1
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Gutiérrez-Valencia J, Zervakis PI, Postel Z, Fracassetti M, Losvik A, Mehrabi S, Bunikis I, Soler L, Hughes PW, Désamoré A, Laenen B, Abdelaziz M, Pettersson OV, Arroyo J, Slotte T. Genetic Causes and Genomic Consequences of Breakdown of Distyly in Linum trigynum. Mol Biol Evol 2024; 41:msae087. [PMID: 38709782 PMCID: PMC11114476 DOI: 10.1093/molbev/msae087] [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: 11/17/2023] [Revised: 03/22/2024] [Accepted: 04/29/2024] [Indexed: 05/08/2024] Open
Abstract
Distyly is an iconic floral polymorphism governed by a supergene, which promotes efficient pollen transfer and outcrossing through reciprocal differences in the position of sexual organs in flowers, often coupled with heteromorphic self-incompatibility. Distyly has evolved convergently in multiple flowering plant lineages, but has also broken down repeatedly, often resulting in homostylous, self-compatible populations with elevated rates of self-fertilization. Here, we aimed to study the genetic causes and genomic consequences of the shift to homostyly in Linum trigynum, which is closely related to distylous Linum tenue. Building on a high-quality genome assembly, we show that L. trigynum harbors a genomic region homologous to the dominant haplotype of the distyly supergene conferring long stamens and short styles in L. tenue, suggesting that loss of distyly first occurred in a short-styled individual. In contrast to homostylous Primula and Fagopyrum, L. trigynum harbors no fixed loss-of-function mutations in coding sequences of S-linked distyly candidate genes. Instead, floral gene expression analyses and controlled crosses suggest that mutations downregulating the S-linked LtWDR-44 candidate gene for male self-incompatibility and/or anther height could underlie homostyly and self-compatibility in L. trigynum. Population genomic analyses of 224 whole-genome sequences further demonstrate that L. trigynum is highly self-fertilizing, exhibits significantly lower genetic diversity genome-wide, and is experiencing relaxed purifying selection and less frequent positive selection on nonsynonymous mutations relative to L. tenue. Our analyses shed light on the loss of distyly in L. trigynum, and advance our understanding of a common evolutionary transition in flowering plants.
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Affiliation(s)
- Juanita Gutiérrez-Valencia
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Panagiotis-Ioannis Zervakis
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Zoé Postel
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Marco Fracassetti
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Aleksandra Losvik
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Sara Mehrabi
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Ignas Bunikis
- Department of Immunology, Genetics and Pathology, Uppsala Genome Center, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology, Uppsala University, National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - P William Hughes
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Aurélie Désamoré
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Benjamin Laenen
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | | | - Olga Vinnere Pettersson
- Department of Immunology, Genetics and Pathology, Uppsala Genome Center, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Juan Arroyo
- Department of Plant Biology and Ecology, University of Seville, Seville, Spain
| | - Tanja Slotte
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
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2
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Fyon F, Berbel‐Filho WM. Influence of the mutation load on the genomic composition of hybrids between outcrossing and self-fertilizing species. Ecol Evol 2023; 13:e10538. [PMID: 37720059 PMCID: PMC10502466 DOI: 10.1002/ece3.10538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/24/2023] [Accepted: 09/04/2023] [Indexed: 09/19/2023] Open
Abstract
Hybridization is a natural process whereby two diverging evolutionary lineages reproduce and create offspring of mixed ancestry. Differences in mating systems (e.g., self-fertilization and outcrossing) are expected to affect the direction and extent of hybridization and introgression in hybrid zones. Among other factors, selfers and outcrossers are expected to differ in their mutation loads. This has been studied both theoretically and empirically; however, conflicting predictions have been made on the effects mutation loads of parental species with different mating systems can have on the genomic composition of hybrids. Here, we develop a multi-locus, selective model to study how the different mutation load built up in selfers and outcrossers as a result of selective interference and homozygosity impact the long-term genetic composition of hybrid populations. Notably, our results emphasize that genes from the parental population with lesser mutation load get rapidly overrepresented in hybrid genomes, regardless of the hybrids own mating system. When recombination tends to be more important than mutation, outcrossers' genomes tend to be of higher quality and prevail. When recombination rates are low, however, selfers' genomes may reach higher quality than outcrossers' genomes and prevail in the hybrids. Taken together, these results provide concrete insights into one of the multiple factors influencing hybrid genome ancestry and introgression patterns in hybrid zones containing species with different mating systems.
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Affiliation(s)
- Fréderic Fyon
- Department of BiologyRoyal Holloway University of LondonEghamUK
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3
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Inbreeding in Chinese Fir: Insight into the Rare Self-Fertilizing Event from a Genetic View. Genes (Basel) 2022; 13:genes13112105. [DOI: 10.3390/genes13112105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/11/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is a fast-growing conifer with great forestation value and prefers outcrossing with high inbreeding depression effect. Previously, we captured a special Chinese fir parent clone named as ‘cx569’ that lacks early inbreeding depression. In view of the fact that very little has been published about the rare self-fertilizing event in Chinese fir from a genetic view, herein, we conduct an SSR-based study on the variation of open- and self-pollinated offspring of this parent to gain a view of the rare self-fertilizing event. The results indicated that genetic diversity of self-pollinated offspring was significantly reduced by half (Ho: 0.302, vs. 0.595, p = 0.001; He: 0.274 vs. 0.512, p = 0.002) when compared to an open-pollinated set. Self-pollinated offspring also had significantly positive FIS values (FIS = 0.057, p = 0.034) with a much higher proportion of common allele (20.59% vs. 0), reflecting their heterozygote deficiency. Clustering analysis further indicated a separation of the self- and opened- pollinated groups, implying a natural preference of outcrossing for cx569. However, the cx569 still had 6% acceptance for selfing. When accepted 100% for its own pollen, the cx569 led to a genetically unique selfing group. Additionally, this selfing group seemed to be consistently homozygous at seven particular loci. These findings gave us more genetic clues to gain insight into the rare self-fertilizing event in conifer (Chinese fir).
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4
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Yi H, Wang J, Wang J, Rausher M, Kang M. Genomic insights into inter- and intraspecific mating system shifts in Primulina. Mol Ecol 2022; 31:5699-5713. [PMID: 36178058 DOI: 10.1111/mec.16706] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 08/17/2022] [Accepted: 09/21/2022] [Indexed: 01/13/2023]
Abstract
The mating system shift from outcrossing to selfing is one of the most frequent evolutionary trends in flowering plants. However, the genomic consequences of this shift remain poorly understood. Specifically, the relative importance of the demographic and genetic processes causing changes in genetic variation and selection efficacy associated with the evolution of selfing is unclear. Here we sequenced the genomes of two Primulina species with contrasting mating systems: P. eburnea (outcrossing) versus P. tabacum (outcrossing, mixed-mating and selfing populations). Whole-genome resequencing data were used to investigate the genomic consequences of mating system shifts within and between species. We found that highly selfing populations of P. tabacum display loss of genetic diversity, increased deleterious mutations, higher genomic burden and fewer adaptive substitutions. However, compared with outcrossing populations, mixed-mating populations did not display loss of genetic diversity and accumulation of genetic load. We find no evidence of population bottlenecks associated with the shift to selfing, which suggests that the genetic effects of selfing on Ne and possibly linked selection, rather than demographic history, are the primary drivers of diversity reduction in highly selfing populations. Our results highlight the importance of distinguishing the relative contribution of mating system and demography on the genomic consequences associated with mating system evolution in plants.
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Affiliation(s)
- Huiqin Yi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jieyu Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Mark Rausher
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
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5
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Chak STC, Harris SE, Hultgren KM, Duffy JE, Rubenstein DR. Demographic inference provides insights into the extirpation and ecological dominance of eusocial snapping shrimps. J Hered 2022; 113:552-562. [PMID: 35921239 DOI: 10.1093/jhered/esac035] [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: 11/08/2021] [Accepted: 07/27/2022] [Indexed: 11/14/2022] Open
Abstract
Although eusocial animals often achieve ecological dominance in the ecosystems where they occur, many populations are unstable, resulting in local extinction. Both patterns may be linked to the characteristic demography of eusocial species-high reproductive skew and reproductive division of labor support stable effective population sizes that make eusocial groups more competitive in some species, but also lower effective population sizes that increase susceptibility to population collapse in others. Here, we examine the relationship between demography and social organization in Synalpheus snapping shrimps, a group in which eusociality has evolved recently and repeatedly. We show using coalescent demographic modelling that eusocial species have had lower but more stable effective population sizes across 100,000 generations. Our results are consistent with the idea that stable population sizes may enable competitive dominance in eusocial shrimps, but they also suggest that recent population declines are likely caused by eusocial shrimps' heightened sensitivity to environmental changes, perhaps as a result of their low effective population sizes and localized dispersal. Thus, although the unique life histories and demography of eusocial shrimps have likely contributed to their persistence and ecological dominance over evolutionary timescales, these social traits may also make them vulnerable to contemporary environmental change.
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Affiliation(s)
- Solomon T C Chak
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA.,Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, USA.,Department of Biological Sciences, SUNY College at Old Westbury, Old Westbury, NY, USA
| | - Stephen E Harris
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA.,Biology Department, SUNY Purchase College, Purchase, NY, USA
| | | | - J Emmett Duffy
- Tennenbaum Marine Observatories Network, Smithsonian Institution, Edgewater, MD, USA
| | - Dustin R Rubenstein
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
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6
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David P, Degletagne C, Saclier N, Jennan A, Jarne P, Plénet S, Konecny L, François C, Guéguen L, Garcia N, Lefébure T, Luquet E. Extreme mitochondrial DNA divergence underlies genetic conflict over sex determination. Curr Biol 2022; 32:2325-2333.e6. [PMID: 35483362 DOI: 10.1016/j.cub.2022.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/28/2022] [Accepted: 04/06/2022] [Indexed: 01/06/2023]
Abstract
Cytoplasmic male sterility (CMS) is a form of genetic conflict over sex determination that results from differences in modes of inheritance between genomic compartments.1-3 Indeed, maternally transmitted (usually mitochondrial) genes sometimes enhance their transmission by suppressing the male function in a hermaphroditic organism to the detriment of biparentally inherited nuclear genes. Therefore, these hermaphrodites become functionally female and may coexist with regular hermaphrodites in so-called gynodioecious populations.3 CMS has been known in plants since Darwin's times4 but is previously unknown in the animal kingdom.5-8 We relate the first observation of CMS in animals. It occurs in a freshwater snail population, where some individuals appear unable to sire offspring in controlled crosses and show anatomical, physiological, and behavioral characters consistent with a suppression of the male function. Male sterility is associated with a mitochondrial lineage that underwent a spectacular acceleration of DNA substitution rates, affecting the entire mitochondrial genome-this acceleration concerns both synonymous and non-synonymous substitutions and therefore results from increased mitogenome mutation rates. Consequently, mitochondrial haplotype divergence within the population is exceptionally high, matching that observed between snail taxa that diverged 475 million years ago. This result is reminiscent of similar accelerations in mitogenome evolution observed in plant clades where gynodioecy is frequent,9,10 both being consistent with arms-race evolution of genome regions implicated in CMS.11,12 Our study shows that genomic conflicts can trigger independent evolution of similar sex-determination systems in plants and animals and dramatically accelerate molecular evolution.
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Affiliation(s)
- Patrice David
- CEFE, CNRS, University of Montpellier, IRD, EPHE, Montpellier, France.
| | - Cyril Degletagne
- University of Lyon, CNRS, ENTPE, UMR5023 LEHNA, 69622 Villeurbanne, France
| | | | - Aurel Jennan
- University of Lyon, CNRS, ENTPE, UMR5023 LEHNA, 69622 Villeurbanne, France
| | - Philippe Jarne
- CEFE, CNRS, University of Montpellier, IRD, EPHE, Montpellier, France
| | - Sandrine Plénet
- University of Lyon, CNRS, ENTPE, UMR5023 LEHNA, 69622 Villeurbanne, France
| | - Lara Konecny
- University of Lyon, CNRS, ENTPE, UMR5023 LEHNA, 69622 Villeurbanne, France
| | | | - Laurent Guéguen
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Noéline Garcia
- University of Lyon, CNRS, ENTPE, UMR5023 LEHNA, 69622 Villeurbanne, France
| | - Tristan Lefébure
- University of Lyon, CNRS, ENTPE, UMR5023 LEHNA, 69622 Villeurbanne, France
| | - Emilien Luquet
- University of Lyon, CNRS, ENTPE, UMR5023 LEHNA, 69622 Villeurbanne, France
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7
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Abstract
The nearly neutral theory is a common framework to describe natural selection at the molecular level. This theory emphasizes the importance of slightly deleterious mutations by recognizing their ability to segregate and eventually get fixed due to genetic drift in spite of the presence of purifying selection. As genetic drift is stronger in smaller than in larger populations, a correlation between population size and molecular measures of natural selection is expected within the nearly neutral theory. However, this hypothesis was originally formulated under equilibrium conditions. As most natural populations are not in equilibrium, testing the relationship empirically may lead to confounded outcomes. Demographic nonequilibria, for instance following a change in population size, are common scenarios that are expected to push the selection–drift relationship off equilibrium. By explicitly modeling the effects of a change in population size on allele frequency trajectories in the Poisson random field framework, we obtain analytical solutions of the nonstationary allele frequency spectrum. This enables us to derive exact results of measures of natural selection and effective population size in a demographic nonequilibrium. The study of their time-dependent relationship reveals a substantial deviation from the equilibrium selection–drift balance after a change in population size. Moreover, we show that the deviation is sensitive to the combination of different measures. These results therefore constitute relevant tools for empirical studies to choose suitable measures for investigating the selection–drift relationship in natural populations. Additionally, our new modeling approach extends existing population genetics theory and can serve as foundation for methodological developments.
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Affiliation(s)
- Rebekka Müller
- Department of Mathematics, Uppsala University, 752 37 Uppsala, Sweden
| | - Ingemar Kaj
- Department of Mathematics, Uppsala University, 752 37 Uppsala, Sweden
| | - Carina F. Mugal
- Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden
- Corresponding author: E-mail:
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8
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Wang XJ, Barrett SCH, Zhong L, Wu ZK, Li DZ, Wang H, Zhou W. The Genomic Selfing Syndrome Accompanies the Evolutionary Breakdown of Heterostyly. Mol Biol Evol 2021; 38:168-180. [PMID: 32761213 PMCID: PMC7782863 DOI: 10.1093/molbev/msaa199] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The evolutionary transition from outcrossing to selfing can have important genomic consequences. Decreased effective population size and the reduced efficacy of selection are predicted to play an important role in the molecular evolution of the genomes of selfing species. We investigated evidence for molecular signatures of the genomic selfing syndrome using 66 species of Primula including distylous (outcrossing) and derived homostylous (selfing) taxa. We complemented our comparative analysis with a microevolutionary study of P. chungensis, which is polymorphic for mating system and consists of both distylous and homostylous populations. We generated chloroplast and nuclear genomic data sets for distylous, homostylous, and distylous–homostylous species and identified patterns of nonsynonymous to synonymous divergence (dN/dS) and polymorphism (πN/πS) in species or lineages with contrasting mating systems. Our analysis of coding sequence divergence and polymorphism detected strongly reduced genetic diversity and heterozygosity, decreased efficacy of purifying selection, purging of large-effect deleterious mutations, and lower rates of adaptive evolution in samples from homostylous compared with distylous populations, consistent with theoretical expectations of the genomic selfing syndrome. Our results demonstrate that self-fertilization is a major driver of molecular evolutionary processes with genomic signatures of selfing evident in both old and relatively young homostylous populations.
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Affiliation(s)
- Xin-Jia Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Li Zhong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhi-Kun Wu
- Department of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - De-Zhu Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Hong Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Wei Zhou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
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9
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Systematics and geographical distribution of Galba species, a group of cryptic and worldwide freshwater snails. Mol Phylogenet Evol 2020; 157:107035. [PMID: 33285288 DOI: 10.1016/j.ympev.2020.107035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 09/18/2020] [Accepted: 11/30/2020] [Indexed: 01/06/2023]
Abstract
Cryptic species can present a significant challenge to the application of systematic and biogeographic principles, especially if they are invasive or transmit parasites or pathogens. Detecting cryptic species requires a pluralistic approach in which molecular markers facilitate the detection of coherent taxonomic units that can then be analyzed using various traits (e.g., internal morphology) and crosses. In asexual or self-fertilizing species, the latter criteria are of limited use. We studied a group of cryptic freshwater snails (genus Galba) from the family Lymnaeidae that have invaded almost all continents, reproducing mainly by self-fertilization and transmitting liver flukes to humans and livestock. We aim to clarify the systematics, distribution, and phylogeny of these species with an integrative approach that includes morphology, molecular markers, wide-scale sampling across America, and data retrieved from GenBank (to include Old World samples). Our phylogenetic analysis suggests that the genus Galba originated ca. 22 Myr ago and today comprises six species or species complexes. Four of them show an elongated-shell cryptic phenotype and exhibit wide variation in their genetic diversity, geographic distribution, and invasiveness. The remaining two species have more geographically restricted distributions and exhibit a globose-shell cryptic phenotype, most likely phylogenetically derived from the elongated one. We emphasize that no Galba species should be identified without molecular markers. We also discuss several hypotheses that can explain the origin of cryptic species in Galba, such as convergence and morphological stasis.
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10
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Kočí J, Röslein J, Pačes J, Kotusz J, Halačka K, Koščo J, Fedorčák J, Iakovenko N, Janko K. No evidence for accumulation of deleterious mutations and fitness degradation in clonal fish hybrids: Abandoning sex without regrets. Mol Ecol 2020; 29:3038-3055. [PMID: 32627290 PMCID: PMC7540418 DOI: 10.1111/mec.15539] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/18/2020] [Accepted: 06/22/2020] [Indexed: 02/07/2023]
Abstract
Despite its inherent costs, sexual reproduction is ubiquitous in nature, and the mechanisms to protect it from a competitive displacement by asexuality remain unclear. Popular mutation-based explanations, like the Muller's ratchet and the Kondrashov's hatchet, assume that purifying selection may not halt the accumulation of deleterious mutations in the nonrecombining genomes, ultimately leading to their degeneration. However, empirical evidence is scarce and it remains particularly unclear whether mutational degradation proceeds fast enough to ensure the decay of clonal organisms and to prevent them from outcompeting their sexual counterparts. To test this hypothesis, we jointly analysed the exome sequences and the fitness-related phenotypic traits of the sexually reproducing fish species and their clonal hybrids, whose evolutionary ages ranged from F1 generations to 300 ky. As expected, mutations tended to accumulate in the clonal genomes in a time-dependent manner. However, contrary to the predictions, we found no trend towards increased nonsynonymity of mutations acquired by clones, nor higher radicality of their amino acid substitutions. Moreover, there was no evidence for fitness degeneration in the old clones compared with that in the younger ones. In summary, although an efficacy of purifying selection may still be reduced in the asexual genomes, our data indicate that its efficiency is not drastically decreased. Even the oldest investigated clone was found to be too young to suffer fitness consequences from a mutation accumulation. This suggests that mechanisms other than mutation accumulation may be needed to explain the competitive advantage of sex in the short term.
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Affiliation(s)
- Jan Kočí
- Department of Biology and Ecology, University of Ostrava, Ostrava, Czechia.,Institute of Animal Physiology and Genetics, Czech Academy of Science, Liběchov, Czechia
| | - Jan Röslein
- Department of Biology and Ecology, University of Ostrava, Ostrava, Czechia.,Institute of Animal Physiology and Genetics, Czech Academy of Science, Liběchov, Czechia
| | - Jan Pačes
- Institute of Animal Physiology and Genetics, Czech Academy of Science, Liběchov, Czechia.,Institute of Molecular Genetics, Czech Academy of Science, Prague, Czechia
| | - Jan Kotusz
- Museum of Natural History, University of Wrocław, Wrocław, Poland
| | - Karel Halačka
- Institute of Vertebrate Biology, Czech Academy of Science, Brno, Czechia
| | - Ján Koščo
- Department of Ecology, University of Prešov, Prešov, Slovakia
| | - Jakub Fedorčák
- Department of Ecology, University of Prešov, Prešov, Slovakia
| | - Nataliia Iakovenko
- Department of Biology and Ecology, University of Ostrava, Ostrava, Czechia.,Institute of Animal Physiology and Genetics, Czech Academy of Science, Liběchov, Czechia
| | - Karel Janko
- Department of Biology and Ecology, University of Ostrava, Ostrava, Czechia.,Institute of Animal Physiology and Genetics, Czech Academy of Science, Liběchov, Czechia
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11
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Cutter AD. Reproductive transitions in plants and animals: selfing syndrome, sexual selection and speciation. THE NEW PHYTOLOGIST 2019; 224:1080-1094. [PMID: 31336389 DOI: 10.1111/nph.16075] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 07/17/2019] [Indexed: 05/23/2023]
Abstract
The evolution of predominant self-fertilisation frequently coincides with the evolution of a collection of phenotypes that comprise the 'selfing syndrome', in both plants and animals. Genomic features also display a selfing syndrome. Selfing syndrome traits often involve changes to male and female reproductive characters that were subject to sexual selection and sexual conflict in the obligatorily outcrossing ancestor, including the gametic phase for both plants and animals. Rapid evolution of reproductive traits, due to both relaxed selection and directional selection under the new status of predominant selfing, lays the genetic groundwork for reproductive isolation. Consequently, shifts in sexual selection pressures coupled to transitions to selfing provide a powerful paradigm for investigating the speciation process. Plant and animal studies, however, emphasise distinct selective forces influencing reproductive-mode transitions: genetic transmission advantage to selfing or reproductive assurance outweighing the costs of inbreeding depression vs the costs of males and meiosis. Here, I synthesise links between sexual selection, evolution of selfing and speciation, with particular focus on identifying commonalities and differences between plant and animal systems and pointing to areas warranting further synergy.
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Affiliation(s)
- Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
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12
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Ho EKH, Bartkowska M, Wright SI, Agrawal AF. Population genomics of the facultatively asexual duckweed Spirodela polyrhiza. THE NEW PHYTOLOGIST 2019; 224:1361-1371. [PMID: 31298732 DOI: 10.1111/nph.16056] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/18/2019] [Indexed: 06/10/2023]
Abstract
Clonal propagation allows some plant species to achieve massive population sizes quickly but also reduces the evolutionary independence of different sites in the genome. We examine genome-wide genetic diversity in Spirodela polyrhiza, a duckweed that reproduces primarily asexually. We find that this geographically widespread and numerically abundant species has very low levels of genetic diversity. Diversity at nonsynonymous sites relative to synonymous sites is high, suggesting that purifying selection is weak. A potential explanation for this observation is that a very low frequency of sex renders selection ineffective. However, there is a pronounced decay in linkage disequilibrium over 40 kb, suggesting that though sex may be rare at the individual level it is not too infrequent at the population level. In addition, neutral diversity is affected by the physical proximity of selected sites, which would be unexpected if sex was exceedingly rare at the population level. The amount of genetic mixing as assessed by the decay in linkage disequilibrium is not dissimilar from selfing species such as Arabidopsis thaliana, yet selection appears to be much less effective in duckweed. We discuss alternative explanations for the signature of weak purifying selection.
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Affiliation(s)
- Eddie K H Ho
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Magdalena Bartkowska
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
- Center for Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Aneil F Agrawal
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
- Center for Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
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13
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Martin H, Carpentier F, Gallina S, Godé C, Schmitt E, Muyle A, Marais GAB, Touzet P. Evolution of Young Sex Chromosomes in Two Dioecious Sister Plant Species with Distinct Sex Determination Systems. Genome Biol Evol 2019; 11:350-361. [PMID: 30649306 PMCID: PMC6364797 DOI: 10.1093/gbe/evz001] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2019] [Indexed: 12/14/2022] Open
Abstract
In the last decade, progress has been made in methods to identify the sex determination system in plants. This gives the opportunity to study sex chromosomes that arose independently at different phylogenetic scales, and thus allows the discovery and the understanding of early stages of sex chromosome evolution. In the genus Silene, sex chromosomes have evolved independently in at least two clades from a nondioecious ancestor, the Melandrium and Otites sections. In the latter, sex chromosomes could be younger than in the section Melandrium, based on phylogenetic studies and as no heteromorphic sex chromosomes have been detected. This section might also exhibit lability in sex determination, because male heterogamy and female heterogamy have been suggested to occur. In this study, we investigated the sex determination system of two dioecious species in the section Otites (Silene otites and its close relative Silene pseudotites). Applying the new probabilistic method SEX-DETector on RNA-seq data from cross-controlled progenies, we inferred their most likely sex determination system and a list of putative autosomal and sex-linked contigs. We showed that the two phylogenetically close species differed in their sex determination system (XY versus ZW) with sex chromosomes that derived from two different pairs of autosomes. We built a genetic map of the sex chromosomes and showed that both pairs exhibited a large region with lack of recombination. However, the sex-limited chromosomes exhibited no strong degeneration. Finally, using the “ancestral” autosomal expression of sex-linked orthologs of nondioecious S. nutans, we found a slight signature of dosage compensation in the heterogametic females of S. otites.
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Affiliation(s)
- Hélène Martin
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, France.,Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Fantin Carpentier
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, France.,Ecologie Systématique Evolution, Université Paris Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | | | - Cécile Godé
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, France
| | - Eric Schmitt
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, France
| | - Aline Muyle
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France.,Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine
| | - Gabriel A B Marais
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
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14
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Abstract
A major current molecular evolution challenge is to link comparative genomic patterns to species' biology and ecology. Breeding systems are pivotal because they affect many population genetic processes and thus genome evolution. We review theoretical predictions and empirical evidence about molecular evolutionary processes under three distinct breeding systems-outcrossing, selfing, and asexuality. Breeding systems may have a profound impact on genome evolution, including molecular evolutionary rates, base composition, genomic conflict, and possibly genome size. We present and discuss the similarities and differences between the effects of selfing and clonality. In reverse, comparative and population genomic data and approaches help revisiting old questions on the long-term evolution of breeding systems.
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Affiliation(s)
- Sylvain Glémin
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France
| | - Clémentine M François
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France
| | - Nicolas Galtier
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France.
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15
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Ho EKH, Agrawal AF. Mutation accumulation in selfing populations under fluctuating selection. Evolution 2018; 72:1759-1772. [DOI: 10.1111/evo.13553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 06/26/2018] [Accepted: 07/01/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Eddie K. H. Ho
- Department of Ecology and Evolutionary Biology University of Toronto 25 Willcocks Street Toronto ON M5S 3B2 Canada
| | - Aneil F. Agrawal
- Department of Ecology and Evolutionary Biology University of Toronto 25 Willcocks Street Toronto ON M5S 3B2 Canada
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16
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Petrone Mendoza S, Lascoux M, Glémin S. Competitive ability of Capsella species with different mating systems and ploidy levels. ANNALS OF BOTANY 2018; 121:1257-1264. [PMID: 29471370 PMCID: PMC5946883 DOI: 10.1093/aob/mcy014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 01/19/2018] [Indexed: 05/31/2023]
Abstract
BACKGROUND AND AIMS Capsella is a model genus for studying the transition from outcrossing to selfing, with or without change in ploidy levels. The genomic consequences and changes in reproductive traits (selfing syndrome) associated with these shifts have been studied in depth. However, potential ecological divergence among species of the genus has not been determined. Among ecological traits, competitive ability could be relevant for selfing evolution, as selfing has been shown to be statistically associated with reduced competitiveness in a recent meta-analysis. METHODS We assessed the effect of competition on three Capsella species differing in their mating system and ploidy level. We used an experimental design where fitness related traits were measured in focal individuals with and without competitors. KEY RESULTS The diploid selfer (C. rubella) was most sensitive to competition, whereas the tetraploid selfer (C. bursa-pastoris) performed the best, with the diploid outcrosser (C. grandiflora) being intermediate. CONCLUSIONS These results add to the detailed characterization of Capsella species and highlight the possible roles of ecological context and ploidy in the evolutionary trajectories of selfing species.
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Affiliation(s)
- Sandra Petrone Mendoza
- Department of Ecology and Genetics, Evolutionary Biology Center and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Center and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sylvain Glémin
- Department of Ecology and Genetics, Evolutionary Biology Center and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Institut des Sciences de l’Evolution (ISEM - UMR 5554 Université de Montpellier-CNRS-IRD-EPHE), France
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17
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Lounnas M, Correa A, Alda P, David P, Dubois MP, Calvopiña M, Caron Y, Celi-Erazo M, Dung B, Jarne P, Loker E, Noya O, Rodríguez-Hidalgo R, Toty C, Uribe N, Pointier JP, Hurtrez-Boussès S. Population structure and genetic diversity in the invasive freshwater snail Galba schirazensis (Lymnaeidae). CAN J ZOOL 2018. [DOI: 10.1139/cjz-2016-0319] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We studied the population genetic structure of the freshwater snail Galba schirazensis (Küster, 1862), a potential vector of infectious diseases such as fascioliasis. Galba schirazensis has now a worldwide distribution but a poorly known origin because this species has been distinguished only recently from the morphologically similar and cosmopolitan Galba truncatula (O.F. Müller, 1774). We developed specific microsatellite markers and sequenced a mitochondrial gene (cytochrome oxidase subunit I (CO1)) to study individuals of G. schirazensis from the Old World and the New World. We found very low genetic diversity within populations, no heterozygotes, and marked population structure — a pattern observed in other highly selfing lymnaeid species with recently enlarged distributions as a result of biological invasions. The total lack of observed heterozygosity in the few populations of G. schirazensis that displayed some allelic diversity suggests high selfing rates. We also found that the center of diversity, and by extension the origin area of this species, should be found in the New World, whereas Old World populations should rather result from a recent introduction of a genetically uniform population. The microsatellite markers developed here will help to clarify the history of expansion of G. schirazensis and might help to understand its role as a potential vector of infectious diseases.
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Affiliation(s)
- M. Lounnas
- MIVEGEC, UMR UM – CNRS 5290 – IRD 224 Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle, Centre IRD, BP 64501, 34394 Montpellier CEDEX 5, France
| | - A.C. Correa
- MIVEGEC, UMR UM – CNRS 5290 – IRD 224 Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle, Centre IRD, BP 64501, 34394 Montpellier CEDEX 5, France
| | - P. Alda
- MIVEGEC, UMR UM – CNRS 5290 – IRD 224 Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle, Centre IRD, BP 64501, 34394 Montpellier CEDEX 5, France
- Laboratorio de Zoología de Invertebrados I, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, San Juan No. 670, B8000ICN, Bahía Blanca, Buenos Aires, Argentina
| | - P. David
- Centre d’Ecologie Fonctionnelle et d’Evolution, UMR 5175, CNRS – Université de Montpellier – Université Paul Valéry Montpellier – EPHE, 1919 route de Mende, 34293 Montpellier CEDEX 5, France
| | - M.-P. Dubois
- Centre d’Ecologie Fonctionnelle et d’Evolution, UMR 5175, CNRS – Université de Montpellier – Université Paul Valéry Montpellier – EPHE, 1919 route de Mende, 34293 Montpellier CEDEX 5, France
| | - M. Calvopiña
- Carrera de Medicina, Facultad de Ciencias Médicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Y. Caron
- Research Unit in Parasitology and Parasitic Diseases, Fundamental and Applied Research for Animals and Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Belgium
| | | | - B.T. Dung
- Research Unit in Parasitology and Parasitic Diseases, Fundamental and Applied Research for Animals and Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Belgium
| | - P. Jarne
- Centre d’Ecologie Fonctionnelle et d’Evolution, UMR 5175, CNRS – Université de Montpellier – Université Paul Valéry Montpellier – EPHE, 1919 route de Mende, 34293 Montpellier CEDEX 5, France
| | - E.S. Loker
- Center for Evolutionary and Theoretical Immunology, Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - O. Noya
- Centro para Estudios Sobre Malaria, Instituto de Altos Estudios “Dr. Arnoldo Gabaldón” – Instituto Nacional de Higiene “Rafael Rangel” del Ministerio del Poder Popular para la Salud y Sección de Biohelmintiasis, Instituto de Medicina Tropical, Facultad de Medicina, Universidad Central de Venezuela, Caracas, Venezuela
| | - R. Rodríguez-Hidalgo
- CIZ, Universidad Central de Ecuador, Quito, Ecuador
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Central del Ecuador, Quito, Ecuador
| | - C. Toty
- MIVEGEC, UMR UM – CNRS 5290 – IRD 224 Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle, Centre IRD, BP 64501, 34394 Montpellier CEDEX 5, France
| | - N. Uribe
- Escuela de Bacteriología y Laboratorio Clínico, Facultad de Salud, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - J.-P. Pointier
- USR 3278 CNRS–EPHE, CRIOBE Université de Perpignan, 68860 Perpignan-CEDEX, France
| | - S. Hurtrez-Boussès
- MIVEGEC, UMR UM – CNRS 5290 – IRD 224 Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle, Centre IRD, BP 64501, 34394 Montpellier CEDEX 5, France
- Département de Biologie–Ecologie, Faculté des Sciences, Université Montpellier, 34095 Montpellier CEDEX 5, France
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18
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Lins LS, Trojahn S, Sockell A, Yee MC, Tatarenkov A, Bustamante CD, Earley RL, Kelley JL. Whole-genome sequencing reveals the extent of heterozygosity in a preferentially self-fertilizing hermaphroditic vertebrate. Genome 2018; 61:241-247. [DOI: 10.1139/gen-2017-0188] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The mangrove rivulus, Kryptolebias marmoratus, is one of only two self-fertilizing hermaphroditic fish species and inhabits mangrove forests. While selfing can be advantageous, it reduces heterozygosity and decreases genetic diversity. Studies using microsatellites found that there are variable levels of selfing among populations of K. marmoratus, but overall, there is a low rate of outcrossing and, therefore, low heterozygosity. In this study, we used whole-genome data to assess the levels of heterozygosity in different lineages of the mangrove rivulus and infer the phylogenetic relationships among those lineages. We sequenced whole genomes from 15 lineages that were completely homozygous at microsatellite loci and used single nucleotide polymorphisms (SNPs) to determine heterozygosity levels. More variation was uncovered than in studies using microsatellite data because of the resolution of full genome sequencing data. Moreover, missense polymorphisms were found most often in genes associated with immune function and reproduction. Inferred phylogenetic relationships suggest that lineages largely group by their geographic distribution. The use of whole-genome data provided further insight into genetic diversity in this unique species. Although this study was limited by the number of lineages that were available, these data suggest that there is previously undescribed variation within lineages of K. marmoratus that could have functional consequences and (or) inform us about the limits to selfing (e.g., genetic load, accumulation of deleterious mutations) and selection that might favor the maintenance of heterozygosity. These results highlight the need to sequence additional individuals within and among lineages.
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Affiliation(s)
- Luana S.F. Lins
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, 100 Dairy Road, Pullman, WA 99164, USA
| | - Shawn Trojahn
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, 100 Dairy Road, Pullman, WA 99164, USA
| | - Alexandra Sockell
- Department of Genetics, Stanford University, 300 Pasteur Dr., Stanford, CA 94305, USA
| | - Muh-Ching Yee
- Stanford Functional Genomics Facility, Stanford University, CCSR 0120, 269 Campus Drive, Stanford, CA 94305, USA
| | - Andrey Tatarenkov
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
| | - Carlos D. Bustamante
- Department of Genetics, Stanford University, 300 Pasteur Dr., Stanford, CA 94305, USA
- Department of Biomedical Data Science, Stanford University, 365 Lasuen Street, Littlefield Center, Room 303, Stanford, CA 94305, USA
| | - Ryan L. Earley
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Joanna L. Kelley
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, 100 Dairy Road, Pullman, WA 99164, USA
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19
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Abu Awad D, Roze D. Effects of partial selfing on the equilibrium genetic variance, mutation load, and inbreeding depression under stabilizing selection. Evolution 2018; 72:751-769. [DOI: 10.1111/evo.13449] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/17/2018] [Indexed: 01/06/2023]
Affiliation(s)
| | - Denis Roze
- CNRS; UMI 3614 Evolutionary Biology and Ecology of Algae,; 29688 Roscoff France
- Sorbonne Universités; UPMC Université Paris VI,; 29688 Roscoff France
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20
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Valfort AC, Launay C, Sémon M, Delattre M. Evolution of mitotic spindle behavior during the first asymmetric embryonic division of nematodes. PLoS Biol 2018; 16:e2005099. [PMID: 29357348 PMCID: PMC5794175 DOI: 10.1371/journal.pbio.2005099] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 02/01/2018] [Accepted: 01/03/2018] [Indexed: 01/08/2023] Open
Abstract
Asymmetric cell division is essential to generate cellular diversity. In many animal cells, the cleavage plane lies perpendicular to the mitotic spindle, and it is the spindle positioning that dictates the size of the daughter cells. Although some properties of spindle positioning are conserved between distantly related model species and different cell types, little is known of the evolutionary robustness of the mechanisms underlying this event. We recorded the first embryonic division of 42 species of nematodes closely related to Caenorhabditis elegans, which is an excellent model system to study the biophysical properties of asymmetric spindle positioning. Our recordings, corresponding to 128 strains from 27 Caenorhabditis and 15 non-Caenorhabditis species (accessible at http://www.ens-lyon.fr/LBMC/NematodeCell/videos/), constitute a powerful collection of subcellular phenotypes to study the evolution of various cellular processes across species. In the present work, we analyzed our collection to the study of asymmetric spindle positioning. Although all the strains underwent an asymmetric first cell division, they exhibited large intra- and inter-species variations in the degree of cell asymmetry and in several parameters controlling spindle movement, including spindle oscillation, elongation, and displacement. Notably, these parameters changed frequently during evolution with no apparent directionality in the species phylogeny, with the exception of spindle transverse oscillations, which were an evolutionary innovation at the base of the Caenorhabditis genus. These changes were also unrelated to evolutionary variations in embryo size. Importantly, spindle elongation, displacement, and oscillation each evolved independently. This finding contrasts starkly with expectations based on C. elegans studies and reveals previously unrecognized evolutionary changes in spindle mechanics. Collectively, these data demonstrate that, while the essential process of asymmetric cell division has been conserved over the course of nematode evolution, the underlying spindle movement parameters can combine in various ways. Like other developmental processes, asymmetric cell division is subject to system drift.
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Affiliation(s)
- Aurore-Cécile Valfort
- Department of Pharmacology & Physiology (Colin Flaveny lab), Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Caroline Launay
- UnivLyon, ENS de Lyon, Univ Claude Bernard, Laboratory of Biology and Modelling of the Cell, Lyon University, Lyon, France
| | - Marie Sémon
- UnivLyon, ENS de Lyon, Univ Claude Bernard, Laboratory of Biology and Modelling of the Cell, Lyon University, Lyon, France
| | - Marie Delattre
- UnivLyon, ENS de Lyon, Univ Claude Bernard, Laboratory of Biology and Modelling of the Cell, Lyon University, Lyon, France
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21
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Correa AC, De Meeûs T, Dreyfuss G, Rondelaud D, Hurtrez-Boussès S. Galba truncatula and Fasciola hepatica: Genetic costructures and interactions with intermediate host dispersal. INFECTION GENETICS AND EVOLUTION 2017; 55:186-194. [PMID: 28917540 DOI: 10.1016/j.meegid.2017.09.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 09/12/2017] [Accepted: 09/12/2017] [Indexed: 12/07/2022]
Abstract
Antagonistic interactions between hosts and parasites are key structuring forces in natural populations. Demographic factors like extinction, migration and the effective population size shape host-parasite metapopulational dynamics. Therefore, to understand the evolution of host-parasite systems it is necessary to study the distribution of the genetic variation of both entities simultaneously. In this paper, we investigate the population genetics co-structure of parasites and hosts within a metapopulation of the liver fluke, Fasciola hepatica, and two of its intermediate hosts, the main intermediate host in Europe, Galba truncatula, and a new intermediate host, Omphiscola glabra, in Central France. Our results reveal an absence of specificity of flukes as regard to the two alternative hosts though O. glabra shows higher prevalence of F. hepatica. Host and parasites displayed contrasting population genetics structure with very small, highly inbred (selfing) and strongly isolated G. truncatula populations and much bigger, panmictic and more dispersive F. hepatica. This could indicate a local adaptation of the parasite and a local maladaptation of the host. We also unveil a parasite-mediated biased population genetics structure suggesting that infected G. truncatula disperse more; have higher dispersal survival than uninfected snails or, more likely, that immigrant snails are infected more often than local snails (local parasites are less adapted to local hosts). Finally, an absence, or at least an ambiguous signature of isolation by distance was observed in both host and parasite population. A very weak migration rate for G. truncatula provides a reasonable explanation for this ambiguous result. Alternatively, smaller sample sizes combined with modest migration rates might explain the difficulties to unveil the signal in F. hepatica.
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Affiliation(s)
- Ana C Correa
- Mivegec UMR UM, CNRS 5290 - IRD 224 Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, Centre IRD, BP 64501, 34394 Montpellier Cedex 5, France
| | - Thierry De Meeûs
- IRD, UMR Interactions hôtes - vecteurs - parasites dans les infections par des trypanosomatidae - (Intertryp) UMR IRD 177, CIRAD 17, TA A-17/G, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France.
| | - Gilles Dreyfuss
- Inserm 1094, Facultés de Médecine et de Pharmacie, Limoges, 2 Rue du Docteur Raymond Marcland, 87025 Limoges, France
| | - Daniel Rondelaud
- Inserm 1094, Facultés de Médecine et de Pharmacie, Limoges, 2 Rue du Docteur Raymond Marcland, 87025 Limoges, France
| | - Sylvie Hurtrez-Boussès
- Mivegec UMR UM, CNRS 5290 - IRD 224 Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, Centre IRD, BP 64501, 34394 Montpellier Cedex 5, France; Département de Biologie-Ecologie, Faculté des Sciences, Université Montpellier, 34095 Montpellier Cedex 5, France
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22
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Pellissier L, Kostikova A, Litsios G, Salamin N, Alvarez N. High Rate of Protein Coding Sequence Evolution and Species Diversification in the Lycaenids. Front Ecol Evol 2017. [DOI: 10.3389/fevo.2017.00090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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23
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Settepani V, Schou MF, Greve M, Grinsted L, Bechsgaard J, Bilde T. Evolution of sociality in spiders leads to depleted genomic diversity at both population and species levels. Mol Ecol 2017; 26:4197-4210. [DOI: 10.1111/mec.14196] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 04/06/2017] [Accepted: 04/10/2017] [Indexed: 12/21/2022]
Affiliation(s)
- V. Settepani
- Department of Bioscience; Aarhus University; Aarhus C Denmark
| | - M. F. Schou
- Department of Bioscience; Aarhus University; Aarhus C Denmark
| | - M. Greve
- Department of Plant Science; University of Pretoria; Hatfield South Africa
| | - L. Grinsted
- School of Biological Sciences; Royal Holloway University of London; Egham UK
| | - J. Bechsgaard
- Department of Bioscience; Aarhus University; Aarhus C Denmark
| | - T. Bilde
- Department of Bioscience; Aarhus University; Aarhus C Denmark
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24
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Szövényi P, Ullrich KK, Rensing SA, Lang D, van Gessel N, Stenøien HK, Conti E, Reski R. Selfing in Haploid Plants and Efficacy of Selection: Codon Usage Bias in the Model Moss Physcomitrella patens. Genome Biol Evol 2017; 9:1528-1546. [PMID: 28549175 PMCID: PMC5507605 DOI: 10.1093/gbe/evx098] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2017] [Indexed: 12/15/2022] Open
Abstract
A long-term reduction in effective population size will lead to major shift in genome evolution. In particular, when effective population size is small, genetic drift becomes dominant over natural selection. The onset of self-fertilization is one evolutionary event considerably reducing effective size of populations. Theory predicts that this reduction should be more dramatic in organisms capable for haploid than for diploid selfing. Although theoretically well-grounded, this assertion received mixed experimental support. Here, we test this hypothesis by analyzing synonymous codon usage bias of genes in the model moss Physcomitrella patens frequently undergoing haploid selfing. In line with population genetic theory, we found that the effect of natural selection on synonymous codon usage bias is very weak. Our conclusion is supported by four independent lines of evidence: 1) Very weak or nonsignificant correlation between gene expression and codon usage bias, 2) no increased codon usage bias in more broadly expressed genes, 3) no evidence that codon usage bias would constrain synonymous and nonsynonymous divergence, and 4) predominant role of genetic drift on synonymous codon usage predicted by a model-based analysis. These findings show striking similarity to those observed in AT-rich genomes with weak selection for optimal codon usage and GC content overall. Our finding is in contrast to a previous study reporting adaptive codon usage bias in the moss P. patens.
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Affiliation(s)
- Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Switzerland
| | - Kristian K. Ullrich
- Plant Cell Biology, Faculty of Biology, University of Marburg, Germany
- Present address: Max-Planck-Insitut für Evolutionsbiologie, Plön, Germany
| | - Stefan A. Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Germany
- BIOSS—Centre for Biological Signalling Studies, University of Freiburg, Germany
| | - Daniel Lang
- Plant Genome and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Nico van Gessel
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Germany
| | | | - Elena Conti
- Department of Systematic and Evolutionary Botany, University of Zurich, Switzerland
| | - Ralf Reski
- BIOSS—Centre for Biological Signalling Studies, University of Freiburg, Germany
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Germany
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25
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Ho EKH, Agrawal AF. Aging asexual lineages and the evolutionary maintenance of sex. Evolution 2017; 71:1865-1875. [PMID: 28444897 DOI: 10.1111/evo.13260] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 04/13/2017] [Accepted: 04/17/2017] [Indexed: 12/24/2022]
Abstract
Finite populations of asexual and highly selfing species suffer from a reduced efficacy of selection. Such populations are thought to decline in fitness over time due to accumulating slightly deleterious mutations or failing to adapt to changing conditions. These within-population processes that lead nonrecombining species to extinction may help maintain sex and outcrossing through species level selection. Although inefficient selection is proposed to elevate extinction rates over time, previous models of species selection for sex assumed constant diversification rates. For sex to persist, classic models require that asexual species diversify at rates lower than sexual species; the validity of this requirement is questionable, both conceptually and empirically. We extend past models by allowing asexual lineages to decline in diversification rates as they age, that is nonrecombining lineages "senesce" in diversification rates. At equilibrium, senescing diversification rates maintain sex even when asexual lineages, at young ages, diversify faster than their sexual progenitors. In such cases, the age distribution of asexual lineages contains a peak at intermediate values rather than showing the exponential decline predicted by the classic model. Coexistence requires only that the average rate of diversification in asexuals be lower than that of sexuals.
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Affiliation(s)
- Eddie K H Ho
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
| | - Aneil F Agrawal
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
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26
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Hartfield M, Bataillon T, Glémin S. The Evolutionary Interplay between Adaptation and Self-Fertilization. Trends Genet 2017; 33:420-431. [PMID: 28495267 PMCID: PMC5450926 DOI: 10.1016/j.tig.2017.04.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 03/31/2017] [Accepted: 04/03/2017] [Indexed: 11/29/2022]
Abstract
Genome-wide surveys of nucleotide polymorphisms, obtained from next-generation sequencing, have uncovered numerous examples of adaptation in self-fertilizing organisms, especially regarding changes to climate, geography, and reproductive systems. Yet existing models for inferring attributes of adaptive mutations often assume idealized outcrossing populations, which risks mischaracterizing properties of these variants. Recent theoretical work is emphasizing how various aspects of self-fertilization affects adaptation, yet empirical data on these properties are lacking. We review theoretical and empirical studies demonstrating how self-fertilization alters the process of adaptation, illustrated using examples from current sequencing projects. We propose ideas for how future research can more accurately quantify aspects of adaptation in self-fertilizers, including incorporating the effects of standing variation, demographic history, and polygenic adaptation. Analysis of large-scale next-generation sequencing datasets are finding more examples of adaptive evolution at the genomic level. Advances in theoretical work has demonstrated how self-fertilisation affects different aspects of adaptation in these organisms, compared to outcrossers. Current software and statistical methods do not take different mating systems into account, which risks mischaracterising the presence or strength of adaptive mutations from genome scans. Development of new mathematical and statistical methods that explicitly consider self-fertilization and associated demographic effects will enable researchers to more accurately quantify adaptation in these organisms.
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Affiliation(s)
- Matthew Hartfield
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto ON, Canada M5S 3B2; Bioinformatics Research Centre, Aarhus University, 8000C, Aarhus, Denmark.
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, 8000C, Aarhus, Denmark
| | - Sylvain Glémin
- Institut des Sciences de l'Evolution (ISEM - UMR 5554 Universite de Montpellier-CNRS-IRD-EPHE), Place Eugene Bataillon, 34075 Montpellier, France; Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
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27
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Patterns of cross-contamination in a multispecies population genomic project: detection, quantification, impact, and solutions. BMC Biol 2017; 15:25. [PMID: 28356154 PMCID: PMC5370491 DOI: 10.1186/s12915-017-0366-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/13/2017] [Indexed: 01/06/2023] Open
Abstract
Background Contamination is a well-known but often neglected problem in molecular biology. Here, we investigated the prevalence of cross-contamination among 446 samples from 116 distinct species of animals, which were processed in the same laboratory and subjected to subcontracted transcriptome sequencing. Results Using cytochrome oxidase 1 as a barcode, we identified a minimum of 782 events of between-species contamination, with approximately 80% of our samples being affected. An analysis of laboratory metadata revealed a strong effect of the sequencing center: nearly all the detected events of between-species contamination involved species that were sent the same day to the same company. We introduce new methods to address the amount of within-species, between-individual contamination, and to correct for this problem when calling genotypes from base read counts. Conclusions We report evidence for pervasive within-species contamination in this data set, and show that classical population genomic statistics, such as synonymous diversity, the ratio of non-synonymous to synonymous diversity, inbreeding coefficient FIT, and Tajima’s D, are sensitive to this problem to various extents. Control analyses suggest that our published results are probably robust to the problem of contamination. Recommendations on how to prevent or avoid contamination in large-scale population genomics/molecular ecology are provided based on this analysis. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0366-6) contains supplementary material, which is available to authorized users.
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28
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Lounnas M, Correa AC, Vázquez AA, Dia A, Escobar JS, Nicot A, Arenas J, Ayaqui R, Dubois MP, Gimenez T, Gutiérrez A, González-Ramírez C, Noya O, Prepelitchi L, Uribe N, Wisnivesky-Colli C, Yong M, David P, Loker ES, Jarne P, Pointier JP, Hurtrez-Boussès S. Self-fertilization, long-distance flash invasion and biogeography shape the population structure ofPseudosuccinea columellaat the worldwide scale. Mol Ecol 2017; 26:887-903. [DOI: 10.1111/mec.13984] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 11/11/2016] [Accepted: 11/21/2016] [Indexed: 12/30/2022]
Affiliation(s)
- M. Lounnas
- MIVEGEC; UMR IRD 224 CNRS 5290 UM1-UM2; 911 Avenue Agropolis, BP 64501 34394 Montpellier Cedex 5 France
| | - A. C. Correa
- MIVEGEC; UMR IRD 224 CNRS 5290 UM1-UM2; 911 Avenue Agropolis, BP 64501 34394 Montpellier Cedex 5 France
| | - A. A. Vázquez
- MIVEGEC; UMR IRD 224 CNRS 5290 UM1-UM2; 911 Avenue Agropolis, BP 64501 34394 Montpellier Cedex 5 France
- Laboratorio de Malacología; Instituto de Medicina Tropical Pedro Kourí; Apartado Postal 601, Marianao 13 La Habana Cuba
| | - A. Dia
- MIVEGEC; UMR IRD 224 CNRS 5290 UM1-UM2; 911 Avenue Agropolis, BP 64501 34394 Montpellier Cedex 5 France
| | - J. S. Escobar
- Vidarium Nutrition, Health and Wellness Research Center; Grupo Empresarial Nutresa; Calle 8 sur #50-67 Medellín Colombia
| | - A. Nicot
- MIVEGEC; UMR IRD 224 CNRS 5290 UM1-UM2; 911 Avenue Agropolis, BP 64501 34394 Montpellier Cedex 5 France
| | - J. Arenas
- Facultad de Biología Marina; Universidad Científica del Sur; Lima Perú
| | - R. Ayaqui
- Departamento de Microbiología y Patología de la; Facultad de Medicina de la Universidad Nacional de San Agustín; Arequipa Perú
| | - M. P. Dubois
- Centre d'Ecologie Fonctionnelle et d'Evolution; UMR 5175, CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE; 1919 route de Mende 34293 Montpellier Cedex 5 France
| | - T. Gimenez
- Departamento de Parasitología; Facultad de Ciencias Veterinarias; Universidad Nacional de Asunción; Casilla 1061 San Lorenzo Paraguay
| | - A. Gutiérrez
- Laboratorio de Malacología; Instituto de Medicina Tropical Pedro Kourí; Apartado Postal 601, Marianao 13 La Habana Cuba
| | - C. González-Ramírez
- Laboratorio de Investigaciones Parasitológicas ‘Dr Jesús Moreno Rangel’ Cátedra de Parasitología; Departamento de Microbiología y Parasitología; Facultad de Farmacia y Bioanálisis; Universidad de los Andes; Urb. Campo de Oro 5101 Mérida Venezuela
| | - O. Noya
- Sección de Biohelmintiasis; Instituto de Medicina Tropical; Facultad de Medicina; Universidad Central de Venezuela y Centro para Estudios Sobre Malaria; Instituto de Altos Estudios ‘Dr. Arnoldo Gabaldón’-Instituto Nacional de Higiene ‘Rafael Rangel’ del Ministerio del Poder Popular para la Salud; Caracas Venezuela
| | - L. Prepelitchi
- Unidad de Ecología de Reservorios y Vectores de Parásitos; Departamento de Ecología, Genética y Evolución; Facultad de Ciencias Exactas y Naturales; Universidad de Buenos Aires; Ciudad Universitaria, Pabellón 2, 4 piso, Laboratorio 55 Ciudad Autónoma de Buenos Aires C1428EGA Argentina
| | - N. Uribe
- Escuela de Bacteriología y Laboratorio Clínico; Facultad de Salud; Universidad Industrial de Santander; Bucaramanga Colombia
| | - C. Wisnivesky-Colli
- Unidad de Ecología de Reservorios y Vectores de Parásitos; Departamento de Ecología, Genética y Evolución; Facultad de Ciencias Exactas y Naturales; Universidad de Buenos Aires; Ciudad Universitaria, Pabellón 2, 4 piso, Laboratorio 55 Ciudad Autónoma de Buenos Aires C1428EGA Argentina
| | - M. Yong
- Laboratorio de Malacología; Instituto de Medicina Tropical Pedro Kourí; Apartado Postal 601, Marianao 13 La Habana Cuba
| | - P. David
- Centre d'Ecologie Fonctionnelle et d'Evolution; UMR 5175, CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE; 1919 route de Mende 34293 Montpellier Cedex 5 France
| | - E. S. Loker
- Department of Biology; Center for Evolutionary and Theoretical Immunology; University of New Mexico; Albuquerque NM 87131 USA
| | - P. Jarne
- Centre d'Ecologie Fonctionnelle et d'Evolution; UMR 5175, CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE; 1919 route de Mende 34293 Montpellier Cedex 5 France
| | - J. P. Pointier
- USR 3278 CNRS-EPHE; CRIOBE Université de Perpignan; 68860 Perpignan-Cedex France
| | - S. Hurtrez-Boussès
- MIVEGEC; UMR IRD 224 CNRS 5290 UM1-UM2; 911 Avenue Agropolis, BP 64501 34394 Montpellier Cedex 5 France
- Département de Biologie-Ecologie; Faculté des Sciences - cc 046; Université Montpellier; 4 Place Eugène Bataillon 34095 Montpellier Cedex 5 France
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Iglesias-Piñeiro J, González-Warleta M, Castro-Hermida JA, Córdoba M, González-Lanza C, Manga-González Y, Mezo M. Transmission of Calicophoron daubneyi and Fasciola hepatica in Galicia (Spain): Temporal follow-up in the intermediate and definitive hosts. Parasit Vectors 2016; 9:610. [PMID: 27894356 PMCID: PMC5126829 DOI: 10.1186/s13071-016-1892-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/17/2016] [Indexed: 12/27/2022] Open
Abstract
Background Paramphistomosis caused by Calicophoron daubneyi and fasciolosis caused by Fasciola hepatica are common parasitic diseases of livestock animals. Transmission of the diseases depends on the presence of intermediate hosts, i.e. freshwater gastropods such as lymnaeids. We carried out a 2-year-long study of the dynamics of the snail population acting as the intermediate host for these parasites, considering the population structure in terms of size/age and infection status. In addition, we determined the kinetics of trematode egg excretion in grazing cows. Generalized Additive Models (GAMs) were used to analyze the associations between different response variables and snail size, sampling month and weather-related variables. Results Of the molluscan species examined, Galba truncatula, Radix peregra, Anisus (Anisus) leucostoma and Pisidium casertanum (n = 2802), only G. truncatula was infected with C. daubneyi or F. hepatica, at prevalence rates of 8.2% and 4.4% respectively. The probability of infection with C. daubneyi or F. hepatica was linearly related to snail size, although in different ways (negative for C. daubneyi and positive for F. hepatica). The total snail population increased in winter, when specimens of all size classes were found. Infected snails were more abundant during spring-autumn. Mature cercariae of both parasites were found in most seasons. In the statistical models, the sampling month accounted for a high percentage (71.9–78.2%) of the observed variability in snail abundance. The inclusion of climatic variables in the models moderately increased the percentage of deviance explained (77.7–91.9%). Excretion of C. daubneyi eggs in cow faeces was always higher than that of F. hepatica eggs. Conclusions Particular care should be taken to prevent pastures and the surrounding environment being contaminated with parasite eggs during winter-spring, when the number of snails susceptible to miracidial infections is maximal. This is therefore the optimal time for treating grazing animals. Nevertheless, control of trematodosis based only on chemotherapy is difficult in an area such as the study area, where environmental factors favour the regular appearance of snail populations harbouring mature cercariae. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1892-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Javier Iglesias-Piñeiro
- Departamento de Zooloxía, Xenética e Antropoloxía Física, Facultade de Bioloxía, Campus Vida, Universidade de Santiago de Compostela, 15706, Santiago de Compostela (A Coruña), Spain
| | - Marta González-Warleta
- Laboratorio de Parasitología, Centro de Investigaciones Agrarias de Mabegondo, Instituto Galego de Calidade Alimentaria-Xunta de Galicia, Carretera AC-542 de Betanzos a Mesón do Vento, Km 7, 15318, Abegondo (A Coruña), Spain
| | - José Antonio Castro-Hermida
- Laboratorio de Parasitología, Centro de Investigaciones Agrarias de Mabegondo, Instituto Galego de Calidade Alimentaria-Xunta de Galicia, Carretera AC-542 de Betanzos a Mesón do Vento, Km 7, 15318, Abegondo (A Coruña), Spain
| | - María Córdoba
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Camino González-Lanza
- Departamento de Sanidad Animal, Instituto de Ganadería de Montaña, Consejo Superior de Investigaciones Científicas (CSIC)-ULE, 24346, Grulleros (León), Spain
| | - Yolanda Manga-González
- Departamento de Sanidad Animal, Instituto de Ganadería de Montaña, Consejo Superior de Investigaciones Científicas (CSIC)-ULE, 24346, Grulleros (León), Spain
| | - Mercedes Mezo
- Laboratorio de Parasitología, Centro de Investigaciones Agrarias de Mabegondo, Instituto Galego de Calidade Alimentaria-Xunta de Galicia, Carretera AC-542 de Betanzos a Mesón do Vento, Km 7, 15318, Abegondo (A Coruña), Spain.
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Abstract
Genetic polymorphism varies among species and within genomes, and has important implications for the evolution and conservation of species. The determinants of this variation have been poorly understood, but population genomic data from a wide range of organisms now make it possible to delineate the underlying evolutionary processes, notably how variation in the effective population size (Ne) governs genetic diversity. Comparative population genomics is on its way to providing a solution to 'Lewontin's paradox' - the discrepancy between the many orders of magnitude of variation in population size and the much narrower distribution of diversity levels. It seems that linked selection plays an important part both in the overall genetic diversity of a species and in the variation in diversity within the genome. Genetic diversity also seems to be predictable from the life history of a species.
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31
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Roze D. Background Selection in Partially Selfing Populations. Genetics 2016; 203:937-57. [PMID: 27075726 PMCID: PMC4896204 DOI: 10.1534/genetics.116.187955] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/07/2016] [Indexed: 12/18/2022] Open
Abstract
Self-fertilizing species often present lower levels of neutral polymorphism than their outcrossing relatives. Indeed, selfing automatically increases the rate of coalescence per generation, but also enhances the effects of background selection and genetic hitchhiking by reducing the efficiency of recombination. Approximations for the effect of background selection in partially selfing populations have been derived previously, assuming tight linkage between deleterious alleles and neutral loci. However, loosely linked deleterious mutations may have important effects on neutral diversity in highly selfing populations. In this article, I use a general method based on multilocus population genetics theory to express the effect of a deleterious allele on diversity at a linked neutral locus in terms of moments of genetic associations between loci. Expressions for these genetic moments at equilibrium are then computed for arbitrary rates of selfing and recombination. An extrapolation of the results to the case where deleterious alleles segregate at multiple loci is checked using individual-based simulations. At high selfing rates, the tight linkage approximation underestimates the effect of background selection in genomes with moderate to high map length; however, another simple approximation can be obtained for this situation and provides accurate predictions as long as the deleterious mutation rate is not too high.
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Affiliation(s)
- Denis Roze
- Centre National de la Recherche Scientifique, Unité Mixte Internationale 3614, Evolutionary Biology and Ecology of Algae, Roscoff, FranceSorbonne Universités, Université Pierre et Marie Curie Université Paris VI, 29688 Roscoff, France
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32
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Limits to Adaptation in Partially Selfing Species. Genetics 2016; 203:959-74. [PMID: 27098913 DOI: 10.1534/genetics.116.188821] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/15/2016] [Indexed: 12/26/2022] Open
Abstract
In outcrossing populations, "Haldane's sieve" states that recessive beneficial alleles are less likely to fix than dominant ones, because they are less exposed to selection when rare. In contrast, selfing organisms are not subject to Haldane's sieve and are more likely to fix recessive types than outcrossers, as selfing rapidly creates homozygotes, increasing overall selection acting on mutations. However, longer homozygous tracts in selfers also reduce the ability of recombination to create new genotypes. It is unclear how these two effects influence overall adaptation rates in partially selfing organisms. Here, we calculate the fixation probability of beneficial alleles if there is an existing selective sweep in the population. We consider both the potential loss of the second beneficial mutation if it has a weaker advantage than the first one, and the possible replacement of the initial allele if the second mutant is fitter. Overall, loss of weaker adaptive alleles during a first selective sweep has a larger impact on preventing fixation of both mutations in highly selfing organisms. Furthermore, the presence of linked mutations has two opposing effects on Haldane's sieve. First, recessive mutants are disproportionally likely to be lost in outcrossers, so it is likelier that dominant mutations will fix. Second, with elevated rates of adaptive mutation, selective interference annuls the advantage in selfing organisms of not suffering from Haldane's sieve; outcrossing organisms are more able to fix weak beneficial mutations of any dominance value. Overall, weakened recombination effects can greatly limit adaptation in selfing organisms.
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33
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Brandvain Y, Wright SI. The Limits of Natural Selection in a Nonequilibrium World. Trends Genet 2016; 32:201-210. [PMID: 26874998 DOI: 10.1016/j.tig.2016.01.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 12/23/2015] [Accepted: 01/19/2016] [Indexed: 11/19/2022]
Abstract
Evolutionary theory predicts that factors such as a small population size or low recombination rate can limit the action of natural selection. The emerging field of comparative population genomics offers an opportunity to evaluate these hypotheses. However, classical theoretical predictions assume that populations are at demographic equilibrium. This assumption is likely to be violated in the very populations researchers use to evaluate selection's limits: populations that have experienced a recent shift in population size and/or effective recombination rates. Here we highlight theory and data analyses concerning limitations on the action of natural selection in nonequilibrial populations and argue that substantial care is needed to appropriately test whether species and populations show meaningful differences in selection efficacy. A move toward model-based inferences that explicitly incorporate nonequilibrium dynamics provides a promising approach to more accurately contrast selection efficacy across populations and interpret its significance.
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Affiliation(s)
- Yaniv Brandvain
- Department of Plant Biology, University of Minnesota, St Paul, MN 55108, USA
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
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34
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Agrawal AF, Hartfield M. Coalescence with Background and Balancing Selection in Systems with Bi- and Uniparental Reproduction: Contrasting Partial Asexuality and Selfing. Genetics 2016; 202:313-26. [PMID: 26584901 PMCID: PMC4701095 DOI: 10.1534/genetics.115.181024] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 11/13/2015] [Indexed: 11/18/2022] Open
Abstract
Uniparental reproduction in diploids, via asexual reproduction or selfing, reduces the independence with which separate loci are transmitted across generations. This is expected to increase the extent to which a neutral marker is affected by selection elsewhere in the genome. Such effects have previously been quantified in coalescent models involving selfing. Here we examine the effects of background selection and balancing selection in diploids capable of both sexual and asexual reproduction (i.e., partial asexuality). We find that the effect of background selection on reducing coalescent time (and effective population size) can be orders of magnitude greater when rates of sex are low than when sex is common. This is because asexuality enhances the effects of background selection through both a recombination effect and a segregation effect. We show that there are several reasons that the strength of background selection differs between systems with partial asexuality and those with comparable levels of uniparental reproduction via selfing. Expectations for reductions in Ne via background selection have been verified using stochastic simulations. In contrast to background selection, balancing selection increases the coalescence time for a linked neutral site. With partial asexuality, the effect of balancing selection is somewhat dependent upon the mode of selection (e.g., heterozygote advantage vs. negative frequency-dependent selection) in a manner that does not apply to selfing. This is because the frequency of heterozygotes, which are required for recombination onto alternative genetic backgrounds, is more dependent on the pattern of selection with partial asexuality than with selfing.
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Affiliation(s)
- Aneil F Agrawal
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Matthew Hartfield
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada Bioinformatics Research Centre, University of Aarhus, 8000C Aarhus, Denmark
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35
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Hartfield M. Evolutionary genetic consequences of facultative sex and outcrossing. J Evol Biol 2015; 29:5-22. [DOI: 10.1111/jeb.12770] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/24/2015] [Accepted: 09/28/2015] [Indexed: 01/16/2023]
Affiliation(s)
- M. Hartfield
- Department of Ecology and Evolutionary Biology; University of Toronto; Toronto ON Canada
- Bioinformatics Research Centre; University of Aarhus; Aarhus Denmark
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36
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Mugal CF, Weber CC, Ellegren H. GC-biased gene conversion links the recombination landscape and demography to genomic base composition. Bioessays 2015; 37:1317-26. [DOI: 10.1002/bies.201500058] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Carina F. Mugal
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Claudia C. Weber
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
- Department of Biology; Center for Computational Genetics and Genomics; Temple University; Philadelphia PA USA
| | - Hans Ellegren
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
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