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Krueger-Hadfield SA. Let's talk about sex: Why reproductive systems matter for understanding algae. JOURNAL OF PHYCOLOGY 2024; 60:581-597. [PMID: 38743848 DOI: 10.1111/jpy.13462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/16/2024]
Abstract
Sex is a crucial process that has molecular, genetic, cellular, organismal, and population-level consequences for eukaryotic evolution. Eukaryotic life cycles are composed of alternating haploid and diploid phases but are constrained by the need to accommodate the phenotypes of these different phases. Critical gaps in our understanding of evolutionary drivers of the diversity in algae life cycles include how selection acts to stabilize and change features of the life cycle. Moreover, most eukaryotes are partially clonal, engaging in both sexual and asexual reproduction. Yet, our understanding of the variation in their reproductive systems is largely based on sexual reproduction in animals or angiosperms. The relative balance of sexual versus asexual reproduction not only controls but also is in turn controlled by standing genetic variability, thereby shaping evolutionary trajectories. Thus, we must quantitatively assess the consequences of the variation in life cycles on reproductive systems. Algae are a polyphyletic group spread across many of the major eukaryotic lineages, providing powerful models by which to resolve this knowledge gap. There is, however, an alarming lack of data about the population genetics of most algae and, therefore, the relative frequency of sexual versus asexual processes. For many algae, the occurrence of sexual reproduction is unknown, observations have been lost in overlooked papers, or data on population genetics do not yet exist. This greatly restricts our ability to forecast the consequences of climate change on algal populations inhabiting terrestrial, aquatic, and marine ecosystems. This perspective summarizes our extant knowledge and provides some future directions to pursue broadly across micro- and macroalgal species.
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Boulanger L, Planchon C, Taudière A, McCoy KD, Burgess STG, Nisbet AJ, Bartley K, Galliot P, Creach P, Sleeckx N, Roy L. The Poultry Red Mite, Dermanyssus gallinae, travels far but not frequently, and takes up permanent residence on farms. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 120:105584. [PMID: 38521481 DOI: 10.1016/j.meegid.2024.105584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/13/2024] [Accepted: 03/15/2024] [Indexed: 03/25/2024]
Abstract
Management of Dermanyssus gallinae, a cosmopolitan hematophagous mite responsible for damage in layer poultry farming, is hampered by a lack of knowledge of its spatio-temporal population dynamics. Previous studies have shown that the circulation of this pest between farms is of strictly anthropogenic origin, that a mitochondrial haplogroup has been expanding on European farms since the beginning of the 21st century and that its local population growth may be particularly rapid. To refine our understanding of how D. gallinae spreads within and among farms, we characterized the genetic structure of mite populations at different spatial scales and sought to identify the main factors interrupting gene flow between poultry houses and between mitochondrial haplogroups. To this end, we selected and validated the first set of nuclear microsatellite markers for D. gallinae and sequenced a region of the CO1-encoding mitochondrial gene in a subsample of microsatellite-genotyped mites. We also tested certain conditions required for effective contamination of a poultry house through field experimentation, and conducted a survey of practices during poultry transfers. Our results confirm the role of poultry transport in the dissemination of mite populations, but the frequency of effective contamination after the introduction of contaminated material into poultry houses seems lower than expected. The high persistence of mites on farms, even during periods when poultry houses are empty and cleaned, and the very large number of nodes in the logistic network (large number of companies supplying pullets or transporting animals) undoubtedly explain the very high prevalence on farms. Substantial genetic diversity was measured in farm populations, probably as a result of the mite's known haplodiploid mode of sexual reproduction, coupled with the dense logistic network. The possibility of the occasional occurrence of asexual reproduction in this sexually reproducing mite was also revealed in our analyses, which could explain the extreme aggressiveness of its demographic dynamics under certain conditions.
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Affiliation(s)
- L Boulanger
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, 1919 route de Mende, 3400 Montpellier, France
| | - C Planchon
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, 1919 route de Mende, 3400 Montpellier, France
| | - A Taudière
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, 1919 route de Mende, 3400 Montpellier, France
| | - K D McCoy
- Université de Montpellier, CNRS, IRD, MIVEGEC, Domaine La Valette - 900, rue Jean François BRETON, 34090 Montpellier, France
| | - S T G Burgess
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian EH26 0PZ, UK
| | - A J Nisbet
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian EH26 0PZ, UK
| | - K Bartley
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian EH26 0PZ, UK
| | - P Galliot
- Institut Technique de l'AVIculture (ITAVI), FranceITAVI, 41 rue Beaucemaine, 22440 Ploufragan, France
| | - P Creach
- Institut Technique de l'AVIculture (ITAVI), FranceITAVI, 41 rue Beaucemaine, 22440 Ploufragan, France
| | - N Sleeckx
- Experimental Poultry Centre, 77 Poiel, Geel 2440, Belgium
| | - Lise Roy
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, 1919 route de Mende, 3400 Montpellier, France.
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Reichel K, Herklotz V, Smolka A, Nybom H, Kellner A, De Riek J, Smulders MJM, Wissemann V, Ritz CM. Untangling the hedge: Genetic diversity in clonally and sexually transmitted genomes of European wild roses, Rosa L. PLoS One 2023; 18:e0292634. [PMID: 37797054 PMCID: PMC10553836 DOI: 10.1371/journal.pone.0292634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/25/2023] [Indexed: 10/07/2023] Open
Abstract
While European wild roses are abundant and widely distributed, their morphological taxonomy is complicated and ambiguous. In particular, the polyploid Rosa section Caninae (dogroses) is characterised by its unusual meiosis, causing simultaneous clonal and sexual transmission of sub-genomes. This hemisexual reproduction, which often co-occurs with vegetative reproduction, defies the standard definition of species boundaries. We analysed seven highly polymorphic microsatellite loci, scored for over 2 600 Rosa samples of differing ploidy, collected across Europe within three independent research projects. Based on their morphology, these samples had been identified as belonging to 21 dogrose and five other native rose species. We quantified the degree of clonality within species and at individual sampling sites. We then compared the genetic structure within our data to current rose morpho-systematics and searched for hemisexually co-inherited sets of alleles at individual loci. We found considerably fewer copies of identical multi-locus genotypes in dogroses than in roses with regular meiosis, with some variation recorded among species. While clonality showed no detectable geographic pattern, some genotypes appeared to be more widespread. Microsatellite data confirmed the current classification of subsections, but they did not support most of the generally accepted dogrose microspecies. Under canina meiosis, we found co-inherited sets of alleles as expected, but could not distinguish between sexually and clonally inherited sub-genomes, with only some of the detected allele combinations being lineage-specific.
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Affiliation(s)
- Katja Reichel
- Institute of Biology, Dahlem Center of Plant Sciences, Freie Universität Berlin, Berlin, Germany
| | - Veit Herklotz
- Department of Botany, Senckenberg Museum for Natural History Görlitz, Senckenberg–Member of the Leibniz Association, Görlitz, Germany
| | - Alisia Smolka
- Institute of Biology, Dahlem Center of Plant Sciences, Freie Universität Berlin, Berlin, Germany
- Department of Botany, Senckenberg Museum for Natural History Görlitz, Senckenberg–Member of the Leibniz Association, Görlitz, Germany
| | - Hilde Nybom
- Department of Plant Breeding, Balsgård, Swedish University of Agricultural Sciences, Kristianstad, Sweden
| | - Alexandra Kellner
- Institute of Botany, Systematic Botany Group, Justus-Liebig-University, Gießen, Germany
| | - Jan De Riek
- Flanders Research Institute for Agricultural, Fisheries and Food Research (ILVO), Plant Sciences Unit, Melle, Belgium
| | | | - Volker Wissemann
- Institute of Botany, Systematic Botany Group, Justus-Liebig-University, Gießen, Germany
| | - Christiane M. Ritz
- Department of Botany, Senckenberg Museum for Natural History Görlitz, Senckenberg–Member of the Leibniz Association, Görlitz, Germany
- International Institute (IHI) Zittau, Chair of Biodiversity of Higher Plants, Technical University Dresden, Zittau, Germany
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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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Gargiulo R, Waples RS, Grow AK, Shefferson RP, Viruel J, Fay MF, Kull T. Effective population size in a partially clonal plant is not predicted by the number of genetic individuals. Evol Appl 2023; 16:750-766. [PMID: 36969138 PMCID: PMC10033856 DOI: 10.1111/eva.13535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/22/2022] [Accepted: 02/02/2023] [Indexed: 02/23/2023] Open
Abstract
Estimating effective population size (N e) is important for theoretical and practical applications in evolutionary biology and conservation. Nevertheless, estimates of N e in organisms with complex life-history traits remain scarce because of the challenges associated with estimation methods. Partially clonal plants capable of both vegetative (clonal) growth and sexual reproduction are a common group of organisms for which the discrepancy between the apparent number of individuals (ramets) and the number of genetic individuals (genets) can be striking, and it is unclear how this discrepancy relates to N e. In this study, we analysed two populations of the orchid Cypripedium calceolus to understand how the rate of clonal versus sexual reproduction affected N e. We genotyped >1000 ramets at microsatellite and SNP loci, and estimated contemporary N e with the linkage disequilibrium method, starting from the theoretical expectation that variance in reproductive success among individuals caused by clonal reproduction and by constraints on sexual reproduction would lower N e. We considered factors potentially affecting our estimates, including different marker types and sampling strategies, and the influence of pseudoreplication in genomic data sets on N e confidence intervals. The magnitude of N e/N ramets and N e/N genets ratios we provide may be used as reference points for other species with similar life-history traits. Our findings demonstrate that N e in partially clonal plants cannot be predicted based on the number of genets generated by sexual reproduction, because demographic changes over time can strongly influence N e. This is especially relevant in species of conservation concern in which population declines may not be detected by only ascertaining the number of genets.
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Affiliation(s)
| | - Robin S. Waples
- NOAA Fisheries, Northwest Fisheries Science Center Seattle Washington USA
- University of Washington Seattle Washington USA
| | - Adri K. Grow
- Department of Biological Sciences Smith College Northampton Massachusetts USA
| | | | | | - Michael F. Fay
- Royal Botanic Gardens, Kew Richmond UK
- School of Biological Sciences University of Western Australia Crawley Western Australia Australia
| | - Tiiu Kull
- Estonian University of Life Sciences Tartu Estonia
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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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Pierre JS, Stoeckel S, Wajnberg E. The advantage of sex: Reinserting fluctuating selection in the pluralist approach. PLoS One 2022; 17:e0272134. [PMID: 35917359 PMCID: PMC9345338 DOI: 10.1371/journal.pone.0272134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 07/13/2022] [Indexed: 11/29/2022] Open
Abstract
The advantage of sex, and its fixation in some clades and species all over the eukaryote tree of life, is considered an evolutionary enigma, especially regarding its assumed two-fold cost. Several likely hypotheses have been proposed such as (1) a better response to the negative frequency-dependent selection imposed by the “Red Queen” hypothesis; (2) the competition between siblings induced by the Tangled Bank hypothesis; (3) the existence of genetic and of (4) ecological factors that can diminish the cost of sex to less than the standard assumed two-fold; and (5) a better maintenance of genetic diversity and its resulting phenotypic variation, providing a selective advantage in randomly fluctuating environments. While these hypotheses have mostly been studied separately, they can also act simultaneously. This was advocated by several studies which presented a pluralist point of view. Only three among the five causes cited above were considered yet in such a framework: the Red Queen hypothesis, the Tangled Bank and the genetic factors lowering the cost of sex. We thus simulated the evolution of a finite mutating population undergoing negative frequency-dependent selection on phenotypes and a two-fold (or less) cost of sexuality, experiencing randomly fluctuating selection along generations. The individuals inherited their reproductive modes, either clonal or sexual. We found that exclusive sexuality begins to fix in populations exposed to environmental variation that exceeds the width of one ecological niche (twice the standard deviation of a Gaussian response to environment). This threshold was lowered by increasing negative frequency-dependent selection and when reducing the two-fold cost of sex. It contributes advocating that the different processes involved in a short-term advantage of sex and recombination can act in combination to favor the fixation of sexual reproduction in populations.
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Affiliation(s)
- Jean-Sébastien Pierre
- UMR 6553 Ecologie Biodiversité Evolution, CNRS INEE, Université de Rennes 1, OSUR, Campus de Beaulieu, Rennes Cedex, France
- * E-mail:
| | - Solenn Stoeckel
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, France
| | - Eric Wajnberg
- INRAE, Sophia Antipolis Cedex, France
- Projet Hephaistos, INRIA, Sophia Antipolis Cedex, France
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Hart MW, Guerra VI, Allen JD, Byrne M. Cloning and Selfing Affect Population Genetic Variation in Simulations of Outcrossing, Sexual Sea Stars. THE BIOLOGICAL BULLETIN 2021; 241:286-302. [PMID: 35015625 DOI: 10.1086/717293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
AbstractMany sea stars are well known for facultative or obligate asexual reproduction in both the adult and larval life-cycle stages. Some species and lineages are also capable of facultative or obligate hermaphroditic reproduction with self-fertilization. However, models of population genetic variation and empirical analyses of genetic data typically assume only sexual reproduction and outcrossing. A recent reanalysis of previously published empirical data (microsatellite genotypes) from two studies of one of the most well-known sea star species (the crown-of-thorns sea star; Acanthaster sp.) concluded that cloning and self-fertilization in that species are rare and contribute little to patterns of population genetic variation. Here we reconsider that conclusion by simulating the contribution of cloning and selfing to genetic variation in a series of models of sea star demography. Simulated variation in two simple models (analogous to previous analyses of empirical data) was consistent with high rates of cloning or selfing or both. More realistic scenarios that characterize population flux in sea stars of ecological significance, including outbreaks of crown-of-thorns sea stars that devastate coral reefs, invasions by Asterias amurensis, and epizootics of sea star wasting disease that kill Pisaster ochraceus, also showed significant but smaller effects of cloning and selfing on variation within subpopulations and differentiation between subpopulations. Future models or analyses of genetic variation in similar study systems might benefit from simulation modeling to characterize possible contributions of cloning or selfing to genetic variation in population samples or to understand the limits on inferring the effects of cloning or selfing in nature.
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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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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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Ryan WH, Aida J, Krueger-Hadfield SA. The Contribution of Clonality to Population Genetic Structure in the Sea Anemone, Diadumene lineata. J Hered 2021; 112:122-139. [PMID: 33507264 DOI: 10.1093/jhered/esaa050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 12/22/2020] [Indexed: 01/06/2023] Open
Abstract
Ecological and evolutionary processes differ depending on how genetic diversity is organized in space. For clonal organisms, the organization of both genetic and genotypic diversity can influence the fitness effects of competition, the mating system, and reproductive mode, which are key drivers of life cycle evolution. Understanding how individual reproductive behavior contributes to population genetic structure is essential for disentangling these forces, particularly in species with complex and plastic life cycles. The widespread sea anemone, Diadumene lineata, exhibits temperature-dependent fission, which contributes to predictable variation in clonal rate along the Atlantic coast of the United States, part of its non-native range. Because warmer conditions lead to higher rates of clonality, we expected to find lower genotypic and genetic diversity in lower versus higher latitude populations. We developed primers for 11 microsatellite loci and genotyped 207 anemones collected from 8 sites ranging from Florida to Massachusetts. We found clonal influence at all sites, and as predicted, the largest clones were found at lower latitude sites. We also found genetic signatures of sex in the parts of the range where gametogenesis is most common. Evidence of sex outside the native range is novel for this species and provides insights into the dynamics of this successful invader. Our findings also illustrate challenges that partially clonal taxa pose for eco-evolutionary studies, such as difficulty sampling statistically robust numbers of genets and interpretating common population genetic metrics. For example, we found high among-locus variation in FIS, which makes the meaning of mean multilocus FIS unclear.
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Affiliation(s)
- Will H Ryan
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL.,Department of Biological Science, Florida State University, Tallahassee, FL
| | - Jaclyn Aida
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL
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