sciences The University of Adelaide Adelaide SA Australia
- Department of Biogeography and Global Change Museo Nacional de Ciencias NaturalesSpanish National Research Council (CSIC) Madrid Spain
| | - Raymond Tobler
- Australian Centre for Ancient DNA School of Biological Sciences The University of Adelaide Adelaide SA Australia
- Evolution of Cultural Diversity Initiative Australian National University Canberra ACT Australia
| | - Christian D. Huber
- Australian Centre for Ancient DNA School of Biological Sciences The University of Adelaide Adelaide SA Australia
- Department of Biology The Pennsylvania State University University Park PA USA
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Bourgeois YXC, Warren BH. An overview of current population genomics methods for the analysis of whole-genome resequencing data in eukaryotes. Mol Ecol 2021; 30:6036-6071. [PMID: 34009688 DOI: 10.1111/mec.15989] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/26/2021] [Accepted: 05/11/2021] [Indexed: 01/01/2023]
Abstract
Characterizing the population history of a species and identifying loci underlying local adaptation is crucial in functional ecology, evolutionary biology, conservation and agronomy. The constant improvement of high-throughput sequencing techniques has facilitated the production of whole genome data in a wide range of species. Population genomics now provides tools to better integrate selection into a historical framework, and take into account selection when reconstructing demographic history. However, this improvement has come with a profusion of analytical tools that can confuse and discourage users. Such confusion limits the amount of information effectively retrieved from complex genomic data sets, and impairs the diffusion of the most recent analytical tools into fields such as conservation biology. It may also lead to redundancy among methods. To address these isssues, we propose an overview of more than 100 state-of-the-art methods that can deal with whole genome data. We summarize the strategies they use to infer demographic history and selection, and discuss some of their limitations. A website listing these methods is available at www.methodspopgen.com.
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Affiliation(s)
| | - Ben H Warren
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, CP 51, Paris, France
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5
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Zanin M, Gonzalez-Borrajo N, ChÁvez C, Rubio Y, Harmsen B, Keller C, Villalva P, Srbek-Araujo AC, Costa LP, Palomares F. The differential genetic signatures related to climatic landscapes for jaguars and pumas on a continental scale. Integr Zool 2020; 16:2-18. [PMID: 32929877 DOI: 10.1111/1749-4877.12486] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Modern and paleoclimate changes may have altered species dynamics by shifting species' niche suitability over space and time. We analyze whether the current genetic structure and isolation of the two large American felids, jaguar (Panthera onca) and puma (Puma concolor), are mediated by changes in climatic suitability and connection routes over modern and paleoclimatic landscapes. We estimate species distribution under 5 climatic landscapes (modern, Holocene, last maximum glaciations [LMG], average suitability, and climatic instability) and correlate them with individuals' genetic isolation through causal modeling on a resemblance matrix. Both species exhibit genetic isolation patterns correlated with LMG climatic suitability, suggesting that these areas may have worked as "allele refuges." However, the jaguar showed higher vulnerability to climate changes, responding to modern climatic suitability and connection routes, whereas the puma showed a continuous and gradual transition of genetic variation. Despite differential responsiveness to climate change, both species are subjected to the climatic effects on genetic configuration, which may make them susceptible to future climatic changes, since these are progressing faster and with higher intensity than changes in the paleoclimate. Thus, the effects of climatic changes should be considered in the design of conservation strategies to ensure evolutionary and demographic processes mediated by gene flow for both species.
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Affiliation(s)
- Marina Zanin
- Biology Department, Federal University of Maranhão, São Luís, Brazil
| | - Noa Gonzalez-Borrajo
- Departamento de Biologia de la Conservación, Estación Biológica de Doñana, Sevilla, Spain
| | - Cuauhtémoc ChÁvez
- Departamento de Ciencias Ambientales, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Yamel Rubio
- Escuela de Biologia, Universidad Autónoma de Sinaloa, Culiacán, Mexico
| | | | - Claudia Keller
- Biodiversity Coordination, Amazon Research Institute, Manaus, Brazil
| | - Pablo Villalva
- Departamento de Biologia de la Conservación, Estación Biológica de Doñana, Sevilla, Spain
| | | | - Leonora Pires Costa
- Biological Sciences Department, Federal University of Espírito Santo, Vitória, Brazil
| | - Francisco Palomares
- Departamento de Biologia de la Conservación, Estación Biológica de Doñana, Sevilla, Spain
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Adamo M, Mammola S, Noble V, Mucciarelli M. Integrating Multiple Lines of Evidence to Explore Intraspecific Variability in a Rare Endemic Alpine Plant and Implications for Its Conservation. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1160. [PMID: 32911798 PMCID: PMC7569986 DOI: 10.3390/plants9091160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/03/2020] [Accepted: 09/06/2020] [Indexed: 11/17/2022]
Abstract
We studied the ecology, distribution, and phylogeography of Tephroseris balbisiana, a rare plant whose range is centered to the South-Western Alps. Our aim was to assess the extent of intraspecific variability within the nominal species and the conservation status of isolated populations. We studied genetic diversity across the whole species range. We analyzed leaf traits, which are distinctive morphological characters within the Tephroseris genus. A clear pattern of genetic variation was found among populations of T. balbisiana, which clustered according to their geographic position. On the contrary, there was a strong overlap in the morphological space of individuals across the species' range, with few peripheral populations diverging in their leaf morphology. Studying habitat suitability by means of species distribution models, we observed that T. balbisiana range is primarily explained by solar radiation and precipitation seasonality. Environmental requirements could explain the genetic and morphological uniformity of T. balbisiana in its core distribution area and justify genetic, morphological, and ecological divergences found among the isolated populations of the Apennines. Our findings emphasize the need to account for the whole diversity of a species, comprising peripheral populations, in order to better estimate its status and to prioritize areas for its conservation.
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Affiliation(s)
- Martino Adamo
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, Viale Pier Andrea Mattioli, 25, 10125 Torino, Italy;
| | - Stefano Mammola
- Molecular Ecology Group (MEG), Water Research Institute (IRSA), National Research Council (CNR), Corso Tonolli, 50, 28922 Verbania, Italy;
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History (LUOMUS), University of Helsinki, Pohjoinen Rautatiekatu 13, 00100 Helsinki, Finland
| | - Virgile Noble
- Conservatoire Botanique National Méditerranéen, Avenue Gambetta 34, 83400 Hyères-les-palmiers, France;
| | - Marco Mucciarelli
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, Viale Pier Andrea Mattioli, 25, 10125 Torino, Italy;
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Nali RC, Becker CG, Zamudio KR, Prado CPA. Topography, more than land cover, explains genetic diversity in a Neotropical savanna tree frog. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13154] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Renato C. Nali
- Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Instituto de Biociências Universidade Estadual Paulista Rio Claro São Paulo Brazil
- Department of Ecology and Evolutionary Biology Cornell University Ithaca NY USA
| | | | - Kelly R. Zamudio
- Department of Ecology and Evolutionary Biology Cornell University Ithaca NY USA
| | - Cynthia P. A. Prado
- Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Instituto de Biociências Universidade Estadual Paulista Rio Claro São Paulo Brazil
- Departamento de Morfologia e Fisiologia Animal Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista Jaboticabal São Paulo Brazil
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8
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Cabrera-Toledo D, Vargas-Ponce O, Ascencio-Ramírez S, Valadez-Sandoval LM, Pérez-Alquicira J, Morales-Saavedra J, Huerta-Galván OF. Morphological and Genetic Variation in Monocultures, Forestry Systems and Wild Populations of Agave maximiliana of Western Mexico: Implications for Its Conservation. FRONTIERS IN PLANT SCIENCE 2020; 11:817. [PMID: 32625225 PMCID: PMC7313679 DOI: 10.3389/fpls.2020.00817] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 05/20/2020] [Indexed: 05/04/2023]
Abstract
Forestry systems in Mexico are examples of traditional management of land and biodiversity that integrates the use, conservation and restoration of forest elements. Current in situ management practices of Agave maximiliana in western Mexico include the tolerance of many forest elements, reintroduction of young Agave plants and germination of seeds. More intense forms of management include monocultures, which are agroindustrialized systems developed in more recent times and characterized by the establishment of high densities of A. maximiliana plants in deforested areas and abandoned agricultural lands. We compared monocultures, forestry systems and wild populations (i.e., non/slightly-exploited forests) in order to evaluate whether these practices have had an effect on intraspecific morphological and genetic variation and divergence. We also tested whether divergence has a positive relationship with environmental and geographic distance. We analyzed 16 phenotypic traits in 17 populations of A. maximiliana, and 14 populations were further examined by amplifying 9 SSR loci. We employed multivariate methods and analyses of variance in phenotypic and genetic traits to test whether clusters and the percentage of variation contained in the managed and wild categories can be identified. Tests of isolation by environment (IBE) and distance (IBD) were performed to detect the magnitude of divergence explained by climatic and geographic variables. We found that forestry systems are effective as reservoirs of morphological and genetic diversity, since they maintain levels similar to those of wild populations. Moreover, the monocultures showed similar levels, reflecting their recent emergence. While the species showed high morphological diversity (IMD = 0.638, SE ± 0.07), it had low to intermediate genetic diversity (A = 2.37, H E = 0.418). Similar morphological and genetic divergences were found among populations, but these were not correlated with each other in population pairs. Non-significant morphological differentiation was found among categories. Only IBE was significant in the genetic structure (β = 0.32, p = 0.007), while neither IBE nor IBD was detected in the morphological differentiation. We discuss the implications of these results in the context of the weaknesses and strengths of A. maximiliana in the face of the socio-ecological changes predicted for the study area in the short term.
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Affiliation(s)
- Dánae Cabrera-Toledo
- Laboratorio Nacional de Identificación y Caracterización Vegetal (LaniVeg-CONACYT), Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Mexico
- *Correspondence: Dánae Cabrera-Toledo,
| | - Ofelia Vargas-Ponce
- Laboratorio Nacional de Identificación y Caracterización Vegetal (LaniVeg-CONACYT), Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Mexico
| | - Sabina Ascencio-Ramírez
- Maestría en Ciencias en Recursos Naturales y Desarrollo Rural, Colegio de la Frontera Sur, Tapachula, Mexico
| | - Luis Mario Valadez-Sandoval
- Laboratorio Nacional de Identificación y Caracterización Vegetal (LaniVeg-CONACYT), Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Mexico
| | - Jessica Pérez-Alquicira
- Laboratorio Nacional de Identificación y Caracterización Vegetal (LaniVeg-CONACYT), Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Mexico
- Cátedras CONACYT-Universidad de Guadalajara, Laboratorio Nacional de Identificación y Caracterización Vegetal (LaniVeg), Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Mexico
| | - Judith Morales-Saavedra
- Laboratorio Nacional de Identificación y Caracterización Vegetal (LaniVeg-CONACYT), Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Mexico
| | - Oassis F. Huerta-Galván
- Maestría en Biosistemática y Manejo de Recursos Forestales y Agrícolas, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Mexico
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Sánchez-Montes G, Ariño AH, Vizmanos JL, Wang J, Martínez-Solano Í. Effects of Sample Size and Full Sibs on Genetic Diversity Characterization: A Case Study of Three Syntopic Iberian Pond-Breeding Amphibians. J Hered 2017; 108:535-543. [PMID: 28444211 DOI: 10.1093/jhered/esx038] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 04/21/2017] [Indexed: 11/14/2022] Open
Abstract
Accurate characterization of genetic diversity is essential for understanding population demography, predicting future trends and implementing efficient conservation policies. For that purpose, molecular markers are routinely developed for nonmodel species, but key questions regarding sampling design, such as calculation of minimum sample sizes or the effect of relatives in the sample, are often neglected. We used accumulation curves and sibship analyses to explore how these 2 factors affect marker performance in the characterization of genetic diversity. We illustrate this approach with the analysis of an empirical dataset including newly optimized microsatellite sets for 3 Iberian amphibian species: Hyla molleri, Epidalea calamita, and Pelophylax perezi. We studied 17-21 populations per species (total n = 547, 652, and 516 individuals, respectively), including a reference locality in which the effect of sample size was explored using larger samples (77-96 individuals). As expected, FIS and tests for Hardy-Weinberg equilibrium and linkage disequilibrium were affected by the presence of full sibs, and most initially inferred disequilibria were no longer statistically significant when full siblings were removed from the sample. We estimated that to obtain reliable estimates, the minimum sample size (potentially including full sibs) was close to 20 for expected heterozygosity, and between 50 and 80 for allelic richness. Our pilot study based on a reference population provided a rigorous assessment of marker properties and the effects of sample size and presence of full sibs in the sample. These examples illustrate the advantages of this approach to produce robust and reliable results for downstream analyses.
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Affiliation(s)
- Gregorio Sánchez-Montes
- Department of Environmental Biology, University of Navarra, Pamplona, Spain; Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain; Department of Biochemistry and Genetics, University of Navarra, Pamplona, Spain; Institute of Zoology, Zoological Society of London, London, UK; Instituto de Investigación en Recursos Cinegéticos, Ciudad Real, Spain; and Ecology, Evolution, and Development Group, Department of Wetland Ecology, Doñana Biological Station, CSIC, Seville, Spain
| | - Arturo H Ariño
- Department of Environmental Biology, University of Navarra, Pamplona, Spain; Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain; Department of Biochemistry and Genetics, University of Navarra, Pamplona, Spain; Institute of Zoology, Zoological Society of London, London, UK; Instituto de Investigación en Recursos Cinegéticos, Ciudad Real, Spain; and Ecology, Evolution, and Development Group, Department of Wetland Ecology, Doñana Biological Station, CSIC, Seville, Spain
| | - José L Vizmanos
- Department of Environmental Biology, University of Navarra, Pamplona, Spain; Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain; Department of Biochemistry and Genetics, University of Navarra, Pamplona, Spain; Institute of Zoology, Zoological Society of London, London, UK; Instituto de Investigación en Recursos Cinegéticos, Ciudad Real, Spain; and Ecology, Evolution, and Development Group, Department of Wetland Ecology, Doñana Biological Station, CSIC, Seville, Spain
| | - Jinliang Wang
- Department of Environmental Biology, University of Navarra, Pamplona, Spain; Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain; Department of Biochemistry and Genetics, University of Navarra, Pamplona, Spain; Institute of Zoology, Zoological Society of London, London, UK; Instituto de Investigación en Recursos Cinegéticos, Ciudad Real, Spain; and Ecology, Evolution, and Development Group, Department of Wetland Ecology, Doñana Biological Station, CSIC, Seville, Spain
| | - Íñigo Martínez-Solano
- Department of Environmental Biology, University of Navarra, Pamplona, Spain; Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain; Department of Biochemistry and Genetics, University of Navarra, Pamplona, Spain; Institute of Zoology, Zoological Society of London, London, UK; Instituto de Investigación en Recursos Cinegéticos, Ciudad Real, Spain; and Ecology, Evolution, and Development Group, Department of Wetland Ecology, Doñana Biological Station, CSIC, Seville, Spain
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10
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Noguerales V, Cordero PJ, Ortego J. Testing the role of ancient and contemporary landscapes on structuring genetic variation in a specialist grasshopper. Ecol Evol 2017; 7:3110-3122. [PMID: 28480010 PMCID: PMC5415511 DOI: 10.1002/ece3.2810] [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: 10/04/2016] [Revised: 12/31/2016] [Accepted: 01/24/2017] [Indexed: 12/19/2022] Open
Abstract
Understanding the processes underlying spatial patterns of genetic diversity and structure of natural populations is a central topic in evolutionary biogeography. In this study, we combine data on ancient and contemporary landscape composition to get a comprehensive view of the factors shaping genetic variation across the populations of the scrub‐legume grasshopper (Chorthippus binotatus binotatus) from the biogeographically complex region of southeast Iberia. First, we examined geographical patterns of genetic structure and employed an approximate Bayesian computation (ABC) approach to compare different plausible scenarios of population divergence. Second, we used a landscape genetic framework to test for the effects of (1) Late Miocene paleogeography, (2) Pleistocene climate fluctuations, and (3) contemporary topographic complexity on the spatial patterns of population genetic differentiation. Genetic structure and ABC analyses supported the presence of three genetic clusters and a sequential west‐to‐east splitting model that predated the last glacial maximum (LGM, c. 21 Kya). Landscape genetic analyses revealed that population genetic differentiation was primarily shaped by contemporary topographic complexity, but was not explained by any paleogeographic scenario or resistance distances based on climate suitability in the present or during the LGM. Overall, this study emphasizes the need of integrating information on ancient and contemporary landscape composition to get a comprehensive view of their relative importance to explain spatial patterns of genetic variation in organisms inhabiting regions with complex biogeographical histories.
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Affiliation(s)
- Víctor Noguerales
- Grupo de Investigación de la Biodiversidad Genética y Cultural Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM) Ciudad Real Spain
| | - Pedro J Cordero
- Grupo de Investigación de la Biodiversidad Genética y Cultural Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM) Ciudad Real Spain
| | - Joaquín Ortego
- Department of Integrative Ecology Estación Biológica de Doñana (EBD-CSIC) Seville Spain
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11
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Maia GF, Lima AP, Kaefer IL. Not just the river: genes, shapes, and sounds reveal population-structured diversification in the Amazonian frog Allobates tapajos (Dendrobatoidea). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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12
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Mangombi JB, Brouat C, Loiseau A, Banga O, Leroy EM, Bourgarel M, Duplantier JM. Urban population genetics of the invasive black rats in Franceville, Gabon. J Zool (1987) 2016. [DOI: 10.1111/jzo.12334] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. B. Mangombi
- Centre International de Recherche Médicale de Franceville (CIRMF); Franceville Gabon
- Ird; CBGP (UMR INRA/IRD/Cirad/Montpellier SupAgro); Montferrier-sur-Lez France
- CIRAD; UPR AGIRs; Montpellier France
| | - C. Brouat
- Ird; CBGP (UMR INRA/IRD/Cirad/Montpellier SupAgro); Montferrier-sur-Lez France
| | - A. Loiseau
- INRA; CBGP (UMR INRA/IRD/Cirad/Montpellier SupAgro); Montferrier-sur-Lez France
| | - O. Banga
- Centre International de Recherche Médicale de Franceville (CIRMF); Franceville Gabon
| | - E. M. Leroy
- Centre International de Recherche Médicale de Franceville (CIRMF); Franceville Gabon
| | - M. Bourgarel
- CIRAD; UPR AGIRs; Montpellier France
- CIRAD; UPR AGIRs; Harare Zimbabwe
| | - J.-M. Duplantier
- Ird; CBGP (UMR INRA/IRD/Cirad/Montpellier SupAgro); Montferrier-sur-Lez France
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13
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Population Genetic Structure of the Endangered Kaiser's Mountain Newt, Neurergus kaiseri (Amphibia: Salamandridae). PLoS One 2016; 11:e0149596. [PMID: 26918642 PMCID: PMC4769016 DOI: 10.1371/journal.pone.0149596] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 02/03/2016] [Indexed: 11/19/2022] Open
Abstract
Species often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in an endemic and critically endangered stream breeding mountain newt, Neurergus kaiseri, within its entire range in southwestern Iran. We identified two geographic regions based on phylogenetic relationships using Bayesian inference and maximum likelihood of 779 bp mtDNA (D-loop) in 111 individuals from ten of twelve known breeding populations. This analysis revealed a clear divergence between northern populations, located in more humid habitats at higher elevation, and southern populations, from drier habitats at lower elevations regions. From seven haplotypes found in these populations none was shared between the two regions. Analysis of molecular variance (AMOVA) of N. kaiseri indicates that 94.03% of sequence variation is distributed among newt populations and 5.97% within them. Moreover, a high degree of genetic subdivision, mainly attributable to the existence of significant variance among the two regions is shown (θCT = 0.94, P = 0.002). The positive and significant correlation between geographic and genetic distances (r = 0.61, P = 0.002) following controlling for environmental distance suggests an important influence of geographic divergence of the sites in shaping the genetic variation and may provide tools for a possible conservation based prioritization policy for the endangered species.
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Peñas J, Barrios S, Bobo-Pinilla J, Lorite J, Martínez-Ortega MM. Designing conservation strategies to preserve the genetic diversity of Astragalus edulis Bunge, an endangered species from western Mediterranean region. PeerJ 2016; 4:e1474. [PMID: 26844014 PMCID: PMC4736990 DOI: 10.7717/peerj.1474] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/14/2015] [Indexed: 11/20/2022] Open
Abstract
Astragalus edulis (Fabaceae) is an endangered annual species from the western Mediterranean region that colonized the SE Iberian Peninsula, NE and SW Morocco, and the easternmost Macaronesian islands (Lanzarote and Fuerteventura). Although in Spain some conservation measures have been adopted, it is still necessary to develop an appropriate management plan to preserve genetic diversity across the entire distribution area of the species. Our main objective was to use population genetics as well as ecological and phylogeographic data to select Relevant Genetic Units for Conservation (RGUCs) as the first step in designing conservation plans for A. edulis. We identified six RGUCs for in situ conservation, based on estimations of population genetic structure and probabilities of loss of rare alleles. Additionally, further population parameters, i.e. occupation area, population size, vulnerability, legal status of the population areas, and the historical haplotype distribution, were considered in order to establish which populations deserve conservation priority. Three populations from the Iberian Peninsula, two from Morocco, and one from the Canary Islands represent the total genetic diversity of the species and the rarest allelic variation. Ex situ conservation is recommended to complement the preservation of A. edulis, given that effective in situ population protection is not feasible in all cases. The consideration of complementary phylogeographic and ecological data is useful for management efforts to preserve the evolutionary potential of the species.
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Affiliation(s)
- Julio Peñas
- Plant Conservation Unit, Department of Botany, University of Granada, Granada, Spain
| | - Sara Barrios
- Department of Botany, University of Salamanca, Salamanca, Spain
| | - Javier Bobo-Pinilla
- Department of Botany, University of Salamanca, Salamanca, Spain
- Biobanco de ADN Vegetal, Edificio Multiusos I+D+i, Calle Espejo s/n, Salamanca, Spain
| | - Juan Lorite
- Plant Conservation Unit, Department of Botany, University of Granada, Granada, Spain
| | - M. Montserrat Martínez-Ortega
- Department of Botany, University of Salamanca, Salamanca, Spain
- Biobanco de ADN Vegetal, Edificio Multiusos I+D+i, Calle Espejo s/n, Salamanca, Spain
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Bartlewicz J, Vandepitte K, Jacquemyn H, Honnay O. Population genetic diversity of the clonal self-incompatible herbaceous plantLinaria vulgarisalong an urbanization gradient. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12602] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Jacek Bartlewicz
- Biology Department; Plant Conservation and Population Biology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 31 BE-3001 Heverlee Belgium
| | - Katrien Vandepitte
- Biology Department; Plant Conservation and Population Biology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 31 BE-3001 Heverlee Belgium
| | - Hans Jacquemyn
- Biology Department; Plant Conservation and Population Biology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 31 BE-3001 Heverlee Belgium
| | - Olivier Honnay
- Biology Department; Plant Conservation and Population Biology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 31 BE-3001 Heverlee Belgium
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