1
|
Wang C, Liu L, Yin M, Liu B, Wu Y, Eller F, Gao Y, Brix H, Wang T, Guo W, Salojärvi J. Chromosome-level genome assemblies reveal genome evolution of an invasive plant Phragmites australis. Commun Biol 2024; 7:1007. [PMID: 39154094 PMCID: PMC11330502 DOI: 10.1038/s42003-024-06660-1] [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: 01/22/2024] [Accepted: 07/30/2024] [Indexed: 08/19/2024] Open
Abstract
Biological invasions pose a significant threat to ecosystems, disrupting local biodiversity and ecosystem functions. The genomic underpinnings of invasiveness, however, are still largely unknown, making it difficult to predict and manage invasive species effectively. The common reed (Phragmites australis) is a dominant grass species in wetland ecosystems and has become particularly invasive when transferred from Europe to North America. Here, we present a high-quality gap-free, telomere-to-telomere genome assembly of Phragmites australis consisting of 24 pseudochromosomes and a B chromosome. Fully phased subgenomes demonstrated considerable subgenome dominance and revealed the divergence of diploid progenitors approximately 30.9 million years ago. Comparative genomics using chromosome-level scaffolds for three other lineages and a previously published draft genome assembly of an invasive lineage revealed that gene family expansions in the form of tandem duplications may have contributed to the invasiveness of the lineage. This study sheds light on the genome evolution of Arundinoideae grasses and suggests that genetic drivers, such as gene family expansions and tandem duplications, may underly the processes of biological invasion in plants. These findings provide a crucial step toward understanding and managing the genetic basis of invasiveness in plant species.
Collapse
Affiliation(s)
- Cui Wang
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, Ministry of Natural Resources, School of Life Sciences, Shandong University, Qingdao, PR China
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Lele Liu
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, Ministry of Natural Resources, School of Life Sciences, Shandong University, Qingdao, PR China
| | - Meiqi Yin
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, Ministry of Natural Resources, School of Life Sciences, Shandong University, Qingdao, PR China
| | - Bingbing Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Yiming Wu
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, Ministry of Natural Resources, School of Life Sciences, Shandong University, Qingdao, PR China
| | | | - Yingqi Gao
- Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Hans Brix
- Department of Biology, Aarhus University, Aarhus, Denmark
| | - Tong Wang
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, China
| | - Weihua Guo
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, Ministry of Natural Resources, School of Life Sciences, Shandong University, Qingdao, PR China.
| | - Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Population Genomic Analyses Suggest a Hybrid Origin, Cryptic Sexuality, and Decay of Genes Regulating Seed Development for the Putatively Strictly Asexual Kingdonia uniflora (Circaeasteraceae, Ranunculales). Int J Mol Sci 2023; 24:ijms24021451. [PMID: 36674965 PMCID: PMC9866071 DOI: 10.3390/ijms24021451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/20/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
Asexual lineages are perceived to be short-lived on evolutionary timescales. Hence, reports for exceptional cases of putative 'ancient asexuals' usually raise questions about the persistence of such species. So far, there have been few studies to solve the mystery in plants. The monotypic Kingdonia dating to the early Eocene, contains only K. uniflora that has no known definitive evidence for sexual reproduction nor records for having congeneric sexual species, raising the possibility that the species has persisted under strict asexuality for a long period of time. Here, we analyze whole genome polymorphism and divergence in K. uniflora. Our results show that K. uniflora is characterized by high allelic heterozygosity and elevated πN/πS ratio, in line with theoretical expectations under asexual evolution. Allele frequency spectrum analysis reveals the origin of asexuality in K. uniflora occurred prior to lineage differentiation of the species. Although divergence within K. uniflora individuals exceeds that between populations, the topologies of the two haplotype trees, however, fail to match each other, indicating long-term asexuality is unlikely to account for the high allele divergence and K. uniflora may have a recent hybrid origin. Phi-test shows a statistical probability of recombination for the conflicting phylogenetic signals revealed by the split network, suggesting K. uniflora engages in undetected sexual reproduction. Detection of elevated genetic differentiation and premature stop codons (in some populations) in genes regulating seed development indicates mutational degradation of sexuality-specific genes in K. uniflora. This study unfolds the origin and persistence mechanism of a plant lineage that has been known to reproduce asexually and presents the genomic consequences of lack of sexuality.
Collapse
|
4
|
Zhao Q, Shao F, Li Y, Yi SV, Peng Z. Novel genome sequence of Chinese cavefish (Triplophysa rosa) reveals pervasive relaxation of natural selection in cavefish genomes. Mol Ecol 2022; 31:5831-5845. [PMID: 36125323 PMCID: PMC9828065 DOI: 10.1111/mec.16700] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 09/15/2022] [Indexed: 01/13/2023]
Abstract
All cavefishes, living exclusively in caves across the globe, exhibit similar phenotypic traits, including the characteristic loss of eyes. To understand whether such phenotypic convergence shares similar genomic bases, here we investigated genome-wide evolutionary signatures of cavefish phenotypes by comparing whole-genome sequences of three pairs of cavefishes and their surface fish relatives. Notably, we newly sequenced and generated a whole-genome assembly of the Chinese cavefish Triplophysa rosa. Our comparative analyses revealed several shared features of cavefish genome evolution. Cavefishes had lower mutation rates than their surface fish relatives. In contrast, the ratio of nonsynonymous to synonymous substitutions (ω) was significantly elevated in cavefishes compared to in surface fishes, consistent with the relaxation of purifying selection. In addition, cavefish genomes had an increased mutational load, including mutations that alter protein hydrophobicity profiles, which were considered harmful. Interestingly, however, we found no overlap in positively selected genes among different cavefish lineages, indicating that the phenotypic convergence in cavefishes was not caused by positive selection of the same sets of genes. Analyses of previously identified candidate genes associated with cave phenotypes supported this conclusion. Genes belonging to the lipid metabolism functional ontology were under relaxed purifying selection in all cavefish genomes, which may be associated with the nutrient-poor habitat of cavefishes. Our work reveals previously uncharacterized patterns of cavefish genome evolution and provides comparative insights into the evolution of cave-associated phenotypic traits.
Collapse
Affiliation(s)
- Qingyuan Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Southwest University School of Life SciencesChongqingChina,Department of Laboratory Animal Science, College of Basic Medical SciencesArmy Medical University (Third Military Medical University)ChongqingChina
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Southwest University School of Life SciencesChongqingChina
| | - Yanping Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Southwest University School of Life SciencesChongqingChina,Key Laboratory of Sichuan Province for Fish Conservation and Utilization in the Upper Reaches of the Yangtze RiverNeijiang Normal University College of Life SciencesNeijiangChina
| | - Soojin V. Yi
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraCaliforniaUSA
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Southwest University School of Life SciencesChongqingChina,Academy of Plateau Science and SustainabilityQinghai Normal UniversityXiningChina
| |
Collapse
|
5
|
Maldonado JA, Firneno TJ, Hall AS, Fujita MK. Parthenogenesis doubles the rate of amino acid substitution in whiptail mitochondria. Evolution 2022; 76:1434-1442. [PMID: 35580923 DOI: 10.1111/evo.14509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 03/10/2022] [Accepted: 03/21/2022] [Indexed: 01/21/2023]
Abstract
Sexual reproduction is ubiquitous in the natural world, suggesting that sex must have extensive benefits to overcome the cost of males compared to asexual reproduction. One hypothesized advantage of sex with strong theoretical support is that sex plays a role in removing deleterious mutations from the genome. Theory predicts that transitions to asexuality should lead to the suppression of recombination and segregation and, in turn, weakened natural selection, allowing for the accumulation of slightly deleterious mutations. We tested this prediction by estimating the dN/dS ratios in asexual vertebrate lineages in the genus Aspidoscelis using whole mitochondrial genomes from seven asexual and five sexual species. We found higher dN/dS ratios in asexual Aspidoscelis species, indicating that asexual whiptails accumulate nonsynonymous substitutions due to weaker purifying selection. Additionally, we estimated nucleotide diversity and found that asexuals harbor significantly less diversity. Thus, despite their recent origins, slightly deleterious mutations accumulated rapidly enough in asexual lineages to be detected. We provide empirical evidence to corroborate the connection between asexuality and increased amino acid substitutions in asexual vertebrate lineages.
Collapse
Affiliation(s)
- Jose A Maldonado
- Amphibian and Reptile Diversity Research Center, Department of Biology, The University of Texas, Arlington, Texas, USA
| | - Thomas J Firneno
- Amphibian and Reptile Diversity Research Center, Department of Biology, The University of Texas, Arlington, Texas, USA
| | - Alexander S Hall
- Amphibian and Reptile Diversity Research Center, Department of Biology, The University of Texas, Arlington, Texas, USA
| | - Matthew K Fujita
- Amphibian and Reptile Diversity Research Center, Department of Biology, The University of Texas, Arlington, Texas, USA
| |
Collapse
|
6
|
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.
Collapse
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:
| |
Collapse
|
7
|
Ohtsuki H, Norimatsu H, Makino T, Urabe J. Invasions of an obligate asexual daphnid species support the nearly neutral theory. Sci Rep 2022; 12:7305. [PMID: 35508526 PMCID: PMC9068809 DOI: 10.1038/s41598-022-11218-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/20/2022] [Indexed: 11/09/2022] Open
Abstract
To verify the "nearly neutral theory (NNT)," the ratio of nonsynonymous to synonymous substitutions (dN/dS) was compared among populations of different species. To determine the validity of NNT, however, populations that are genetically isolated from each other but share the same selection agents and differ in size should be compared. Genetically different lineages of obligate asexual Daphnia pulex invading Japan from North America are an ideal example as they satisfy these prerequisites. Therefore, we analyzed the whole-genome sequences of 18 genotypes, including those of the two independently invaded D. pulex lineages (JPN1 and JPN2) and compared the dN/dS ratio between the lineages. The base substitution rate of each genotype demonstrated that the JPN1 lineage having a larger distribution range diverged earlier and thus was older than the JPN2 lineage. Comparisons of the genotypes within lineages revealed that changes in dN/dS occurred after the divergence and were larger in the younger lineage, JPN2. These results imply that the JPN1 lineage has been more effectively subjected to purification selections, while slightly deteriorating mutations are less purged in JPN2 with smaller population size. Altogether, the lineage-specific difference in the dN/dS ratio for the obligate asexual D. pulex was well explained by the NNT.
Collapse
Affiliation(s)
- Hajime Ohtsuki
- Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Hirotomo Norimatsu
- Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Takashi Makino
- Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Jotaro Urabe
- Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan.
| |
Collapse
|
8
|
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.
Collapse
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.)
| |
Collapse
|
9
|
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.
Collapse
Affiliation(s)
- Marco Archetti
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| |
Collapse
|
10
|
Picard MAL, Vicoso B, Bertrand S, Escriva H. Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates, and the Putative Contribution of Genetic Conflict. Genes (Basel) 2021; 12:1136. [PMID: 34440310 PMCID: PMC8391622 DOI: 10.3390/genes12081136] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/08/2021] [Accepted: 07/11/2021] [Indexed: 12/30/2022] Open
Abstract
About eight million animal species are estimated to live on Earth, and all except those belonging to one subphylum are invertebrates. Invertebrates are incredibly diverse in their morphologies, life histories, and in the range of the ecological niches that they occupy. A great variety of modes of reproduction and sex determination systems is also observed among them, and their mosaic-distribution across the phylogeny shows that transitions between them occur frequently and rapidly. Genetic conflict in its various forms is a long-standing theory to explain what drives those evolutionary transitions. Here, we review (1) the different modes of reproduction among invertebrate species, highlighting sexual reproduction as the probable ancestral state; (2) the paradoxical diversity of sex determination systems; (3) the different types of genetic conflicts that could drive the evolution of such different systems.
Collapse
Affiliation(s)
- Marion Anne Lise Picard
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; (S.B.); (H.E.)
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria;
| | - Stéphanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; (S.B.); (H.E.)
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; (S.B.); (H.E.)
| |
Collapse
|
11
|
Greimann ES, Ward SF, Woodell JD, Hennessey S, Kline MR, Moreno JA, Peters M, Cruise JL, Montooth KL, Neiman M, Sharbrough J. Phenotypic Variation in Mitochondria-Related Performance Traits Across New Zealand Snail Populations. Integr Comp Biol 2021; 60:275-287. [PMID: 32589742 DOI: 10.1093/icb/icaa066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mitochondrial function is critical for energy homeostasis and should shape how genetic variation in metabolism is transmitted through levels of biological organization to generate stability in organismal performance. Mitochondrial function is encoded by genes in two distinct and separately inherited genomes-the mitochondrial genome and the nuclear genome-and selection is expected to maintain functional mito-nuclear interactions. The documented high levels of polymorphism in genes involved in these mito-nuclear interactions and wide variation for mitochondrial function demands an explanation for how and why variability in such a fundamental trait is maintained. Potamopyrgus antipodarum is a New Zealand freshwater snail with coexisting sexual and asexual individuals and, accordingly, contrasting systems of separate vs. co-inheritance of nuclear and mitochondrial genomes. As such, this snail provides a powerful means to dissect the evolutionary and functional consequences of mito-nuclear variation. The lakes inhabited by P. antipodarum span wide environmental gradients, with substantial across-lake genetic structure and mito-nuclear discordance. This situation allows us to use comparisons across reproductive modes and lakes to partition variation in cellular respiration across genetic and environmental axes. Here, we integrated cellular, physiological, and behavioral approaches to quantify variation in mitochondrial function across a diverse set of wild P. antipodarum lineages. We found extensive across-lake variation in organismal oxygen consumption and behavioral response to heat stress and differences across sexes in mitochondrial membrane potential but few global effects of reproductive mode. Taken together, our data set the stage for applying this important model system for sexual reproduction and polyploidy to dissecting the complex relationships between mito-nuclear variation, performance, plasticity, and fitness in natural populations.
Collapse
Affiliation(s)
- Emma S Greimann
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Samuel F Ward
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, USA
| | - James D Woodell
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | | | - Michael R Kline
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Jorge A Moreno
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Madeline Peters
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Jennifer L Cruise
- Department of Biology, University of St. Thomas, Saint Paul, MN, USA
| | - Kristi L Montooth
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Joel Sharbrough
- Department of Biology, University of Iowa, Iowa City, IA, USA
- Colorado State University, Fort Collins, CO, USA
| |
Collapse
|
12
|
Fujita MK, Singhal S, Brunes TO, Maldonado JA. Evolutionary Dynamics and Consequences of Parthenogenesis in Vertebrates. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-011720-114900] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Parthenogenesis is asexual reproduction without any required participation from males and, as such, is a null model for sexual reproduction. In a comparative context, we can expand our understanding of the evolution and ecology of sex by investigating the consequences of parthenogenesis. In this review, we examine the theoretical predictions of and empirical results on the evolution of asexual reproduction in vertebrates, focusing on recent studies addressing the origins and geographic spread of parthenogenetic lineages and the genomic consequences of an asexual life history. With advances in computational methods and genome technologies, researchers are poised to make rapid and significant progress in studying the origin and evolution of parthenogenesis in vertebrates, thus providing an important perspective on understanding biodiversity patterns of both asexual and sexual populations.
Collapse
Affiliation(s)
- Matthew K. Fujita
- Amphibian and Reptile Diversity Research Center and Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Sonal Singhal
- Department of Biology, California State University, Dominguez Hills, Carson, California 90747, USA
| | - Tuliana O. Brunes
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Jose A. Maldonado
- Amphibian and Reptile Diversity Research Center and Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Agatha S, Utz LRP, Zufall RA, Warren A. Symposium on Ciliates in Memory of Denis Lynn. Eur J Protistol 2020; 78:125694. [PMID: 33500175 DOI: 10.1016/j.ejop.2020.125694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/10/2020] [Indexed: 10/24/2022]
Abstract
Denis Lynn (1947-2018) was an outstanding protistologist, applying multiple techniques and data sources and thus pioneering an integrative approach in order to investigate ciliate biology. For example, he recognized the importance of the ultrastructure for inferring ciliate phylogeny, based on which he developed his widely accepted classification scheme for the phylum Ciliophora. In this paper, recent findings regarding the evolution and systematics of both peritrichs and the mainly marine planktonic oligotrichean spirotrichs are discussed and compared with the concepts and hypotheses formulated by Denis Lynn. Additionally, the state of knowledge concerning the diversity of ciliates in bromeliad phytotelmata and amitosis in ciliates is reviewed.
Collapse
Affiliation(s)
- Sabine Agatha
- Department of Biosciences, Paris Lodron University of Salzburg, Salzburg, Austria.
| | - Laura R P Utz
- School of Health and Life Sciences, PUCRS, Porto Alegre, Brazil
| | - Rebecca A Zufall
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, UK.
| |
Collapse
|
15
|
Leria L, Vila-Farré M, Solà E, Riutort M. Outstanding intraindividual genetic diversity in fissiparous planarians (Dugesia, Platyhelminthes) with facultative sex. BMC Evol Biol 2019; 19:130. [PMID: 31221097 PMCID: PMC6587288 DOI: 10.1186/s12862-019-1440-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 05/15/2019] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Predicted genetic consequences of asexuality include high intraindividual genetic diversity (i.e., the Meselson effect) and accumulation of deleterious mutations (i.e., Muller's Ratchet), among others. These consequences have been largely studied in parthenogenetic organisms, but studies on fissiparous species are scarce. Differing from parthenogens, fissiparous organisms inherit part of the soma of the progenitor, including somatic mutations. Thus, in the long term, fissiparous reproduction may also result in genetic mosaicism, besides the presence of the Meselson effect and Muller's Ratchet. Dugesiidae planarians show outstanding regeneration capabilities, allowing them to naturally reproduce by fission, either strictly or combined with sex (facultative). Therefore, they are an ideal model to analyze the genetic footprint of fissiparous reproduction, both when it is alternated with sex and when it is the only mode of reproduction. RESULTS In the present study, we generate and analyze intraindividual cloned data of a nuclear and a mitochondrial gene of sexual, fissiparous and facultative wild populations of the species Dugesia subtentaculata. We find that most individuals, independently of their reproductive strategy, are mosaics. However, the intraindividual haplotype and nucleotide diversity of fissiparous and facultative individuals is significantly higher than in sexual individuals, with no signs of Muller's Ratchet. Finally, we also find that this high intraindividual genetic diversity of fissiparous and facultative individuals is composed by different combinations of ancestral and derived haplotypes of the species. CONCLUSIONS The intraindividual analyses of genetic diversity point out that fissiparous reproduction leaves a very special genetic footprint in individuals, characterized by mosaicism combined with the Meselson effect (named in the present study as the mosaic Meselson effect). Interestingly, the different intraindividual combinations of ancestral and derivate genetic diversity indicate that haplotypes generated during periods of fissiparous reproduction can be also transmitted to the progeny through sexual events, resulting in offspring showing a wide range of genetic diversity and putatively allowing purifying selection to act at both intraindividual and individual level. Further investigations, using Dugesia planarians as model organisms, would be of great value to delve into this new model of genetic evolution by the combination of fission and sex.
Collapse
Affiliation(s)
- Laia Leria
- Department de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, and Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia Spain
| | - Miquel Vila-Farré
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Eduard Solà
- Department de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, and Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia Spain
| | - Marta Riutort
- Department de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, and Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia Spain
| |
Collapse
|
16
|
Bast J, Parker DJ, Dumas Z, Jalvingh KM, Tran Van P, Jaron KS, Figuet E, Brandt A, Galtier N, Schwander T. Consequences of Asexuality in Natural Populations: Insights from Stick Insects. Mol Biol Evol 2019; 35:1668-1677. [PMID: 29659991 PMCID: PMC5995167 DOI: 10.1093/molbev/msy058] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Recombination is a fundamental process with significant impacts on genome evolution. Predicted consequences of the loss of recombination include a reduced effectiveness of selection, changes in the amount of neutral polymorphisms segregating in populations, and an arrest of GC-biased gene conversion. Although these consequences are empirically well documented for nonrecombining genome portions, it remains largely unknown if they extend to the whole genome scale in asexual organisms. We identify the consequences of asexuality using de novo transcriptomes of five independently derived, obligately asexual lineages of stick insects, and their sexual sister-species. We find strong evidence for higher rates of deleterious mutation accumulation, lower levels of segregating polymorphisms and arrested GC-biased gene conversion in asexuals as compared with sexuals. Taken together, our study conclusively shows that predicted consequences of genome evolution under asexuality can indeed be found in natural populations.
Collapse
Affiliation(s)
- Jens Bast
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Darren J Parker
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Kirsten M Jalvingh
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Patrick Tran Van
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kamil S Jaron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Emeric Figuet
- Institute of Evolutionary Sciences, University of Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Alexander Brandt
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, Goettingen, Germany
| | - Nicolas Galtier
- Institute of Evolutionary Sciences, University of Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
17
|
Brandt A, Bast J, Scheu S, Meusemann K, Donath A, Schütte K, Machida R, Kraaijeveld K. No signal of deleterious mutation accumulation in conserved gene sequences of extant asexual hexapods. Sci Rep 2019; 9:5338. [PMID: 30926861 PMCID: PMC6441085 DOI: 10.1038/s41598-019-41821-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/18/2019] [Indexed: 11/15/2022] Open
Abstract
Loss of sex and recombination is generally assumed to impede the effectiveness of purifying selection and to result in the accumulation of slightly deleterious mutations. Empirical evidence for this has come from several studies investigating mutational load in a small number of individual genes. However, recent whole transcriptome based studies have yielded inconsistent results, hence questioning the validity of the assumption of mutational meltdown in asexual populations. Here, we study the effectiveness of purifying selection in eight asexual hexapod lineages and their sexual relatives, as present in the 1 K Insect Transcriptome Evolution (1KITE) project, covering eight hexapod groups. We analyse the accumulation of slightly deleterious nonsynonymous and synonymous point mutations in 99 single copy orthologue protein-coding loci shared among the investigated taxa. While accumulation rates of nonsynonymous mutations differed between genes and hexapod groups, we found no effect of reproductive mode on the effectiveness of purifying selection acting at nonsynonymous and synonymous sites. Although the setup of this study does not fully rule out nondetection of subtle effects, our data does not support the established consensus of asexual lineages undergoing ‘mutational meltdown’.
Collapse
Affiliation(s)
- Alexander Brandt
- University of Göttingen, JF Blumenbach Institute of Zoology and Anthropology, Untere Karspüle 2, D-37073, Göttingen, Germany.
| | - Jens Bast
- University of Lausanne, Department of Ecology and Evolution, UNIL Sorge, Le Biophore, CH-1015, Lausanne, Switzerland
| | - Stefan Scheu
- University of Göttingen, JF Blumenbach Institute of Zoology and Anthropology, Untere Karspüle 2, D-37073, Göttingen, Germany
| | - Karen Meusemann
- University of Freiburg, Biology I, Evolutionary Biology & Ecology, Hauptstraße 1, D-79104, Freiburg, Germany.,Center for Molecular Biodiversity Research (ZMB), Zoological Research Museum Alexander König, Adenauerallee 160, D-53113, Bonn, Germany
| | - Alexander Donath
- Center for Molecular Biodiversity Research (ZMB), Zoological Research Museum Alexander König, Adenauerallee 160, D-53113, Bonn, Germany
| | - Kai Schütte
- University of Hamburg, Faculty of Mathematics, Informatics and Natural Sciences, Department of Biology, Institute of Zoology, Research Unit Animal Ecology and Conservation, Martin-Luther-King-Platz 3, D-20146, Hamburg, Germany
| | - Ryuichiro Machida
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, 1278-294, Sugadaira Kogen, Ueda, Nagano, 386-2204, Japan
| | - Ken Kraaijeveld
- University of Amsterdam, Institute for Biodiversity and Ecosystem Dynamics, Science Park 904, 1090 GE, Amsterdam, The Netherlands
| |
Collapse
|
18
|
Tvedte ES, Logsdon JM, Forbes AA. Sex loss in insects: causes of asexuality and consequences for genomes. CURRENT OPINION IN INSECT SCIENCE 2019; 31:77-83. [PMID: 31109677 DOI: 10.1016/j.cois.2018.11.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/03/2018] [Accepted: 11/20/2018] [Indexed: 06/09/2023]
Abstract
Boasting a staggering diversity of reproductive strategies, insects provide attractive models for the comparative study of the causes and consequences of transitions to asexuality. We provide an overview of some contemporary studies of reproductive systems in insects and compile an initial database of asexual insect genome resources. Insect systems have already yielded some important insights into various mechanisms by which sex is lost, including genetic, endosymbiont-mediated, and hybridization. Studies of mutation and substitution after loss of sex provide the strongest empirical support for hypothesized effects of asexuality, whereas there is mixed evidence for ecological hypotheses such as increased parasite load and altered niche breadth in asexuals. Most hypotheses have been explored in a select few taxa (e.g. stick insects, aphids), such that much of the great taxonomic breadth of insects remain understudied. Given the variation in the proximate causes of asexuality in insects, we argue for expanding the taxonomic breadth of study systems. Despite some challenges for investigating sex in insects, the increasing cost-effectiveness of genomic sequencing makes data generation for closely-related asexual and sexual lineages increasingly feasible.
Collapse
Affiliation(s)
- Eric S Tvedte
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States.
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, IA, United States
| | - Andrew A Forbes
- Department of Biology, University of Iowa, Iowa City, IA, United States
| |
Collapse
|
19
|
Abstract
A major current molecular evolution challenge is to link comparative genomic patterns to species' biology and ecology. Breeding systems are pivotal because they affect many population genetic processes and thus genome evolution. We review theoretical predictions and empirical evidence about molecular evolutionary processes under three distinct breeding systems-outcrossing, selfing, and asexuality. Breeding systems may have a profound impact on genome evolution, including molecular evolutionary rates, base composition, genomic conflict, and possibly genome size. We present and discuss the similarities and differences between the effects of selfing and clonality. In reverse, comparative and population genomic data and approaches help revisiting old questions on the long-term evolution of breeding systems.
Collapse
Affiliation(s)
- Sylvain Glémin
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France
| | - Clémentine M François
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France
| | - Nicolas Galtier
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France.
| |
Collapse
|
20
|
Tahir D, Glémin S, Lascoux M, Kaj I. Modeling a trait-dependent diversification process coupled with molecular evolution on a random species tree. J Theor Biol 2018; 461:189-203. [PMID: 30340056 DOI: 10.1016/j.jtbi.2018.10.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 10/10/2018] [Accepted: 10/12/2018] [Indexed: 12/23/2022]
Abstract
Understanding the evolution of binary traits, which affects the birth and survival of species and also the rate of molecular evolution, remains challenging. In this work, we present a probabilistic modeling framework for binary trait, random species trees, in which the number of species and their traits are represented by an asymmetric, two-type, continuous time Markov branching process. The model involves a number of different parameters describing both character and molecular evolution on the so-called 'reduced' tree, consisting of only extant species at the time of observation. We expand our model by considering the impact of binary traits on dN/dS, the normalized ratio of nonsynonymous to synonymous substitutions. We also develop mechanisms which enable us to understand the substitution rates on a phylogenetic tree with regards to the observed traits. The properties obtained from the model are illustrated with a phylogeny of outcrossing and selfing plant species, which allows us to investigate not only the branching tree rates, but also the molecular rates and the intensity of selection.
Collapse
Affiliation(s)
- Daniah Tahir
- Department of Mathematics, Uppsala University, Box 480, Uppsala SE-751 06, Sweden.
| | - Sylvain Glémin
- Department of Plant Ecology and Evolution, Uppsala University, Norbyvägen 18D, Uppsala SE-752 36, Sweden; UMR 5554 ISEM (Université de Montpellier-CNRS-IRD-EPHE), Montpellier Cedex 5 FR-34095, France.
| | - Martin Lascoux
- Department of Plant Ecology and Evolution, Uppsala University, Norbyvägen 18D, Uppsala SE-752 36, Sweden.
| | - Ingemar Kaj
- Department of Mathematics, Uppsala University, Box 480, Uppsala SE-751 06, Sweden.
| |
Collapse
|
21
|
Neiman M, Meirmans PG, Schwander T, Meirmans S. Sex in the wild: How and why field-based studies contribute to solving the problem of sex. Evolution 2018; 72:1194-1203. [PMID: 29645091 DOI: 10.1111/evo.13485] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/27/2018] [Indexed: 02/06/2023]
Abstract
Why and how sexual reproduction is maintained in natural populations, the so-called "queen of problems," is a key unanswered question in evolutionary biology. Recent efforts to solve the problem of sex have often emphasized results generated from laboratory settings. Here, we use a survey of representative "sex in the wild" literature to review and synthesize the outcomes of empirical studies focused on natural populations. Especially notable results included relatively strong support for mechanisms involving niche differentiation and a near absence of attention to adaptive evolution. Support for a major role of parasites is largely confined to a single study system, and only three systems contribute most of the support for mutation accumulation hypotheses. This evidence for taxon specificity suggests that outcomes of particular studies should not be more broadly extrapolated without extreme caution. We conclude by suggesting steps forward, highlighting tests of niche differentiation mechanisms in both laboratory and nature, and empirical evaluation of adaptive evolution-focused hypotheses in the wild. We also emphasize the value of leveraging the growing body of genomic resources for nonmodel taxa to address whether the clearance of harmful mutations and spread of beneficial variants in natural populations proceeds as expected under various hypotheses for sex.
Collapse
Affiliation(s)
- Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Patrick G Meirmans
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94248, 1090GE Amsterdam, The Netherlands
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Stephanie Meirmans
- Academic Medical Center (AMC), University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| |
Collapse
|
22
|
Tvedte ES, Forbes AA, Logsdon JM. Retention of Core Meiotic Genes Across Diverse Hymenoptera. J Hered 2018; 108:791-806. [PMID: 28992199 DOI: 10.1093/jhered/esx062] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 07/13/2017] [Indexed: 12/20/2022] Open
Abstract
The cellular mechanisms of meiosis are critical for proper gamete formation in sexual organisms. Functional studies in model organisms have identified genes essential for meiosis, yet the extent to which this core meiotic machinery is conserved across non-model systems is not fully understood. Moreover, it is unclear whether deviation from canonical modes of sexual reproduction is accompanied by modifications in the genetic components involved in meiosis. We used a robust approach to identify and catalogue meiosis genes in Hymenoptera, an insect order typically characterized by haplodiploid reproduction. Using newly available genome data, we searched for 43 genes involved in meiosis in 18 diverse hymenopterans. Seven of eight genes with roles specific to meiosis were found across a majority of surveyed species, suggesting the preservation of core meiotic machinery in haplodiploid hymenopterans. Phylogenomic analyses of the inventory of meiosis genes and the identification of shared gene duplications and losses provided support for the grouping of species within Proctotrupomorpha, Ichneumonomorpha, and Aculeata clades, along with a paraphyletic Symphyta. The conservation of meiosis genes across Hymenoptera provides a framework for studying transitions between reproductive modes in this insect group.
Collapse
Affiliation(s)
- Eric S Tvedte
- Department of Biology, University of Iowa, Iowa City, IA 52242
| | - Andrew A Forbes
- Department of Biology, University of Iowa, Iowa City, IA 52242
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, IA 52242
| |
Collapse
|
23
|
Sharbrough J, Luse M, Boore JL, Logsdon JM, Neiman M. Radical amino acid mutations persist longer in the absence of sex. Evolution 2018. [PMID: 29520921 DOI: 10.1111/evo.13465] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Harmful mutations are ubiquitous and inevitable, and the rate at which these mutations are removed from populations is a critical determinant of evolutionary fate. Closely related sexual and asexual taxa provide a particularly powerful setting to study deleterious mutation elimination because sexual reproduction should facilitate mutational clearance by reducing selective interference between sites and by allowing the production of offspring with different mutational complements than their parents. Here, we compared the rate of removal of conservative (i.e., similar biochemical properties) and radical (i.e., distinct biochemical properties) nonsynonymous mutations from mitochondrial genomes of sexual versus asexual Potamopyrgus antipodarum, a New Zealand freshwater snail characterized by coexisting and ecologically similar sexual and asexual lineages. Our analyses revealed that radical nonsynonymous mutations are cleared at higher rates than conservative changes and that sexual lineages eliminate radical changes more rapidly than asexual counterparts. These results are consistent with reduced efficacy of purifying selection in asexual lineages allowing harmful mutations to remain polymorphic longer than in sexual lineages. Together, these data illuminate some of the population-level processes contributing to mitochondrial mutation accumulation and suggest that mutation accumulation could influence the outcome of competition between sexual and asexual lineages.
Collapse
Affiliation(s)
- Joel Sharbrough
- Department of Biology, University of Iowa, Iowa City, Iowa 52242.,Department of Biology, Colorado State University, Fort Collins, Colorado 80523
| | - Meagan Luse
- Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Jeffrey L Boore
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California 94720.,Providence St. Joseph Health and Institute for Systems Biology, Seattle, Washington 98109
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, Iowa 52242
| |
Collapse
|
24
|
Vogt G. Investigating the genetic and epigenetic basis of big biological questions with the parthenogenetic marbled crayfish: A review and perspectives. J Biosci 2018. [DOI: 10.1007/s12038-018-9741-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
25
|
Fyon F, Lenormand T. Cis-regulator runaway and divergence in asexuals. Evolution 2018; 72:426-439. [DOI: 10.1111/evo.13424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/06/2017] [Accepted: 12/09/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Frédéric Fyon
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier 3, EPHE, IRD; Montpellier France
| | - Thomas Lenormand
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier 3, EPHE, IRD; Montpellier France
| |
Collapse
|
26
|
Brandt A, Schaefer I, Glanz J, Schwander T, Maraun M, Scheu S, Bast J. Effective purifying selection in ancient asexual oribatid mites. Nat Commun 2017; 8:873. [PMID: 29026136 PMCID: PMC5638860 DOI: 10.1038/s41467-017-01002-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/08/2017] [Indexed: 11/29/2022] Open
Abstract
Sex is beneficial in the long term because it can prevent mutational meltdown through increased effectiveness of selection. This idea is supported by empirical evidence of deleterious mutation accumulation in species with a recent transition to asexuality. Here, we study the effectiveness of purifying selection in oribatid mites which have lost sex millions of years ago and diversified into different families and species while reproducing asexually. We compare the accumulation of deleterious nonsynonymous and synonymous mutations between three asexual and three sexual lineages using transcriptome data. Contrasting studies of young asexual lineages, we find evidence for strong purifying selection that is more effective in asexual as compared to sexual oribatid mite lineages. Our results suggest that large populations likely sustain effective purifying selection and facilitate the escape of mutational meltdown in the absence of sex. Thus, sex per se is not a prerequisite for the long-term persistence of animal lineages. Asexual reproduction is thought to be an evolutionary dead end in eukaryotes because deleterious mutations will not be purged effectively. Here, Brandt and colleagues show that anciently asexual oribatid mites in fact have reduced accumulation of deleterious mutations compared to their sexual relatives.
Collapse
Affiliation(s)
- Alexander Brandt
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, Georg-August-University Goettingen, Untere Karspuele 2, DE-37073, Goettingen, Germany.
| | - Ina Schaefer
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, Georg-August-University Goettingen, Untere Karspuele 2, DE-37073, Goettingen, Germany
| | - Julien Glanz
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, Georg-August-University Goettingen, Untere Karspuele 2, DE-37073, Goettingen, Germany
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, UNIL Sorge, Le Biophore, CH-1015, Lausanne, Switzerland
| | - Mark Maraun
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, Georg-August-University Goettingen, Untere Karspuele 2, DE-37073, Goettingen, Germany
| | - Stefan Scheu
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, Georg-August-University Goettingen, Untere Karspuele 2, DE-37073, Goettingen, Germany.,Center of Biodiversity and Sustainable Land Use, Georg-August-University Goettingen, Untere Karspuele 2, DE-37073, Goettingen, Germany
| | - Jens Bast
- Department of Ecology and Evolution, University of Lausanne, UNIL Sorge, Le Biophore, CH-1015, Lausanne, Switzerland.
| |
Collapse
|
27
|
Krasovec M, Eyre-Walker A, Sanchez-Ferandin S, Piganeau G. Spontaneous Mutation Rate in the Smallest Photosynthetic Eukaryotes. Mol Biol Evol 2017; 34:1770-1779. [PMID: 28379581 PMCID: PMC5455958 DOI: 10.1093/molbev/msx119] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Mutation is the ultimate source of genetic variation, and knowledge of mutation rates is fundamental for our understanding of all evolutionary processes. High throughput sequencing of mutation accumulation lines has provided genome wide spontaneous mutation rates in a dozen model species, but estimates from nonmodel organisms from much of the diversity of life are very limited. Here, we report mutation rates in four haploid marine bacterial-sized photosynthetic eukaryotic algae; Bathycoccus prasinos, Ostreococcus tauri, Ostreococcus mediterraneus, and Micromonas pusilla. The spontaneous mutation rate between species varies from μ = 4.4 × 10-10 to 9.8 × 10-10 mutations per nucleotide per generation. Within genomes, there is a two-fold increase of the mutation rate in intergenic regions, consistent with an optimization of mismatch and transcription-coupled DNA repair in coding sequences. Additionally, we show that deviation from the equilibrium GC content increases the mutation rate by ∼2% to ∼12% because of a GC bias in coding sequences. More generally, the difference between the observed and equilibrium GC content of genomes explains some of the inter-specific variation in mutation rates.
Collapse
Affiliation(s)
- Marc Krasovec
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls/Mer, France
| | - Adam Eyre-Walker
- Evolution, behaviour and environment, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Sophie Sanchez-Ferandin
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls/Mer, France
| | - Gwenael Piganeau
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls/Mer, France
| |
Collapse
|
28
|
Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes. PLoS Genet 2017; 13:e1006777. [PMID: 28594822 PMCID: PMC5465968 DOI: 10.1371/journal.pgen.1006777] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/24/2017] [Indexed: 11/19/2022] Open
Abstract
Root-knot nematodes (genus Meloidogyne) exhibit a diversity of reproductive modes ranging from obligatory sexual to fully asexual reproduction. Intriguingly, the most widespread and devastating species to global agriculture are those that reproduce asexually, without meiosis. To disentangle this surprising parasitic success despite the absence of sex and genetic exchanges, we have sequenced and assembled the genomes of three obligatory ameiotic and asexual Meloidogyne. We have compared them to those of relatives able to perform meiosis and sexual reproduction. We show that the genomes of ameiotic asexual Meloidogyne are large, polyploid and made of duplicated regions with a high within-species average nucleotide divergence of ~8%. Phylogenomic analysis of the genes present in these duplicated regions suggests that they originated from multiple hybridization events and are thus homoeologs. We found that up to 22% of homoeologous gene pairs were under positive selection and these genes covered a wide spectrum of predicted functional categories. To biologically assess functional divergence, we compared expression patterns of homoeologous gene pairs across developmental life stages using an RNAseq approach in the most economically important asexually-reproducing nematode. We showed that >60% of homoeologous gene pairs display diverged expression patterns. These results suggest a substantial functional impact of the genome structure. Contrasting with high within-species nuclear genome divergence, mitochondrial genome divergence between the three ameiotic asexuals was very low, signifying that these putative hybrids share a recent common maternal ancestor. Transposable elements (TE) cover a ~1.7 times higher proportion of the genomes of the ameiotic asexual Meloidogyne compared to the sexual relative and might also participate in their plasticity. The intriguing parasitic success of asexually-reproducing Meloidogyne species could be partly explained by their TE-rich composite genomes, resulting from allopolyploidization events, and promoting plasticity and functional divergence between gene copies in the absence of sex and meiosis.
Collapse
|
29
|
Ho EKH, Agrawal AF. Aging asexual lineages and the evolutionary maintenance of sex. Evolution 2017; 71:1865-1875. [PMID: 28444897 DOI: 10.1111/evo.13260] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 04/13/2017] [Accepted: 04/17/2017] [Indexed: 12/24/2022]
Abstract
Finite populations of asexual and highly selfing species suffer from a reduced efficacy of selection. Such populations are thought to decline in fitness over time due to accumulating slightly deleterious mutations or failing to adapt to changing conditions. These within-population processes that lead nonrecombining species to extinction may help maintain sex and outcrossing through species level selection. Although inefficient selection is proposed to elevate extinction rates over time, previous models of species selection for sex assumed constant diversification rates. For sex to persist, classic models require that asexual species diversify at rates lower than sexual species; the validity of this requirement is questionable, both conceptually and empirically. We extend past models by allowing asexual lineages to decline in diversification rates as they age, that is nonrecombining lineages "senesce" in diversification rates. At equilibrium, senescing diversification rates maintain sex even when asexual lineages, at young ages, diversify faster than their sexual progenitors. In such cases, the age distribution of asexual lineages contains a peak at intermediate values rather than showing the exponential decline predicted by the classic model. Coexistence requires only that the average rate of diversification in asexuals be lower than that of sexuals.
Collapse
Affiliation(s)
- Eddie K H Ho
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
| | - Aneil F Agrawal
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
| |
Collapse
|
30
|
Variation in Recombination Rate: Adaptive or Not? Trends Genet 2017; 33:364-374. [DOI: 10.1016/j.tig.2017.03.003] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 01/30/2023]
|
31
|
Ament-Velásquez SL, Figuet E, Ballenghien M, Zattara EE, Norenburg JL, Fernández-Álvarez FA, Bierne J, Bierne N, Galtier N. Population genomics of sexual and asexual lineages in fissiparous ribbon worms (Lineus, Nemertea): hybridization, polyploidy and the Meselson effect. Mol Ecol 2016; 25:3356-69. [DOI: 10.1111/mec.13717] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 04/18/2016] [Accepted: 05/02/2016] [Indexed: 12/28/2022]
Affiliation(s)
- S. L. Ament-Velásquez
- Institute of Evolutionary Sciences; University Montpellier; CNRS, IRD, EPHE; Place Eugène Bataillon; 34095 Montpellier France
- Department of Organismal Biology; Systematic Biology; Uppsala University; PO Box 256 SE-751 05 Uppsala Sweden
| | - E. Figuet
- Institute of Evolutionary Sciences; University Montpellier; CNRS, IRD, EPHE; Place Eugène Bataillon; 34095 Montpellier France
| | - M. Ballenghien
- Institute of Evolutionary Sciences; University Montpellier; CNRS, IRD, EPHE; Place Eugène Bataillon; 34095 Montpellier France
| | - E. E. Zattara
- Department of Biology; Indiana University; 107 S Indiana Ave Bloomington IN 47405 USA
- Department of Invertebrate Zoology; National Museum of Natural History; Smithsonian Institution; 10th St. & Constitution Ave. NW Washington DC 20560 USA
| | - J. L. Norenburg
- Department of Invertebrate Zoology; National Museum of Natural History; Smithsonian Institution; 10th St. & Constitution Ave. NW Washington DC 20560 USA
| | | | - J. Bierne
- Laboratoire de Biologie Cellulaire et Moléculaire; Université de Reims Champagne-Ardenne; 9 Boulevard de la Paix 51100 Reims France
| | - N. Bierne
- Institute of Evolutionary Sciences; University Montpellier; CNRS, IRD, EPHE; Place Eugène Bataillon; 34095 Montpellier France
| | - N. Galtier
- Institute of Evolutionary Sciences; University Montpellier; CNRS, IRD, EPHE; Place Eugène Bataillon; 34095 Montpellier France
| |
Collapse
|
32
|
Bast J, Schaefer I, Schwander T, Maraun M, Scheu S, Kraaijeveld K. No Accumulation of Transposable Elements in Asexual Arthropods. Mol Biol Evol 2015; 33:697-706. [PMID: 26560353 PMCID: PMC4760076 DOI: 10.1093/molbev/msv261] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Transposable elements (TEs) and other repetitive DNA can accumulate in the absence of recombination, a process contributing to the degeneration of Y-chromosomes and other nonrecombining genome portions. A similar accumulation of repetitive DNA is expected for asexually reproducing species, given their entire genome is effectively nonrecombining. We tested this expectation by comparing the whole-genome TE loads of five asexual arthropod lineages and their sexual relatives, including asexual and sexual lineages of crustaceans (Daphnia water fleas), insects (Leptopilina wasps), and mites (Oribatida). Surprisingly, there was no evidence for increased TE load in genomes of asexual as compared to sexual lineages, neither for all classes of repetitive elements combined nor for specific TE families. Our study therefore suggests that nonrecombining genomes do not accumulate TEs like nonrecombining genomic regions of sexual lineages. Even if a slight but undetected increase of TEs were caused by asexual reproduction, it appears to be negligible compared to variance between species caused by processes unrelated to reproductive mode. It remains to be determined if molecular mechanisms underlying genome regulation in asexuals hamper TE activity. Alternatively, the differences in TE dynamics between nonrecombining genomes in asexual lineages versus nonrecombining genome portions in sexual species might stem from selection for benign TEs in asexual lineages because of the lack of genetic conflict between TEs and their hosts and/or because asexual lineages may only arise from sexual ancestors with particularly low TE loads.
Collapse
Affiliation(s)
- Jens Bast
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Ina Schaefer
- J.F. Blumenbach Institute of Zoology and Anthropology, Georg August University Goettingen, Goettingen, Germany
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Mark Maraun
- J.F. Blumenbach Institute of Zoology and Anthropology, Georg August University Goettingen, Goettingen, Germany
| | - Stefan Scheu
- J.F. Blumenbach Institute of Zoology and Anthropology, Georg August University Goettingen, Goettingen, Germany
| | - Ken Kraaijeveld
- Department of Ecological Science, VU University Amsterdam, Amsterdam, The Netherlands Leiden Genome Technology Center, Department of Human genetics, Leiden University Medical Center, Leiden, The Netherlands
| |
Collapse
|
33
|
Vogt G, Falckenhayn C, Schrimpf A, Schmid K, Hanna K, Panteleit J, Helm M, Schulz R, Lyko F. The marbled crayfish as a paradigm for saltational speciation by autopolyploidy and parthenogenesis in animals. Biol Open 2015; 4:1583-94. [PMID: 26519519 PMCID: PMC4728364 DOI: 10.1242/bio.014241] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 10/05/2015] [Indexed: 12/31/2022] Open
Abstract
The parthenogenetic all-female marbled crayfish is a novel research model and potent invader of freshwater ecosystems. It is a triploid descendant of the sexually reproducing slough crayfish, Procambarus fallax, but its taxonomic status has remained unsettled. By cross-breeding experiments and parentage analysis we show here that marbled crayfish and P. fallax are reproductively separated. Both crayfish copulate readily, suggesting that the reproductive barrier is set at the cytogenetic rather than the behavioural level. Analysis of complete mitochondrial genomes of marbled crayfish from laboratory lineages and wild populations demonstrates genetic identity and indicates a single origin. Flow cytometric comparison of DNA contents of haemocytes and analysis of nuclear microsatellite loci confirm triploidy and suggest autopolyploidisation as its cause. Global DNA methylation is significantly reduced in marbled crayfish implying the involvement of molecular epigenetic mechanisms in its origination. Morphologically, both crayfish are very similar but growth and fecundity are considerably larger in marbled crayfish, making it a different animal with superior fitness. These data and the high probability of a divergent future evolution of the marbled crayfish and P. fallax clusters suggest that marbled crayfish should be considered as an independent asexual species. Our findings also establish the P. fallax-marbled crayfish pair as a novel paradigm for rare chromosomal speciation by autopolyploidy and parthenogenesis in animals and for saltational evolution in general.
Collapse
Affiliation(s)
- Günter Vogt
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Cassandra Falckenhayn
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Anne Schrimpf
- Institute for Environmental Sciences, University of Koblenz-Landau, Forststrasse 7, 76829 Landau, Germany
| | - Katharina Schmid
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Katharina Hanna
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Jörn Panteleit
- Institute for Environmental Sciences, University of Koblenz-Landau, Forststrasse 7, 76829 Landau, Germany
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Ralf Schulz
- Institute for Environmental Sciences, University of Koblenz-Landau, Forststrasse 7, 76829 Landau, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| |
Collapse
|
34
|
Hartfield M. Evolutionary genetic consequences of facultative sex and outcrossing. J Evol Biol 2015; 29:5-22. [DOI: 10.1111/jeb.12770] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/24/2015] [Accepted: 09/28/2015] [Indexed: 01/16/2023]
Affiliation(s)
- M. Hartfield
- Department of Ecology and Evolutionary Biology; University of Toronto; Toronto ON Canada
- Bioinformatics Research Centre; University of Aarhus; Aarhus Denmark
| |
Collapse
|
35
|
Flores-López CA, Machado CA. Differences in inferred genome-wide signals of positive selection during the evolution of Trypanosoma cruzi and Leishmania spp. lineages: A result of disparities in host and tissue infection ranges? INFECTION GENETICS AND EVOLUTION 2015; 33:37-46. [DOI: 10.1016/j.meegid.2015.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 03/19/2015] [Accepted: 04/09/2015] [Indexed: 01/21/2023]
|
36
|
Schwander T, Marais G, Roze D. Sex uncovered: the evolutionary biology of reproductive systems. J Evol Biol 2015; 27:1287-91. [PMID: 24975885 DOI: 10.1111/jeb.12424] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- T Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | | |
Collapse
|
37
|
Becks L, Alavi Y. Using Microevolution to Explain the Macroevolutionary Observations for the Evolution of Sex. INTERDISCIPLINARY EVOLUTION RESEARCH 2015. [DOI: 10.1007/978-3-319-15045-1_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
38
|
Hollister JD, Greiner S, Wang W, Wang J, Zhang Y, Wong GKS, Wright SI, Johnson MT. Recurrent Loss of Sex Is Associated with Accumulation of Deleterious Mutations in Oenothera. Mol Biol Evol 2014; 32:896-905. [DOI: 10.1093/molbev/msu345] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
|
39
|
Lovell JT, Grogan K, Sharbel TF, McKay JK. Mating system and environmental variation drive patterns of adaptation inBoechera spatifolia(Brassicaceae). Mol Ecol 2014; 23:4486-97. [DOI: 10.1111/mec.12879] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 07/22/2014] [Accepted: 07/28/2014] [Indexed: 12/27/2022]
Affiliation(s)
- John T. Lovell
- Graduate Degree Program in Ecology; Department of BioAgricultural Sciences and Pest Management; Colorado State University; Fort Collins CO 80523-1177 USA
- Apomixis Research Group; Institute for Plant Genetics and Crop Plant Improvement (IPK); Gatersleben D-06466 Germany
| | - Kelsi Grogan
- Graduate Degree Program in Ecology; Department of BioAgricultural Sciences and Pest Management; Colorado State University; Fort Collins CO 80523-1177 USA
| | - Timothy F. Sharbel
- Apomixis Research Group; Institute for Plant Genetics and Crop Plant Improvement (IPK); Gatersleben D-06466 Germany
| | - John K. McKay
- Graduate Degree Program in Ecology; Department of BioAgricultural Sciences and Pest Management; Colorado State University; Fort Collins CO 80523-1177 USA
| |
Collapse
|
40
|
Glémin S, Muyle A. Mating systems and selection efficacy: a test using chloroplastic sequence data in Angiosperms. J Evol Biol 2014; 27:1386-99. [PMID: 24674012 DOI: 10.1111/jeb.12356] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 02/10/2014] [Accepted: 02/12/2014] [Indexed: 12/26/2022]
Abstract
Selfing is assumed to reduce selection efficacy, especially purifying selection. This can be tested using molecular data, for example by comparing the Dn/Ds ratio between selfing and outcrossing lineages. So far, little evidence of relaxed selection against weakly deleterious mutations (as inferred by a higher Dn/Ds ratio) in selfers as compared to outcrossers has been found, contrary to the pattern often observed between asexual and sexual lineages. However, few groups have been studied to date. To further test this hypothesis, we compiled and analysed chloroplastic sequence data sets in several plant groups. We found a general trend towards relaxed selection in selfers in our data sets but with weak statistical support. Simulations suggested that the results were compatible with weak-to-moderate Dn/Ds ratio differences in selfing lineages. Simple theoretical predictions also showed that the ability to detect relaxed selection in selfers could strongly depend on the distribution of the effects of deleterious mutations on fitness. Our results are compatible with a recent origin of selfing lineages whereby deleterious mutations potentially have a strong impact on population extinction or with a more ancient origin but without a marked effect of deleterious mutations on the extinction dynamics.
Collapse
Affiliation(s)
- S Glémin
- Institut des Sciences de l'Evolution de Montpellier, UMR CNRS 5554, Montpellier, France
| | | |
Collapse
|
41
|
Forbes AA, Rice LA, Stewart NB, Yee WL, Neiman M. Niche differentiation and colonization of a novel environment by an asexual parasitic wasp. J Evol Biol 2013; 26:1330-40. [PMID: 23517017 DOI: 10.1111/jeb.12135] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 01/17/2013] [Accepted: 01/19/2013] [Indexed: 12/23/2022]
Abstract
How do asexual taxa become adapted to a diversity of environments, and how do they persist despite changing environmental conditions? These questions are linked by their mutual focus on the relationship between genetic variation, which is often limited in asexuals, and the ability to respond to environmental variation. Asexual taxa originating from a single ancestor present a unique opportunity to assess rates of phenotypic and genetic change when access to new genetic variation is limited to mutation. Diachasma muliebre is an asexual Hymenopteran wasp that is geographically and genetically isolated from all sexual relatives. D. muliebre attack larvae of the western cherry fruit fly (Rhagoletis indifferens), which in turn feed inside bitter cherry fruit (Prunus emarginata) in August and September. R. indifferens has recently colonized a new host plant with an earlier fruiting phenology (June/July), domesticated sweet cherries (P. avium), and D. muliebre has followed its host into this temporally earlier niche. We tested three hypotheses: 1) that all D. muliebre lineages originate from a single asexual ancestor; 2) that different D. muliebre lineages (as defined by unique mtDNA haplotypes) have differentiated on their ancestral host in an important life-history trait, eclosion timing; and 3) that early-eclosing lineages have preferentially colonized the new sweet cherry niche. We find that mitochondrial COI and microsatellite data provide strong support for a single ancestral origin for all lineages. Furthermore, COI sequencing revealed five mitochondrial haplotypes among D. muliebre, and individual wasps possessing one distinctive mitochondrial haplotype (haplotype II) eclosed as reproductive adults significantly earlier than wasps with all other haplotypes. In addition, this early-eclosing lineage of D. muliebre is one of two lineages that have colonized the P. avium habitat, consistent with the preferential colonization hypothesis. These data suggest that D. muliebre has evolved adaptive phenotypic variation despite limited genetic variation, and that this variation has subsequently allowed an expansion of some wasps into a novel habitat. The D. muliebre system may allow for in-depth study of adaptation and long-term persistence of asexual taxa.
Collapse
Affiliation(s)
- A A Forbes
- Department of Biology, The University of Iowa, Iowa City, IA 52242, USA.
| | | | | | | | | |
Collapse
|
42
|
|
43
|
Jiang FF, Wang ZW, Zhou L, Jiang L, Zhang XJ, Apalikova OV, Brykov VA, Gui JF. High male incidence and evolutionary implications of triploid form in northeast Asia Carassius auratus complex. Mol Phylogenet Evol 2012; 66:350-9. [PMID: 23099150 DOI: 10.1016/j.ympev.2012.10.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 10/01/2012] [Accepted: 10/08/2012] [Indexed: 10/27/2022]
Abstract
Carassius auratus complex is believed to originate from East Eurasia and consist of diploid and triploid forms. Diploid form reproduces sexually, whereas triploid form possesses mixture modes of unisexual gynogenesis and sexual reproduction, which makes it a unique case to study evolutionary issues among vertebrates. In this study, we identified 337 triploid individuals from 386 specimens of Carassius auratus complex sampled from 4 different sites of Xingkai Lake and Suifen River on the northeast Asia transboundary areas of Russia and China, and found that triploids were ubiquitous, whereas diploids existed only in SII site of Suifen River. Triploid males were detected in all surveyed sites, and an unusually high triploid male incidence (23%) was found in the Chinese reach of Suifen River. Then, nuclear and cytoplasmic markers were used to analyze their genetic diversity and phylogenetic relationship. A total of 61 distinct tf alleles and 35 mtDNA CR haplotypes were revealed. Higher genetic diversity and divergence were confirmed in triploids than in diploids, and identical genetic background between triploid males and females was demonstrated. Moreover, evolutionary implications and roles of triploid males were suggested in population proliferation and diversity creation of the triploid form.
Collapse
Affiliation(s)
- Fang-Fang Jiang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Ross L, Hardy NB, Okusu A, Normark BB. LARGE POPULATION SIZE PREDICTS THE DISTRIBUTION OF ASEXUALITY IN SCALE INSECTS. Evolution 2012; 67:196-206. [DOI: 10.1111/j.1558-5646.2012.01784.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
45
|
Co-phylogeography and morphological evolution of sika deer lice (Damalinia sika) with their hosts (Cervus nippon). Parasitology 2012; 139:1614-29. [DOI: 10.1017/s0031182012000996] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|