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Yarbrough E, Chandler C. Patterns of molecular evolution in a parthenogenic terrestrial isopod ( Trichoniscus pusillus). PeerJ 2024; 12:e17780. [PMID: 39071119 PMCID: PMC11276757 DOI: 10.7717/peerj.17780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 06/30/2024] [Indexed: 07/30/2024] Open
Abstract
The "paradox of sex" refers to the question of why sexual reproduction is maintained in the wild, despite how costly it is compared to asexual reproduction. Because of these costs, one might expect nature to select for asexual reproduction, yet sex seems to be continually selected for. Multiple hypotheses have been proposed to explain this incongruence, including the niche differentiation hypothesis, the Red Queen hypothesis, and accumulation of harmful mutations in asexual species due to inefficient purifying selection. This study focuses on the accumulation of mutations in two terrestrial isopods, Trichoniscus pusillus, which has sexual diploid and parthenogenic triploid forms, and Hyloniscus riparius, an obligately sexual relative. We surveyed sex ratios of both species in an upstate New York population and obtained RNA-seq data from wild-caught individuals of both species to examine within- and between-species patterns of molecular evolution in protein-coding genes. The sex ratio and RNA-seq data together provide strong evidence that this T. pusillus population is entirely asexual and triploid, while the H. riparius population is sexual and diploid. Although all the wild T. pusillus individuals used for sequencing shared identical genotypes at nearly all SNPs, supporting a clonal origin, heterozygosity and SNP density were much higher in T. pusillus than in the sexually reproducing H. riparius. This observation suggests this parthenogenic lineage may have arisen via mating between two divergent diploid lineages. Between-species sequence comparisons showed no evidence of ineffective purifying selection in the asexual T. pusillus lineage, as measured by the ratio of nonsynonymous to synonymous substitutions (dN/dS ratios). Likewise, there was no difference between T. pusillus and H. riparius in the ratios of nonsynonymous to synonymous SNPs overall (pN/pS). However, pN/pS ratios in T. pusillus were significantly higher when considering only SNPs that may have arisen via recent mutation after the transition to parthenogenesis. Thus, these recent SNPs are consistent with the hypothesis that purifying selection is less effective against new mutations in asexual lineages, but only over long time scales. This system provides a useful model for future studies on the evolutionary tradeoffs between sexual and asexual reproduction in nature.
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Affiliation(s)
- Emily Yarbrough
- Department of Biological Sciences, State University of New York at Oswego, Oswego, NY, United States of America
- Department of Biological Sciences, State University of New York at Binghamton, Binghamton, NY, United States of America
| | - Christopher Chandler
- Department of Biological Sciences, State University of New York at Oswego, Oswego, NY, United States of America
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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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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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Bartoš O, Bohlen J, Šlechtová VB, Kočí J, Röslein J, Janko K. Sequence capture: Obsolete or irreplaceable? A thorough validation across phylogenetic distances and its applicability to hybrids and allopolyploids. Mol Ecol Resour 2023. [PMID: 37122140 DOI: 10.1111/1755-0998.13806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 05/02/2023]
Abstract
As whole-genome sequencing has become pervasive, some have suggested that reduced genomic representation approaches, for example, sequence capture, are becoming obsolete. In the present study, we argue that these techniques still provide excellent tools in terms of price and quality of data as well as in their ability to provide markers with specific features, as required, for example, in phylogenomics. A potential drawback of the wide-scale application of reduced representation approaches could be their drop in efficiency with increasing phylogenetic distance from the reference species. While some studies have focused on the degree and performance of reduced representation techniques in such situations, to our knowledge, none of them evaluated their applicability to inter-specific hybrids and polyploids. This highlights a significant gap in current knowledge since there is increasing evidence for the frequent occurrence of natural hybrids and polyploids, as well as for the major importance of both phenomena in evolution. The main aim of the present study was to carry out a thorough validation of SEQcap applicability to (1) a set of non-model taxa with a wide range of phylogenetic relatedness and (2) inter-specific hybrids of various ploidies and genomic compositions. Considering the latter point, we especially focused on mechanisms causing allelic bias and consequent allelic dropout, as these could have confounding effects with respect to the evolutionary genomic dynamics of hybrids, especially in asexuals, which virtually reproduce as a frozen F1 generation.
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Affiliation(s)
- Oldřich Bartoš
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Libechov, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jörg Bohlen
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Libechov, Czech Republic
| | - Vendula Bohlen Šlechtová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Libechov, Czech Republic
| | - Jan Kočí
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Libechov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jan Röslein
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Libechov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Karel Janko
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Libechov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
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Yadav V, Sun S, Heitman J. On the evolution of variation in sexual reproduction through the prism of eukaryotic microbes. Proc Natl Acad Sci U S A 2023; 120:e2219120120. [PMID: 36867686 PMCID: PMC10013875 DOI: 10.1073/pnas.2219120120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/23/2023] [Indexed: 03/05/2023] Open
Abstract
Almost all eukaryotes undergo sexual reproduction to generate diversity and select for fitness in their population pools. Interestingly, the systems by which sex is defined are highly diverse and can even differ between evolutionarily closely related species. While the most commonly known form of sex determination involves males and females in animals, eukaryotic microbes can have as many as thousands of different mating types for the same species. Furthermore, some species have found alternatives to sexual reproduction and prefer to grow clonally and yet undergo infrequent facultative sexual reproduction. These organisms are mainly invertebrates and microbes, but several examples are also present among vertebrates suggesting that alternative modes of sexual reproduction evolved multiple times throughout evolution. In this review, we summarize the sex-determination modes and variants of sexual reproduction found across the eukaryotic tree of life and suggest that eukaryotic microbes provide unique opportunities to study these processes in detail. We propose that understanding variations in modes of sexual reproduction can serve as a foundation to study the evolution of sex and why and how it evolved in the first place.
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Affiliation(s)
- Vikas Yadav
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC27710
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC27710
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC27710
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Morozov-Leonov SY. Reproduction and the Evolutionary Potential of the Hybrid Form Pelophylax Esculentus-Bidibundus (Amphibia, Ranidae) within the Drainages of Pripyat, Dniester, and Southern Bug Rivers. CYTOL GENET+ 2023. [DOI: 10.3103/s0095452723010085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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7
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Paetzold C, Barke BH, Hörandl E. Evolution of Transcriptomes in Early-Generation Hybrids of the Apomictic Ranunculus auricomus Complex ( Ranunculaceae). Int J Mol Sci 2022; 23:ijms232213881. [PMID: 36430360 PMCID: PMC9697309 DOI: 10.3390/ijms232213881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/12/2022] Open
Abstract
Hybridisation in plants may cause a shift from sexual to asexual seed formation (apomixis). Indeed, natural apomictic plants are usually hybrids, but it is still unclear how hybridisation could trigger the shift to apomixis. The genome evolution of older apomictic lineages is influenced by diverse processes such as polyploidy, mutation accumulation, and allelic sequence divergence. To disentangle the effects of hybridisation from these other factors, we analysed the transcriptomes of flowering buds from artificially produced, diploid F2 hybrids of the Ranunculus auricomus complex. The hybrids exhibited unreduced embryo sac formation (apospory) as one important component of apomixis, whereas their parental species were sexual. We revealed 2915 annotated single-copy genes that were mostly under purifying selection according to dN/dS ratios. However, pairwise comparisons revealed, after rigorous filtering, 79 genes under diversifying selection between hybrids and parents, whereby gene annotation assigned ten of them to reproductive processes. Four genes belong to the meiosis-sporogenesis phase (ASY1, APC1, MSP1, and XRI1) and represent, according to literature records, candidate genes for apospory. We conclude that hybridisation could combine novel (or existing) mutations in key developmental genes in certain hybrid lineages, and establish (together with altered gene expression profiles, as observed in other studies) a heritable regulatory mechanism for aposporous development.
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Affiliation(s)
- Claudia Paetzold
- Department of Botany and Molecular Evolution, Senckenberg Research Institute, 60325 Frankfurt am Main, Germany
| | - Birthe H. Barke
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, 37073 Goettingen, Germany
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, 37073 Goettingen, Germany
- Correspondence:
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Pierre JS, Stoeckel S, Wajnberg E. The advantage of sex: Reinserting fluctuating selection in the pluralist approach. PLoS One 2022; 17:e0272134. [PMID: 35917359 PMCID: PMC9345338 DOI: 10.1371/journal.pone.0272134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 07/13/2022] [Indexed: 11/29/2022] Open
Abstract
The advantage of sex, and its fixation in some clades and species all over the eukaryote tree of life, is considered an evolutionary enigma, especially regarding its assumed two-fold cost. Several likely hypotheses have been proposed such as (1) a better response to the negative frequency-dependent selection imposed by the “Red Queen” hypothesis; (2) the competition between siblings induced by the Tangled Bank hypothesis; (3) the existence of genetic and of (4) ecological factors that can diminish the cost of sex to less than the standard assumed two-fold; and (5) a better maintenance of genetic diversity and its resulting phenotypic variation, providing a selective advantage in randomly fluctuating environments. While these hypotheses have mostly been studied separately, they can also act simultaneously. This was advocated by several studies which presented a pluralist point of view. Only three among the five causes cited above were considered yet in such a framework: the Red Queen hypothesis, the Tangled Bank and the genetic factors lowering the cost of sex. We thus simulated the evolution of a finite mutating population undergoing negative frequency-dependent selection on phenotypes and a two-fold (or less) cost of sexuality, experiencing randomly fluctuating selection along generations. The individuals inherited their reproductive modes, either clonal or sexual. We found that exclusive sexuality begins to fix in populations exposed to environmental variation that exceeds the width of one ecological niche (twice the standard deviation of a Gaussian response to environment). This threshold was lowered by increasing negative frequency-dependent selection and when reducing the two-fold cost of sex. It contributes advocating that the different processes involved in a short-term advantage of sex and recombination can act in combination to favor the fixation of sexual reproduction in populations.
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Affiliation(s)
- Jean-Sébastien Pierre
- UMR 6553 Ecologie Biodiversité Evolution, CNRS INEE, Université de Rennes 1, OSUR, Campus de Beaulieu, Rennes Cedex, France
- * E-mail:
| | - Solenn Stoeckel
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, France
| | - Eric Wajnberg
- INRAE, Sophia Antipolis Cedex, France
- Projet Hephaistos, INRIA, Sophia Antipolis Cedex, France
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9
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Yan ZC, Qi GY, Yao TY, Li YX. Mitochondrial Genomes of Two Asexual Trichogramma (Hymenoptera: Trichogrammatidae) Strains and Comparison with Their Sexual Relatives. INSECTS 2022; 13:insects13060549. [PMID: 35735886 PMCID: PMC9224637 DOI: 10.3390/insects13060549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 05/30/2022] [Accepted: 06/15/2022] [Indexed: 02/05/2023]
Abstract
Simple Summary Sexual reproduction is dominant in animals, while asexual lineages are rare and evolutionarily short-lived. However, sexual reproduction has substantial costs, such as male production, inputs to courtship and mating, increased risk of predator exposure, and sexually transmitted diseases. A large body of theories has been proposed to explain the paradox of sex. One favored explanation is that asexuals are more likely to accumulate a greater number of deleterious mutations, known as Muller’s ratchet. Trichogramma is a genus of egg parasitoid wasps and is widely used as a biological control agent for agricultural and forest pests. With asexual lineages in at least 16 species, Trichogramma provides an excellent model to investigate the causes and consequences of asexual reproduction. In this study, we sequenced and assembled two asexual Trichogramma mitogenomes, representing two divergent origins of asexual reproduction. The asexual T. pretiosum is induced by the endosymbiont Wolbachia, while T. cacoeciae presumably originates from interspecific hybridization. To test Muller’s ratchet hypothesis, we compared these two asexual mitogenomes with their sexual relatives and found no association between asexual reproduction and mutation accumulation. This study provides a basis for further investigation into mitochondrial evolution and asexual reproduction in Trichogramma. Abstract Despite its substantial costs, sexual reproduction dominates in animals. One popular explanation for the paradox of sex is that asexual reproduction is more likely to accumulate deleterious mutations than sexual reproduction. To test this hypothesis, we compared the mitogenomes of two asexual wasp strains, Trichogramma cacoeciae and T. pretiosum, to their sexual relatives. These two asexual strains represent two different transition mechanisms in Trichogramma from sexual to asexual reproduction. Asexual T. pretiosum is induced by Wolbachia, while T. cacoeciae presumably originated from interspecific hybridization. We sequenced and assembled complete mitochondrial genomes of asexual T. cacoeciae and T. pretiosum. Compared to four sexual relatives, we found no evidence of higher mutation accumulation in asexual Trichogramma mitogenomes than in their sexual relatives. We also did not detect any relaxed selection in asexual Trichogramma mitogenomes. In contrast, the intensified selection was detected in Nad1 and Nad4 of the asexual T. pretiosum mitogenome, suggesting more purifying selection. In summary, no higher mitochondrial mutation accumulation was detected in these two asexual Trichogramma strains. This study provides a basis for further investigating mitochondrial evolution and asexual reproduction in Trichogramma.
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Affiliation(s)
- Zhi-Chao Yan
- Department of Entomology, Nanjing Agricultural University, Nanjing 210095, China; (Z.-C.Y.); (G.-Y.Q.); (T.-Y.Y.)
- Key Laboratory of Integrated Pest Management in Crops in Eastern China (Nanjing Agricultural University), Ministry of Agriculture, Nanjing 210095, China
| | - Guang-Yuan Qi
- Department of Entomology, Nanjing Agricultural University, Nanjing 210095, China; (Z.-C.Y.); (G.-Y.Q.); (T.-Y.Y.)
| | - Tian-Yi Yao
- Department of Entomology, Nanjing Agricultural University, Nanjing 210095, China; (Z.-C.Y.); (G.-Y.Q.); (T.-Y.Y.)
| | - Yuan-Xi Li
- Department of Entomology, Nanjing Agricultural University, Nanjing 210095, China; (Z.-C.Y.); (G.-Y.Q.); (T.-Y.Y.)
- Key Laboratory of Integrated Pest Management in Crops in Eastern China (Nanjing Agricultural University), Ministry of Agriculture, Nanjing 210095, China
- Correspondence:
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10
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Kearney MR, Jasper ME, White VL, Aitkenhead IJ, Blacket MJ, Kong JD, Chown SL, Hoffmann AA. Parthenogenesis without costs in a grasshopper with hybrid origins. Science 2022; 376:1110-1114. [PMID: 35653484 DOI: 10.1126/science.abm1072] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The rarity of parthenogenetic species is typically attributed to the reduced genetic variability that accompanies the absence of sex, yet natural parthenogens can be surprisingly successful. Ecological success is often proposed to derive from hybridization through enhanced genetic diversity from repetitive origins or enhanced phenotypic breadth from heterosis. Here, we tested and rejected both hypotheses in a classic parthenogen, the diploid grasshopper Warramaba virgo. Genetic data revealed a single hybrid mating origin at least 0.25 million years ago, and comparative analyses of 14 physiological and life history traits showed no evidence for altered fitness relative to its sexual progenitors. Our findings imply that the rarity of parthenogenesis is due to constraints on origin rather than to rapid extinction.
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Affiliation(s)
- Michael R Kearney
- School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Moshe E Jasper
- Bio21 Institute, School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Vanessa L White
- School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Ian J Aitkenhead
- School of Biological Sciences, Monash University, Victoria 3800, Australia
| | - Mark J Blacket
- School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Jacinta D Kong
- School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Steven L Chown
- School of Biological Sciences, Monash University, Victoria 3800, Australia
| | - Ary A Hoffmann
- Bio21 Institute, School of BioSciences, The University of Melbourne, Victoria 3010, Australia
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11
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Normark BB. The clones are all right. Science 2022; 376:1052-1053. [PMID: 35653466 DOI: 10.1126/science.abq3024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Parthenogenetic grasshoppers confound predictions by showing no signs of decline.
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Affiliation(s)
- Benjamin B Normark
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
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12
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Archetti M. Evidence from automixis with inverted meiosis for the maintenance of sex by loss of complementation. J Evol Biol 2021; 35:40-50. [PMID: 34927297 DOI: 10.1111/jeb.13975] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 11/30/2022]
Abstract
The adaptive value of sexual reproduction is still debated. A short-term disadvantage of asexual reproduction is loss of heterozygosity, which leads to the unmasking of recessive deleterious mutations. The cost of this loss of complementation is predicted to be higher than the twofold cost of meiosis for most types of asexual reproduction. Automixis with terminal fusion of sister nuclei is especially vulnerable to the effect of loss of complementation. It is found, however, in some taxa including oribatid mites, the most prominent group of ancient asexuals. Here, I show that automixis with terminal fusion is stable if it is associated with inverted meiosis and that this appears to be the case in nature, notably in oribatid mites. The existence of automixis with terminal fusion, and its co-occurrence with inverted meiosis, therefore, is consistent with the hypothesis that loss of complementation is important in the evolution of sexual reproduction.
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Affiliation(s)
- Marco Archetti
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
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13
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Janko K, Bartoš O, Kočí J, Roslein J, Drdová EJ, Kotusz J, Eisner J, Mokrejš M, Štefková-Kašparová E. Genome Fractionation and Loss of Heterozygosity in Hybrids and Polyploids: Mechanisms, Consequences for Selection, and Link to Gene Function. Mol Biol Evol 2021; 38:5255-5274. [PMID: 34410426 PMCID: PMC8662595 DOI: 10.1093/molbev/msab249] [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] [Indexed: 12/28/2022] Open
Abstract
Hybridization and genome duplication have played crucial roles in the evolution of many animal and plant taxa. The subgenomes of parental species undergo considerable changes in hybrids and polyploids, which often selectively eliminate segments of one subgenome. However, the mechanisms underlying these changes are not well understood, particularly when the hybridization is linked with asexual reproduction that opens up unexpected evolutionary pathways. To elucidate this problem, we compared published cytogenetic and RNAseq data with exome sequences of asexual diploid and polyploid hybrids between three fish species; Cobitis elongatoides, C. taenia, and C. tanaitica. Clonal genomes remained generally static at chromosome-scale levels but their heterozygosity gradually deteriorated at the level of individual genes owing to allelic deletions and conversions. Interestingly, the impact of both processes varies among animals and genomic regions depending on ploidy level and the properties of affected genes. Namely, polyploids were more tolerant to deletions than diploid asexuals where conversions prevailed, and genomic restructuring events accumulated preferentially in genes characterized by high transcription levels and GC-content, strong purifying selection and specific functions like interacting with intracellular membranes. Although hybrids were phenotypically more similar to C. taenia, we found that they preferentially retained C. elongatoides alleles. This demonstrates that favored subgenome is not necessarily the transcriptionally dominant one. This study demonstrated that subgenomes in asexual hybrids and polyploids evolve under a complex interplay of selection and several molecular mechanisms whose efficiency depends on the organism's ploidy level, as well as functional properties and parental ancestry of the genomic region.
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Affiliation(s)
- Karel Janko
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Oldřich Bartoš
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Kočí
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jan Roslein
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Edita Janková Drdová
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jan Kotusz
- Museum of Natural History, University of Wroclaw, Wroclaw, Poland
| | - Jan Eisner
- Department of Mathematics, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
| | - Martin Mokrejš
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- IT4Innovations, VŠB—Technical University of Ostrava, Ostrava-Poruba, Czech Republic
| | - Eva Štefková-Kašparová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Genetics and Breeding, FAFNR, Czech University of Life Sciences Prague, Czech Republic
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14
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Dedukh D, Marta A, Janko K. Challenges and Costs of Asexuality: Variation in Premeiotic Genome Duplication in Gynogenetic Hybrids from Cobitis taenia Complex. Int J Mol Sci 2021; 22:ijms222212117. [PMID: 34830012 PMCID: PMC8622741 DOI: 10.3390/ijms222212117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/25/2021] [Accepted: 11/04/2021] [Indexed: 02/07/2023] Open
Abstract
The transition from sexual reproduction to asexuality is often triggered by hybridization. The gametogenesis of many hybrid asexuals involves premeiotic genome endoreplication leading to bypass hybrid sterility and forming clonal gametes. However, it is still not clear when endoreplication occurs, how many gonial cells it affects and whether its rate differs among clonal lineages. Here, we investigated meiotic and premeiotic cells of diploid and triploid hybrids of spined loaches (Cypriniformes: Cobitis) that reproduce by gynogenesis. We found that in naturally and experimentally produced F1 hybrids asexuality is achieved by genome endoreplication, which occurs in gonocytes just before entering meiosis or, rarely, one or a few divisions before meiosis. However, genome endoreplication was observed only in a minor fraction of the hybrid's gonocytes, while the vast majority of gonocytes were unable to duplicate their genomes and consequently could not proceed beyond pachytene due to defects in bivalent formation. We also noted that the rate of endoreplication was significantly higher among gonocytes of hybrids from natural clones than of experimentally produced F1 hybrids. Thus, asexuality and hybrid sterility are intimately related phenomena and the transition from sexual reproduction to asexuality must overcome significant problems with genome incompatibilities with a possible impact on reproductive potential.
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Affiliation(s)
- Dmitrij Dedukh
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the CAS, Rumburská 89, 277 21 Liběchov, Czech Republic;
- Correspondence: (D.D.); (K.J.)
| | - Anatolie Marta
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the CAS, Rumburská 89, 277 21 Liběchov, Czech Republic;
- Department of Zoology, Faculty of Science, Charles University in Prague, 128 00 Prague, Czech Republic
- Institute of Zoology, MD-2028, Academiei 1, 2001 Chisinau, Moldova
| | - Karel Janko
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the CAS, Rumburská 89, 277 21 Liběchov, Czech Republic;
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
- Correspondence: (D.D.); (K.J.)
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15
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Moreira MO, Fonseca C, Rojas D. Parthenogenesis is self-destructive for scaled reptiles. Biol Lett 2021; 17:20210006. [PMID: 33975486 PMCID: PMC8113917 DOI: 10.1098/rsbl.2021.0006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 04/20/2021] [Indexed: 11/12/2022] Open
Abstract
Parthenogenesis is rare in nature. With 39 described true parthenogens, scaled reptiles (Squamata) are the only vertebrates that evolved this reproductive strategy. Parthenogenesis is ecologically advantageous in the short term, but the young age and rarity of parthenogenetic species indicate it is less advantageous in the long term. This suggests parthenogenesis is self-destructive: it arises often but is lost due to increased extinction rates, high rates of reversal or both. However, this role of parthenogenesis as a self-destructive trait remains unknown. We used a phylogeny of Squamata (5388 species), tree metrics, null simulations and macroevolutionary scenarios of trait diversification to address the factors that best explain the rarity of parthenogenetic species. We show that parthenogenesis can be considered as self-destructive, with high extinction rates mainly responsible for its rarity in nature. Since these parthenogenetic species occur, this trait should be ecologically relevant in the short term.
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Affiliation(s)
- Matthew Owen Moreira
- CESAM - Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Carlos Fonseca
- CESAM - Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
- ForestWISE - Collaborative Laboratory for Integrated Forest and Fire Management, Quinta de Prados, 5001-801 Vila Real, Portugal
| | - Danny Rojas
- Department of Natural Sciences and Mathematics, Pontificia Universidad Javeriana Cali, Cali, Colombia
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16
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Kočí J, Röslein J, Pačes J, Kotusz J, Halačka K, Koščo J, Fedorčák J, Iakovenko N, Janko K. No evidence for accumulation of deleterious mutations and fitness degradation in clonal fish hybrids: Abandoning sex without regrets. Mol Ecol 2020; 29:3038-3055. [PMID: 32627290 PMCID: PMC7540418 DOI: 10.1111/mec.15539] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/18/2020] [Accepted: 06/22/2020] [Indexed: 02/07/2023]
Abstract
Despite its inherent costs, sexual reproduction is ubiquitous in nature, and the mechanisms to protect it from a competitive displacement by asexuality remain unclear. Popular mutation-based explanations, like the Muller's ratchet and the Kondrashov's hatchet, assume that purifying selection may not halt the accumulation of deleterious mutations in the nonrecombining genomes, ultimately leading to their degeneration. However, empirical evidence is scarce and it remains particularly unclear whether mutational degradation proceeds fast enough to ensure the decay of clonal organisms and to prevent them from outcompeting their sexual counterparts. To test this hypothesis, we jointly analysed the exome sequences and the fitness-related phenotypic traits of the sexually reproducing fish species and their clonal hybrids, whose evolutionary ages ranged from F1 generations to 300 ky. As expected, mutations tended to accumulate in the clonal genomes in a time-dependent manner. However, contrary to the predictions, we found no trend towards increased nonsynonymity of mutations acquired by clones, nor higher radicality of their amino acid substitutions. Moreover, there was no evidence for fitness degeneration in the old clones compared with that in the younger ones. In summary, although an efficacy of purifying selection may still be reduced in the asexual genomes, our data indicate that its efficiency is not drastically decreased. Even the oldest investigated clone was found to be too young to suffer fitness consequences from a mutation accumulation. This suggests that mechanisms other than mutation accumulation may be needed to explain the competitive advantage of sex in the short term.
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Affiliation(s)
- Jan Kočí
- Department of Biology and Ecology, University of Ostrava, Ostrava, Czechia.,Institute of Animal Physiology and Genetics, Czech Academy of Science, Liběchov, Czechia
| | - Jan Röslein
- Department of Biology and Ecology, University of Ostrava, Ostrava, Czechia.,Institute of Animal Physiology and Genetics, Czech Academy of Science, Liběchov, Czechia
| | - Jan Pačes
- Institute of Animal Physiology and Genetics, Czech Academy of Science, Liběchov, Czechia.,Institute of Molecular Genetics, Czech Academy of Science, Prague, Czechia
| | - Jan Kotusz
- Museum of Natural History, University of Wrocław, Wrocław, Poland
| | - Karel Halačka
- Institute of Vertebrate Biology, Czech Academy of Science, Brno, Czechia
| | - Ján Koščo
- Department of Ecology, University of Prešov, Prešov, Slovakia
| | - Jakub Fedorčák
- Department of Ecology, University of Prešov, Prešov, Slovakia
| | - Nataliia Iakovenko
- Department of Biology and Ecology, University of Ostrava, Ostrava, Czechia.,Institute of Animal Physiology and Genetics, Czech Academy of Science, Liběchov, Czechia
| | - Karel Janko
- Department of Biology and Ecology, University of Ostrava, Ostrava, Czechia.,Institute of Animal Physiology and Genetics, Czech Academy of Science, Liběchov, Czechia
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