1
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Hörandl E. Apomixis and the paradox of sex in plants. ANNALS OF BOTANY 2024; 134:1-18. [PMID: 38497809 PMCID: PMC11161571 DOI: 10.1093/aob/mcae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/15/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND The predominance of sex in eukaryotes, despite the high costs of meiosis and mating, remains an evolutionary enigma. Many theories have been proposed, none of them being conclusive on its own, and they are, in part, not well applicable to land plants. Sexual reproduction is obligate in embryophytes for the great majority of species. SCOPE This review compares the main forms of sexual and asexual reproduction in ferns and angiosperms, based on the generation cycling of sporophyte and gametophyte (leaving vegetative propagation aside). The benefits of sexual reproduction for maintenance of genomic integrity in comparison to asexuality are discussed in the light of developmental, evolutionary, genetic and phylogenetic studies. CONCLUSIONS Asexual reproduction represents modifications of the sexual pathway, with various forms of facultative sexuality. For sexual land plants, meiosis provides direct DNA repair mechanisms for oxidative damage in reproductive tissues. The ploidy alternations of meiosis-syngamy cycles and prolonged multicellular stages in the haploid phase in the gametophytes provide a high efficiency of purifying selection against recessive deleterious mutations. Asexual lineages might buffer effects of such mutations via polyploidy and can purge the mutational load via facultative sexuality. The role of organelle-nuclear genome compatibility for maintenance of genome integrity is not well understood. In plants in general, the costs of mating are low because of predominant hermaphroditism. Phylogenetic patterns in the archaeplastid clade suggest that high frequencies of sexuality in land plants are concomitant with a stepwise increase of intrinsic and extrinsic stress factors. Furthermore, expansion of genome size in land plants would increase the potential mutational load. Sexual reproduction appears to be essential for keeping long-term genomic integrity, and only rare combinations of extrinsic and intrinsic factors allow for shifts to asexuality.
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Affiliation(s)
- Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with herbarium), University of Göttingen, Göttingen, Germany
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2
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Woodruff GC, Willis JH, Phillips PC. Patterns of Genomic Diversity in a Fig-Associated Close Relative of Caenorhabditis elegans. Genome Biol Evol 2024; 16:evae020. [PMID: 38302111 PMCID: PMC10883733 DOI: 10.1093/gbe/evae020] [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: 08/22/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/03/2024] Open
Abstract
The evolution of reproductive mode is expected to have profound impacts on the genetic composition of populations. At the same time, ecological interactions can generate close associations among species, which can in turn generate a high degree of overlap in their spatial distributions. Caenorhabditis elegans is a hermaphroditic nematode that has enabled extensive advances in developmental genetics. Caenorhabditis inopinata, the sister species of C. elegans, is a gonochoristic nematode that thrives in figs and obligately disperses on fig wasps. Here, we describe patterns of genomic diversity in C. inopinata. We performed RAD-seq on individual worms isolated from the field across three Okinawan island populations. C. inopinata is about five times more diverse than C. elegans. Additionally, C. inopinata harbors greater differences in diversity among functional genomic regions (such as between genic and intergenic sequences) than C. elegans. Conversely, C. elegans harbors greater differences in diversity between high-recombining chromosome arms and low-recombining chromosome centers than C. inopinata. FST is low among island population pairs, and clear population structure could not be easily detected among islands, suggesting frequent migration of wasps between islands. These patterns of population differentiation appear comparable with those previously reported in its fig wasp vector. These results confirm many theoretical population genetic predictions regarding the evolution of reproductive mode and suggest C. inopinata population dynamics may be driven by wasp dispersal. This work sets the stage for future evolutionary genomic studies aimed at understanding the evolution of sex as well as the evolution of ecological interactions.
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Affiliation(s)
- Gavin C Woodruff
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
- Present address: Department of Biology, University of Oklahoma, Norman, OK 73019, USA
| | - John H Willis
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
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3
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Böhne A, Oğuzhan Z, Chrysostomakis I, Vitt S, Meuthen D, Martin S, Kukowka S, Thünken T. Evidence for selfing in a vertebrate from whole-genome sequencing. Genome Res 2023; 33:2133-2142. [PMID: 38190641 PMCID: PMC10760518 DOI: 10.1101/gr.277368.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/07/2023] [Indexed: 01/10/2024]
Abstract
A growing number of recent genomic studies report asexual parthenogenetic reproduction in a wide range of taxa, including vertebrate species from the reptile, bird, and fish lineages. Yet, self-fertilization (selfing) has been recorded only in a single vertebrate, the mangrove killifish Kryptolebias marmoratus In cichlid fishes, sex determination is notably diverse and can be influenced by the environment, and sequential hermaphroditism has been reported for some species. Here, we present evidence for a case of facultative selfing in the cichlid fish Benitochromis nigrodorsalis, which is otherwise known as biparentally reproducing ovophilic mouthbrooder from Western Africa. Our laboratory observations revealed that a wild-caught individual produced repeatedly viable offspring in absence of a mating partner. By analyzing genome-wide single-nucleotide polymorphism (SNP) data, we compare that individual and two of its offspring to shed light on its reproductive mode. First, our results confirm uniparental reproduction. Second, overall heterozygosity is reduced in the offspring compared with outbred individuals. Retained maternal heterozygosity in the offspring is ∼51%, which is close to the theoretically expected value of a heterozygosity reduction of 50% by selfing. Heterozygosity patterns along individual chromosomes do not point to alternative parthenogenetic reproductive mechanisms like automixis by terminal or central fusion. Facultative selfing may represent an adaptive strategy ensuring reproduction when mating partners are absent and, hence, contribute to the cichlids' enormous evolutionary success.
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Affiliation(s)
- Astrid Böhne
- Leibniz Institute for the Analysis of Biodiversity Change LIB, Museum Koenig Bonn, 53113 Bonn, Germany;
| | - Zeynep Oğuzhan
- Leibniz Institute for the Analysis of Biodiversity Change LIB, Museum Koenig Bonn, 53113 Bonn, Germany
| | - Ioannis Chrysostomakis
- Leibniz Institute for the Analysis of Biodiversity Change LIB, Museum Koenig Bonn, 53113 Bonn, Germany
| | - Simon Vitt
- Bonn Institute of Organismic Biology (BIOB), Department of Animal Biodiversity, University of Bonn, 53121 Bonn, Germany
| | - Denis Meuthen
- Bonn Institute of Organismic Biology (BIOB), Department of Animal Biodiversity, University of Bonn, 53121 Bonn, Germany
- Evolutionary Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Sebastian Martin
- Leibniz Institute for the Analysis of Biodiversity Change LIB, Museum Koenig Bonn, 53113 Bonn, Germany
| | - Sandra Kukowka
- Leibniz Institute for the Analysis of Biodiversity Change LIB, Museum Koenig Bonn, 53113 Bonn, Germany
| | - Timo Thünken
- Bonn Institute of Organismic Biology (BIOB), Department of Animal Biodiversity, University of Bonn, 53121 Bonn, Germany;
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4
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Janko K, Mikulíček P, Hobza R, Schlupp I. Sperm-dependent asexual species and their role in ecology and evolution. Ecol Evol 2023; 13:e10522. [PMID: 37780083 PMCID: PMC10534198 DOI: 10.1002/ece3.10522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 08/16/2023] [Accepted: 08/24/2023] [Indexed: 10/03/2023] Open
Abstract
Sexual reproduction is the primary mode of reproduction in eukaryotes, but some organisms have evolved deviations from classical sex and switched to asexuality. These asexual lineages have sometimes been viewed as evolutionary dead ends, but recent research has revealed their importance in many areas of general biology. Our review explores the understudied, yet important mechanisms by which sperm-dependent asexuals that produce non-recombined gametes but rely on their fertilization, can have a significant impact on the evolution of coexisting sexual species and ecosystems. These impacts are concentrated around three major fields. Firstly, sperm-dependent asexuals can potentially impact the gene pool of coexisting sexual species by either restricting their population sizes or by providing bridges for interspecific gene flow whose type and consequences substantially differ from gene flow mechanisms expected under sexual reproduction. Secondly, they may impact on sexuals' diversification rates either directly, by serving as stepping-stones in speciation, or indirectly, by promoting the formation of pre- and postzygotic reproduction barriers among nascent species. Thirdly, they can potentially impact on spatial distribution of species, via direct or indirect (apparent) types of competition and Allee effects. For each such mechanism, we provide empirical examples of how natural sperm-dependent asexuals impact the evolution of their sexual counterparts. In particular, we highlight that these broad effects may last beyond the tenure of the individual asexual lineages causing them, which challenges the traditional perception that asexual lineages are short-lived evolutionary dead ends and minor sideshows. Our review also proposes new research directions to incorporate the aforementioned impacts of sperm-dependent asexuals. These research directions will ultimately enhance our understanding of the evolution of genomes and biological interactions in general.
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Affiliation(s)
- Karel Janko
- Laboratory of Non‐Mendelian Evolution, Institute of Animal Physiology and GeneticsAcademy of Sciences of the Czech RepublicLiběchovCzech Republic
- Department of Biology and Ecology, Faculty of ScienceUniversity of OstravaOstravaCzech Republic
| | - Peter Mikulíček
- Department of Zoology, Faculty of Natural SciencesComenius University in BratislavaBratislavaSlovakia
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of BiophysicsAcademy of Sciences of the Czech RepublicBrnoCzech Republic
| | - Ingo Schlupp
- Department of BiologyUniversity of OklahomaOklahomaNormanUSA
- Department of BiologyInternational Stock Center for Livebearing FishesOklahomaNormanUSA
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5
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Li LL, Xiao Y, Wang X, He ZH, Lv YW, Hu XS. The Ka /Ks and πa /πs Ratios under Different Models of Gametophytic and Sporophytic Selection. Genome Biol Evol 2023; 15:evad151. [PMID: 37561000 PMCID: PMC10443736 DOI: 10.1093/gbe/evad151] [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: 01/11/2023] [Revised: 08/06/2023] [Accepted: 08/08/2023] [Indexed: 08/11/2023] Open
Abstract
Alternation of generations in plant life cycle provides a biological basis for natural selection occurring in either the gametophyte or the sporophyte phase or in both. Divergent biphasic selection could yield distinct evolutionary rates for phase-specific or pleiotropic genes. Here, we analyze models that deal with antagonistic and synergistic selection between alternative generations in terms of the ratio of nonsynonymous to synonymous divergence (Ka/Ks). Effects of biphasic selection are opposite under antagonistic selection but cumulative under synergistic selection for pleiotropic genes. Under the additive and comparable strengths of biphasic allelic selection, the absolute Ka/Ks for the gametophyte gene is equal to in outcrossing but smaller than, in a mixed mating system, that for the sporophyte gene under antagonistic selection. The same pattern is predicted for Ka/Ks under synergistic selection. Selfing reduces efficacy of gametophytic selection. Other processes, including pollen and seed flow and genetic drift, reduce selection efficacy. The polymorphism (πa) at a nonsynonymous site is affected by the joint effects of selfing with gametophytic or sporophytic selection. Likewise, the ratio of nonsynonymous to synonymous polymorphism (πa/πs) is also affected by the same joint effects. Gene flow and genetic drift have opposite effects on πa or πa/πs in interacting with gametophytic and sporophytic selection. We discuss implications of this theory for detecting natural selection in terms of Ka/Ks and for interpreting the evolutionary divergence among gametophyte-specific, sporophyte-specific, and pleiotropic genes.
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Affiliation(s)
- Ling-Ling Li
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Yu Xiao
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Xi Wang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Zi-Han He
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Yan-Wen Lv
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Xin-Sheng Hu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
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6
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Teterina AA, Willis JH, Lukac M, Jovelin R, Cutter AD, Phillips PC. Genomic diversity landscapes in outcrossing and selfing Caenorhabditis nematodes. PLoS Genet 2023; 19:e1010879. [PMID: 37585484 PMCID: PMC10461856 DOI: 10.1371/journal.pgen.1010879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 08/28/2023] [Accepted: 07/21/2023] [Indexed: 08/18/2023] Open
Abstract
Caenorhabditis nematodes form an excellent model for studying how the mode of reproduction affects genetic diversity, as some species reproduce via outcrossing whereas others can self-fertilize. Currently, chromosome-level patterns of diversity and recombination are only available for self-reproducing Caenorhabditis, making the generality of genomic patterns across the genus unclear given the profound potential influence of reproductive mode. Here we present a whole-genome diversity landscape, coupled with a new genetic map, for the outcrossing nematode C. remanei. We demonstrate that the genomic distribution of recombination in C. remanei, like the model nematode C. elegans, shows high recombination rates on chromosome arms and low rates toward the central regions. Patterns of genetic variation across the genome are also similar between these species, but differ dramatically in scale, being tenfold greater for C. remanei. Historical reconstructions of variation in effective population size over the past million generations echo this difference in polymorphism. Evolutionary simulations demonstrate how selection, recombination, mutation, and selfing shape variation along the genome, and that multiple drivers can produce patterns similar to those observed in natural populations. The results illustrate how genome organization and selection play a crucial role in shaping the genomic pattern of diversity whereas demographic processes scale the level of diversity across the genome as a whole.
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Affiliation(s)
- Anastasia A. Teterina
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
- Center of Parasitology, Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
| | - John H. Willis
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Matt Lukac
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Richard Jovelin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Asher D. Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Patrick C. Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
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7
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Thorn CS, Maness RW, Hulke JM, Delmore KE, Criscione CD. Population genomics of helminth parasites. J Helminthol 2023; 97:e29. [PMID: 36927601 DOI: 10.1017/s0022149x23000123] [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] [Indexed: 03/18/2023]
Abstract
Next generation sequencing technologies have facilitated a shift from a few targeted loci in population genetic studies to whole genome approaches. Here, we review the types of questions and inferences regarding the population biology and evolution of parasitic helminths being addressed within the field of population genomics. Topics include parabiome, hybridization, population structure, loci under selection and linkage mapping. We highlight various advances, and note the current trends in the field, particularly a focus on human-related parasites despite the inherent biodiversity of helminth species. We conclude by advocating for a broader application of population genomics to reflect the taxonomic and life history breadth displayed by helminth parasites. As such, our basic knowledge about helminth population biology and evolution would be enhanced while the diversity of helminths in itself would facilitate population genomic comparative studies to address broader ecological and evolutionary concepts.
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Affiliation(s)
- C S Thorn
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843, USA
| | - R W Maness
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843, USA
| | - J M Hulke
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843, USA
| | - K E Delmore
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843, USA
| | - C D Criscione
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843, USA
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8
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Zhang Z, Kryvokhyzha D, Orsucci M, Glémin S, Milesi P, Lascoux M. How broad is the selfing syndrome? Insights from convergent evolution of gene expression across species and tissues in the Capsella genus. THE NEW PHYTOLOGIST 2022; 236:2344-2357. [PMID: 36089898 PMCID: PMC9828073 DOI: 10.1111/nph.18477] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
The shift from outcrossing to selfing is one of the main evolutionary transitions in plants. It is accompanied by profound effects on reproductive traits, the so-called selfing syndrome. Because the transition to selfing also implies deep genomic and ecological changes, one also expects to observe a genomic selfing syndrome. We took advantage of the three independent transitions from outcrossing to selfing in the Capsella genus to characterize the overall impact of mating system change on RNA expression, in flowers but also in leaves and roots. We quantified the extent of both selfing and genomic syndromes, and tested whether changes in expression corresponded to adaptation to selfing or to relaxed selection on traits that were constrained in outcrossers. Mating system change affected gene expression in all three tissues but more so in flowers than in roots and leaves. Gene expression in selfing species tended to converge in flowers but diverged in the two other tissues. Hence, convergent adaptation to selfing dominates in flowers, whereas genetic drift plays a more important role in leaves and roots. The effect of mating system transition is not limited to reproductive tissues and corresponds to both adaptation to selfing and relaxed selection on previously constrained traits.
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Affiliation(s)
- Zebin Zhang
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityNorbyvägen 18D752 36UppsalaSweden
| | - Dmytro Kryvokhyzha
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityNorbyvägen 18D752 36UppsalaSweden
- Department of Clinical SciencesLund University Diabetes Centre214 28MalmöSweden
| | - Marion Orsucci
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityNorbyvägen 18D752 36UppsalaSweden
- Department of Plant BiologySwedish University of Agricultural Sciences, Uppsala BioCenter750 07UppsalaSweden
| | - Sylvain Glémin
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityNorbyvägen 18D752 36UppsalaSweden
- Université de Rennes, Centre National de la Recherche Scientifique (CNRS), ECOBIO (Ecosystèmes, Biodiversité, Evolution) – Unité Mixte de Recherche (UMR) 6553F‐35042RennesFrance
| | - Pascal Milesi
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityNorbyvägen 18D752 36UppsalaSweden
- Science For Life Laboratory (SciLifeLab)752 37UppsalaSweden
| | - Martin Lascoux
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityNorbyvägen 18D752 36UppsalaSweden
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9
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Cerbin S, Ou S, Li Y, Sun Y, Jiang N. Distinct composition and amplification dynamics of transposable elements in sacred lotus (Nelumbo nucifera Gaertn.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:172-192. [PMID: 35959634 PMCID: PMC9804982 DOI: 10.1111/tpj.15938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/19/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Sacred lotus (Nelumbo nucifera Gaertn.) is a basal eudicot plant with a unique lifestyle, physiological features, and evolutionary characteristics. Here we report the unique profile of transposable elements (TEs) in the genome, using a manually curated repeat library. TEs account for 59% of the genome, and hAT (Ac/Ds) elements alone represent 8%, more than in any other known plant genome. About 18% of the lotus genome is comprised of Copia LTR retrotransposons, and over 25% of them are associated with non-canonical termini (non-TGCA). Such high abundance of non-canonical LTR retrotransposons has not been reported for any other organism. TEs are very abundant in genic regions, with retrotransposons enriched in introns and DNA transposons primarily in flanking regions of genes. The recent insertion of TEs in introns has led to significant intron size expansion, with a total of 200 Mb in the 28 455 genes. This is accompanied by declining TE activity in intergenic regions, suggesting distinct control efficacy of TE amplification in different genomic compartments. Despite the prevalence of TEs in genic regions, some genes are associated with fewer TEs, such as those involved in fruit ripening and stress responses. Other genes are enriched with TEs, and genes in epigenetic pathways are the most associated with TEs in introns, indicating a dynamic interaction between TEs and the host surveillance machinery. The dramatic differential abundance of TEs with genes involved in different biological processes as well as the variation of target preference of different TEs suggests the composition and activity of TEs influence the path of evolution.
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Affiliation(s)
- Stefan Cerbin
- Department of HorticultureMichigan State University1066 Bogue StreetEast LansingMI48824USA
- Present address:
Department of Ecology & Evolutionary BiologyUniversity of Kansas1200 Sunnyside AvenueLawrenceKS66045USA
| | - Shujun Ou
- Department of HorticultureMichigan State University1066 Bogue StreetEast LansingMI48824USA
- Present address:
Department of Computer ScienceJohns Hopkins UniversityBaltimoreMD21218USA
| | - Yang Li
- Department of Electrical EngineeringCity University of Hong KongKowloonHong Kong SARChina
| | - Yanni Sun
- Department of Electrical EngineeringCity University of Hong KongKowloonHong Kong SARChina
| | - Ning Jiang
- Department of HorticultureMichigan State University1066 Bogue StreetEast LansingMI48824USA
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10
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Quevarec L, Réale D, Dufourcq‐Sekatcheff E, Car C, Armant O, Dubourg N, Adam‐Guillermin C, Bonzom J. Male frequency in Caenorhabditis elegans increases in response to chronic irradiation. Evol Appl 2022; 15:1331-1343. [PMID: 36187185 PMCID: PMC9488675 DOI: 10.1111/eva.13420] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 01/09/2023] Open
Abstract
Outcrossing can be advantageous in a changing environment because it promotes the purge of deleterious mutations and increases the genetic diversity within a population, which may improve population persistence and evolutionary potential. Some species may, therefore, switch their reproductive mode from inbreeding to outcrossing when under environmental stress. This switch may have consequences on the demographic dynamics and evolutionary trajectory of populations. For example, it may directly influence the sex ratio of a population. However, much remains to be discovered about the mechanisms and evolutionary implications of sex ratio changes in a population in response to environmental stress. Populations of the androdioecious nematode Caenorhabditis elegans, are composed of selfing hermaphrodites and rare males. Here, we investigate the changes in the sex ratio of C. elegans populations exposed to radioactive pollution for 60 days or around 20 generations. We experimentally exposed populations to three levels of ionizing radiation (i.e., 0, 1.4, and 50 mGy.h-1). We then performed reciprocal transplant experiments to evaluate genetic divergence between populations submitted to different treatments. Finally, we used a mathematical model to examine the evolutionary mechanisms that could be responsible for the change in sex ratio. Our results showed an increase in male frequency in irradiated populations, and this effect increased with the dose rate. The model showed that an increase in male fertilization success or a decrease in hermaphrodite self-fertilization could explain this increase in the frequency of males. Moreover, males persisted in populations after transplant back into the control conditions. These results suggested selection favoring outcrossing under irradiation conditions. This study shows that ionizing radiation can sustainably alter the reproductive strategy of a population, likely impacting its long-term evolutionary history. This study highlights the need to evaluate the impact of pollutants on the reproductive strategies of populations when assessing the ecological risks.
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Affiliation(s)
- Loïc Quevarec
- PSE‐ENV/SRTE/LECO, CadaracheInstitut de Radioprotection et de Sûreté Nucléaire (IRSN)Saint Paul Lez DuranceFrance
| | - Denis Réale
- Département des Sciences BiologiquesUniversité du Québec à MontréalMontréalQuebecCanada
| | | | - Clément Car
- PSE‐ENV/SRTE/LECO, CadaracheInstitut de Radioprotection et de Sûreté Nucléaire (IRSN)Saint Paul Lez DuranceFrance
| | - Olivier Armant
- PSE‐ENV/SRTE/LECO, CadaracheInstitut de Radioprotection et de Sûreté Nucléaire (IRSN)Saint Paul Lez DuranceFrance
| | - Nicolas Dubourg
- PSE‐ENV/SRTE/LECO, CadaracheInstitut de Radioprotection et de Sûreté Nucléaire (IRSN)Saint Paul Lez DuranceFrance
| | - Christelle Adam‐Guillermin
- PSE‐SANTE/SDOS/LMDN, CadaracheInstitut de Radioprotection et de Sûreté Nucléaire (IRSN)Saint Paul Lez DuranceFrance
| | - Jean‐Marc Bonzom
- PSE‐ENV/SRTE/LECO, CadaracheInstitut de Radioprotection et de Sûreté Nucléaire (IRSN)Saint Paul Lez DuranceFrance
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11
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Tsuchimatsu T, Fujii S. The selfing syndrome and beyond: diverse evolutionary consequences of mating system transitions in plants. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200510. [PMID: 35634918 PMCID: PMC9149797 DOI: 10.1098/rstb.2020.0510] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/04/2021] [Indexed: 07/20/2023] Open
Abstract
The shift from outcrossing to self-fertilization (selfing) is considered one of the most prevalent evolutionary transitions in flowering plants. Selfing species tend to share similar reproductive traits in morphology and function, and such a set of traits is called the 'selfing syndrome'. Although the genetic basis of the selfing syndrome has been of great interest to evolutionary biologists, knowledge of the causative genes or mutations was limited until recently. Thanks to advances in population genomic methodologies combined with high-throughput sequencing technologies, several studies have successfully unravelled the molecular and genetic basis for evolution of the selfing syndrome in Capsella, Arabidopsis, Solanum and other genera. Here we first introduce recent research examples that have explored the loci, genes and mutations responsible for the selfing syndrome traits, such as reductions in petal size or in pollen production, that are mainly relevant to pre-pollination processes. Second, we review the relationship between the evolution of selfing and interspecific pollen transfer, highlighting the findings of post-pollination reproductive barriers at the molecular level. We then discuss the emerging view of patterns in evolution of the selfing syndrome, such as the pervasive involvement of loss-of-function mutations and the relative importance of selection versus neutral degradation. This article is part of the theme issue 'Genetic basis of adaptation and speciation: from loci to causative mutations'.
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Affiliation(s)
- Takashi Tsuchimatsu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku 113-0033, Japan
| | - Sota Fujii
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku 113-8657, Japan
- Suntory Rising Stars Encouragement Program in Life Sciences (SunRiSE) Fellow, Bunkyo, Japan
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12
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Cornille A, Tiret M, Salcedo A, Huang HR, Orsucci M, Milesi P, Kryvokhyzha D, Holm K, Ge XJ, Stinchcombe JR, Glémin S, Wright SI, Lascoux M. The relative role of plasticity and demographic history in Capsella bursa-pastoris: a common garden experiment in Asia and Europe. AOB PLANTS 2022; 14:plac011. [PMID: 35669442 PMCID: PMC9162126 DOI: 10.1093/aobpla/plac011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 03/28/2022] [Indexed: 05/15/2023]
Abstract
The colonization success of a species depends on the interplay between its phenotypic plasticity, adaptive potential and demographic history. Assessing their relative contributions during the different phases of a species range expansion is challenging, and requires large-scale experiments. Here, we investigated the relative contributions of plasticity, performance and demographic history to the worldwide expansion of the shepherd's purse, Capsella bursa-pastoris. We installed two large common gardens of the shepherd's purse, a young, self-fertilizing, allopolyploid weed with a worldwide distribution. One common garden was located in Europe, the other in Asia. We used accessions from three distinct genetic clusters (Middle East, Europe and Asia) that reflect the demographic history of the species. Several life-history traits were measured. To explain the phenotypic variation between and within genetic clusters, we analysed the effects of (i) the genetic clusters, (ii) the phenotypic plasticity and its association to fitness and (iii) the distance in terms of bioclimatic variables between the sampling site of an accession and the common garden, i.e. the environmental distance. Our experiment showed that (i) the performance of C. bursa-pastoris is closely related to its high phenotypic plasticity; (ii) within a common garden, genetic cluster was a main determinant of phenotypic differences; and (iii) at the scale of the experiment, the effect of environmental distance to the common garden could not be distinguished from that of genetic clusters. Phenotypic plasticity and demographic history both play important role at different stages of range expansion. The success of the worldwide expansion of C. bursa-pastoris was undoubtedly influenced by its strong phenotypic plasticity.
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Affiliation(s)
| | | | | | | | - Marion Orsucci
- Department of Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Pascal Milesi
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
- Science for Life Laboratory, 752 37 Uppsala, Sweden
| | - Dmytro Kryvokhyzha
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Karl Holm
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, M5S 3B2 Toronto, ON, Canada
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13
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Jaron KS, Parker DJ, Anselmetti Y, Tran Van P, Bast J, Dumas Z, Figuet E, François CM, Hayward K, Rossier V, Simion P, Robinson-Rechavi M, Galtier N, Schwander T. Convergent consequences of parthenogenesis on stick insect genomes. SCIENCE ADVANCES 2022; 8:eabg3842. [PMID: 35196080 PMCID: PMC8865771 DOI: 10.1126/sciadv.abg3842] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The shift from sexual reproduction to parthenogenesis has occurred repeatedly in animals, but how the loss of sex affects genome evolution remains poorly understood. We generated reference genomes for five independently evolved parthenogenetic species in the stick insect genus Timema and their closest sexual relatives. Using these references and population genomic data, we show that parthenogenesis results in an extreme reduction of heterozygosity and often leads to genetically uniform populations. We also find evidence for less effective positive selection in parthenogenetic species, suggesting that sex is ubiquitous in natural populations because it facilitates fast rates of adaptation. Parthenogenetic species did not show increased transposable element (TE) accumulation, likely because there is little TE activity in the genus. By using replicated sexual-parthenogenetic comparisons, our study reveals how the absence of sex affects genome evolution in natural populations, providing empirical support for the negative consequences of parthenogenesis as predicted by theory.
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Affiliation(s)
- Kamil S. Jaron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
- Corresponding author. (D.J.P.); (K.S.J.); (T.S.)
| | - Darren J. Parker
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Corresponding author. (D.J.P.); (K.S.J.); (T.S.)
| | | | - Patrick Tran Van
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jens Bast
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Emeric Figuet
- ISEM—Institut des Sciences de l’Evolution, Montpellier, France
| | | | - Keith Hayward
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Victor Rossier
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Paul Simion
- ISEM—Institut des Sciences de l’Evolution, Montpellier, France
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicolas Galtier
- ISEM—Institut des Sciences de l’Evolution, Montpellier, France
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Corresponding author. (D.J.P.); (K.S.J.); (T.S.)
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14
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Brand JN, Harmon LJ, Schärer L. Mating behavior and reproductive morphology predict macroevolution of sex allocation in hermaphroditic flatworms. BMC Biol 2022; 20:35. [PMID: 35130880 PMCID: PMC8822660 DOI: 10.1186/s12915-022-01234-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/18/2022] [Indexed: 11/10/2022] Open
Abstract
Background Sex allocation is the distribution of resources to male or female reproduction. In hermaphrodites, this concerns an individual’s resource allocation to, for example, the production of male or female gametes. Macroevolutionary studies across hermaphroditic plants have revealed that the self-pollination rate and the pollination mode are strong predictors of sex allocation. Consequently, we expect similar factors such as the selfing rate and aspects of the reproductive biology, like the mating behaviour and the intensity of postcopulatory sexual selection, to predict sex allocation in hermaphroditic animals. However, comparative work on hermaphroditic animals is limited. Here, we study sex allocation in 120 species of the hermaphroditic free-living flatworm genus Macrostomum. We ask how hypodermic insemination, a convergently evolved mating behaviour where sperm are traumatically injected through the partner’s epidermis, affects the evolution of sex allocation. We also test the commonly-made assumption that investment into male and female reproduction should trade-off. Finally, we ask if morphological indicators of the intensity of postcopulatory sexual selection (female genital complexity, male copulatory organ length, and sperm length) can predict sex allocation. Results We find that the repeated evolution of hypodermic insemination predicts a more female-biased sex allocation (i.e., a relative shift towards female allocation). Moreover, transcriptome-based estimates of heterozygosity reveal reduced heterozygosity in hypodermically mating species, indicating that this mating behavior is linked to increased selfing or biparental inbreeding. Therefore, hypodermic insemination could represent a selfing syndrome. Furthermore, across the genus, allocation to male and female gametes is negatively related, and larger species have a more female-biased sex allocation. Finally, increased female genital complexity, longer sperm, and a longer male copulatory organ predict a more male-biased sex allocation. Conclusions Selfing syndromes have repeatedly originated in plants. Remarkably, this macroevolutionary pattern is replicated in Macrostomum flatworms and linked to repeated shifts in reproductive behavior. We also find a trade-off between male and female reproduction, a fundamental assumption of most theories of sex allocation. Beyond that, no theory predicts a more female-biased allocation in larger species, suggesting avenues for future work. Finally, morphological indicators of more intense postcopulatory sexual selection appear to predict more intense sperm competition. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01234-1.
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Affiliation(s)
- Jeremias N Brand
- Department of Environmental Sciences, Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland. .,Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany.
| | - Luke J Harmon
- Department of Biological Sciences, University of Idaho, Life Sciences South 252, 875 Perimeter Dr MS 3051, Moscow, ID, USA
| | - Lukas Schärer
- Department of Environmental Sciences, Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
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15
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López Hernández JF, Helston RM, Lange JJ, Billmyre RB, Schaffner SH, Eickbush MT, McCroskey S, Zanders SE. Diverse mating phenotypes impact the spread of wtf meiotic drivers in Schizosaccharomyces pombe. eLife 2021; 10:e70812. [PMID: 34895466 PMCID: PMC8789285 DOI: 10.7554/elife.70812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 12/10/2021] [Indexed: 11/13/2022] Open
Abstract
Meiotic drivers are genetic elements that break Mendel's law of segregation to be transmitted into more than half of the offspring produced by a heterozygote. The success of a driver relies on outcrossing (mating between individuals from distinct lineages) because drivers gain their advantage in heterozygotes. It is, therefore, curious that Schizosaccharomyces pombe, a species reported to rarely outcross, harbors many meiotic drivers. To address this paradox, we measured mating phenotypes in S. pombe natural isolates. We found that the propensity for cells from distinct clonal lineages to mate varies between natural isolates and can be affected both by cell density and by the available sexual partners. Additionally, we found that the observed levels of preferential mating between cells from the same clonal lineage can slow, but not prevent, the spread of a wtf meiotic driver in the absence of additional fitness costs linked to the driver. These analyses reveal parameters critical to understanding the evolution of S. pombe and help explain the success of meiotic drivers in this species.
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Affiliation(s)
| | | | - Jeffrey J Lange
- Stowers Institute for Medical ResearchKansas CityUnited States
| | | | - Samantha H Schaffner
- Stowers Institute for Medical ResearchKansas CityUnited States
- Kenyon CollegeGambierUnited States
| | | | - Scott McCroskey
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Sarah E Zanders
- Stowers Institute for Medical ResearchKansas CityUnited States
- Department of Molecular and Integrative Physiology, University of Kansas Medical CenterKansas CityUnited States
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16
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Wiberg RAW, Brand JN, Schärer L. Faster Rates of Molecular Sequence Evolution in Reproduction-Related Genes and in Species with Hypodermic Sperm Morphologies. Mol Biol Evol 2021; 38:5685-5703. [PMID: 34534329 PMCID: PMC8662610 DOI: 10.1093/molbev/msab276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Sexual selection drives the evolution of many striking behaviors and morphologies and should leave signatures of selection at loci underlying these phenotypes. However, although loci thought to be under sexual selection often evolve rapidly, few studies have contrasted rates of molecular sequence evolution at such loci across lineages with different sexual selection contexts. Furthermore, work has focused on separate sexed animals, neglecting alternative sexual systems. We investigate rates of molecular sequence evolution in hermaphroditic flatworms of the genus Macrostomum. Specifically, we compare species that exhibit contrasting sperm morphologies, strongly associated with multiple convergent shifts in the mating strategy, reflecting different sexual selection contexts. Species donating and receiving sperm in every mating have sperm with bristles, likely to prevent sperm removal. Meanwhile, species that hypodermically inject sperm lack bristles, potentially as an adaptation to the environment experienced by hypodermic sperm. Combining functional annotations from the model, Macrostomum lignano, with transcriptomes from 93 congeners, we find genus-wide faster sequence evolution in reproduction-related versus ubiquitously expressed genes, consistent with stronger sexual selection on the former. Additionally, species with hypodermic sperm morphologies had elevated molecular sequence evolution, regardless of a gene's functional annotation. These genome-wide patterns suggest reduced selection efficiency following shifts to hypodermic mating, possibly due to higher selfing rates in these species. Moreover, we find little evidence for convergent amino acid changes across species. Our work not only shows that reproduction-related genes evolve rapidly also in hermaphroditic animals, but also that well-replicated contrasts of different sexual selection contexts can reveal underappreciated genome-wide effects.
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Affiliation(s)
- R Axel W Wiberg
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
| | - Jeremias N Brand
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
| | - Lukas Schärer
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
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17
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Huylmans AK, Macon A, Hontoria F, Vicoso B. Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. Proc Biol Sci 2021; 288:20211720. [PMID: 34547909 PMCID: PMC8456138 DOI: 10.1098/rspb.2021.1720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 08/31/2021] [Indexed: 11/12/2022] Open
Abstract
While sexual reproduction is widespread among many taxa, asexual lineages have repeatedly evolved from sexual ancestors. Despite extensive research on the evolution of sex, it is still unclear whether this switch represents a major transition requiring major molecular reorganization, and how convergent the changes involved are. In this study, we investigated the phylogenetic relationship and patterns of gene expression of sexual and asexual lineages of Eurasian Artemia brine shrimp, to assess how gene expression patterns are affected by the transition to asexuality. We find only a few genes that are consistently associated with the evolution of asexuality, suggesting that this shift may not require an extensive overhauling of the meiotic machinery. While genes with sex-biased expression have high rates of expression divergence within Eurasian Artemia, neither female- nor male-biased genes appear to show unusual evolutionary patterns after sexuality is lost, contrary to theoretical expectations.
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Affiliation(s)
- Ann Kathrin Huylmans
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
| | - Ariana Macon
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
| | - Francisco Hontoria
- Instituto de Acuicultura de Torre de la Sal (IATS-CSIC), 12595 Ribera de Cabanes, Castellón, Spain
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
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18
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Linde AM, Eklund DM, Cronberg N, Bowman JL, Lagercrantz U. Rates and patterns of molecular evolution in bryophyte genomes, with focus on complex thalloid liverworts, Marchantiopsida. Mol Phylogenet Evol 2021; 165:107295. [PMID: 34438050 DOI: 10.1016/j.ympev.2021.107295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/30/2021] [Accepted: 08/19/2021] [Indexed: 10/20/2022]
Abstract
Plants commonly referred to as "bryophytes" belong to three major lineages of non-vascular plants: the liverworts, the hornworts and the mosses. They are unique among land plants in having a dominant haploid generation and a short-lived diploid sporophytic generation. The dynamics of selection acting on a haploid genome differs from those acting on a diploid genome: new mutations are directly exposed to selection. The general aim of this paper is to investigate the diversification rateof bryophytes - measured as silent site substitution rate representing neutral evolution (mutation rate) and the nonsynonymous to synonymous substitution rate ratio (dN/dS) representing selective evolution - and compare it with earlier studies on vascular plants. Results show that the silent site substitution rate is lower for liverworts as compared to angiosperms, but not as low as for gymnosperms. The selection pressure, measured as dN/dS, isnot remarkably lower for bryophytes as compared to other diploid dominant plants as would be expected by the masking hypothesis, indicating that other factors are more important than ploidy.
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Affiliation(s)
- Anna-Malin Linde
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
| | - D Magnus Eklund
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
| | - Nils Cronberg
- Biodiversity, Department of Biology, Lund University, Ecology Building, SE-223 62 Lund, Sweden.
| | - John L Bowman
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Ulf Lagercrantz
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
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19
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McElroy KE, Müller S, Lamatsch DK, Bankers L, Fields PD, Jalinsky JR, Sharbrough J, Boore JL, Logsdon JM, Neiman M. Asexuality Associated with Marked Genomic Expansion of Tandemly Repeated rRNA and Histone Genes. Mol Biol Evol 2021; 38:3581-3592. [PMID: 33885820 PMCID: PMC8382920 DOI: 10.1093/molbev/msab121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
How does asexual reproduction influence genome evolution? Although is it clear that genomic structural variation is common and important in natural populations, we know very little about how one of the most fundamental of eukaryotic traits-mode of genomic inheritance-influences genome structure. We address this question with the New Zealand freshwater snail Potamopyrgus antipodarum, which features multiple separately derived obligately asexual lineages that coexist and compete with otherwise similar sexual lineages. We used whole-genome sequencing reads from a diverse set of sexual and asexual individuals to analyze genomic abundance of a critically important gene family, rDNA (the genes encoding rRNAs), that is notable for dynamic and variable copy number. Our genomic survey of rDNA in P. antipodarum revealed two striking results. First, the core histone and 5S rRNA genes occur between tandem copies of the 18S-5.8S-28S gene cluster, a unique architecture for these crucial gene families. Second, asexual P. antipodarum harbor dramatically more rDNA-histone copies than sexuals, which we validated through molecular and cytogenetic analysis. The repeated expansion of this genomic region in asexual P. antipodarum lineages following distinct transitions to asexuality represents a dramatic genome structural change associated with asexual reproduction-with potential functional consequences related to the loss of sexual reproduction.
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Affiliation(s)
- Kyle E McElroy
- Ecology, Evolutionary, and Organismal Biology, Iowa State University, Ames, IA, USA
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Stefan Müller
- Institute of Human Genetics, Munich University Hospital, Ludwig-Maximilians University, Munich, Germany
| | - Dunja K Lamatsch
- Research Department for Limnology, University of Innsbruck, Mondsee, Mondsee, Austria
| | - Laura Bankers
- Division of Infectious Diseases, University of Colorado—Anschutz Medical Campus, Aurora, CO, USA
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | | | - Joel Sharbrough
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, USA
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Jeffrey L Boore
- Providence St. Joseph Health and Institute for Systems Biology, Seattle, WA, USA
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, IA, USA
- Department of Gender, Women's, and Sexuality Studies, University of Iowa, Iowa City, IA, USA
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20
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Kozlowski DKL, Hassanaly‐Goulamhoussen R, Da Rocha M, Koutsovoulos GD, Bailly‐Bechet M, Danchin EGJ. Movements of transposable elements contribute to the genomic plasticity and species diversification in an asexually reproducing nematode pest. Evol Appl 2021; 14:1844-1866. [PMID: 34295368 PMCID: PMC8288018 DOI: 10.1111/eva.13246] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 12/14/2022] Open
Abstract
Despite reproducing without sexual recombination, Meloidogyne incognita is an adaptive and versatile phytoparasitic nematode. This species displays a global distribution, can parasitize a large range of plants, and can overcome plant resistance in a few generations. The mechanisms underlying this adaptability remain poorly known. At the whole-genome level, only a few single nucleotide variations have been observed across different geographical isolates with distinct ranges of compatible hosts. Exploring other factors possibly involved in genomic plasticity is thus important. Transposable elements (TEs), by their repetitive nature and mobility, can passively and actively impact the genome dynamics. This is particularly expected in polyploid hybrid genomes such as the one of M. incognita. Here, we have annotated the TE content of M. incognita, analyzed the statistical properties of this TE landscape, and used whole-genome pool-seq data to estimate the mobility of these TEs across twelve geographical isolates, presenting variations in ranges of compatible host plants. DNA transposons are more abundant than retrotransposons, and the high similarity of TE copies to their consensus sequences suggests they have been at least recently active. We have identified loci in the genome where the frequencies of presence of a TE showed substantial variations across the different isolates. Overall, variations in TE frequencies across isolates followed their phylogenetic divergence, suggesting TEs participate in the species diversification. Compared with the M. incognita reference genome, we detected isolate and lineage-specific de novo insertion of some TEs, including within genic regions or in the upstream regulatory regions. We validated by PCR the insertion of some of these TEs inside genic regions, confirming TE movements have possible functional impacts. Overall, we show DNA transposons can drive genomic plasticity in M. incognita and their role in genome evolution of other parthenogenetic animal deserves further investigation.
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21
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Hyun DY, Sebastin R, Lee GA, Lee KJ, Kim SH, Yoo E, Lee S, Kang MJ, Lee SB, Jang I, Ro NY, Cho GT. Genome-Wide SNP Markers for Genotypic and Phenotypic Differentiation of Melon ( Cucumis melo L.) Varieties Using Genotyping-by-Sequencing. Int J Mol Sci 2021; 22:ijms22136722. [PMID: 34201603 PMCID: PMC8268568 DOI: 10.3390/ijms22136722] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/16/2021] [Accepted: 06/16/2021] [Indexed: 12/29/2022] Open
Abstract
Melon (Cucumis melo L.) is an economically important horticultural crop with abundant morphological and genetic variability. Complex genetic variations exist even among melon varieties and remain unclear to date. Therefore, unraveling the genetic variability among the three different melon varieties, muskmelon (C. melo subsp. melo), makuwa (C. melo L. var. makuwa), and cantaloupes (C. melo subsp. melo var. cantalupensis), could provide a basis for evolutionary research. In this study, we attempted a systematic approach with genotyping-by-sequencing (GBS)-derived single nucleotide polymorphisms (SNPs) to reveal the genetic structure and diversity, haplotype differences, and marker-based varieties differentiation. A total of 6406 GBS-derived SNPs were selected for the diversity analysis, in which the muskmelon varieties showed higher heterozygote SNPs. Linkage disequilibrium (LD) decay varied significantly among the three melon varieties, in which more rapid LD decay was observed in muskmelon (r2 = 0.25) varieties. The Bayesian phylogenetic tree provided the intraspecific relationships among the three melon varieties that formed, as expected, individual clusters exhibiting the greatest genetic distance based on the posterior probability. The haplotype analysis also supported the phylogeny result by generating three major networks for 48 haplotypes. Further investigation for varieties discrimination allowed us to detect a total of 52 SNP markers that discriminated muskmelon from makuwa varieties, of which two SNPs were converted into cleaved amplified polymorphic sequence markers for practical use. In addition to these markers, the genome-wide association study identified two SNPs located in the genes on chromosome 6, which were significantly associated with the phenotypic traits of melon seed. This study demonstrated that a systematic approach using GBS-derived SNPs could serve to efficiently classify and manage the melon varieties in the genebank.
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Affiliation(s)
- Do Yoon Hyun
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
- Correspondence:
| | - Raveendar Sebastin
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Gi-An Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Kyung Jun Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
- Honam National Institute of Biological Resources, Mokpo-si 58762, Korea
| | - Seong-Hoon Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Eunae Yoo
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Sookyeong Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Man-Jung Kang
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Seung Bum Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Ik Jang
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Na-Young Ro
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Gyu-Taek Cho
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
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Liang Y, Liu HJ, Yan J, Tian F. Natural Variation in Crops: Realized Understanding, Continuing Promise. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:357-385. [PMID: 33481630 DOI: 10.1146/annurev-arplant-080720-090632] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Crops feed the world's population and shape human civilization. The improvement of crop productivity has been ongoing for almost 10,000 years and has evolved from an experience-based to a knowledge-driven practice over the past three decades. Natural alleles and their reshuffling are long-standing genetic changes that affect how crops respond to various environmental conditions and agricultural practices. Decoding the genetic basis of natural variation is central to understanding crop evolution and, in turn, improving crop breeding. Here, we review current advances in the approaches used to map the causal alleles of natural variation, provide refined insights into the genetics and evolution of natural variation, and outline how this knowledge promises to drive the development of sustainable agriculture under the dome of emerging technologies.
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Affiliation(s)
- Yameng Liang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; ,
| | - Hai-Jun Liu
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, 1030 Vienna, Austria;
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
| | - Feng Tian
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; ,
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Tran Van P, Anselmetti Y, Bast J, Dumas Z, Galtier N, Jaron KS, Martens K, Parker DJ, Robinson-Rechavi M, Schwander T, Simion P, Schön I. First annotated draft genomes of nonmarine ostracods (Ostracoda, Crustacea) with different reproductive modes. G3 (BETHESDA, MD.) 2021; 11:jkab043. [PMID: 33591306 PMCID: PMC8049415 DOI: 10.1093/g3journal/jkab043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/05/2021] [Indexed: 11/14/2022]
Abstract
Ostracods are one of the oldest crustacean groups with an excellent fossil record and high importance for phylogenetic analyses but genome resources for this class are still lacking. We have successfully assembled and annotated the first reference genomes for three species of nonmarine ostracods; two with obligate sexual reproduction (Cyprideis torosa and Notodromas monacha) and the putative ancient asexual Darwinula stevensoni. This kind of genomic research has so far been impeded by the small size of most ostracods and the absence of genetic resources such as linkage maps or BAC libraries that were available for other crustaceans. For genome assembly, we used an Illumina-based sequencing technology, resulting in assemblies of similar sizes for the three species (335-382 Mb) and with scaffold numbers and their N50 (19-56 kb) in the same orders of magnitude. Gene annotations were guided by transcriptome data from each species. The three assemblies are relatively complete with BUSCO scores of 92-96. The number of predicted genes (13,771-17,776) is in the same range as Branchiopoda genomes but lower than in most malacostracan genomes. These three reference genomes from nonmarine ostracods provide the urgently needed basis to further develop ostracods as models for evolutionary and ecological research.
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Affiliation(s)
- Patrick Tran Van
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Yoann Anselmetti
- ISEM—Institut des Sciences de l’Evolution, Montpellier 34090, France
| | - Jens Bast
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Nicolas Galtier
- ISEM—Institut des Sciences de l’Evolution, Montpellier 34090, France
| | - Kamil S Jaron
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Koen Martens
- Royal Belgian Institute of Natural Sciences, OD Nature, Freshwater Biology, Brussels 1000, Belgium
- Department of Biology, University of Ghent, Ghent 9000, Belgium
| | - Darren J Parker
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Paul Simion
- ISEM—Institut des Sciences de l’Evolution, Montpellier 34090, France
- Université de Namur, LEGE, URBE, Namur 5000, Belgium
| | - Isa Schön
- Royal Belgian Institute of Natural Sciences, OD Nature, Freshwater Biology, Brussels 1000, Belgium
- University of Hasselt, Research Group Zoology, Diepenbeek 3590, Belgium
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Ferrer MM, Tapia-Gómez CA, Estrada-Medina H, Ruenes-Morales MDR, Montañez-Escalante PI, Jiménez-Osornio JJ. Growing Out of the Tropical Forests: Gene Flow of Native Mesoamerican Trees Among Forest and Mayan Homegardens. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.628765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
This work aimed to evaluate domestication effects on the genetic structure of two dioecious speciesBrosimum alicastrumSw. (Moraceae) andSpondias purpureaL. (Anacardiaceae), and a heterostylous oneCordia dodecandraA. DC. (Cordiaceae), growing in remnant forests and homegardens within two climatic regions of the Peninsula of Yucatan. The trees ofB. alicastrumandC. dodecandraare propagated by seeds in both population types, while those ofS. purpureaare propagated asexually in the homegardens. ISSRs genetic markers were amplified from foliar tissue of 18 to 21 plants per population type/region combination for each species. Genetic diversity, genetic differentiation, and genetic structure estimators were obtained and compared among species at the regional and population level. We found higher polymorphism (37.5–41), but lower private alleles (4–4.4) and similar heterozygosity (0.1–0.12) in the species with sexual reproduction compared toS. purpurea(34, 8, and 0.11, respectively). Genetic diversity inB. alicastrumpopulations varied with the region; inC. dodecandra, to the population type; and inS. purpurea, to both the population type and the region. Unrestricted gene flow among regions was suggested by low ΦRTinC. dodecandraandS. purpurea(−0.006 and 0.002) but not forB. alicastrum(0.1). Gene flow between populations within the regions for the sexually reproducing species was suggested by lower θII(0.005–0.07 and 0.008–0.1) estimates than those ofS. purpurea(0.09 and 0.13). Even though the lowest paired FST(0.002–0.05) and ΦST(0.002–0.12) values were found between the northeastern forest and homegarden populations for the three species, the dendrogram, Bayesian assignment, and K-Means analyses suggest that the least differentiated populations are southwestern forest and homegarden populations ofB. alicastrumandS. purpurea, and the southwestern forest and northeastern homegarden ofC. dodecandra. The sexual reproduction, biotic interactions, and extensive management ofB. alicastrumandC. dodecandrain the agroforestry and the urban systems may contribute to connectivity between wild and domesticated populations, while inS. purpureathis connectivity is interrupted by the clonal propagation of the species in the homegardens.
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Glémin S. Balancing selection in self-fertilizing populations. Evolution 2021; 75:1011-1029. [PMID: 33675041 DOI: 10.1111/evo.14194] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/17/2021] [Indexed: 11/30/2022]
Abstract
Self-fertilization commonly occurs in hermaphroditic species, either occasionally or as the main reproductive mode. It strongly affects the genetic functioning of a population by increasing homozygosity and genetic drift and reducing the effectiveness of recombination. Balancing selection is a form of selection that maintains polymorphism, which has been extensively studied in outcrossing species. Yet, despite recent developments, the analysis of balancing selection in partially selfing species is limited to specific cases and a general treatment is still lacking. In particular, it is unclear whether selfing globally reduced the efficacy of balancing selection as in the well-known case of overdominance. I provide a unifying framework, quantify how selfing affects the maintenance of polymorphism and the efficacy of the different form of balancing selection, and show that they can be classified into two main categories: overdominance-like selection (including true overdominance, selection variable in space and time, and antagonistic selection), which is strongly affected by selfing, and negative frequency dependent selection, which is barely affected by selfing, even at multiple loci. I also provide simple analytical results for all cases under the assumption of weak selection. This framework provides theoretical background to analyze the genomic signature of balancing selection in partially selfing species. It also sheds new light on the evolution of selfing species, including the evolution of selfing syndrome, the interaction with pathogens, and the evolutionary fate of selfing lineages.
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Affiliation(s)
- Sylvain Glémin
- CNRS, ECOBIO (Ecosystèmes, biodiversité, évolution), University of Rennes 1, UMR 6553, Rennes, France.,Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, 752 36, Sweden
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A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod Darwinula stevensoni. Genes (Basel) 2021; 12:genes12030401. [PMID: 33799706 PMCID: PMC7998251 DOI: 10.3390/genes12030401] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/02/2021] [Accepted: 03/06/2021] [Indexed: 11/17/2022] Open
Abstract
How asexual reproduction shapes transposable element (TE) content and diversity in eukaryotic genomes remains debated. We performed an initial survey of TE load and diversity in the putative ancient asexual ostracod Darwinula stevensoni. We examined long contiguous stretches of DNA in clones from a genomic fosmid library, totaling about 2.5 Mb, and supplemented these data with results on TE abundance and diversity from an Illumina draft genome. In contrast to other TE studies in putatively ancient asexuals, which revealed relatively low TE content, we found that at least 19% of the fosmid dataset and 26% of the genome assembly corresponded to known transposons. We observed a high diversity of transposon families, including LINE, gypsy, PLE, mariner/Tc, hAT, CMC, Sola2, Ginger, Merlin, Harbinger, MITEs and helitrons, with the prevalence of DNA transposons. The predominantly low levels of sequence diversity indicate that many TEs are or have recently been active. In the fosmid data, no correlation was found between telomeric repeats and non-LTR retrotransposons, which are present near telomeres in other taxa. Most TEs in the fosmid data were located outside of introns and almost none were found in exons. We also report an N-terminal Myb/SANT-like DNA-binding domain in site-specific R4/Dong non-LTR retrotransposons. Although initial results on transposable loads need to be verified with high quality draft genomes, this study provides important first insights into TE dynamics in putative ancient asexual ostracods.
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Muyle A, Martin H, Zemp N, Mollion M, Gallina S, Tavares R, Silva A, Bataillon T, Widmer A, Glémin S, Touzet P, Marais GAB. Dioecy Is Associated with High Genetic Diversity and Adaptation Rates in the Plant Genus Silene. Mol Biol Evol 2021; 38:805-818. [PMID: 32926156 PMCID: PMC7947750 DOI: 10.1093/molbev/msaa229] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
About 15,000 angiosperm species (∼6%) have separate sexes, a phenomenon known as dioecy. Why dioecious taxa are so rare is still an open question. Early work reported lower species richness in dioecious compared with nondioecious sister clades, raising the hypothesis that dioecy may be an evolutionary dead-end. This hypothesis has been recently challenged by macroevolutionary analyses that detected no or even positive effect of dioecy on diversification. However, the possible genetic consequences of dioecy at the population level, which could drive the long-term fate of dioecious lineages, have not been tested so far. Here, we used a population genomics approach in the Silene genus to look for possible effects of dioecy, especially for potential evidence of evolutionary handicaps of dioecy underlying the dead-end hypothesis. We collected individual-based RNA-seq data from several populations in 13 closely related species with different sexual systems: seven dioecious, three hermaphroditic, and three gynodioecious species. We show that dioecy is associated with increased genetic diversity, as well as higher selection efficacy both against deleterious mutations and for beneficial mutations. The results hold after controlling for phylogenetic inertia, differences in species census population sizes and geographic ranges. We conclude that dioecious Silene species neither show signs of increased mutational load nor genetic evidence for extinction risk. We discuss these observations in the light of the possible demographic differences between dioecious and self-compatible hermaphroditic species and how this could be related to alternatives to the dead-end hypothesis to explain the rarity of dioecy.
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Affiliation(s)
- Aline Muyle
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA
| | - Hélène Martin
- University of Lille, CNRS, UMR 8198—Evo-Eco-Paleo, F-59000 Lille, France
- Département de Biologie, Institut de Biologie Integrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Niklaus Zemp
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Genetic Diversity Centre (GDC), ETH Zurich, Zurich, Switzerland
| | - Maéva Mollion
- Bioinformatics Research Centre, Aarhus University, Aarhus C, Denmark
| | - Sophie Gallina
- University of Lille, CNRS, UMR 8198—Evo-Eco-Paleo, F-59000 Lille, France
| | - Raquel Tavares
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
| | - Alexandre Silva
- Centro de Interpretação da Serra da Estrela (CISE), Seia, Portugal
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus C, Denmark
| | - Alex Widmer
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Sylvain Glémin
- CNRS, ECOBIO [(Ecosystèmes, Biodiversité, Évolution)]—UMR 6553, University of Rennes, Rennes, France
- Department of Ecology and Genetics, Evolutionary Biology Center and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Pascal Touzet
- University of Lille, CNRS, UMR 8198—Evo-Eco-Paleo, F-59000 Lille, France
| | - Gabriel A B Marais
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
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Woodruff GC, Teterina AA. Degradation of the Repetitive Genomic Landscape in a Close Relative of Caenorhabditis elegans. Mol Biol Evol 2020; 37:2549-2567. [PMID: 32359146 PMCID: PMC7475029 DOI: 10.1093/molbev/msaa107] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The abundance, diversity, and genomic distribution of repetitive elements is highly variable among species. These patterns are thought to be driven in part by reproductive mode and the interaction of selection and recombination, and recombination rates typically vary by chromosomal position. In the nematode Caenorhabditis elegans, repetitive elements are enriched at chromosome arms and depleted on centers, and this mirrors the chromosomal distributions of other genomic features such as recombination rate. How conserved is this genomic landscape of repeats, and what evolutionary forces maintain it? To address this, we compared the genomic organization of repetitive elements across five Caenorhabditis species with chromosome-level assemblies. As previously reported, repeat content is enriched on chromosome arms in most Caenorhabditis species, and no obvious patterns of repeat content associated with reproductive mode were observed. However, the fig-associated C. inopinata has experienced repetitive element expansion and reveals no association of global repeat density with chromosome position. Patterns of repeat superfamily specific distributions reveal this global pattern is driven largely by a few repeat superfamilies that in C. inopinata have expanded in number and have weak associations with chromosome position. Additionally, 15% of predicted protein-coding genes in C. inopinata align to transposon-related proteins. When these are excluded, C. inopinata has no enrichment of genes in chromosome centers, in contrast to its close relatives who all have such clusters. Forward evolutionary simulations reveal that chromosomal heterogeneity in recombination rate alone can generate structured repetitive genomic landscapes when insertions are weakly deleterious, whereas chromosomal heterogeneity in the fitness effects of transposon insertion can promote such landscapes across a variety of evolutionary scenarios. Thus, patterns of gene density along chromosomes likely contribute to global repetitive landscapes in this group, although other historical or genomic factors are needed to explain the idiosyncrasy of genomic organization of various transposable element taxa within C. inopinata. Taken together, these results highlight the power of comparative genomics and evolutionary simulations in testing hypotheses regarding the causes of genome organization.
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Affiliation(s)
- Gavin C Woodruff
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR
| | - Anastasia A Teterina
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR
- Center of Parasitology, Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
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Ruane LG, Mangum SM, Horner KM, Moeller DA. The opportunity for outcrossing varies across the geographic range of the primarily selfing Clarkia xantiana ssp. parviflora. AMERICAN JOURNAL OF BOTANY 2020; 107:1198-1207. [PMID: 32700343 DOI: 10.1002/ajb2.1510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 02/22/2020] [Indexed: 06/11/2023]
Abstract
PREMISE The timing of self-fertilization has potentially important consequences for the trajectory of mating system evolution, the opportunity for outcrossing, and the maintenance of genetic variation in populations. For primarily selfing taxa, it remains poorly understood as to how floral variation influences the opportunity for outcrossing and whether those attributes vary among populations across geographic ranges. METHODS We examined variation in floral traits (herkogamy, protandry, flower size, stigma stage at anthesis, timing of stigma receptivity) in seven populations of Clarkia xantiana ssp. parviflora, a primarily selfing taxon, spanning from the western to eastern margins of its distribution. We also performed experimental emasculations and pollinations (followed by stigma severing) to quantify the extent of opportunities for outcrossing across flower development. RESULTS There was marked among-population variation in all floral traits, particularly between far eastern and western populations. Emasculation experiments showed that the eastern populations had minimal autonomous selfing, but western populations had high rates of selfing within 24 h after anthesis. Population variation in autofertility was significantly predicted by floral trait variation, especially protandry and petal size. CONCLUSIONS Greater protandry both extended the time over which outcrossing could potentially occur and reduced the probability of autonomous selfing, suggesting that there may be a tradeoff that results in fitness loss when pollinator visits are not common. The east-west pattern of differentiation in some floral traits parallels that of postglacial range expansion, suggesting that selection on the mating system may have been strong in the process of range expansion.
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Affiliation(s)
- Lauren G Ruane
- Department of Organismal and Environmental Biology, Christopher Newport University, 1 Avenue of the Arts, Newport News, Virginia, 23606, United States
| | - Samantha M Mangum
- Department of Organismal and Environmental Biology, Christopher Newport University, 1 Avenue of the Arts, Newport News, Virginia, 23606, United States
| | - Kaitlyn M Horner
- Department of Organismal and Environmental Biology, Christopher Newport University, 1 Avenue of the Arts, Newport News, Virginia, 23606, United States
| | - David A Moeller
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota, 55108, United States
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Cutter AD, Morran LT, Phillips PC. Males, Outcrossing, and Sexual Selection in Caenorhabditis Nematodes. Genetics 2019; 213:27-57. [PMID: 31488593 PMCID: PMC6727802 DOI: 10.1534/genetics.119.300244] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 06/06/2019] [Indexed: 12/15/2022] Open
Abstract
Males of Caenorhabditis elegans provide a crucial practical tool in the laboratory, but, as the rarer and more finicky sex, have not enjoyed the same depth of research attention as hermaphrodites. Males, however, have attracted the attention of evolutionary biologists who are exploiting the C. elegans system to test longstanding hypotheses about sexual selection, sexual conflict, transitions in reproductive mode, and genome evolution, as well as to make new discoveries about Caenorhabditis organismal biology. Here, we review the evolutionary concepts and data informed by study of males of C. elegans and other Caenorhabditis We give special attention to the important role of sperm cells as a mediator of inter-male competition and male-female conflict that has led to drastic trait divergence across species, despite exceptional phenotypic conservation in many other morphological features. We discuss the evolutionary forces important in the origins of reproductive mode transitions from males being common (gonochorism: females and males) to rare (androdioecy: hermaphrodites and males) and the factors that modulate male frequency in extant androdioecious populations, including the potential influence of selective interference, host-pathogen coevolution, and mutation accumulation. Further, we summarize the consequences of males being common vs rare for adaptation and for trait divergence, trait degradation, and trait dimorphism between the sexes, as well as for molecular evolution of the genome, at both micro-evolutionary and macro-evolutionary timescales. We conclude that C. elegans male biology remains underexploited and that future studies leveraging its extensive experimental resources are poised to discover novel biology and to inform profound questions about animal function and evolution.
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Affiliation(s)
- Asher D Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario M5S3B2, Canada
| | - Levi T Morran
- Department of Biology, Emory University, Atlanta, Georgia 30322, and
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
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