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Tamagawa K, Dayi M, Sun S, Hata R, Kikuchi T, Haruta N, Sugimoto A, Makino T. Evolutionary changes of noncoding elements associated with transition of sexual mode in Caenorhabditis nematodes. SCIENCE ADVANCES 2024; 10:eadn9913. [PMID: 39270031 PMCID: PMC11397494 DOI: 10.1126/sciadv.adn9913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 08/08/2024] [Indexed: 09/15/2024]
Abstract
The transition of the sexual mode occurs widely in animal evolution. In Caenorhabditis nematodes, androdioecy, a sexual polymorphism composed of males and hermaphrodites having the ability to self-fertilize, has evolved independently multiple times. While the modification of noncoding regulatory elements likely contributed to the evolution of hermaphroditism, little is known about these changes. Here, we conducted a genome-wide analysis of conserved noncoding elements (CNEs) focusing on the evolution of hermaphroditism in Caenorhabditis nematodes. We found that, in androdioecious nematodes, mutations rapidly accumulated in CNEs' neighboring genes associated with sexual traits. Expression analysis indicate that the identified CNEs are involved in spermatogenesis in hermaphrodites and associated with the transition of gene expression from dioecious to androdioecious nematodes. Last, genome editing of a CNE neighboring laf-1 resulted in a change in its expression in the gonadal region undergoing spermatogenesis. Our bioinformatic and experimental analyses highlight the importance of CNEs in gene regulation associated with the development of hermaphrodites.
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Affiliation(s)
- Katsunori Tamagawa
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
| | - Mehmet Dayi
- Forestry Vocational School, Duzce University, 81620 Duzce, Türkiye
| | - Simo Sun
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa City, Japan
| | - Rikako Hata
- Department of Biology, Faculty of Science, Tohoku University, Aoba-ku, Sendai, Japan
| | - Taisei Kikuchi
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa City, Japan
| | - Nami Haruta
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
| | - Asako Sugimoto
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
| | - Takashi Makino
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
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de Mendoza G, Gansfort B, Catalan J, Traunspurger W. Female proportion has a stronger influence on dispersal than body size in nematodes of mountain lakes. PLoS One 2024; 19:e0303864. [PMID: 38758759 PMCID: PMC11101049 DOI: 10.1371/journal.pone.0303864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 05/01/2024] [Indexed: 05/19/2024] Open
Abstract
Nematodes disperse passively and are amongst the smallest invertebrates on Earth. Free-living nematodes in mountain lakes are highly tolerant of environmental variations and are thus excellent model organisms in dispersal studies, since species-environment relationships are unlikely to interfere. In this study, we investigated how population or organism traits influence the stochastic physical nature of passive dispersal in a topologically complex environment. Specifically, we analyzed the influence of female proportion and body size on the geographical distribution of nematode species in the mountain lakes of the Pyrenees. We hypothesized that dispersal is facilitated by (i) a smaller body size, which would increase the rate of wind transport, and (ii) a higher female proportion within a population, which could increase colonization success because many nematode species are capable of parthenogenetic reproduction. The results showed that nematode species with a low proportion of females tend to have clustered spatial distributions that are not associated with patchy environmental conditions, suggesting greater barriers to dispersal. When all species were pooled, the overall proportion of females tended to increase at the highest elevations, where dispersal between lakes is arguably more difficult. The influence of body size was barely relevant for nematode distributions. Our study highlights the relevance of female proportion as a mechanism that enhances the dispersal success of parthenogenetic species, and that female sex is a determining factor in metacommunity connectivity.
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Affiliation(s)
- Guillermo de Mendoza
- Institute of Geography, Faculty of Oceanography and Geography, University of Gdansk, Gdańsk, Poland
- Institute of Biology and Earth Sciences, Pomeranian University in Słupsk, Słupsk, Poland
| | - Birgit Gansfort
- Department of Animal Ecology, Bielefeld University, Bielefeld, Germany
| | - Jordi Catalan
- CREAF, Cerdanyola del Vallès, Barcelona, Spain
- CSIC, Bellaterra, Barcelona, Spain
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3
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Stevens L, Kieninger M, Chan B, Wood JMD, Gonzalez de la Rosa P, Allen J, Blaxter M. The genome of Litomosoides sigmodontis illuminates the origins of Y chromosomes in filarial nematodes. PLoS Genet 2024; 20:e1011116. [PMID: 38227589 PMCID: PMC10817185 DOI: 10.1371/journal.pgen.1011116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/26/2024] [Accepted: 12/26/2023] [Indexed: 01/18/2024] Open
Abstract
Heteromorphic sex chromosomes are usually thought to have originated from a pair of autosomes that acquired a sex-determining locus and subsequently stopped recombining, leading to degeneration of the sex-limited chromosome. The majority of nematode species lack heteromorphic sex chromosomes and determine sex using an X-chromosome counting mechanism, with males being hemizygous for one or more X chromosomes (XX/X0). Some filarial nematode species, including important parasites of humans, have heteromorphic XX/XY karyotypes. It has been assumed that sex is determined by a Y-linked locus in these species. However, karyotypic analyses suggested that filarial Y chromosomes are derived from the unfused homologue of an autosome involved in an X-autosome fusion event. Here, we generated a chromosome-level reference genome for Litomosoides sigmodontis, a filarial nematode with the ancestral filarial karyotype and sex determination mechanism (XX/X0). By mapping the assembled chromosomes to the rhabditid nematode ancestral linkage (or Nigon) elements, we infer that the ancestral filarial X chromosome was the product of a fusion between NigonX (the ancestrally X-linked element) and NigonD (ancestrally autosomal). In the two filarial lineages with XY systems, there have been two independent X-autosome chromosome fusion events involving different autosomal Nigon elements. In both lineages, the region shared by the neo-X and neo-Y chromosomes is within the ancestrally autosomal portion of the X, confirming that the filarial Y chromosomes are derived from the unfused homologue of the autosome. Sex determination in XY filarial nematodes therefore likely continues to operate via the ancestral X-chromosome counting mechanism, rather than via a Y-linked sex-determining locus.
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Affiliation(s)
- Lewis Stevens
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
| | | | - Brian Chan
- Lydia Becker Institute of Immunology and Inflammation, Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, University of Manchester, Manchester, United Kingdom
| | | | | | - Judith Allen
- Lydia Becker Institute of Immunology and Inflammation, Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, University of Manchester, Manchester, United Kingdom
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
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Rödelsperger C. Comparative Genomics of Sex, Chromosomes, and Sex Chromosomes in Caenorhabditis elegans and Other Nematodes. Methods Mol Biol 2024; 2802:455-472. [PMID: 38819568 DOI: 10.1007/978-1-0716-3838-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
The nematode phylum has evolved a remarkable diversity of reproductive modes, including the repeated emergence of asexuality and hermaphroditism across divergent clades. The species-richness and small genome size of nematodes make them ideal systems for investigating the genome-wide causes and consequences of such major transitions. The availability of functional annotations for most Caenorhabditis elegans genes further allows the linking of patterns of gene content evolution with biological processes. Such gene-centric studies were recently complemented by investigations of chromosome evolution that made use of the first chromosome-scale genome assemblies outside the Caenorhabditis genus. This review highlights recent comparative genomic studies of reproductive mode evolution addressing the hybrid origin of asexuality and the parallel gene loss following the emergence of hermaphroditism. It further summarizes ongoing efforts to characterize ancient linkage blocks called Nigon elements, which form central units of chromosome evolution. Fusions between Nigon elements have been demonstrated to impact recombination and speciation. Finally, multiple recent fusions between autosomal and the sex-linked Nigon element reveal insights into the dynamic evolution of sex chromosomes across various timescales.
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Affiliation(s)
- Christian Rödelsperger
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Tübingen, Germany.
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Cossard GG, Godfroy O, Nehr Z, Cruaud C, Cock JM, Lipinska AP, Coelho SM. Selection drives convergent gene expression changes during transitions to co-sexuality in haploid sexual systems. Nat Ecol Evol 2022; 6:579-589. [PMID: 35314785 PMCID: PMC9085613 DOI: 10.1038/s41559-022-01692-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 02/07/2022] [Indexed: 11/25/2022]
Abstract
Co-sexuality has evolved repeatedly from unisexual (dioicous) ancestors across a wide range of taxa. However, the molecular changes underpinning this important transition remain unknown, particularly in organisms with haploid sexual systems such as bryophytes, red algae and brown algae. Here we explore four independent events of emergence of co-sexuality from unisexual ancestors in brown algal clades to examine the nature, evolution and degree of convergence of gene expression changes that accompany the breakdown of dioicy. The amounts of male versus female phenotypic differences in dioicous species were not correlated with the extent of sex-biased gene expression, in stark contrast to what is observed in animals. Although sex-biased genes exhibited a high turnover rate during brown alga diversification, some of their predicted functions were conserved across species. Transitions to co-sexuality consistently involved adaptive gene expression shifts and rapid sequence evolution, particularly for male-biased genes. Gene expression in co-sexual species was more similar to that in females rather than males of related dioicous species, suggesting that co-sexuality may have arisen from ancestral females. Finally, extensive convergent gene expression changes, driven by selection, were associated with the transition to co-sexuality. Together, our observations provide insights on how co-sexual systems arise from ancestral, haploid UV sexual systems.
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Affiliation(s)
- Guillaume G Cossard
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS, Roscoff, France
- Max Plank Institute for Biology Tübingen, Tübingen, Germany
| | - Olivier Godfroy
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS, Roscoff, France
| | - Zofia Nehr
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS, Roscoff, France
| | - Corinne Cruaud
- Genoscope, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - J Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS, Roscoff, France
| | - Agnieszka P Lipinska
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS, Roscoff, France
- Max Plank Institute for Biology Tübingen, Tübingen, Germany
| | - Susana M Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS, Roscoff, France.
- Max Plank Institute for Biology Tübingen, Tübingen, Germany.
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Adams S, Pathak P, Kittelmann M, Jones ARC, Mallon EB, Pires-daSilva A. Sexual morph specialisation in a trioecious nematode balances opposing selective forces. Sci Rep 2022; 12:6402. [PMID: 35431314 PMCID: PMC9013718 DOI: 10.1038/s41598-022-09900-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/10/2022] [Indexed: 11/27/2022] Open
Abstract
The coexistence of different mating strategies, whereby a species can reproduce both by selfing and outcrossing, is an evolutionary enigma. Theory predicts two predominant stable mating states: outcrossing with strong inbreeding depression or selfing with weak inbreeding depression. As these two mating strategies are subject to opposing selective forces, mixed breeding systems are thought to be a rare transitory state yet can persist even after multiple speciation events. We hypothesise that if each mating strategy plays a distinctive role during some part of the species life history, opposing selective pressures could be balanced, permitting the stable co-existence of selfing and outcrossing sexual morphs. In this scenario, we would expect each morph to be specialised in their respective roles. Here we show, using behavioural, physiological and gene expression studies, that the selfing (hermaphrodite) and outcrossing (female) sexual morphs of the trioecious nematode Auanema freiburgensis have distinct adaptations optimised for their different roles during the life cycle. A. freiburgensis hermaphrodites are known to be produced under stressful conditions and are specialised for dispersal to new habitat patches. Here we show that they exhibit metabolic and intestinal changes enabling them to meet the cost of dispersal and reproduction. In contrast, A. freiburgensis females are produced in favourable conditions and facilitate rapid population growth. We found that females compensate for the lack of reproductive assurance by reallocating resources from intestinal development to mate-finding behaviour. The specialisation of each mating system for its role in the life cycle could balance opposing selective forces allowing the stable maintenance of both mating systems in A. freiburgensis.
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Affiliation(s)
- Sally Adams
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
| | - Prachi Pathak
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Maike Kittelmann
- Department of Biological and Medical Sciences, Oxford Brookes University, Headington Campus, Oxford, OX3 0BP, UK
| | - Alun R C Jones
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Eamonn B Mallon
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
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Van Goor J, Herre EA, Gómez A, Nason JD. Extraordinarily precise nematode sex ratios: adaptive responses to vanishingly rare mating opportunities. Proc Biol Sci 2022; 289:20211572. [PMID: 35042409 PMCID: PMC8767218 DOI: 10.1098/rspb.2021.1572] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 12/10/2021] [Indexed: 01/28/2023] Open
Abstract
Sex ratio theory predicts both mean sex ratio and variance under a range of population structures. Here, we compare two genera of phoretic nematodes (Parasitodiplogaster and Ficophagus spp.) associated with 12 fig pollinating wasp species in Panama. The host wasps exhibit classic local mate competition: only inseminated females disperse from natal figs, and their offspring form mating pools that consist of scores of the adult offspring contributed by one or a few foundress mothers. By contrast, in both nematode genera, only sexually undifferentiated juveniles disperse and their mating pools routinely consist of 10 or fewer adults. Across all mating pool sizes, the sex ratios observed in both nematode genera are consistently female-biased (approx. 0.34 males), but markedly less female-biased than is often observed in the host wasps (approx. 0.10 males). In further contrast with their hosts, variances in nematode sex ratios are also consistently precise (significantly less than binomial). The constraints associated with predictably small mating pools within highly subdivided populations appear to select for precise sex ratios that contribute both to the reproductive success of individual nematodes, and to the evolutionary persistence of nematode species. We suggest that some form of environmental sex determination underlies these precise sex ratios.
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Affiliation(s)
- Justin Van Goor
- Department of Biology, University of Maryland College Park, College Park, MD 20742, USA
- Smithsonian Tropical Research Institute, Unit 9100, Box 0948, DPO AA 34002-9998, Miami, FL 34002, USA
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50010, USA
| | - Edward Allen Herre
- Smithsonian Tropical Research Institute, Unit 9100, Box 0948, DPO AA 34002-9998, Miami, FL 34002, USA
| | - Adalberto Gómez
- Smithsonian Tropical Research Institute, Unit 9100, Box 0948, DPO AA 34002-9998, Miami, FL 34002, USA
| | - John D. Nason
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50010, USA
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Van Goor J, Shakes DC, Haag ES. Fisher vs. the Worms: Extraordinary Sex Ratios in Nematodes and the Mechanisms that Produce Them. Cells 2021; 10:1793. [PMID: 34359962 PMCID: PMC8303164 DOI: 10.3390/cells10071793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/08/2021] [Accepted: 07/13/2021] [Indexed: 01/20/2023] Open
Abstract
Parker, Baker, and Smith provided the first robust theory explaining why anisogamy evolves in parallel in multicellular organisms. Anisogamy sets the stage for the emergence of separate sexes, and for another phenomenon with which Parker is associated: sperm competition. In outcrossing taxa with separate sexes, Fisher proposed that the sex ratio will tend towards unity in large, randomly mating populations due to a fitness advantage that accrues in individuals of the rarer sex. This creates a vast excess of sperm over that required to fertilize all available eggs, and intense competition as a result. However, small, inbred populations can experience selection for skewed sex ratios. This is widely appreciated in haplodiploid organisms, in which females can control the sex ratio behaviorally. In this review, we discuss recent research in nematodes that has characterized the mechanisms underlying highly skewed sex ratios in fully diploid systems. These include self-fertile hermaphroditism and the adaptive elimination of sperm competition factors, facultative parthenogenesis, non-Mendelian meiotic oddities involving the sex chromosomes, and environmental sex determination. By connecting sex ratio evolution and sperm biology in surprising ways, these phenomena link two "seminal" contributions of G. A. Parker.
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Affiliation(s)
- Justin Van Goor
- Department of Biology, University of Maryland, College Park, MD 20742, USA;
| | - Diane C. Shakes
- Department of Biology, William and Mary, Williamsburg, VA 23187, USA;
| | - Eric S. Haag
- Department of Biology, University of Maryland, College Park, MD 20742, USA;
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Delattre M, Goehring NW. The first steps in the life of a worm: Themes and variations in asymmetric division in C. elegans and other nematodes. Curr Top Dev Biol 2021; 144:269-308. [PMID: 33992156 DOI: 10.1016/bs.ctdb.2020.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Starting with Boveri in the 1870s, microscopic investigation of early embryogenesis in a broad swath of nematode species revealed the central role of asymmetric cell division in embryonic axis specification, blastomere positioning, and cell fate specification. Notably, across the class Chromadorea, a conserved theme emerges-asymmetry is first established in the zygote and specifies its asymmetric division, giving rise to an anterior somatic daughter cell and a posterior germline daughter cell. Beginning in the 1980s, the emergence of Caenorhabditis elegans as a model organism saw the advent of genetic tools that enabled rapid progress in our understanding of the molecular mechanisms underlying asymmetric division, in many cases defining key paradigms that turn out to regulate asymmetric division in a wide range of systems. Yet, the consequence of this focus on C. elegans came at the expense of exploring the extant diversity of developmental variation exhibited across nematode species. Given the resurgent interest in evolutionary studies facilitated in part by new tools, here we revisit the diversity in this asymmetric first division, juxtaposing molecular insight into mechanisms of symmetry-breaking, spindle positioning and fate specification, with a consideration of plasticity and variability within and between species. In the process, we hope to highlight questions of evolutionary forces and molecular variation that may have shaped the extant diversity of developmental mechanisms observed across Nematoda.
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Affiliation(s)
- Marie Delattre
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Inserm, UCBL, Lyon, France.
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11
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Abstract
In diverse parasite taxa, from scale insects to root-knot nematodes, asexual lineages have exceptionally large host ranges, larger than those of their sexual relatives. Phylogenetic comparative studies of parasite taxa indicate that increases in host range and geographic range increase the probability of establishment of asexual lineages. At first pass, this convergence of traits appears counter-intuitive: intimate, antagonistic association with an enormous range of host taxa correlates with asexual reproduction, which should limit genetic variation within populations. Why would narrow host ranges favor sexual parasites and large host ranges favor asexual parasites? To take on this problem I link theory on ecological specialization to the two predominant hypotheses for the evolution of sex. I argue that both hypotheses predict a positive association between host range and the probability of invasion of asexual parasites, mediated either by variation in population size or in the strength of antagonistic coevolution. I also review hypotheses on colonization and the evolution of niche breadth in asexual lineages. I emphasize parasite taxa, with their diversity of reproductive modes and ecological strategies, as valuable assets in the hunt for solutions to the classic problems of the evolution of sex and geographic parthenogenesis.
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Affiliation(s)
- Amanda K Gibson
- Wissenschaftskolleg zu Berlin, Berlin, Germany.,Department of Biology, University of Virginia, Charlottesville, VA, USA
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12
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Schiffer PH, Danchin EGJ, Burnell AM, Creevey CJ, Wong S, Dix I, O'Mahony G, Culleton BA, Rancurel C, Stier G, Martínez-Salazar EA, Marconi A, Trivedi U, Kroiher M, Thorne MAS, Schierenberg E, Wiehe T, Blaxter M. Signatures of the Evolution of Parthenogenesis and Cryptobiosis in the Genomes of Panagrolaimid Nematodes. iScience 2019; 21:587-602. [PMID: 31759330 PMCID: PMC6889759 DOI: 10.1016/j.isci.2019.10.039] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 07/17/2019] [Accepted: 10/21/2019] [Indexed: 12/12/2022] Open
Abstract
Most animal species reproduce sexually and fully parthenogenetic lineages are usually short lived in evolution. Still, parthenogenesis may be advantageous as it avoids the cost of sex and permits colonization by single individuals. Panagrolaimid nematodes have colonized environments ranging from arid deserts to Arctic and Antarctic biomes. Many are obligatory meiotic parthenogens, and most have cryptobiotic abilities, being able to survive repeated cycles of complete desiccation and freezing. To identify systems that may contribute to these striking abilities, we sequenced and compared the genomes and transcriptomes of parthenogenetic and outcrossing panagrolaimid species, including cryptobionts and non-cryptobionts. The parthenogens are triploids, most likely originating through hybridization. Adaptation to cryptobiosis shaped the genomes of panagrolaimid nematodes and is associated with the expansion of gene families and signatures of selection on genes involved in cryptobiosis. All panagrolaimids have acquired genes through horizontal gene transfer, some of which are likely to contribute to cryptobiosis.
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Affiliation(s)
- Philipp H Schiffer
- CLOE, Department for Biosciences, University College London, London, UK; Zoologisches Institut, Universität zu Köln, 50674 Köln, Germany; Institut für Genetik, Universität zu Köln, 50674 Köln, Germany.
| | | | - Ann M Burnell
- Maynooth University Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
| | | | - Simon Wong
- Irish Centre for High-End Computing, Tower Building, Trinity Technology & Enterprise Campus, Grand Canal Quay, Dublin D02 HP83, Ireland
| | - Ilona Dix
- Maynooth University Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
| | - Georgina O'Mahony
- Maynooth University Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
| | - Bridget A Culleton
- Maynooth University Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland; Megazyme, Bray Business Park, Bray, Co. Wicklow A98 YV29, Ireland
| | | | - Gary Stier
- Zoologisches Institut, Universität zu Köln, 50674 Köln, Germany
| | - Elizabeth A Martínez-Salazar
- Unidad Académica de Ciencias Biológicas, Laboratorio de Colecciones Biológicas y Sistemática Molecular, Universidad Autónoma de Zacatecas, Zacatecas, México
| | - Aleksandra Marconi
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Urmi Trivedi
- Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Michael Kroiher
- Zoologisches Institut, Universität zu Köln, 50674 Köln, Germany
| | - Michael A S Thorne
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | | | - Thomas Wiehe
- Institut für Genetik, Universität zu Köln, 50674 Köln, Germany
| | - Mark Blaxter
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3FL, UK; Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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13
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Cutter AD. Reproductive transitions in plants and animals: selfing syndrome, sexual selection and speciation. THE NEW PHYTOLOGIST 2019; 224:1080-1094. [PMID: 31336389 DOI: 10.1111/nph.16075] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 07/17/2019] [Indexed: 05/23/2023]
Abstract
The evolution of predominant self-fertilisation frequently coincides with the evolution of a collection of phenotypes that comprise the 'selfing syndrome', in both plants and animals. Genomic features also display a selfing syndrome. Selfing syndrome traits often involve changes to male and female reproductive characters that were subject to sexual selection and sexual conflict in the obligatorily outcrossing ancestor, including the gametic phase for both plants and animals. Rapid evolution of reproductive traits, due to both relaxed selection and directional selection under the new status of predominant selfing, lays the genetic groundwork for reproductive isolation. Consequently, shifts in sexual selection pressures coupled to transitions to selfing provide a powerful paradigm for investigating the speciation process. Plant and animal studies, however, emphasise distinct selective forces influencing reproductive-mode transitions: genetic transmission advantage to selfing or reproductive assurance outweighing the costs of inbreeding depression vs the costs of males and meiosis. Here, I synthesise links between sexual selection, evolution of selfing and speciation, with particular focus on identifying commonalities and differences between plant and animal systems and pointing to areas warranting further synergy.
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Affiliation(s)
- Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
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14
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Cutter AD, Morran LT, Phillips PC. Males, Outcrossing, and Sexual Selection in Caenorhabditis Nematodes. Genetics 2019; 213:27-57. [PMID: 31488593 PMCID: PMC6727802 DOI: 10.1534/genetics.119.300244] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 06/06/2019] [Indexed: 12/15/2022] Open
Abstract
Males of Caenorhabditis elegans provide a crucial practical tool in the laboratory, but, as the rarer and more finicky sex, have not enjoyed the same depth of research attention as hermaphrodites. Males, however, have attracted the attention of evolutionary biologists who are exploiting the C. elegans system to test longstanding hypotheses about sexual selection, sexual conflict, transitions in reproductive mode, and genome evolution, as well as to make new discoveries about Caenorhabditis organismal biology. Here, we review the evolutionary concepts and data informed by study of males of C. elegans and other Caenorhabditis We give special attention to the important role of sperm cells as a mediator of inter-male competition and male-female conflict that has led to drastic trait divergence across species, despite exceptional phenotypic conservation in many other morphological features. We discuss the evolutionary forces important in the origins of reproductive mode transitions from males being common (gonochorism: females and males) to rare (androdioecy: hermaphrodites and males) and the factors that modulate male frequency in extant androdioecious populations, including the potential influence of selective interference, host-pathogen coevolution, and mutation accumulation. Further, we summarize the consequences of males being common vs rare for adaptation and for trait divergence, trait degradation, and trait dimorphism between the sexes, as well as for molecular evolution of the genome, at both micro-evolutionary and macro-evolutionary timescales. We conclude that C. elegans male biology remains underexploited and that future studies leveraging its extensive experimental resources are poised to discover novel biology and to inform profound questions about animal function and evolution.
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Affiliation(s)
- Asher D Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario M5S3B2, Canada
| | - Levi T Morran
- Department of Biology, Emory University, Atlanta, Georgia 30322, and
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
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15
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Kanzaki N, Ekino T, Masuya H. Seinura caverna n. sp. (Tylenchomorpha: Aphelenchoididae), an androdioecious species isolated from bat guano in a calcareous cave. NEMATOLOGY 2019. [DOI: 10.1163/15685411-00003207] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Summary
A new species of a predator aphelenchoidid, Seinura caverna n. sp., is described and illustrated. The new species was isolated from bat guano collected from a calcareous cave in Japan. The new species is characterised by its three-lined lateral field, secretory-excretory pore at the level of the posterior two-thirds of the metacorpus, a long post-uterine sac, hermaphrodite tail shape elongate conoid with a filiform tip, and an androdioecious reproductive mode. The new species is typologically and biologically close to S. steineri, but is distinguished by its longer post-uterine sac, slightly longer stylet and slightly larger median bulb. The comparisons with other morphologically similar species, i.e., S. chertkovi, S. tenuicaudata and S. steineri, are discussed. A molecular phylogenetic analysis based on two small and large subunit ribosomal RNA genes revealed that the new species is located at the basal position of clade 3 of the Aphelenchoididae, clearly separate from S. demani, its congener with unclear rectum and anus, which is located at the derived position, suggesting that further generic revision is necessary for the genus. Aphelenchoides lii n. comb. (= Seinura lii) is proposed.
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Affiliation(s)
- Natsumi Kanzaki
- 1Kansai Research Center, Forestry and Forest Products Research Institute (FFPRI), 68 Nagaikyutaroh, Momoyama, Fushimi, Kyoto 612-0855, Japan
| | - Taisuke Ekino
- 2Department of Applied Biological Sciences, Saga University, Saga 840-8502, Japan
- 3The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan
| | - Hayato Masuya
- 4Tohoku Research Center, FFPRI, 92-25 Nabeyashiki, Shimokuriyagawa, Morioka, Iwate 020-0123, Japan
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16
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Rödelsperger C, Röseler W, Prabh N, Yoshida K, Weiler C, Herrmann M, Sommer RJ. Phylotranscriptomics of Pristionchus Nematodes Reveals Parallel Gene Loss in Six Hermaphroditic Lineages. Curr Biol 2018; 28:3123-3127.e5. [DOI: 10.1016/j.cub.2018.07.041] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 06/12/2018] [Accepted: 07/12/2018] [Indexed: 11/28/2022]
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17
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GIBSON AMANDAK, MORRAN LEVIT. A Model for Evolutionary Ecology of Disease: The Case for Caenorhabditis Nematodes and Their Natural Parasites. J Nematol 2018. [DOI: 10.21307/jofnem-2017-083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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18
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Baskaran P, Jaleta TG, Streit A, Rödelsperger C. Duplications and Positive Selection Drive the Evolution of Parasitism-Associated Gene Families in the Nematode Strongyloides papillosus. Genome Biol Evol 2017; 9:790-801. [PMID: 28338804 PMCID: PMC5381570 DOI: 10.1093/gbe/evx040] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2017] [Indexed: 12/29/2022] Open
Abstract
Gene duplication is a major mechanism playing a role in the evolution of phenotypic complexity and in the generation of novel traits. By comparing parasitic and nonparasitic nematodes, a recent study found that the evolution of parasitism in Strongyloididae is associated with a large expansion in the Astacin and CAP gene families.To gain novel insights into the developmental processes in the sheep parasite Strongyloides papillosus, we sequenced transcriptomes of different developmental stages and sexes. Overall, we found that the majority of genes are developmentally regulated and have one-to-one orthologs in the diverged S. ratti genome. Together with the finding of similar expression profiles between S. papillosus and S. ratti, these results indicate a strong evolutionary constraint acting against change at sequence and expression levels. However, the comparison between parasitic and free-living females demonstrates a quite divergent pattern that is mostly due to the previously mentioned expansion in the Astacin and CAP gene families. More detailed phylogenetic analysis of both gene families shows that most members date back to single expansion events early in the Strongyloides lineage and have undergone subfunctionalization resulting in clusters that are highly expressed either in infective larvae or in parasitic females. Finally, we found increased evidence for positive selection in both gene families relative to the genome-wide expectation.In summary, our study reveals first insights into the developmental transcriptomes of S. papillosus and provides a detailed analysis of sequence and expression evolution in parasitism-associated gene families.
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Affiliation(s)
- Praveen Baskaran
- Department for Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Tübingen, Germany
| | - Tegegn G Jaleta
- Department for Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Tübingen, Germany
| | - Adrian Streit
- Department for Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Tübingen, Germany
| | - Christian Rödelsperger
- Department for Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Tübingen, Germany
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19
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Fradin H, Kiontke K, Zegar C, Gutwein M, Lucas J, Kovtun M, Corcoran DL, Baugh LR, Fitch DHA, Piano F, Gunsalus KC. Genome Architecture and Evolution of a Unichromosomal Asexual Nematode. Curr Biol 2017; 27:2928-2939.e6. [PMID: 28943090 PMCID: PMC5659720 DOI: 10.1016/j.cub.2017.08.038] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/14/2017] [Accepted: 08/15/2017] [Indexed: 10/24/2022]
Abstract
Asexual reproduction in animals, though rare, is the main or exclusive mode of reproduction in some long-lived lineages. The longevity of asexual clades may be correlated with the maintenance of heterozygosity by mechanisms that rearrange genomes and reduce recombination. Asexual species thus provide an opportunity to gain insight into the relationship between molecular changes, genome architecture, and cellular processes. Here we report the genome sequence of the parthenogenetic nematode Diploscapter pachys with only one chromosome pair. We show that this unichromosomal architecture is shared by a long-lived clade of asexual nematodes closely related to the genetic model organism Caenorhabditis elegans. Analysis of the genome assembly reveals that the unitary chromosome arose through fusion of six ancestral chromosomes, with extensive rearrangement among neighboring regions. Typical nematode telomeres and telomeric protection-encoding genes are lacking. Most regions show significant heterozygosity; homozygosity is largely concentrated to one region and attributed to gene conversion. Cell-biological and molecular evidence is consistent with the absence of key features of meiosis I, including synapsis and recombination. We propose that D. pachys preserves heterozygosity and produces diploid embryos without fertilization through a truncated meiosis. As a prelude to functional studies, we demonstrate that D. pachys is amenable to experimental manipulation by RNA interference.
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Affiliation(s)
- Hélène Fradin
- Department of Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Karin Kiontke
- Department of Biology, New York University, New York, NY 10003, USA
| | - Charles Zegar
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Michelle Gutwein
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Jessica Lucas
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Mikhail Kovtun
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
| | - David L Corcoran
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
| | - L Ryan Baugh
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - David H A Fitch
- Department of Biology, New York University, New York, NY 10003, USA.
| | - Fabio Piano
- Department of Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
| | - Kristin C Gunsalus
- Department of Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
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20
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Kanzaki N, Kiontke K, Tanaka R, Hirooka Y, Schwarz A, Müller-Reichert T, Chaudhuri J, Pires-daSilva A. Description of two three-gendered nematode species in the new genus Auanema (Rhabditina) that are models for reproductive mode evolution. Sci Rep 2017; 7:11135. [PMID: 28894108 PMCID: PMC5593846 DOI: 10.1038/s41598-017-09871-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 08/01/2017] [Indexed: 01/05/2023] Open
Abstract
The co-existence of males, females and hermaphrodites, a rare mating system known as trioecy, has been considered as an evolutionarily transient state. In nematodes, androdioecy (males/hermaphrodites) as found in Caenorhabditis elegans, is thought to have evolved from dioecy (males/females) through a trioecious intermediate. Thus, trioecious species are good models to understand the steps and requirements for the evolution of new mating systems. Here we describe two new species of nematodes with trioecy, Auanema rhodensis and A. freiburgensis. Along with molecular barcodes, we provide a detailed analysis of the morphology of these species, and document it with drawings and light and SEM micrographs. Based on morphological data, these free-living nematodes were assigned to a new genus, Auanema, together with three other species described previously. Auanema species display convergent evolution in some features with parasitic nematodes with complex life cycles, such as the production of few males after outcrossing and the obligatory development of dauers into self-propagating adults.
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Affiliation(s)
- Natsumi Kanzaki
- Forest Pathology Laboratory, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
| | - Karin Kiontke
- Department of Biology, New York University, 100 Washington Square E., New York, NY, 10003, USA
| | - Ryusei Tanaka
- Forest Pathology Laboratory, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan.,Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Yuuri Hirooka
- Forest Pathology Laboratory, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan.,Department of Clinical Plant Science, Faculty of Bioscience and Applied Chemistry, Hosei University, Kajino-cho 3-7-2, Koganei, Tokyo, 184-8584, Japan
| | - Anna Schwarz
- Experimental Center, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Fiedlerstraße 42, 01307, Dresden, Germany
| | - Thomas Müller-Reichert
- Experimental Center, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Fiedlerstraße 42, 01307, Dresden, Germany
| | - Jyotiska Chaudhuri
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA
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21
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McCaig CM, Lin X, Farrell M, Rehain-Bell K, Shakes DC. Germ cell cysts and simultaneous sperm and oocyte production in a hermaphroditic nematode. Dev Biol 2017; 430:362-373. [PMID: 28844904 DOI: 10.1016/j.ydbio.2017.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/05/2017] [Accepted: 08/08/2017] [Indexed: 11/29/2022]
Abstract
Studies of gamete development in the self-fertile hermaphrodites of Caenorhabditis elegans have significantly contributed to our understanding of fundamental developmental mechanisms. However, evolutionary transitions from outcrossing males and females to self-fertile hermaphrodites have convergently evolved within multiple nematode sub-lineages, and whether the C. elegans pattern of self-fertile hermaphroditism and gamete development is representative remains largely unexplored. Here we describe a pattern of sperm production in the trioecious (male/female/hermaphrodite) nematode Rhabditis sp. SB347 (recently named Auanema rhodensis) that differs from C. elegans in two striking ways. First, while C. elegans hermaphrodites make a one-time switch from sperm to oocyte production, R. sp. SB347 hermaphrodites continuously produce both sperm and oocytes. Secondly, while C. elegans germ cell proliferation is limited to germline stem cells (GSCs), sperm production in R. sp. SB347 includes an additional population of mitotically dividing cells that are a developmental intermediate between GSCs and fully differentiated spermatocytes. These cells are present in males and hermaphrodites but not females, and exhibit key characteristics of spermatogonia - the mitotic progenitors of spermatocytes in flies and vertebrates. Specifically, they exist outside the stem cell niche, increase germ cell numbers by transit-amplifying divisions, and synchronously proliferate within germ cell cysts. We also discovered spermatogonia in other trioecious Rhabditis species, but not in the male/female species Rhabditis axei or the more distant hermaphroditic Oscheius tipulae. The discovery of simultaneous hermaphroditism and spermatogonia in a lab-cultivatable nematode suggests R. sp. SB347 as a richly informative species for comparative studies of gametogenesis.
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Affiliation(s)
- Caitlin M McCaig
- Department of Biology, College of William and Mary, Williamsburg, VA 23187, USA
| | - Xiaoxue Lin
- Department of Biology, College of William and Mary, Williamsburg, VA 23187, USA
| | - Maureen Farrell
- Department of Biology, College of William and Mary, Williamsburg, VA 23187, USA
| | - Kathryn Rehain-Bell
- Department of Biology, College of William and Mary, Williamsburg, VA 23187, USA
| | - Diane C Shakes
- Department of Biology, College of William and Mary, Williamsburg, VA 23187, USA.
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22
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Weadick CJ, Sommer RJ. Unexpected sex-specific post-reproductive lifespan in the free-living nematode Pristionchus exspectatus. Evol Dev 2017; 18:297-307. [PMID: 27870213 DOI: 10.1111/ede.12206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Patterns of senescence (or aging) can vary among life history traits and between the sexes, providing an opportunity to study variation in the aging process within a single species. We previously found that females of the nematode Pristionchus exspectatus outlive males by a substantial margin under laboratory conditions. Here, we show that sex-specific reproductive senescence unfolds in the opposite direction in this species, resulting in a prolonged period of female-specific post-reproductive survival: females lost the ability to reproduce at approximately 4.7 weeks despite a median lifespan of about 12.3 weeks under lab conditions, whereas males lost the ability to reproduce at approximately 6.6 weeks, roughly in line with their median lifespan of around 7.6 weeks. Interestingly, somatic senescence (declining crawling speed) only explained reproductive senescence in males, whereas females lost the ability to reproduce regardless of condition. However, we found that housing females with males significantly increased their mortality rate, indicating that female-specific post-reproductive survival is unlikely to occur in the wild. We discuss our results in light of evolutionary theories of post-reproductive survival and previous studies of nematode behavioral ecology, arguing that premature reproductive senescence may stem from sex-specific condition-dependent survival during the reproductive period. Given the proven lab tractability of Prisitonchus nematodes, our findings provide a foundation for integrative research that combines evolutionary ecology and molecular genetics in the study of sex-specific senescence and post-reproductive survival.
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Affiliation(s)
- Cameron J Weadick
- Department of Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemmanstraße 37, Tübingen, 72076, Germany
| | - Ralf J Sommer
- Department of Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemmanstraße 37, Tübingen, 72076, Germany
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23
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Morgan K, McGaughran A, Rödelsperger C, Sommer RJ. Variation in rates of spontaneous male production within the nematode species Pristionchus pacificus supports an adaptive role for males and outcrossing. BMC Evol Biol 2017; 17:57. [PMID: 28228092 PMCID: PMC5322664 DOI: 10.1186/s12862-017-0873-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 01/05/2017] [Indexed: 12/18/2022] Open
Abstract
Background The nematode species Pristionchus pacificus has an androdioecious mating system in which populations consist of self-fertilizing hermaphrodites and relatively few males. The prevalence of males in such a system is likely to depend on the relative pros and cons of outcrossing. While outcrossing generates novel allelic combinations and can therefore increase adaptive potential, it may also disrupt the potentially beneficial consequences of repeated generations of selfing. These include purging of deleterious alleles, inheritance of co-adapted allele complexes, improved hermaphrodite fitness and increased population growth. Here we use experimental and population genetic approaches to test hypotheses relating to male production and outcrossing in laboratory and natural populations of P. pacificus sampled from the volcanic island of La Réunion. Results We find a significant interaction between sampling locality and temperature treatment influencing rates of spontaneous male production in the laboratory. While strains isolated at higher altitude, cooler localities produce a higher proportion of male offspring at 25 °C relative to 20 or 15 °C, the reverse pattern is seen in strains isolated from warmer, low altitude localities. Linkage disequilibrium extends across long physical distances, but fails to approach levels reported for the partially selfing nematode species Caenorhabditis elegans. Finally, we find evidence for admixture between divergent genetic lineages. Conclusions Elevated rates of laboratory male generation appear to occur under environmental conditions which differ from those experienced by populations in nature. Such elevated male generation may result in higher outcrossing rates, hence driving increased effective recombination and the creation of potentially adaptive novel allelic combinations. Patterns of linkage disequilibrium decay support selfing as the predominant reproductive strategy in P. pacificus. Finally, despite the potential for outcrossing depression, our results suggest admixture has occurred between distinct genetic lineages since their independent colonization of the island, suggesting outcrossing depression may not be uniform in this species. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0873-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katy Morgan
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany. .,Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA70148, USA.
| | - Angela McGaughran
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany.,CSIRO Land & Water, Black Mountain Laboratories, Clunies Ross Street, Canberra, ACT 2601, Australia.,University of Melbourne, School of BioSciences, 30 Flemington Road, Melbourne, VIC, 3010, Australia
| | - Christian Rödelsperger
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Ralf J Sommer
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
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24
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Weadick CJ, Sommer RJ. Hybrid crosses and the genetic basis of interspecific divergence in lifespan in Pristionchus nematodes. J Evol Biol 2016; 30:650-657. [PMID: 27893180 DOI: 10.1111/jeb.13022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/24/2016] [Indexed: 11/30/2022]
Abstract
Characterizing the genetic basis of among-species variation in lifespan is a major goal of evolutionary gerontology research, but the very feature that defines separate species - the inability to interbreed - makes achieving this goal impractical, if not impossible, for most taxa. Pristionchus nematodes provide an intriguing system for tackling this problem, as female lifespan varies among species that can be crossed to form viable (although infertile) hybrids. By conducting reciprocal crosses among three species - two dioecious (long-lived Pristionchus exspectatus and short-lived Pristionchus arcanus) and one androdioecious (short-lived Pristionchus pacificus) - we found that female lifespan was long for all hybrids, consistent with the hypothesis that the relatively short lifespans seen for P. pacificus hermaphrodites and P. arcanus females are caused by independent, recessive alleles that are masked in hybrid genomes. Cross-direction had a small effect on survivorship for crosses involving P. exspectatus, indicating that nuclear-mitochondrial interactions may also influence Pristionchus longevity. Our findings suggest that long lifespan in P. exspectatus reflects the realization of an ancestral potential for extended longevity in the P. pacificus species complex. This work demonstrates the utility of interspecific hybrids for ageing research and provides a foundation for future work on the genetic architecture of interspecific lifespan variation.
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Affiliation(s)
- C J Weadick
- Department of Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - R J Sommer
- Department of Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
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25
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Ellis RE. "The persistence of memory"-Hermaphroditism in nematodes. Mol Reprod Dev 2016; 84:144-157. [PMID: 27291983 DOI: 10.1002/mrd.22668] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 06/01/2016] [Indexed: 12/13/2022]
Abstract
Self-fertility has evolved many times in nematodes. This transition often produces an androdioecious species, with XX hermaphrodites and XO males. Although these hermaphrodites resemble females in most respects, early germ cells differentiate as sperm, and late ones as oocytes. The sperm then receive an activation signal, populate the spermathecae, and are stored for later use in self-fertilization. These traits are controlled by complex modifications to the sex-determination and sperm activation pathways, which have arisen independently during the evolution of each hermaphroditic species. This transformation in reproductive strategy then promotes other major changes in the development, evolution, and population structure of these animals. Mol. Reprod. Dev. 84: 144-157, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ronald E Ellis
- Department of Molecular Biology, Rowan University SOM, Stratford, New Jersey
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26
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Castillo DM, Gibson AK, Moyle LC. Assortative mating and self-fertilization differ in their contributions to reinforcement, cascade speciation, and diversification. Curr Zool 2016; 62:169-181. [PMID: 29491904 PMCID: PMC5804227 DOI: 10.1093/cz/zow004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 01/07/2016] [Indexed: 11/14/2022] Open
Abstract
Cascade speciation and reinforcement can evolve rapidly when traits are pleiotropic and act as both signal/cue in nonrandom mating. Here, we examine the contribution of two key traits-assortative mating and self-fertilization-to reinforcement and (by extension) cascade speciation. First, using a population genetic model of reinforcement we find that both assortative mating and self-fertilization can make independent contributions to increased reproductive isolation, consistent with reinforcement. Self-fertilization primarily evolves due to its 2-fold transmission advantage when inbreeding depression (d) is lower (d < 0.45) but evolves as a function of the cost of hybridization under higher inbreeding depression (0.45 < d < 0.48). When both traits can evolve simultaneously, increased self-fertilization often prohibits the evolution of assortative mating. We infer that, under specific conditions, mating system transitions are more likely to lead to increased reproductive isolation and initiate cascade speciation, than assortative mating. Based on the results of our simulations, we hypothesized that transitions to self-fertilization could contribute to clade-wide diversification if reinforcement or cascade speciation is common. We tested this hypothesis with comparative data from two different groups. Consistent with our hypothesis, there was a trend towards uniparental reproduction being associated with increased diversification rate in the Nematode phylum. For the plant genus Mimulus, however, self-fertilization was associated with reduced diversification. Reinforcement driving speciation via transitions to self-fertilization might be short lived or unsustainable across macroevolutionary scales in some systems (some plants), but not others (such as nematodes), potentially due to differences in susceptibility to inbreeding depression and/or the ability to transition between reproductive modes.
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Affiliation(s)
- Dean M. Castillo
- Department of Biology, 1001 East Third Street, Indiana University, Bloomington, IN 47405, USA
| | - Amanda K. Gibson
- Department of Biology, 1001 East Third Street, Indiana University, Bloomington, IN 47405, USA
| | - Leonie C. Moyle
- Department of Biology, 1001 East Third Street, Indiana University, Bloomington, IN 47405, USA
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27
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Weadick CJ, Sommer RJ. Mating System Transitions Drive Life Span Evolution in Pristionchus Nematodes. Am Nat 2016; 187:517-31. [PMID: 27028079 DOI: 10.1086/685283] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Interactions between the sexes influence evolution at many scales, but not all animal species conform to the familiar male-female (dioecious) mating system; such taxa are powerful tools for studying the evolutionary importance of sexual selection and conflict on all manner of life-history traits, including longevity. We tested for an effect of mating system on adult life span in Pristionchus nematodes, where self-fertile hermaphrodites have replaced females multiple times independently throughout the genus (androdioecy). By measuring adult life span for 11 species (6 dioecious, 5 androdioecious), we found that life span is considerably shorter in hermaphrodites relative to closely related females. This effect is not a cost of reproduction; brood size did not reliably trade off with life span in self-fertilizing hermaphrodites or in mated females. Furthermore, we found that sexual dimorphism in life span varied among dioecious species, with females generally outliving males. Finally, we documented intraspecific variation for life span and cuticular disease (blistering) prevalence in Pristionchus pacificus, a model system for evolutionary-developmental biology. This work demonstrates that mating system transitions and life span evolution are linked in Pristionchus nematodes and provides a foundation for future comparative and mechanistic studies of aging in this genus.
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Fierst JL, Willis JH, Thomas CG, Wang W, Reynolds RM, Ahearne TE, Cutter AD, Phillips PC. Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes. PLoS Genet 2015; 11:e1005323. [PMID: 26114425 PMCID: PMC4482642 DOI: 10.1371/journal.pgen.1005323] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 05/31/2015] [Indexed: 11/18/2022] Open
Abstract
The self-fertile nematode worms Caenorhabditis elegans, C. briggsae, and C. tropicalis evolved independently from outcrossing male-female ancestors and have genomes 20-40% smaller than closely related outcrossing relatives. This pattern of smaller genomes for selfing species and larger genomes for closely related outcrossing species is also seen in plants. We use comparative genomics, including the first high quality genome assembly for an outcrossing member of the genus (C. remanei) to test several hypotheses for the evolution of genome reduction under a change in mating system. Unlike plants, it does not appear that reductions in the number of repetitive elements, such as transposable elements, are an important contributor to the change in genome size. Instead, all functional genomic categories are lost in approximately equal proportions. Theory predicts that self-fertilization should equalize the effective population size, as well as the resulting effects of genetic drift, between the X chromosome and autosomes. Contrary to this, we find that the self-fertile C. briggsae and C. elegans have larger intergenic spaces and larger protein-coding genes on the X chromosome when compared to autosomes, while C. remanei actually has smaller introns on the X chromosome than either self-reproducing species. Rather than being driven by mutational biases and/or genetic drift caused by a reduction in effective population size under self reproduction, changes in genome size in this group of nematodes appear to be caused by genome-wide patterns of gene loss, most likely generated by genomic adaptation to self reproduction per se.
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Affiliation(s)
- Janna L. Fierst
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - John H. Willis
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Cristel G. Thomas
- Department of Ecology and Evolutionary Biology and Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario, Canada
| | - Wei Wang
- Department of Ecology and Evolutionary Biology and Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario, Canada
| | - Rose M. Reynolds
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Timothy E. Ahearne
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Asher D. Cutter
- Department of Ecology and Evolutionary Biology and Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario, Canada
| | - Patrick C. Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
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Gibson AK, Fuentes JA. A phylogenetic test of the Red Queen Hypothesis: outcrossing and parasitism in the Nematode phylum. Evolution 2014; 69:530-40. [PMID: 25403727 DOI: 10.1111/evo.12565] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 11/06/2014] [Indexed: 01/04/2023]
Abstract
Sexual outcrossing is costly relative to selfing and asexuality, yet it is ubiquitous in nature, a paradox that has long puzzled evolutionary biologists. The Red Queen Hypothesis argues that outcrossing is maintained by antagonistic interactions between host and parasites. Most tests of this hypothesis focus on the maintenance of outcrossing in hosts. The Red Queen makes an additional prediction that parasitic taxa are more likely to be outcrossing than their free-living relatives. We test this prediction in the diverse Nematode phylum using phylogenetic comparative methods to evaluate trait correlations. In support of the Red Queen, we demonstrate a significant correlation between parasitism and outcrossing in this clade. We find that this correlation is driven by animal parasites, for which outcrossing is significantly enriched relative to both free-living and plant parasitic taxa. Finally, we test hypotheses for the evolutionary history underlying the correlation of outcrossing and animal parasitism. Our results demonstrate that selfing and asexuality are significantly less likely to arise on parasitic lineages than on free-living ones. The findings of this study are consistent with the Red Queen Hypothesis. Moreover, they suggest that the maintenance of genetic variation is an important factor in the persistence of parasitic lineages.
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How to become a parasite without sex chromosomes: a hypothesis for the evolution of Strongyloides spp. and related nematodes. Parasitology 2014; 141:1244-54. [PMID: 24829037 DOI: 10.1017/s003118201400064x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Parasitic lifestyles evolved many times independently. Just within the phylum Nematoda animal parasitism must have arisen at least four times. Switching to a parasitic lifestyle is expected to lead to changes in various life history traits including reproductive strategies. Parasitic nematode worms of the genus Strongyloides represent an interesting example to study these processes because they are still capable of forming facultative free-living generations in between parasitic ones. The parasitic generation consists of females only, which reproduce parthenogenetically. The sex in the progeny of the parasitic worms is determined by environmental cues, which control a, presumably ancestral, XX/XO chromosomal sex determining system. In some species the X chromosome is fused with an autosome and one copy of the X-derived sequences is removed by sex-specific chromatin diminution in males. Here I propose a hypothesis for how today's Strongyloides sp. might have evolved from a sexual free-living ancestor through dauer larvae forming free-living and facultative parasitic intermediate stages.
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Characterization of genetic diversity in the nematode Pristionchus pacificus from population-scale resequencing data. Genetics 2014; 196:1153-65. [PMID: 24443445 DOI: 10.1534/genetics.113.159855] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The hermaphroditic nematode Pristionchus pacificus is an established model system for comparative studies with Caenorhabditis elegans in developmental biology, ecology, and population genetics. In this study, we present whole-genome sequencing data of 104 P. pacificus strains and the draft assembly of the obligate outcrossing sister species P. exspectatus. We characterize genetic diversity within P. pacificus and investigate the population genetic processes shaping this diversity. P. pacificus is 10 times more diverse than C. elegans and exhibits substantial population structure that allows us to probe its evolution on multiple timescales. Consistent with reduced effective recombination in this self-fertilizing species, we find haplotype blocks that span several megabases. Using the P. exspectatus genome as an outgroup, we polarized variation in P. pacificus and found a site frequency spectrum (SFS) that decays more rapidly than expected in neutral models. The SFS at putatively neutral sites is U shaped, which is a characteristic feature of pervasive linked selection. Based on the additional findings (i) that the majority of nonsynonymous variation is eliminated over timescales on the order of the separation between clades, (ii) that diversity is reduced in gene-rich regions, and (iii) that highly differentiated clades show very similar patterns of diversity, we conclude that purifying selection on many mutations with weak effects is a major force shaping genetic diversity in P. pacificus.
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Gilabert A, Wasmuth JD. Unravelling parasitic nematode natural history using population genetics. Trends Parasitol 2013; 29:438-48. [PMID: 23948430 DOI: 10.1016/j.pt.2013.07.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 07/10/2013] [Accepted: 07/11/2013] [Indexed: 01/01/2023]
Abstract
The health and economic importance of parasitic nematodes cannot be overstated. Moreover, they offer a complex and diverse array of life strategies, raising a multitude of evolutionary questions. Researchers are applying population genetics to parasitic nematodes in order to disentangle some aspects of their life strategies, improve our knowledge about disease epidemiology, and design control strategies. However, population genetics studies of nematodes have been constrained due to the difficulty in sampling nematodes and developing molecular markers. In this context, new computational and sequencing technologies represent promising tools to investigate population genomics of parasitic, non-model, nematode species in an epidemiological context.
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Affiliation(s)
- Aude Gilabert
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, Alberta, T2N 4Z6, Canada
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Wright SI, Kalisz S, Slotte T. Evolutionary consequences of self-fertilization in plants. Proc Biol Sci 2013; 280:20130133. [PMID: 23595268 PMCID: PMC3652455 DOI: 10.1098/rspb.2013.0133] [Citation(s) in RCA: 238] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 03/22/2013] [Indexed: 01/17/2023] Open
Abstract
The transition from outcrossing to self-fertilization is one of the most common evolutionary changes in plants, yet only about 10-15% of flowering plants are predominantly selfing. To explain this phenomenon, Stebbins proposed that selfing may be an 'evolutionary dead end'. According to this hypothesis, transitions from outcrossing to selfing are irreversible, and selfing lineages suffer from an increased risk of extinction owing to a reduced potential for adaptation. Thus, although selfing can be advantageous in the short term, selfing lineages may be mostly short-lived owing to higher extinction rates. Here, we review recent results relevant to the 'dead-end hypothesis' of selfing and the maintenance of outcrossing over longer evolutionary time periods. In particular, we highlight recent results regarding diversification rates in self-incompatible and self-compatible taxa, and review evidence regarding the accumulation of deleterious mutations in selfing lineages. We conclude that while some aspects of the hypothesis of selfing as a dead end are supported by theory and empirical results, the evolutionary and ecological mechanisms remain unclear. We highlight the need for more studies on the effects of quantitative changes in outcrossing rates and on the potential for adaptation, particularly in selfing plants. In addition, there is growing evidence that transitions to selfing may themselves be drivers of speciation, and future studies of diversification and speciation should investigate this further.
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Affiliation(s)
- Stephen I. Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Susan Kalisz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tanja Slotte
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Prosser SWJ, Velarde-Aguilar MG, León-Règagnon V, Hebert PDN. Advancing nematode barcoding: a primer cocktail for the cytochrome c oxidase subunit I gene from vertebrate parasitic nematodes. Mol Ecol Resour 2013; 13:1108-15. [PMID: 23433320 DOI: 10.1111/1755-0998.12082] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 11/09/2012] [Accepted: 11/13/2012] [Indexed: 02/04/2023]
Abstract
Although nematodes are one of the most diverse metazoan phyla, species identification through morphology is difficult. Several genetic markers have been used for their identification, but most do not provide species-level resolution in all groups, and those that do lack primer sets effective across the phylum, precluding high-throughput processing. This study describes a cocktail of three novel primer pairs that overcome this limitation by recovering cytochrome c oxidase I (COI) barcodes from diverse nematode lineages parasitic on vertebrates, including members of three orders and eight families. Its effectiveness across a broad range of nematodes enables high-throughput processing.
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Affiliation(s)
- Sean W J Prosser
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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Weeks SC. The role of androdioecy and gynodioecy in mediating evolutionary transitions between dioecy and hermaphroditism in the animalia. Evolution 2012. [PMID: 23206127 DOI: 10.1111/j.1558-5646.2012.01714.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dioecy (gonochorism) is dominant within the Animalia, although a recent review suggests hermaphroditism is also common. Evolutionary transitions from dioecy to hermaphroditism (or vice versa) have occurred frequently in animals, but few studies suggest the advantage of such transitions. In particular, few studies assess how hermaphroditism evolves from dioecy or whether androdioecy or gynodioecy should be an "intermediate" stage, as noted in plants. Herein, these transitions are assessed by documenting the numbers of androdioecious and gynodioecious animals and inferring their ancestral reproductive mode. Both systems are rare, but androdioecy was an order of magnitude more common than gynodioecy. Transitions from dioecious ancestors were commonly to androdioecy rather than gynodioecy. Hermaphrodites evolving from sexually dimorphic dioecious ancestors appear to be constrained to those with female-biased sex allocation; such hermaphrodites replace females to coexist with males. Hermaphrodites evolving from sexually monomorphic dioecious ancestors were not similarly constrained. Species transitioning from hermaphroditic ancestors were more commonly androdioecious than gynodioecious, contrasting with similar transitions in plants. In animals, such transitions were associated with size specialization between the sexes, whereas in plants these transitions were to avoid inbreeding depression. Further research should frame these reproductive transitions in a theoretical context, similar to botanical studies.
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Affiliation(s)
- Stephen C Weeks
- Department of Biology, Program in Integrated Bioscience, The University of Akron, Akron, Ohio 44325-3908, USA.
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The map-1 gene family in root-knot nematodes, Meloidogyne spp.: a set of taxonomically restricted genes specific to clonal species. PLoS One 2012; 7:e38656. [PMID: 22719916 PMCID: PMC3377709 DOI: 10.1371/journal.pone.0038656] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 05/08/2012] [Indexed: 11/21/2022] Open
Abstract
Taxonomically restricted genes (TRGs), i.e., genes that are restricted to a limited subset of phylogenetically related organisms, may be important in adaptation. In parasitic organisms, TRG-encoded proteins are possible determinants of the specificity of host-parasite interactions. In the root-knot nematode (RKN) Meloidogyne incognita, the map-1 gene family encodes expansin-like proteins that are secreted into plant tissues during parasitism, thought to act as effectors to promote successful root infection. MAP-1 proteins exhibit a modular architecture, with variable number and arrangement of 58 and 13-aa domains in their central part. Here, we address the evolutionary origins of this gene family using a combination of bioinformatics and molecular biology approaches. Map-1 genes were solely identified in one single member of the phylum Nematoda, i.e., the genus Meloidogyne, and not detected in any other nematode, thus indicating that the map-1 gene family is indeed a TRG family. A phylogenetic analysis of the distribution of map-1 genes in RKNs further showed that these genes are specifically present in species that reproduce by mitotic parthenogenesis, with the exception of M. floridensis, and could not be detected in RKNs reproducing by either meiotic parthenogenesis or amphimixis. These results highlight the divergence between mitotic and meiotic RKN species as a critical transition in the evolutionary history of these parasites. Analysis of the sequence conservation and organization of repeated domains in map-1 genes suggests that gene duplication(s) together with domain loss/duplication have contributed to the evolution of the map-1 family, and that some strong selection mechanism may be acting upon these genes to maintain their functional role(s) in the specificity of the plant-RKN interactions.
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Global population genetic structure of Caenorhabditis remanei reveals incipient speciation. Genetics 2012; 191:1257-69. [PMID: 22649079 DOI: 10.1534/genetics.112.140418] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Mating system transitions dramatically alter the evolutionary trajectories of genomes that can be revealed by contrasts of species with disparate modes of reproduction. For such transitions in Caenorhabditis nematodes, some major causes of genome variation in selfing species have been discerned. And yet, we have only limited understanding of species-wide population genetic processes for their outcrossing relatives, which represent the reproductive state of the progenitors of selfing species. Multilocus-multipopulation sequence polymorphism data provide a powerful means to uncover the historical demography and evolutionary processes that shape genomes. Here we survey nucleotide polymorphism across the X chromosome for three populations of the outcrossing nematode Caenorhabditis remanei and demonstrate its divergence from a fourth population describing a closely related new species from China, C. sp. 23. We find high genetic variation globally and within each local population sample. Despite geographic barriers and moderate genetic differentiation between Europe and North America, considerable gene flow connects C. remanei populations. We discovered C. sp. 23 while investigating C. remanei, observing strong genetic differentiation characteristic of reproductive isolation that was confirmed by substantial F2 hybrid breakdown in interspecific crosses. That C. sp. 23 represents a distinct biological species provides a cautionary example of how standard practice can fail for mating tests of species identity in this group. This species pair permits full application of divergence population genetic methods to obligately outcrossing species of Caenorhabditis and also presents a new focus for interrogation of the genetics and evolution of speciation with the Caenorhabditis model system.
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Pires-daSilva A, Parihar M. Evo-devo of the germline and somatic gonad in nematodes. Sex Dev 2012; 7:163-70. [PMID: 22516962 DOI: 10.1159/000337960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Due to recent progress in the development of genetic tools, nematodes have become excellent models to address the mechanistic basis of evolution of development. The gonad is one of the most variable structures in nematodes, reflecting the diverse modes of reproduction and lifestyle in this phylum. During larval development, the gonad primordium has a key role in organizing the neighboring tissues. Therefore, changes in the development of the gonad do not only influence the evolution of its morphology but also the overall body plan of the nematode. Here, we review recent progress on the evolution of development of the germline and somatic gonad in nematodes.
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Affiliation(s)
- A Pires-daSilva
- Department of Biology, University of Texas at Arlington, Arlington, Tex. 76019, USA.
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