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Stoeckel S, Becheler R, Bocharova E, Barloy D. GenAPoPop 1.0: A user-friendly software to analyse genetic diversity and structure from partially clonal and selfed autopolyploid organisms. Mol Ecol Resour 2024; 24:e13886. [PMID: 37902131 DOI: 10.1111/1755-0998.13886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 10/05/2023] [Accepted: 10/16/2023] [Indexed: 10/31/2023]
Abstract
Autopolyploidy is quite common in most clades of eukaryotes. The emergence of sequence-based genotyping methods with individual and marker tags now enables confident allele dosage, overcoming the main obstacle to the democratization of the population genetic approaches when studying ecology and evolution of autopolyploid populations and species. Reproductive modes, including clonality, selfing and allogamy, have deep consequences on the ecology and evolution of population and species. Analysing genetic diversity and its dynamics over generations is one efficient way to infer the relative importance of clonality, selfing and allogamy in populations. GenAPoPop is a user-friendly solution to compute the specific corpus of population genetic indices, including indices about genotypic diversity, needed to analyse partially clonal, selfed and allogamous polysomic populations genotyped with confident allele dosage. It also easily provides the posterior probabilities of quantitative reproductive modes in autopolyploid populations genotyped at two-time steps and a graphical representation of the minimum spanning trees of the genetic distances between polyploid individuals, facilitating the interpretation of the genetic coancestry between individuals in hierarchically structured populations. GenAPoPop complements the previously existing solutions, including SPAGEDI and POLYGENE, to use genotypings to study the ecology and evolution of autopolyploid populations. It was specially developed with a simple graphical interface and workflow, and comes with a simulator to facilitate practical courses and teaching of population genetics for autopolyploid populations.
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Affiliation(s)
- Solenn Stoeckel
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, France
- DECOD (Ecosystem Dynamics and Sustainability), Institut Agro, IFREMER, INRAE, Rennes, France
| | - Ronan Becheler
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, France
- DECOD (Ecosystem Dynamics and Sustainability), Institut Agro, IFREMER, INRAE, Rennes, France
| | - Ekaterina Bocharova
- Evolutionary Developmental Biology laboratory, Koltzov Institute of Developmental Biology of Russian Academy of Sciences (IDB RAS), Moscow, Russia
| | - Dominique Barloy
- DECOD (Ecosystem Dynamics and Sustainability), Institut Agro, IFREMER, INRAE, Rennes, France
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2
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Villegas LI, Ferretti L, Wiehe T, Waldvogel A, Schiffer PH. Parthenogenomics: Insights on mutation rates and nucleotide diversity in parthenogenetic Panagrolaimus nematodes. Ecol Evol 2024; 14:e10831. [PMID: 38192904 PMCID: PMC10771965 DOI: 10.1002/ece3.10831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 01/10/2024] Open
Abstract
Asexual reproduction is assumed to lead to the accumulation of deleterious mutations, and reduced heterozygosity due to the absence of recombination. Panagrolaimid nematode species display different modes of reproduction. Sexual reproduction with distinct males and females, asexual reproduction through parthenogenesis in the genus Panagrolaimus, and hermaphroditism in Propanagrolaimus. Here, we compared genomic features of free-living nematodes in populations and species isolated from geographically distant regions to study diversity, and genome-wide differentiation under different modes of reproduction. We firstly estimated genome-wide spontaneous mutation rates in a triploid parthenogenetic Panagrolaimus, and a diploid hermaphroditic Propanagrolaimus via long-term mutation accumulation lines. Secondly, we calculated population genetic parameters including nucleotide diversity, and fixation index (F ST) between populations of asexually and sexually reproducing nematodes. Thirdly, we used phylogenetic network methods on sexually and asexually reproducing Panagrolaimus populations to understand evolutionary relationships between them. The estimated mutation rate was slightly lower for the asexual population, as expected for taxa with this reproductive mode. Natural polyploid asexual populations revealed higher nucleotide diversity. Despite their common ancestor, a gene network revealed a high level of genetic differentiation among asexual populations. The elevated heterozygosity found in the triploid parthenogens could be explained by the third genome copy. Given their tendentially lower mutation rates it can be hypothesized that this is part of the mechanism to evade Muller's ratchet. Our findings in parthenogenetic triploid nematode populations seem to challenge common expectations of evolution under asexuality.
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Affiliation(s)
| | | | - Thomas Wiehe
- Institute for GeneticsUniversity of CologneKölnGermany
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3
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Tonin R, Wilhelmi S, Gültas M, Gerdol R, Paun O, Trucchi E, Schmitt AO, Wellstein C. Ice holes microrefugia harbor genetically and functionally distinct populations of Vaccinium vitis-idaea (Ericaceae). Sci Rep 2023; 13:13055. [PMID: 37567871 PMCID: PMC10421893 DOI: 10.1038/s41598-023-39772-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
In the mountain terrain, ice holes are little depressions between rock boulders that are characterized by the exit of cold air able to cool down the rock surface even in summer. This cold air creates cold microrefugia in warmer surroundings that preserve plant species probably over thousands of years under extra-zonal climatic conditions. We hypothesized that ice hole populations of the model species Vaccinium vitis-idaea (Ericaceae) show genetic differentiation from nearby zonal subalpine populations, and high functional trait distinctiveness, in agreement with genetic patterns. We genotyped almost 30,000 single nucleotide polymorphisms using restriction site-associated DNA sequencing and measured eight functional traits indicative of individual performance and ecological strategies. Genetic results showed high differentiation among the six populations suggesting isolation. On siliceous bedrock, ice hole individuals exhibited higher levels of admixture than those from subalpine populations which could have experienced more bottlenecks during demographic fluctuations related to glacial cycles. Ice hole and subalpine calcareous populations clearly separated from siliceous populations, indicating a possible effect of bedrock in shaping genetic patterns. Trait analysis reflected the bedrock effect on populations' differentiation. The significant correlation between trait and genetic distances suggests the genetic contribution in shaping intraspecific functional differentiation. In conclusion, extra-zonal populations reveal a prominent genetic and phenotypic differentiation determined by history and ecological contingency. Therefore, microrefugia populations can contribute to the overall variability of the species and lead to intraspecific-driven responses to upcoming environmental changes.
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Affiliation(s)
- Rita Tonin
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100, Bozen, Italy
| | - Selina Wilhelmi
- Breeding Informatics Group, Department of Animal Sciences, University of Göttingen, 37075, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), 37075, Göttingen, Germany
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, 37077, Göttingen, Germany
| | - Mehmet Gültas
- Center for Integrated Breeding Research (CiBreed), 37075, Göttingen, Germany
- Faculty of Agriculture, South Westphalia University of Applied Sciences, 59494, Soest, Germany
| | - Renato Gerdol
- Department of Environmental and Prevention Sciences, University of Ferrara, 44121, Ferrara, Italy
| | - Ovidiu Paun
- Department for Botany and Biodiversity Research, University of Vienna, 1030, Vienna, Austria
| | - Emiliano Trucchi
- Department of Life and Environmental Science, Università Politecnica delle Marche, 60131, Ancona, Italy
| | - Armin Otto Schmitt
- Breeding Informatics Group, Department of Animal Sciences, University of Göttingen, 37075, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), 37075, Göttingen, Germany
| | - Camilla Wellstein
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100, Bozen, Italy.
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4
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Pereyra RT, Rafajlović M, De Wit P, Pinder M, Kinnby A, Töpel M, Johannesson K. Clones on the run: The genomics of a recently expanded partially clonal species. Mol Ecol 2023; 32:4209-4223. [PMID: 37199478 DOI: 10.1111/mec.16996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/19/2023]
Abstract
Why species that in their core areas mainly reproduce sexually become enriched with clones in marginal populations ("geographic parthenogenesis") remains unclear. Earlier hypotheses have emphasized that selection might promote clonality because it protects locally adapted genotypes. On the other hand, it also hampers recombination and adaptation to changing conditions. The aim of the present study was to investigate the early stages of range expansion in a partially clonal species and what drives an increase in cloning during such expansion. We used genome-wide sequencing to investigate the origin and evolution of large clones formed in a macroalgal species (Fucus vesiculosus) during a recent expansion into the postglacial Baltic Sea. We found low but persistent clonality in core populations, while at range margins, large dominant clonal lineages had evolved repeatedly from different sexual populations. A range expansion model showed that even when asexual recruitment is less favourable than sexual recruitment in core populations, repeated bottlenecks at the expansion front can establish a genetically eroded clonal wave that spreads ahead of a sexual wave into the new area. Genetic variation decreases by drift following repeated bottlenecks at the expansion front. This results in the emerging clones having low expected heterozygosity, which corroborated our empirical observations. We conclude that Baker's Law (clones being favoured by uniparental reproductive assurance in new areas) can play an important role during range expansion in partially clonal species, resulting in a complex spatiotemporal mosaic of clonal and sexual lineages that might persist during thousands of generations.
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Affiliation(s)
- Ricardo T Pereyra
- Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
| | - Marina Rafajlović
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Pierre De Wit
- Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
| | - Matthew Pinder
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Alexandra Kinnby
- Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
| | - Mats Töpel
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Kerstin Johannesson
- Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
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Tavares AI, Assis J, Larkin PD, Creed JC, Magalhães K, Horta P, Engelen A, Cardoso N, Barbosa C, Pontes S, Regalla A, Almada C, Ferreira R, Abdoul BM, Ebaye S, Bourweiss M, Dos Santos CVD, Patrício AR, Teodósio A, Santos R, Pearson GA, Serrao EA. Long range gene flow beyond predictions from oceanographic transport in a tropical marine foundation species. Sci Rep 2023; 13:9112. [PMID: 37277448 DOI: 10.1038/s41598-023-36367-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 06/02/2023] [Indexed: 06/07/2023] Open
Abstract
The transport of passively dispersed organisms across tropical margins remains poorly understood. Hypotheses of oceanographic transportation potential lack testing with large scale empirical data. To address this gap, we used the seagrass species, Halodule wrightii, which is unique in spanning the entire tropical Atlantic. We tested the hypothesis that genetic differentiation estimated across its large-scale biogeographic range can be predicted by simulated oceanographic transport. The alternative hypothesis posits that dispersal is independent of ocean currents, such as transport by grazers. We compared empirical genetic estimates and modelled predictions of dispersal along the distribution of H. wrightii. We genotyped eight microsatellite loci on 19 populations distributed across Atlantic Africa, Gulf of Mexico, Caribbean, Brazil and developed a biophysical model with high-resolution ocean currents. Genetic data revealed low gene flow and highest differentiation between (1) the Gulf of Mexico and two other regions: (2) Caribbean-Brazil and (3) Atlantic Africa. These two were more genetically similar despite separation by an ocean. The biophysical model indicated low or no probability of passive dispersal among populations and did not match the empirical genetic data. The results support the alternative hypothesis of a role for active dispersal vectors like grazers.
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Affiliation(s)
- Ana I Tavares
- Center of Marine Sciences (CCMAR-CIMAR), Universidade do Algarve, Faro, Portugal.
| | - Jorge Assis
- Center of Marine Sciences (CCMAR-CIMAR), Universidade do Algarve, Faro, Portugal
- Faculty of Bioscience and Aquaculture, Nord Universitet, Postboks 1490, 8049, Bodø, Norway
| | | | - Joel C Creed
- Departamento de Ecologia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Karine Magalhães
- Área de Ecologia, Departamento de Biologia, Universidade Federal Rural de Pernambuco, R. Dom Manoel de Medeiros, s/n-Dois Irmãos, Recife, PE, CEP 52171-900, Brazil
| | - Paulo Horta
- Laboratório de Ficologia, Departamento de Botânica, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-970, Brazil
| | - Aschwin Engelen
- Center of Marine Sciences (CCMAR-CIMAR), Universidade do Algarve, Faro, Portugal
- CARMABI Foundation, Piscaderabaai z/n, P.O. Box 2090, Willemstad, Curaçao, The Netherlands
| | - Noelo Cardoso
- CIPA, Centro de Investigação Pesqueira Aplicada, Bissau, Guinea-Bissau
| | - Castro Barbosa
- IBAP-Instituto da Biodiversidade e Áreas Protegidas, Bissau, Guinea-Bissau
| | - Samuel Pontes
- IBAP-Instituto da Biodiversidade e Áreas Protegidas, Bissau, Guinea-Bissau
| | - Aissa Regalla
- IBAP-Instituto da Biodiversidade e Áreas Protegidas, Bissau, Guinea-Bissau
| | - Carmen Almada
- Faculdade de Ciências e Tecnologia, Universidade de Cabo Verde, Praia, Cabo Verde
| | - Rogério Ferreira
- Center of Marine Sciences (CCMAR-CIMAR), Universidade do Algarve, Faro, Portugal
- Dragões do Mar, Nova Estrela, Ilha do Príncipe, São Tomé and Príncipe
| | | | - Sidina Ebaye
- Parc Nationale du Banc d'Arguin (PNBA), Chami, Mauritania
| | - Mohammed Bourweiss
- Institut Mauritanien de Recherche Oceanographique et des Peches (IMROP), Nouadhibou, Mauritania
| | | | - Ana R Patrício
- MARE-Marine and Environmental Sciences Centre, ISPA-Instituto Universitário, Lisbon, Portugal
- Centre for Ecology and Conservation, University of Exete, Penryn, UK
| | - Alexandra Teodósio
- Center of Marine Sciences (CCMAR-CIMAR), Universidade do Algarve, Faro, Portugal
| | - Rui Santos
- Center of Marine Sciences (CCMAR-CIMAR), Universidade do Algarve, Faro, Portugal
| | - Gareth A Pearson
- Center of Marine Sciences (CCMAR-CIMAR), Universidade do Algarve, Faro, Portugal
| | - Ester A Serrao
- Center of Marine Sciences (CCMAR-CIMAR), Universidade do Algarve, Faro, Portugal
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Vairão, Portugal
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da Cunha NL, Xue H, Wright SI, Barrett SCH. Genetic variation and clonal diversity in floating aquatic plants: Comparative genomic analysis of water hyacinth species in their native range. Mol Ecol 2022; 31:5307-5325. [PMID: 35984729 DOI: 10.1111/mec.16664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 07/24/2022] [Accepted: 08/10/2022] [Indexed: 12/15/2022]
Abstract
Many eukaryotic organisms reproduce by sexual and asexual reproduction. Genetic diversity in populations can be strongly dependent on the relative importance of these two reproductive modes. Here, we compare the amounts and patterns of genetic diversity in related water hyacinths that differ in their propensity for clonal propagation - highly clonal Eichhornia crassipes and moderately clonal E. azurea (Pontederiaceae). Our comparisons involved genotype-by-sequencing (GBS) of 137 E. crassipes ramets from 60 locations (193,495 nucleotide sites) and 118 E. azurea ramets from 53 locations (198,343 nucleotide sites) among six hydrological basins in central South America, the native range of both species. We predicted that because of more prolific clonal propagation, E. crassipes would exhibit lower clonal diversity than E. azurea. This prediction was supported by all measures of clonal diversity that we examined. Eichhornia crassipes also had a larger excess of heterozygotes at variant sites, another signature of clonality. However, genome-wide heterozygosity was not significantly different between the species. Eichhornia crassipes had weaker spatial genetic structure and lower levels of differentiation among hydrological basins than E. azurea, probably because of higher clonality and more extensive dispersal of its free-floating life form. Our findings for E. crassipes contrast with earlier studies from the invasive range which have reported very low levels of clonal diversity and extensive geographic areas of genetic uniformity.
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Affiliation(s)
- Nicolay Leme da Cunha
- Grupo de Ecología de la Polinización, INIBIOMA, CONICET-Universidad Nacional del Comahue, San Carlos de Bariloche, Rio Negro, Argentina.,Programa de Pós-Graduação em Ecologia e Conservação, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Haoran Xue
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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Species and population genomic differentiation in Pocillopora corals (Cnidaria, Hexacorallia). Genetica 2022; 150:247-262. [PMID: 36083388 DOI: 10.1007/s10709-022-00165-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/01/2022] [Indexed: 11/04/2022]
Abstract
Correctly delimiting species and populations is a prerequisite for studies of connectivity, adaptation and conservation. Genomic data are particularly useful to test species differentiation for organisms with few informative morphological characters or low discrimination of cytoplasmic markers, as in Scleractinians. Here we applied Restriction site Associated DNA sequencing (RAD-sequencing) to the study of species differentiation and genetic structure in populations of Pocillopora spp. from Oman and French Polynesia, with the objectives to test species hypotheses, and to study the genetic structure among sampling sites within species. We focused here on coral colonies morphologically similar to P. acuta (damicornis type β). We tested the impact of different filtering strategies on the stability of the results. The main genetic differentiation was observed between samples from Oman and French Polynesia. These samples corresponded to different previously defined primary species hypotheses (PSH), i.e., PSHs 12 and 13 in Oman, and PSH 5 in French Polynesia. In Oman, we did not observe any clear differentiation between the two putative species PSH 12 and 13, nor between sampling sites. In French Polynesia, where a single species hypothesis was studied, there was no differentiation between sites. Our analyses allowed the identification of clonal lineages in Oman and French Polynesia. The impact of clonality on genetic diversity is discussed in light of individual-based simulations.
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Li F, Liu X, Zhu J, Li J, Gao K, Zhao C. The Role of Genetic Factors in the Differential Invasion Success of Two Spartina Species in China. FRONTIERS IN PLANT SCIENCE 2022; 13:909429. [PMID: 35712568 PMCID: PMC9196123 DOI: 10.3389/fpls.2022.909429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
Biological invasions have become one of the greatest threats to global biodiversity and ecosystem conservation. Most previous studies have revealed how successful invasive species adapt to new environments and climate change through phenotypic and genetic evolution. Some researchers suggested that understanding unsuccessful or less successful biological invasions might be important for understanding the relationships between invasion adaptability and climate factors. We compared the sexual reproduction ability, genetic diversity, and gene × environment interaction in two intentionally introduced alien species in China (Spartina anglica and Spartina alterniflora) based on restriction site-associated DNA (RAD) sequencing. After more than 50 years, the distribution of S. alterniflora has rapidly expanded, while S. anglica has experienced extreme dieback. A total of 212,939 single nucleotide polymorphisms (SNPs) for the two Spartina species were used for analysis. The multilocus genotype (MLG) analysis revealed that clonal reproduction was the prevalent mode of reproduction in both species, indicating that a change in the mode of reproduction was not the key factor enabling successful invasion by Spartina. All genetic diversity indicators (He, Ho, π) in S. alterniflora populations were at least two times higher than those in S. anglica populations, respectively (p < 0.001). Furthermore, the population genetic structure and stronger patterns of climate-associated loci provided support for rapid adaptive evolution in the populations of S. alterniflora in China. Altogether, our results highlight the importance of genetic diversity and local adaptation, which were driven by multiple source populations, in increasing the invasiveness of S. alterniflora.
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Reynes L, Thibaut T, Mauger S, Blanfuné A, Holon F, Cruaud C, Couloux A, Valero M, Aurelle D. Genomic signatures of clonality in the deep water kelp Laminaria rodriguezii. Mol Ecol 2021; 30:1806-1822. [PMID: 33629449 DOI: 10.1111/mec.15860] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/17/2022]
Abstract
The development of population genomic approaches in non-model species allows for renewed studies of the impact of reproductive systems and genetic drift on population diversity. Here, we investigate the genomic signatures of partial clonality in the deep water kelp Laminaria rodriguezii, known to reproduce by both sexual and asexual means. We compared these results with the species Laminaria digitata, a closely related species that differs by different traits, in particular its reproductive mode (no clonal reproduction). We analysed genome-wide variation with dd-RAD sequencing using 4,077 SNPs in L. rodriguezii and 7,364 SNPs in L. digitata. As predicted for partially clonal populations, we show that the distribution of FIS within populations of L. rodriguezii is shifted toward negative values, with a high number of loci showing heterozygote excess. This finding is the opposite of what we observed within sexual populations of L. digitata, characterized by a generalized deficit in heterozygotes. Furthermore, we observed distinct distributions of FIS among populations of L. rodriguezii, which is congruent with the predictions of theoretical models for different levels of clonality and genetic drift. These findings highlight that the empirical distribution of FIS is a promising feature for the genomic study of asexuality in natural populations. Our results also show that the populations of L. rodriguezii analysed here are genetically differentiated and probably isolated. Our study provides a conceptual framework to investigate partial clonality on the basis of RAD-sequencing SNPs. These results could be obtained without any reference genome, and are therefore of interest for various non-model species.
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Affiliation(s)
- Lauric Reynes
- CNRS, IRD, MIO, Aix Marseille Université, Université de Toulon, Marseille, France
| | - Thierry Thibaut
- CNRS, IRD, MIO, Aix Marseille Université, Université de Toulon, Marseille, France
| | - Stéphane Mauger
- IRL 3614, Evolutionary Biology and Ecology of Algae, CNRS, UC, UACH, Sorbonne Université, Roscoff, France
| | - Aurélie Blanfuné
- CNRS, IRD, MIO, Aix Marseille Université, Université de Toulon, Marseille, France
| | | | - Corinne Cruaud
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Arnaud Couloux
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Myriam Valero
- IRL 3614, Evolutionary Biology and Ecology of Algae, CNRS, UC, UACH, Sorbonne Université, Roscoff, France
| | - Didier Aurelle
- CNRS, IRD, MIO, Aix Marseille Université, Université de Toulon, Marseille, France
- Institut de Systématique Évolution Biodiversité (ISYEB, UMR 7205), Muséum National d'Histoire Naturelle, CNRS, EPHE, Sorbonne Université, Paris, France
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10
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Stoeckel S, Arnaud-Haond S, Krueger-Hadfield SA. The Combined Effect of Haplodiplonty and Partial Clonality on Genotypic and Genetic Diversity in a Finite Mutating Population. J Hered 2021; 112:78-91. [PMID: 33710350 DOI: 10.1093/jhered/esaa062] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 12/17/2020] [Indexed: 02/03/2023] Open
Abstract
Partial clonality is known to affect the genetic composition and evolutionary trajectory of diplontic (single, free-living diploid stage) populations. However, many partially clonal eukaryotes exhibit life cycles in which somatic development occurs in both haploid and diploid individuals (haplodiplontic life cycles). Here, we studied how haplodiplontic life cycles and partial clonality structurally constrain, as immutable parameters, the reshuffling of genetic diversity and its dynamics in populations over generations. We assessed the distribution of common population genetic indices at different proportions of haploids, rates of clonality, mutation rates, and sampling efforts. Our results showed that haplodiplontic life cycles alone in finite populations affect effective population sizes and the ranges of distributions of population genetic indices. With nonoverlapping generations, haplodiplonty allowed the evolution of 2 temporal genetic pools that may diverge in sympatry due to genetic drift under full sexuality and clonality. Partial clonality in these life cycles acted as a homogenizing force between those 2 pools. Moreover, the combined effects of proportion of haploids, rate of clonality, and the relative strength of mutation versus genetic drift impacts the distributions of population genetics indices, rendering it difficult to transpose and use knowledge accumulated from diplontic or haplontic species. Finally, we conclude by providing recommendations for sampling and analyzing the population genetics of partially clonal haplodiplontic taxa.
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Affiliation(s)
- Solenn Stoeckel
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, F-35650 Le Rheu, France
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11
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Krueger-Hadfield SA, Guillemin ML, Destombe C, Valero M, Stoeckel S. Exploring the Genetic Consequences of Clonality in Haplodiplontic Taxa. J Hered 2021; 112:92-107. [PMID: 33511982 DOI: 10.1093/jhered/esaa063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/18/2020] [Indexed: 11/15/2022] Open
Abstract
Partially clonality is an incredibly common reproductive mode found across all the major eukaryotic lineages. Yet, population genetic theory is based on exclusive sexuality or exclusive asexuality, and partial clonality is often ignored. This is particularly true in haplodiplontic eukaryotes, including algae, ferns, mosses, and fungi, where somatic development occurs in both the haploid and diploid stages. Haplodiplontic life cycles are predicted to be correlated with asexuality, but tests of this prediction are rare. Moreover, there are unique consequences of having long-lived haploid and diploid stages in the same life cycle. For example, clonal processes uncouple the life cycle such that the repetition of the diploid stage via clonality leads to the loss of the haploid stage. Here, we surveyed the literature to find studies that had genotyped both haploid and diploid stages and recalculated population genetic summary metrics for seven red algae, one green alga, three brown algae, and three mosses. We compared these data to recent simulations that explicitly addressed the population genetic consequences of partial clonality in haplodiplontic life cycles. Not only was partial clonality found to act as a homogenizing force, but the combined effects of proportion of haploids, rate of clonality, and the relative strength of mutation versus genetic drift impacts the distributions of population genetic indices. We found remarkably similar patterns across commonly used population genetic metrics between our empirical and recent theoretical expectations. To facilitate future studies, we provide some recommendations for sampling and analyzing population genetic parameters for haplodiplontic taxa.
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Affiliation(s)
| | - Marie-Laure Guillemin
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Station Biologique de Roscoff, Roscoff, France
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Casilla, Valdivia, Chile
| | - Christophe Destombe
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Station Biologique de Roscoff, Roscoff, France
| | - Myriam Valero
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Station Biologique de Roscoff, Roscoff, France
| | - Solenn Stoeckel
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, Le Rheu, France
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12
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Pánek M, Střížková I, Zouhar M, Kudláček T, Tomšovský M. Mixed-Mating Model of Reproduction Revealed in European Phytophthora cactorum by ddRADseq and Effector Gene Sequence Data. Microorganisms 2021; 9:345. [PMID: 33578718 PMCID: PMC7916502 DOI: 10.3390/microorganisms9020345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/27/2021] [Accepted: 02/06/2021] [Indexed: 02/07/2023] Open
Abstract
A population study of Phytophthora cactorum was performed using ddRADseq sequence variation analysis completed by the analysis of effector genes-RXLR6, RXLR7 and SCR113. The population structure was described by F-statistics, heterozygosity, nucleotide diversity, number of private alleles, number of polymorphic sites, kinship coefficient and structure analysis. The population of P. cactorum in Europe seems to be structured into host-associated groups. The isolates from woody hosts are structured into four groups described previously, while isolates from strawberry form another group. The groups are diverse in effector gene composition and the frequency of outbreeding. When populations from strawberry were analysed, both asexual reproduction and occasional outbreeding confirmed by gene flow among distinct populations were detected. Therefore, distinct P. cactorum populations differ in the level of heterozygosity. The data support the theory of the mixed-mating model for P. cactorum, comprising frequent asexual behaviour and inbreeding alternating with occasional outbreeding. Because P. cactorum is not indigenous to Europe, such variability is probably caused by multiple introductions of different lineages from the area of its original distribution, and the different histories of sexual recombination and host adaptation of particular populations.
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Affiliation(s)
- Matěj Pánek
- Crop Research Institute, Team of Ecology and Diagnostics of Fungal Plant Pathogens, Drnovská 507/73, 161 06 Praha, Czech Republic;
| | - Ivana Střížková
- Crop Research Institute, Team of Ecology and Diagnostics of Fungal Plant Pathogens, Drnovská 507/73, 161 06 Praha, Czech Republic;
| | - Miloslav Zouhar
- Department of Plant Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences in Prague, Kamýcká 129, 165 00 Praha, Czech Republic;
| | - Tomáš Kudláček
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, CZ-613 00 Brno, Czech Republic; (T.K.); (M.T.)
| | - Michal Tomšovský
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, CZ-613 00 Brno, Czech Republic; (T.K.); (M.T.)
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13
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Lozada-Gobilard S, Schwarzer C, Dyer R, Tiedemann R, Joshi J. Genetic Diversity and Connectivity in Plant Species Differing in Clonality and Dispersal Mechanisms in Wetland Island Habitats. J Hered 2021; 112:108-121. [PMID: 33555304 DOI: 10.1093/jhered/esaa059] [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] [Received: 02/01/2020] [Accepted: 12/15/2020] [Indexed: 11/14/2022] Open
Abstract
In plants, long-distance dispersal is both attenuated and directed by specific movement vectors, including animals, wind, and/or water. Hence, movement vectors partly shape metapopulation genetic patterns that are, however, also influenced by other life-history traits such as clonal growth. We studied the relationship between area, isolation, plant-species richness, reproduction, and dispersal mechanisms with genetic diversity and divergence in 4 widespread wetland plant-species in a total of 20 island-like kettle-hole habitats surrounded by an intensive agricultural landscape. Our results showed that genetic parameters reflect the reproduction strategies with the highest genetic diversity being observed in the non-clonal, outcrossing Oenanthe aquatica compared to the clonal Lycopus europaeus, Typha latifolia, and Phragmites australis. Lycopus showed a positive relationship between genetic diversity and kettle-hole area, but a negative relationship with the number of neighboring kettle holes (less isolation). Genetic diversity increased with plant-species richness in the clonal species Phragmites and Lycopus; while it decreased in the non-clonal Oenanthe. Finally, genetic divergence and, therefore, connectivity differed between alternative dispersal strategies, where wind-dispersed Typha and Phragmites had a higher gene flow between the analyzed kettle holes compared with the insect-pollinated, hydrochorous Lycopus and Oenanthe. Our study provides information on genetic patterns related to reproduction and dispersal mechanisms of 4 common wetland species contributing to the understanding of the functioning of plant metacommunities occurring in kettle holes embedded in agricultural landscapes.
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Affiliation(s)
- Sissi Lozada-Gobilard
- Unit of Evolutionary Biology/Systematic Zoology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam, Germany.,The Botanical Garden, School of Plant Sciences and Food Security, G.S. Wise Faculty of Life Science, Tel Aviv University, Israel
| | - Christian Schwarzer
- Plant Systematics and Biodiversity, Humboldt University of Berlin, Späth-Arboretum, Späthstr. 80/81, Berlin, Germany
| | - Rodney Dyer
- Center of Environmental Studies, Virginia Commonwealth University, Richmond, VA
| | - Ralph Tiedemann
- Unit of Evolutionary Biology/Systematic Zoology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam, Germany
| | - Jasmin Joshi
- Institute for Landscape and Open Space, Eastern Switzerland University of Applied Sciences, Seestrasse 10, Rapperswil, Switzerland.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 6, Berlin, Germany
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14
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Stoeckel S, Porro B, Arnaud-Haond S. The discernible and hidden effects of clonality on the genotypic and genetic states of populations: Improving our estimation of clonal rates. Mol Ecol Resour 2021; 21:1068-1084. [PMID: 33386695 DOI: 10.1111/1755-0998.13316] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 11/05/2020] [Accepted: 12/21/2020] [Indexed: 11/29/2022]
Abstract
Partial clonality is widespread across the tree of life, but most population genetic models are designed for exclusively clonal or sexual organisms. This gap hampers our understanding of the influence of clonality on evolutionary trajectories and the interpretation of population genetic data. We performed forward simulations of diploid populations at increasing rates of clonality (c), analysed their relationships with genotypic (clonal richness, R, and distribution of clonal sizes, Pareto β) and genetic (FIS and linkage disequilibrium) indices, and tested predictions of c from population genetic data through supervised machine learning. Two complementary behaviours emerged from the probability distributions of genotypic and genetic indices with increasing c. While the impact of c on R and Pareto β was easily described by simple mathematical equations, its effects on genetic indices were noticeable only at the highest levels (c > 0.95). Consequently, genotypic indices allowed reliable estimates of c, while genetic descriptors led to poorer performances when c < 0.95. These results provide clear baseline expectations for genotypic and genetic diversity and dynamics under partial clonality. Worryingly, however, the use of realistic sample sizes to acquire empirical data systematically led to gross underestimates (often of one to two orders of magnitude) of c, suggesting that many interpretations hitherto proposed in the literature, mostly based on genotypic richness, should be reappraised. We propose future avenues to derive realistic confidence intervals for c and show that, although still approximate, a supervised learning method would greatly improve the estimation of c from population genetic data.
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Affiliation(s)
- Solenn Stoeckel
- Institute for Genetics, Environment and Plant Protection, INRAE, Le Rheu, France
| | - Barbara Porro
- Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France.,MARBEC - Marine Biodiversity Exploitation and Conservation, University of Montpellier, CNRS, Ifremer, IRD, MARBEC, Sète, France
| | - Sophie Arnaud-Haond
- MARBEC - Marine Biodiversity Exploitation and Conservation, University of Montpellier, CNRS, Ifremer, IRD, MARBEC, Sète, France
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15
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White DM, Huang JP, Jara-Muñoz OA, MadriñáN S, Ree RH, Mason-Gamer RJ. The Origins of Coca: Museum Genomics Reveals Multiple Independent Domestications from Progenitor Erythroxylum gracilipes. Syst Biol 2020; 70:1-13. [PMID: 32979264 PMCID: PMC7744036 DOI: 10.1093/sysbio/syaa074] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/08/2020] [Accepted: 09/13/2020] [Indexed: 11/21/2022] Open
Abstract
Coca is the natural source of cocaine as well as a sacred and medicinal plant farmed by South American Amerindians and mestizos. The coca crop comprises four closely related varieties classified into two species (Amazonian and Huánuco varieties within Erythroxylum coca Lam., and Colombian and Trujillo varieties within Erythroxylum novogranatense (D. Morris) Hieron.) but our understanding of the domestication and evolutionary history of these taxa is nominal. In this study, we use genomic data from natural history collections to estimate the geographic origins and genetic diversity of this economically and culturally important crop in the context of its wild relatives. Our phylogeographic analyses clearly demonstrate the four varieties of coca comprise two or three exclusive groups nested within the diverse lineages of the widespread, wild species Erythroxylum gracilipes; establishing a new and robust hypothesis of domestication wherein coca originated two or three times from this wild progenitor. The Colombian and Trujillo coca varieties are descended from a single, ancient domestication event in northwestern South America. Huánuco coca was domesticated more recently, possibly in southeastern Peru. Amazonian coca either shares a common domesticated ancestor with Huánuco coca, or it was the product of a third and most recent independent domestication event in the western Amazon basin. This chronology of coca domestication reveals different Holocene peoples in South America were able to independently transform the same natural resource to serve their needs; in this case, a workaday stimulant. [Erythroxylum; Erythroxylaceae; Holocene; Museomics; Neotropics; phylogeography; plant domestication; target-sequence capture.]
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Affiliation(s)
- Dawson M White
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.,Grainger Bioinformatics Center, The Field Museum, Chicago, IL 60605, USA
| | - Jen-Pan Huang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | | | - Santiago MadriñáN
- Laboratorio de Botánica y Sistemática, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá D.C., Colombia.,Jardín Botánico de Cartagena "Guillermo Piñeres", Turbaco, Bolívar, Colombia
| | - Richard H Ree
- Grainger Bioinformatics Center, The Field Museum, Chicago, IL 60605, USA
| | - Roberta J Mason-Gamer
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
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16
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Becheler R, Guillemin M, Stoeckel S, Mauger S, Saunier A, Brante A, Destombe C, Valero M. After a catastrophe, a little bit of sex is better than nothing: Genetic consequences of a major earthquake on asexual and sexual populations. Evol Appl 2020; 13:2086-2100. [PMID: 32908606 PMCID: PMC7463374 DOI: 10.1111/eva.12967] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 11/27/2022] Open
Abstract
Catastrophic events can have profound effects on the demography of a population and consequently on genetic diversity. The dynamics of postcatastrophic recovery and the role of sexual versus asexual reproduction in buffering the effects of massive perturbations remain poorly understood, in part because the opportunity to document genetic diversity before and after such events is rare. Six natural (purely sexual) and seven cultivated (mainly clonal due to farming practices) populations of the red alga Agarophyton chilense were surveyed along the Chilean coast before, in the days after and 2 years after the 8.8 magnitude earthquake in 2010. The genetic diversity of sexual populations appeared sensitive to this massive perturbation, notably through the loss of rare alleles immediately after the earthquake. By 2012, the levels of diversity returned to those observed before the catastrophe, probably due to migration. In contrast, enhanced rates of clonality in cultivated populations conferred a surprising ability to buffer the instantaneous loss of diversity. After the earthquake, farmers increased the already high rate of clonality to maintain the few surviving beds, but most of them collapsed rapidly. Contrasting fates between sexual and clonal populations suggest that betting on strict clonality to sustain production is risky, probably because this extreme strategy hampered adaptation to the brutal environmental perturbation induced by the catastrophe.
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Affiliation(s)
- Ronan Becheler
- Centro de Conservación MarinaDepartamento de EcologíaFacultad de Ciencias BiológicasPontificia Universidad Católica de ChileCasillaChile
- UMI 3614Evolutionary Biology and Ecology of AlgaeCNRSSorbonne UniversitéUniversidad Austral de ChilePontificia Universidad Católica de ChileRoscoffFrance
| | - Marie‐Laure Guillemin
- UMI 3614Evolutionary Biology and Ecology of AlgaeCNRSSorbonne UniversitéUniversidad Austral de ChilePontificia Universidad Católica de ChileRoscoffFrance
- Instituto de Ciencias Ambientales y EvolutivasFacultad de CienciasUniversidad Austral de ChileValdiviaChile
| | - Solenn Stoeckel
- UMR1349 Institute for Genetics, Environment and Plant ProtectionINRALe RheuFrance
| | - Stéphane Mauger
- UMI 3614Evolutionary Biology and Ecology of AlgaeCNRSSorbonne UniversitéUniversidad Austral de ChilePontificia Universidad Católica de ChileRoscoffFrance
| | - Alice Saunier
- UMI 3614Evolutionary Biology and Ecology of AlgaeCNRSSorbonne UniversitéUniversidad Austral de ChilePontificia Universidad Católica de ChileRoscoffFrance
- Instituto de Ciencias Ambientales y EvolutivasFacultad de CienciasUniversidad Austral de ChileValdiviaChile
| | - Antonio Brante
- Departamento de EcologíaFacultad de CienciasUniversidad Católica de la Santísima Concepción (UCSC)ConcepciónChile
- Centro de Investigación en Biodiversidad y Ambientes Sustentables (CIBAS)UCSCConcepciónChile
| | - Christophe Destombe
- UMI 3614Evolutionary Biology and Ecology of AlgaeCNRSSorbonne UniversitéUniversidad Austral de ChilePontificia Universidad Católica de ChileRoscoffFrance
| | - Myriam Valero
- UMI 3614Evolutionary Biology and Ecology of AlgaeCNRSSorbonne UniversitéUniversidad Austral de ChilePontificia Universidad Católica de ChileRoscoffFrance
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17
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Arnaud-Haond S, Stoeckel S, Bailleul D. New insights into the population genetics of partially clonal organisms: When seagrass data meet theoretical expectations. Mol Ecol 2020; 29:3248-3260. [PMID: 32613610 DOI: 10.1111/mec.15532] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/30/2020] [Accepted: 06/11/2020] [Indexed: 01/23/2023]
Abstract
Seagrass meadows are among the most important coastal ecosystems in terms of both spatial extent and ecosystem services, but they are also declining worldwide. Understanding the drivers of seagrass meadow dynamics is essential for designing sound management, conservation and restoration strategies. However, poor knowledge of the effect of clonality on the population genetics of natural populations severely limits our understanding of the dynamics and connectivity of meadows. Recent modelling approaches have described the expected distributions of genotypic and genetic descriptors under increasing clonal rates, which may help us better understand and interpret population genetics data obtained for partial asexuals. Here, in the light of these recent theoretical developments, we revisited population genetics data for 165 meadows of four seagrass species. Contrasting shoot lifespan and rhizome turnover led to the prediction that the influence of asexual reproduction would increase along a gradient from Zostera noltii to Zostera marina, Cymodocea nodosa and Posidonia oceanica, with increasing departure from Hardy-Weinberg equilibrium (Fis ), mostly towards heterozygote excess, and decreasing genotypic richness (R). This meta-analysis provides a nested validation of this hypothesis at both the species and meadow scales through a significant relationship between Fis and R within each species. By empirically demonstrating the theoretical expectations derived from recent modelling approaches, this work calls for the use of Hardy-Weinberg equilibrium (Fis ) rather than only the strongly sampling-sensitive R to assess the importance of clonal reproduction (c), at least when the impact of selfing on Fis can be neglected. The results also emphasize the need to revise our appraisal of the extent of clonality and its influence on the dynamics, connectivity and evolutionary trajectory of partial asexuals in general, including in seagrass meadows, to develop the most accurate management strategies.
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Affiliation(s)
| | - Solenn Stoeckel
- IGEPP INRAE, Institut Agro, University of Rennes, Le Rheu, France
| | - Diane Bailleul
- Université de Montpellier, Ifremer, CNRS, IRD, MARBEC, Sète, France
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18
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Haponski AE, Ó Foighil D. Phylogenomic analyses confirm a novel invasive North American Corbicula (Bivalvia: Cyrenidae) lineage. PeerJ 2019; 7:e7484. [PMID: 31497390 PMCID: PMC6708575 DOI: 10.7717/peerj.7484] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 07/15/2019] [Indexed: 11/20/2022] Open
Abstract
The genus Corbicula consists of estuarine or freshwater clams native to temperate/tropical regions of Asia, Africa, and Australia that collectively encompass both sexual species and clonal (androgenetic) lineages. The latter have become globally invasive in freshwater systems and they represent some of the most successful aquatic invasive lineages. Previous studies have documented four invasive clonal lineages, Forms A, B, C, and Rlc, with varying known distributions. Form A (R in Europe) occurs globally, Form B is found solely in North America, mainly the western United States, Form C (S in Europe) occurs both in European watersheds and in South America, and Rlc is known from Europe. A putative fifth invasive morph, Form D, was recently described in the New World from the Illinois River (Great Lakes watershed), where it occurs in sympatry with Forms A and B. An initial study showed Form D to be conchologically distinct: possessing rust-colored rays and white nacre with purple teeth. However, its genetic distinctiveness using standard molecular markers (mitochondrial cytochrome c oxidase subunit I and nuclear ribosomal 28S RNA) was ambiguous. To resolve this issue, we performed a phylogenomic analysis using 1,699-30,027 nuclear genomic loci collected via the next generation double digested restriction-site associated DNA sequencing method. Our results confirmed Form D to be a distinct invasive New World lineage with a population genomic profile consistent with clonality. A majority (7/9) of the phylogenomic analyses recovered the four New World invasive Corbicula lineages (Forms A, B, C, and D) as members of a clonal clade, sister to the non-clonal Lake Biwa (Japan) endemic, Corbicula sandai. The age of the clonal clade was estimated at 1.49 million years (my; ± 0.401-2.955 my) whereas the estimated ages of the four invasive lineage crown clades ranged from 0.27 to 0.44 my. We recovered very little evidence of nuclear genomic admixture among the four invasive lineages in our study populations. In contrast, 2/6 C. sandai individuals displayed partial nuclear genomic Structure assignments with multiple invasive clonal lineages. These results provide new insights into the origin and maintenance of clonality in this complex system.
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Affiliation(s)
- Amanda E. Haponski
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Diarmaid Ó Foighil
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
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19
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Xu NN, Jiang K, Biswas SR, Tong X, Wang R, Chen XY. Clone Configuration and Spatial Genetic Structure of Two Halophila ovalis Populations With Contrasting Internode Lengths. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00170] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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20
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Bouteiller XP, Verdu CF, Aikio E, Bloese P, Dainou K, Delcamp A, De Thier O, Guichoux E, Mengal C, Monty A, Pucheu M, van Loo M, Josée Porté A, Lassois L, Mariette S. A few north Appalachian populations are the source of European black locust. Ecol Evol 2019; 9:2398-2414. [PMID: 30891188 PMCID: PMC6405530 DOI: 10.1002/ece3.4776] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 11/12/2018] [Accepted: 11/13/2018] [Indexed: 12/24/2022] Open
Abstract
The role of evolution in biological invasion studies is often overlooked. In order to evaluate the evolutionary mechanisms behind invasiveness, it is crucial to identify the source populations of the introduction. Studies in population genetics were carried out on Robinia pseudoacacia L., a North American tree which is now one of the worst invasive tree species in Europe. We realized large-scale sampling in both the invasive and native ranges: 63 populations were sampled and 818 individuals were genotyped using 113 SNPs. We identified clonal genotypes in each population and analyzed between and within range population structure, and then, we compared genetic diversity between ranges, enlarging the number of SNPs to mitigate the ascertainment bias. First, we demonstrated that European black locust was introduced from just a limited number of populations located in the Appalachian Mountains, which is in agreement with the historical documents briefly reviewed in this study. Within America, population structure reflected the effects of long-term processes, whereas in Europe it was largely impacted by human activities. Second, we showed that there is a genetic bottleneck between the ranges with a decrease in allelic richness and total number of alleles in Europe. Lastly, we found more clonality within European populations. Black locust became invasive in Europe despite being introduced from a reduced part of its native distribution. Our results suggest that human activity, such as breeding programs in Europe and the seed trade throughout the introduced range, had a major role in promoting invasion; therefore, the introduction of the missing American genetic cluster to Europe should be avoided.
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Affiliation(s)
| | - Cindy Frédérique Verdu
- Biodiversity and Landscape Unit, Gembloux Agro‐Bio TechUniversity of LiègeGemblouxBelgium
| | - Emmi Aikio
- Department of Genetics and PhysiologyUniversity of OuluOuluFinland
| | - Paul Bloese
- Department of ForestryMichigan State UniversityEast LansingMichigan
| | - Kasso Dainou
- Biodiversity and Landscape Unit, Gembloux Agro‐Bio TechUniversity of LiègeGemblouxBelgium
| | | | - Olivier De Thier
- Biodiversity and Landscape Unit, Gembloux Agro‐Bio TechUniversity of LiègeGemblouxBelgium
| | | | - Coralie Mengal
- Biodiversity and Landscape Unit, Gembloux Agro‐Bio TechUniversity of LiègeGemblouxBelgium
| | - Arnaud Monty
- Forest Management Unit, Gembloux Agro‐Bio TechUniversity of LiègeGemblouxBelgium
| | | | - Marcela van Loo
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | | | - Ludivine Lassois
- Biodiversity and Landscape Unit, Gembloux Agro‐Bio TechUniversity of LiègeGemblouxBelgium
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21
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Garcia-Cisneros A, Palacín C, Ventura CRR, Feital B, Paiva PC, Pérez-Portela R. Intraspecific genetic structure, divergence and high rates of clonality in an amphi-Atlantic starfish. Mol Ecol 2018; 27:752-772. [PMID: 29218784 DOI: 10.1111/mec.14454] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 08/28/2017] [Accepted: 11/08/2017] [Indexed: 12/14/2022]
Abstract
Intraspecific genetic diversity and divergence have a large influence on the adaption and evolutionary potential of species. The widely distributed starfish, Coscinasterias tenuispina, combines sexual reproduction with asexual reproduction via fission. Here we analyse the phylogeography of this starfish to reveal historical and contemporary processes driving its intraspecific genetic divergence. We further consider whether asexual reproduction is the most important method of propagation throughout the distribution range of this species. Our study included 326 individuals from 16 populations, covering most of the species' distribution range. A total of 12 nuclear microsatellite loci and sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene were analysed. COI and microsatellites were clustered in two isolated lineages: one found along the southwestern Atlantic and the other along the northeastern Atlantic and Mediterranean Sea. This suggests the existence of two different evolutionary units. Marine barriers along the European coast would be responsible for population clustering: the Almeria-Oran Front that limits the entrance of migrants from the Atlantic to the Mediterranean, and the Siculo-Tunisian strait that divides the two Mediterranean basins. The presence of identical genotypes was detected in all populations, although two monoclonal populations were found in two sites where annual mean temperatures and minimum values were the lowest. Our results based on microsatellite loci showed that intrapopulation genetic diversity was significantly affected by clonality whereas it had lower effect for the global phylogeography of the species, although still some impact on populations' genetic divergence could be observed between some populations.
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Affiliation(s)
- Alex Garcia-Cisneros
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Research Institute of Biodiversity (IRBIO), Barcelona, Spain.,Center for Advanced Studies of Blanes (CEAB-CSIC), Accès a la Cala Sant Francesc, Girona, Spain
| | - Creu Palacín
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Research Institute of Biodiversity (IRBIO), Barcelona, Spain
| | - Carlos Renato Rezende Ventura
- Invertebrate Department, National Museum, Federal University of Rio de Janeiro, Quinta da Boa Vista, Rio de Janeiro, Brazil
| | - Barbara Feital
- Invertebrate Department, National Museum, Federal University of Rio de Janeiro, Quinta da Boa Vista, Rio de Janeiro, Brazil.,Department of Zoology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo Cesar Paiva
- Department of Zoology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rocío Pérez-Portela
- Center for Advanced Studies of Blanes (CEAB-CSIC), Accès a la Cala Sant Francesc, Girona, Spain
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22
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Clonal expansion behind a marine diatom bloom. ISME JOURNAL 2017; 12:463-472. [PMID: 29160864 PMCID: PMC5776461 DOI: 10.1038/ismej.2017.181] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 09/10/2017] [Accepted: 09/14/2017] [Indexed: 11/08/2022]
Abstract
Genetic diversity is what selection acts on, thus shaping the adaptive potential of populations. We studied micro-evolutionary patterns of the key planktonic diatom Pseudo-nitzschia multistriata at a long-term sampling site over 2 consecutive years by genotyping isolates with 22 microsatellite markers. We show that both sex and vegetative growth interplay in shaping intraspecific diversity. We document a brief but massive demographic and clonal expansion driven by strains of the same mating type. The analysis of an extended data set (6 years) indicates that the genetic fingerprint of P. multistriata changed over time with a nonlinear pattern, with intermittent periods of weak and strong diversification related to the temporary predominance of clonal expansions over sexual recombination. These dynamics, rarely documented for phytoplankton, contribute to the understanding of bloom formation and of the mechanisms that drive microevolution in diatoms.
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23
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Postaire B, Gélin P, Bruggemann JH, Pratlong M, Magalon H. Population differentiation or species formation across the Indian and the Pacific Oceans? An example from the brooding marine hydrozoan Macrorhynchia phoenicea. Ecol Evol 2017; 7:8170-8186. [PMID: 29075441 PMCID: PMC5648676 DOI: 10.1002/ece3.3236] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/09/2017] [Accepted: 06/20/2017] [Indexed: 01/18/2023] Open
Abstract
Assessing population connectivity is necessary to construct effective marine protected areas. This connectivity depends, among other parameters, inherently on species dispersal capacities. Isolation by distance (IBD) is one of the main modes of differentiation in marine species, above all in species presenting low dispersal abilities. This study reports the genetic structuring in the tropical hydrozoan Macrorhynchia phoenicea α (sensu Postaire et al., 2016a), a brooding species, from 30 sampling sites in the Western Indian Ocean and the Tropical Southwestern Pacific, using 15 microsatellite loci. At the local scale, genet dispersal relied on asexual propagation at short distance, which was not found at larger scales. Considering one representative per clone, significant positive FIS values (from −0.327*** to 0.411***) were found within almost all sites. Gene flow was extremely low at all spatial scales, among sites within islands (<10 km distance) and among islands (100 to >11,000 km distance), with significant pairwise FST values (from 0.035*** to 0.645***). A general pattern of IBD was found at the Indo‐Pacific scale, but also within ecoregions in the Western Indian Ocean province. Clustering and network analyses identified each island as a potential independent population, while analysis of molecular variance indicated that population genetic differentiation was significant at small (within island) and intermediate (among islands within province) spatial scales. As shown by this species, a brooding life cycle might be corollary of the high population differentiation found in some coastal marine species, thwarting regular dispersal at distances more than a few kilometers and probably leading to high cryptic diversity, each island housing independent evolutionary lineages.
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Affiliation(s)
- Bautisse Postaire
- UMR ENTROPIE Université de La Réunion/CNRS/IRD Université de La Réunion Saint Denis France.,Laboratoire d'Excellence CORAIL Perpignan France.,IMBE UMR 7263 Aix Marseille Université/CNRS/IRD/Avignon Université Marseille France
| | - Pauline Gélin
- UMR ENTROPIE Université de La Réunion/CNRS/IRD Université de La Réunion Saint Denis France.,Laboratoire d'Excellence CORAIL Perpignan France
| | - J Henrich Bruggemann
- UMR ENTROPIE Université de La Réunion/CNRS/IRD Université de La Réunion Saint Denis France.,Laboratoire d'Excellence CORAIL Perpignan France
| | - Marine Pratlong
- IMBE UMR 7263 Aix Marseille Université/CNRS/IRD/Avignon Université Marseille France.,I2M Equipe Evolution Biologique et Modélisation Aix Marseille Université/CNRS/Centrale Marseille Marseille France
| | - Hélène Magalon
- UMR ENTROPIE Université de La Réunion/CNRS/IRD Université de La Réunion Saint Denis France.,Laboratoire d'Excellence CORAIL Perpignan France
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24
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Becheler R, Masson JP, Arnaud-Haond S, Halkett F, Mariette S, Guillemin ML, Valero M, Destombe C, Stoeckel S. ClonEstiMate, a Bayesian method for quantifying rates of clonality of populations genotyped at two-time steps. Mol Ecol Resour 2017; 17:e251-e267. [DOI: 10.1111/1755-0998.12698] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 06/01/2017] [Accepted: 06/22/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Ronan Becheler
- Evolutionary Biology and Ecology of Algae; CNRS; Sorbonne Universités; UPMC; University of Paris VI; UC; UACH; UMI 3614; Roscoff France
| | - Jean-Pierre Masson
- Institute for Genetics; Environment and Plant Protection; INRA; UMR1349; Le Rheu France
| | - Sophie Arnaud-Haond
- Ifremer; MARBEC (Marine Biodiversity, Exploitation and Conservation); Boulevard Jean Monet; 34200 SETE
| | | | | | - Marie-Laure Guillemin
- Evolutionary Biology and Ecology of Algae; CNRS; Sorbonne Universités; UPMC; University of Paris VI; UC; UACH; UMI 3614; Roscoff France
- Facultad de Ciencias; Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Valdivia Chile
| | - Myriam Valero
- Evolutionary Biology and Ecology of Algae; CNRS; Sorbonne Universités; UPMC; University of Paris VI; UC; UACH; UMI 3614; Roscoff France
| | - Christophe Destombe
- Evolutionary Biology and Ecology of Algae; CNRS; Sorbonne Universités; UPMC; University of Paris VI; UC; UACH; UMI 3614; Roscoff France
| | - Solenn Stoeckel
- Institute for Genetics; Environment and Plant Protection; INRA; UMR1349; Le Rheu France
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25
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Cubry P, Scotti I, Oddou-Muratorio S, Lefèvre F. Generalization of the Q ST framework in hierarchically structured populations: Impacts of inbreeding and dominance. Mol Ecol Resour 2017; 17:e76-e83. [PMID: 28681534 DOI: 10.1111/1755-0998.12693] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 05/12/2017] [Accepted: 05/22/2017] [Indexed: 11/30/2022]
Abstract
QST is a differentiation parameter based on the decomposition of the genetic variance of a trait. In the case of additive inheritance and absence of selection, it is analogous to the genic differentiation measured on individual loci, FST . Thus, QST -FST comparison is used to infer selection: selective divergence when QST > FST , or convergence when QST < FST. The definition of Q-statistics was extended to two-level hierarchical population structures with Hardy-Weinberg equilibrium. Here, we generalize the Q-statistics framework to any hierarchical population structure. First, we developed the analytical definition of hierarchical Q-statistics for populations not at Hardy-Weinberg equilibrium. We show that the Q-statistics values obtained with the Hardy-Weinberg definition are lower than their corresponding F-statistics when FIS > 0 (higher when FIS < 0). Then, we used an island model simulation approach to investigate the impact of inbreeding and dominance on the QST -FST framework in a hierarchical population structure. We show that, while differentiation at the lower hierarchical level (QSR ) is a monotonic function of migration, differentiation at the upper level (QRT ) is not. In the case of additive inheritance, we show that inbreeding inflates the variance of QRT , which can increase the frequency of QRT > FRT cases. We also show that dominance drastically reduces Q-statistics below F-statistics for any level of the hierarchy. Therefore, high values of Q-statistics are good indicators of selection, but low values are not in the case of dominance.
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Affiliation(s)
- Philippe Cubry
- INRA, UR 629 Ecologie des Forêts Méditerranéennes, URFM, Avignon Cedex9, France.,IRD, UMR DIADE, Montpellier Cedex 5, France
| | - Ivan Scotti
- INRA, UR 629 Ecologie des Forêts Méditerranéennes, URFM, Avignon Cedex9, France
| | | | - François Lefèvre
- INRA, UR 629 Ecologie des Forêts Méditerranéennes, URFM, Avignon Cedex9, France
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26
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Effects of complex life cycles on genetic diversity: cyclical parthenogenesis. Heredity (Edinb) 2016; 117:336-347. [PMID: 27436524 DOI: 10.1038/hdy.2016.52] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 06/02/2016] [Accepted: 06/08/2016] [Indexed: 11/08/2022] Open
Abstract
Neutral patterns of population genetic diversity in species with complex life cycles are difficult to anticipate. Cyclical parthenogenesis (CP), in which organisms undergo several rounds of clonal reproduction followed by a sexual event, is one such life cycle. Many species, including crop pests (aphids), human parasites (trematodes) or models used in evolutionary science (Daphnia), are cyclical parthenogens. It is therefore crucial to understand the impact of such a life cycle on neutral genetic diversity. In this paper, we describe distributions of genetic diversity under conditions of CP with various clonal phase lengths. Using a Markov chain model of CP for a single locus and individual-based simulations for two loci, our analysis first demonstrates that strong departures from full sexuality are observed after only a few generations of clonality. The convergence towards predictions made under conditions of full clonality during the clonal phase depends on the balance between mutations and genetic drift. Second, the sexual event of CP usually resets the genetic diversity at a single locus towards predictions made under full sexuality. However, this single recombination event is insufficient to reshuffle gametic phases towards full-sexuality predictions. Finally, for similar levels of clonality, CP and acyclic partial clonality (wherein a fixed proportion of individuals are clonally produced within each generation) differentially affect the distribution of genetic diversity. Overall, this work provides solid predictions of neutral genetic diversity that may serve as a null model in detecting the action of common evolutionary or demographic processes in cyclical parthenogens (for example, selection or bottlenecks).
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27
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Reichel K, Masson JP, Malrieu F, Arnaud-Haond S, Stoeckel S. Rare sex or out of reach equilibrium? The dynamics of F IS in partially clonal organisms. BMC Genet 2016; 17:76. [PMID: 27286682 PMCID: PMC4902967 DOI: 10.1186/s12863-016-0388-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 06/01/2016] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Partially clonal organisms are very common in nature, yet the influence of partial asexuality on the temporal dynamics of genetic diversity remains poorly understood. Mathematical models accounting for clonality predict deviations only for extremely rare sex and only towards mean inbreeding coefficient [Formula: see text]. Yet in partially clonal species, both F IS < 0 and F IS > 0 are frequently observed also in populations where there is evidence for a significant amount of sexual reproduction. Here, we studied the joint effects of partial clonality, mutation and genetic drift with a state-and-time discrete Markov chain model to describe the dynamics of F IS over time under increasing rates of clonality. RESULTS Results of the mathematical model and simulations show that partial clonality slows down the asymptotic convergence to F IS = 0. Thus, although clonality alone does not lead to departures from Hardy-Weinberg expectations once reached the final equilibrium state, both negative and positive F IS values can arise transiently even at intermediate rates of clonality. More importantly, such "transient" departures from Hardy Weinberg proportions may last long as clonality tunes up the temporal variation of F IS and reduces its rate of change over time, leading to a hyperbolic increase of the maximal time needed to reach the final mean [Formula: see text] value expected at equilibrium. CONCLUSION Our results argue for a dynamical interpretation of F IS in clonal populations. Negative values cannot be interpreted as unequivocal evidence for extremely scarce sex but also as intermediate rates of clonality in finite populations. Complementary observations (e.g. frequency distribution of multiloci genotypes, population history) or time series data may help to discriminate between different possible conclusions on the extent of clonality when mean [Formula: see text] values deviating from zero and/or a large variation of F IS over loci are observed.
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Affiliation(s)
- Katja Reichel
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, 35650, Le Rheu, France
| | - Jean-Pierre Masson
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, 35650, Le Rheu, France
| | - Florent Malrieu
- Université de Tours, CNRS-UMR7350 LMPT, F-37200, Tours, France
| | | | - Solenn Stoeckel
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, 35650, Le Rheu, France.
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28
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Ali S, Soubeyrand S, Gladieux P, Giraud T, Leconte M, Gautier A, Mboup M, Chen W, de Vallavieille-Pope C, Enjalbert J. cloncase: Estimation of sex frequency and effective population size by clonemate resampling in partially clonal organisms. Mol Ecol Resour 2016; 16:845-61. [DOI: 10.1111/1755-0998.12511] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 01/29/2016] [Accepted: 02/02/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Sajid Ali
- UMR1290, BIOGER; INRA-AgroParisTech; BP01 78850 Thiverval-Grignon France
- Institute of Biotechnology and Genetic Engineering; the University of Agriculture, Peshawar; 25000 Peshawar Pakistan
| | - Samuel Soubeyrand
- UR546 Biostatistics and Spatial Processes; INRA; 84914 Avignon France
| | - Pierre Gladieux
- Ecologie Systématique Evolution; CNRS; Univ. Paris-Sud; AgroParisTech; Université Paris-Saclay; 91400 Orsay France
- UMR385 Biologie et Génétique des Interactions Plante-Parasite; CIRAD; INRA; F-34398 Montpellier France
| | - Tatiana Giraud
- Ecologie Systématique Evolution; CNRS; Univ. Paris-Sud; AgroParisTech; Université Paris-Saclay; 91400 Orsay France
| | - Marc Leconte
- UMR1290, BIOGER; INRA-AgroParisTech; BP01 78850 Thiverval-Grignon France
| | - Angélique Gautier
- UMR1290, BIOGER; INRA-AgroParisTech; BP01 78850 Thiverval-Grignon France
| | - Mamadou Mboup
- DuPont de Nemours (France) SAS Crop Protection - European Research & Development Center; 24, rue du Moulin 68740 Nambsheim France
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests; Institute of Plant Protection; Chinese Academy of Agricultural Sciences; No. 2 Yuanmingyuan West Road Beijing 100193 China
| | | | - Jérôme Enjalbert
- Ecologie Systématique Evolution; CNRS; Univ. Paris-Sud; AgroParisTech; Université Paris-Saclay; 91400 Orsay France
- GQE - Le Moulon; INRA; Univ. Paris-Sud; CNRS; AgroParisTech; Université Paris-Saclay; F-91190 Gif-sur-Yvette France
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29
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Reichel K, Bahier V, Midoux C, Parisey N, Masson JP, Stoeckel S. Interpretation and approximation tools for big, dense Markov chain transition matrices in population genetics. Algorithms Mol Biol 2015; 10:31. [PMID: 26719759 PMCID: PMC4696214 DOI: 10.1186/s13015-015-0061-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 12/04/2015] [Indexed: 11/14/2022] Open
Abstract
Background Markov chains are a common framework for individual-based state and time discrete models in evolution. Though they played an important role in the development of basic population genetic theory, the analysis of more complex evolutionary scenarios typically involves approximation with other types of models. As the number of states increases, the big, dense transition matrices involved
become increasingly unwieldy. However, advances in computational technology continue to reduce the challenges of “big data”, thus giving new potential to state-rich Markov chains in theoretical population genetics. Results Using a population genetic model based on genotype frequencies as an example, we propose a set of methods to assist in the computation and interpretation of big, dense Markov chain transition matrices. With the help of network analysis, we demonstrate how they can be transformed into clear and easily interpretable graphs, providing a new perspective even on the classic case of a randomly mating, finite population with mutation. Moreover, we describe an algorithm to save computer memory by substituting the original matrix with a sparse approximate while preserving its mathematically important properties, including a closely corresponding dominant (normalized) eigenvector. A global sensitivity analysis of the approximation results in our example shows that size reduction of more than 90 % is possible without significantly affecting the basic model results. Sample implementations of our methods are collected in the Python module mamoth. Conclusion Our methods help to make stochastic population genetic models involving big, dense transition matrices computationally feasible. Our visualization techniques provide new ways to explore such models and concisely present the results. Thus, our methods will contribute to establish state-rich Markov chains as a valuable supplement to the diversity of population genetic models currently employed, providing interesting new details about evolution e.g. under non-standard reproductive systems such as partial clonality. Electronic supplementary material The online version of this article (doi:10.1186/s13015-015-0061-5) contains supplementary material, which is available to authorized users.
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30
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Nougué O, Rode NO, Jabbour-zahab R, Ségard A, Chevin LM, Haag CR, Lenormand T. Automixis in Artemia: solving a century-old controversy. J Evol Biol 2015; 28:2337-48. [DOI: 10.1111/jeb.12757] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 08/26/2015] [Accepted: 09/07/2015] [Indexed: 12/11/2022]
Affiliation(s)
- O. Nougué
- UMR 5175 CEFE; CNRS - Université Montpellier - Université P. Valéry - EPHE; Montpellier Cedex 5 France
| | - N. O. Rode
- UMR 5175 CEFE; CNRS - Université Montpellier - Université P. Valéry - EPHE; Montpellier Cedex 5 France
- INRA - UMR 1334 AGAP; Montpellier France
| | - R. Jabbour-zahab
- UMR 5175 CEFE; CNRS - Université Montpellier - Université P. Valéry - EPHE; Montpellier Cedex 5 France
| | - A. Ségard
- UMR 5175 CEFE; CNRS - Université Montpellier - Université P. Valéry - EPHE; Montpellier Cedex 5 France
| | - L.-M. Chevin
- UMR 5175 CEFE; CNRS - Université Montpellier - Université P. Valéry - EPHE; Montpellier Cedex 5 France
| | - C. R. Haag
- UMR 5175 CEFE; CNRS - Université Montpellier - Université P. Valéry - EPHE; Montpellier Cedex 5 France
| | - T. Lenormand
- UMR 5175 CEFE; CNRS - Université Montpellier - Université P. Valéry - EPHE; Montpellier Cedex 5 France
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