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Barnard-Kubow KB, Becker D, Murray CS, Porter R, Gutierrez G, Erickson P, Nunez JCB, Voss E, Suryamohan K, Ratan A, Beckerman A, Bergland AO. Genetic Variation in Reproductive Investment Across an Ephemerality Gradient in Daphnia pulex. Mol Biol Evol 2022; 39:msac121. [PMID: 35642301 PMCID: PMC9198359 DOI: 10.1093/molbev/msac121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Species across the tree of life can switch between asexual and sexual reproduction. In facultatively sexual species, the ability to switch between reproductive modes is often environmentally dependent and subject to local adaptation. However, the ecological and evolutionary factors that influence the maintenance and turnover of polymorphism associated with facultative sex remain unclear. We studied the ecological and evolutionary dynamics of reproductive investment in the facultatively sexual model species, Daphnia pulex. We found that patterns of clonal diversity, but not genetic diversity varied among ponds consistent with the predicted relationship between ephemerality and clonal structure. Reconstruction of a multi-year pedigree demonstrated the coexistence of clones that differ in their investment into male production. Mapping of quantitative variation in male production using lab-generated and field-collected individuals identified multiple putative quantitative trait loci (QTL) underlying this trait, and we identified a plausible candidate gene. The evolutionary history of these QTL suggests that they are relatively young, and male limitation in this system is a rapidly evolving trait. Our work highlights the dynamic nature of the genetic structure and composition of facultative sex across space and time and suggests that quantitative genetic variation in reproductive strategy can undergo rapid evolutionary turnover.
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Affiliation(s)
- Karen B Barnard-Kubow
- Department of Biology, University of Virginia, Charlottesville, VA, USA
- Department of Biology, James Madison University, Harrisonburg, VA, USA
| | - Dörthe Becker
- Department of Biology, University of Virginia, Charlottesville, VA, USA
- School of Biosciences, Ecology and Evolutionary Biology, University of Sheffield, Sheffield, UK
- Department of Biology, University of Marburg, Marburg, Germany
| | - Connor S Murray
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Robert Porter
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Grace Gutierrez
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | | | - Joaquin C B Nunez
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Erin Voss
- Department of Biology, University of Virginia, Charlottesville, VA, USA
- Department of Integrative Biology, UC Berkeley, Berkeley, CA, USA
| | | | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Andrew Beckerman
- School of Biosciences, Ecology and Evolutionary Biology, University of Sheffield, Sheffield, UK
| | - Alan O Bergland
- Department of Biology, University of Virginia, Charlottesville, VA, USA
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2
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Ye Z, Jiang X, Pfrender ME, Lynch M. Genome-Wide Allele-Specific Expression in Obligately Asexual Daphnia pulex and the Implications for the Genetic Basis of Asexuality. Genome Biol Evol 2021; 13:6415829. [PMID: 34726699 PMCID: PMC8598174 DOI: 10.1093/gbe/evab243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2021] [Indexed: 01/17/2023] Open
Abstract
Although obligately asexual lineages are thought to experience selective disadvantages associated with reduced efficiency of fixing beneficial mutations and purging deleterious mutations, such lineages are phylogenetically and geographically widespread. However, despite several genome-wide association studies, little is known about the genetic elements underlying the origin of obligate asexuality and how they spread. Because many obligately asexual lineages have hybrid origins, it has been suggested that asexuality is caused by the unbalanced expression of alleles from the hybridizing species. Here, we investigate this idea by identifying genes with allele-specific expression (ASE) in a Daphnia pulex population, in which obligate parthenogens (OP) and cyclical parthenogens (CP) coexist, with the OP clones having been originally derived from hybridization between CP D. pulex and its sister species, Daphnia pulicaria. OP D. pulex have significantly more ASE genes (ASEGs) than do CP D. pulex. Whole-genomic comparison of OP and CP clones revealed ∼15,000 OP-specific markers and 42 consistent ASEGs enriched in marker-defined regions. Ten of the 42 ASEGs have alleles coding for different protein sequences, suggesting functional differences between the products of the two parental alleles. At least three of these ten genes appear to be directly involved in meiosis-related processes, for example, RanBP2 can cause abnormal chromosome segregation in anaphase I, and the presence of Wee1 in immature oocytes leads to failure to enter meiosis II. These results provide a guide for future molecular resolution of the genetic basis of the transition to ameiotic parthenogenesis.
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Affiliation(s)
- Zhiqiang Ye
- Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona
| | | | - Michael E Pfrender
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana
| | - Michael Lynch
- Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona
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3
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Ye Z, Williams E, Zhao C, Burns CW, Lynch M. The rapid, mass invasion of New Zealand by North American Daphnia " pulex". LIMNOLOGY AND OCEANOGRAPHY 2021; 66:2672-2683. [PMID: 39175934 PMCID: PMC11340258 DOI: 10.1002/lno.11780] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 04/08/2021] [Indexed: 08/24/2024]
Abstract
Nonindigenous members of the Daphnia pulex complex have been found in many lakes in New Zealand (NZ) in the past 20 years, suggesting a recent invasion. However, very little is known about the precise phylogenetic origin of invasive Daphnia, whether each lake is invaded by a single clone or multiple clones, the lineage of the invasive clones, and whether they are obligately asexual clones. Furthermore, the source and time of arrival of the invasive genotype(s) are unclear. We address these questions by genomic sequencing of Daphnia populations from 13 lakes in the South Island and 1 lake in the North Island, NZ. All biallelic sites in these NZ populations have similar numbers of reads for the two parental alleles, suggesting each NZ population originates from a single asexual clone. Based on 25,643 monomorphic lineage-specific markers, the invasive Daphnia in the South Island were found to be Daphnia pulicaria Forbes, while those in the North Island are hybrids of D. pulicaria Forbes and D. cf. pulex sensu Hebert. Both the South and North Island Daphnia are phylogenetically clustered with North American Daphnia, thereby suggesting their North American origins. We found also that all South Island clones contain identical mitochondrial genomes, suggesting the origin and proliferation from a single founder clone, which we experimentally verified to be an obligate asexual. Estimates from molecular data imply a colonization time for the South Island clones of ~60 years ago, with a likely invasion route associated with the introduction of salmonids from North America.
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Affiliation(s)
- Zhiqiang Ye
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona
| | - Emily Williams
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona
| | - Chaoxian Zhao
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona
| | - Carolyn W. Burns
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona
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4
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Wang P, Yang F, Ma Z, Zhang R. Chromosome Unipolar Division and Low Expression of Tws May Cause Parthenogenesis of Rice Water Weevil ( Lissorhoptrus oryzophilus Kuschel). INSECTS 2021; 12:278. [PMID: 33805047 PMCID: PMC8064085 DOI: 10.3390/insects12040278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 11/28/2022]
Abstract
Rice water weevil (RWW) is divided into two types of population, triploid parthenogenesis and diploid bisexual reproduction. In this study, we explored the meiosis of triploid parthenogenesis RWW (Shangzhuang Town, Haidian District, Beijing, China) by marking the chromosomes and microtubules of parthenogenetic RWW oocytes via immunostaining. The immunostaining results show that there is a canonical meiotic spindle formed in the triploid parthenogenetic RWW oocytes, but chromosomes segregate at only one pole, which means that there is a chromosomal unipolar division during the oogenesis of the parthenogenetic RWW. Furthermore, we cloned the conserved sequences of parthenogenetic RWW REC8 and Tws, and designed primers based on the parthenogenetic RWW sequence to detect expression patterns by quantitative PCR (Q-PCR). Q-PCR results indicate that the expression of REC8 and Tws in ovarian tissue of bisexual Drosophila melanogaster is 0.98 and 10,000.00 times parthenogenetic RWW, respectively (p < 0.01). The results show that Tws had low expression in parthenogenetic RWW ovarian tissue, and REC8 was expressed normally. Our study suggests that the chromosomal unipolar division and deletion of Tws may cause parthenogenesis in RWW.
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Affiliation(s)
- Pengcheng Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (P.W.); (F.Y.); (Z.M.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangyuan Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (P.W.); (F.Y.); (Z.M.)
- Department of Entomology, Guizhou University, Guiyang 550025, Guizhou, China
| | - Zhuo Ma
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (P.W.); (F.Y.); (Z.M.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Runzhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (P.W.); (F.Y.); (Z.M.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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5
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Chin TA, Cristescu ME. Speciation in Daphnia. Mol Ecol 2021; 30:1398-1418. [PMID: 33522056 DOI: 10.1111/mec.15824] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/11/2021] [Accepted: 01/20/2021] [Indexed: 11/26/2022]
Abstract
The microcrustacean Daphnia is arguably one of the most studied zooplankton species, having a well understood ecology, life history, and a relatively well studied evolutionary history. Despite this wealth of knowledge, species boundaries within closely related species in this genus often remain elusive and the major evolutionary forces driving the diversity of daphniids remain controversial. This genus contains more than 80 species with multiple cryptic species complexes, with many closely related species able to hybridize. Here, we review speciation research in Daphnia within the framework of current speciation theory. We evaluate the role of geography, ecology, and biology in restricting gene flow and promoting diversification. Of the 253 speciation studies on Daphnia, the majority of studies examine geographic barriers (55%). While evidence shows that geographic barriers play a role in species divergence, ecological barriers are also probably prominent in Daphnia speciation. We assess the contribution of ecological and nonecological reproductive isolating barriers between closely related species of Daphnia and found that none of the reproductive isolating barriers are restricting gene flow completely. Research on reproductive isolating barriers has disproportionally focused on two species complexes, the Daphnia pulex and Daphnia longispina species complexes. Finally, we identify areas of research that remain relatively unexplored and discuss future research directions that build our understanding of speciation in daphniids.
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Affiliation(s)
- Tiffany A Chin
- Department of Biology, McGill University, Montreal, QC, Canada
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6
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Maiakovska O, Andriantsoa R, Tönges S, Legrand C, Gutekunst J, Hanna K, Pârvulescu L, Novitsky R, Weiperth A, Sciberras A, Deidun A, Ercoli F, Kouba A, Lyko F. Genome analysis of the monoclonal marbled crayfish reveals genetic separation over a short evolutionary timescale. Commun Biol 2021; 4:74. [PMID: 33462402 PMCID: PMC7814009 DOI: 10.1038/s42003-020-01588-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 12/10/2020] [Indexed: 12/20/2022] Open
Abstract
The marbled crayfish (Procambarus virginalis) represents a very recently evolved parthenogenetic freshwater crayfish species that has invaded diverse habitats in Europe and in Madagascar. However, population genetic analyses have been hindered by the homogeneous genetic structure of the population and the lack of suitable tools for data analysis. We have used whole-genome sequencing to characterize reference specimens from various known wild populations. In parallel, we established a whole-genome sequencing data analysis pipeline for the population genetic analysis of nearly monoclonal genomes. Our results provide evidence for systematic genetic differences between geographically separated populations and illustrate the emerging differentiation of the marbled crayfish genome. We also used mark-recapture population size estimation in combination with genetic data to model the growth pattern of marbled crayfish populations. Our findings uncover evolutionary dynamics in the marbled crayfish genome over a very short evolutionary timescale and identify the rapid growth of marbled crayfish populations as an important factor for ecological monitoring. Olena Maiakovska et al. provide whole-genome sequencing of the parthenogenetic and invasive marbled crayfish and develop a computational framework for data analysis of monoclonal genomes. These data and methodology allow the authors to demonstrate genetic separation between two populations and provide the first size estimate for a marbled crayfish colony, which they used to model population growth patterns.
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Affiliation(s)
- Olena Maiakovska
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Ranja Andriantsoa
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Sina Tönges
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Carine Legrand
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Julian Gutekunst
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Katharina Hanna
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Lucian Pârvulescu
- Department of Biology-Chemistry, West University of Timisoara, 16A Pestalozzi St., 300115, Timisoara, Romania
| | - Roman Novitsky
- Department of Water Bioresources and Aquaculture, Dnipro State Agrarian and Economic University, 25 Serhii Efremov St., Dnipro, 49600, Ukraine
| | - András Weiperth
- Department of Aquaculture, Institute for Natural Resources Conservation, Faculty of Agriculture and Environmental Sciences, Szent István University, Páter Károly utca 1, 2100, Gödöllő, Hungary
| | - Arnold Sciberras
- Physical Oceanography Research Group, Department of Geosciences, University of Malta, Msida, MSD 2080, Malta
| | - Alan Deidun
- Physical Oceanography Research Group, Department of Geosciences, University of Malta, Msida, MSD 2080, Malta
| | - Fabio Ercoli
- Chair of Hydrobiology and Fisheries, Institute of Agricultural and Environment Sciences, Estonian University of Life Sciences, Kreutzwaldi 5D, 51006, Tartu, Estonia.,Natural Resources and Environment, Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014, Jyväskylä, Finland
| | - Antonin Kouba
- Faculty of Fisheries and Protection of Waters, CENAKVA, University of South Bohemia in České Budějovice, Zátiší 728/II, 38925, Vodňany, Czech Republic
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.
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7
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Li X, Zhang Z, Zhang J, Huang J, Wang L, Li Y, Hafeez M, Lu Y. Population Genetic Diversity and Structure of Thrips tabaci (Thysanoptera: Thripidae) on Allium Hosts in China, Inferred From Mitochondrial COI Gene Sequences. JOURNAL OF ECONOMIC ENTOMOLOGY 2020; 113:1426-1435. [PMID: 31982906 DOI: 10.1093/jee/toaa001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Indexed: 06/10/2023]
Abstract
Thrips tabaci Lindeman is a widely distributed agricultural pest China, which causes damage to many vegetables and cash crops. However, the population genetic variation of this pest in China remains unknown. In this study, the genetic diversity and structure of T. tabaci on Allium hosts collected from 12 geographic locations were evaluated based on mitochondrial cytochrome oxidase subunit I (COI) sequences. Six haplotypes were identified in 247 T. tabaci individuals from 12 geographic locations. All the identified T. tabaci haplotypes were thelytokous populations. The strongest genetic differentiation and relatively low gene flow were found between QHXN and other locations, which might be due to geographic barriers, such as high altitude Qinghai-Tibet Plateau. The lowest genetic variation was found in eastern and southern regions, with only one haplotype identified. The Mantel test showed no correlation between genetic distance and geographical distances. High gene flow between locations with substantial geographical distances suggested that migration of T. tabaci across China might be facilitated through human activities. The results of demographic analysis suggested that T. tabaci in China have undergone a recent demographic expansion. The possible influences of T. tabaci invasion history and human activities on the current haplotype geographical distribution were interpreted and the implications of these findings for T. tabaci management were discussed.
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Affiliation(s)
- Xiaowei Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Zhijun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Jinming Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Jun Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Likun Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Yehua Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Muhammad Hafeez
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Yaobin Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
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8
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Lohr JN, Haag CR. Parasite-driven replacement of a sexual by a closely related asexual taxon in nature. Ecology 2020; 101:e03105. [PMID: 32452541 DOI: 10.1002/ecy.3105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/22/2020] [Accepted: 04/15/2020] [Indexed: 11/09/2022]
Abstract
Asexual species are thought to suffer more from coevolving parasites than related sexuals. Yet a variety of studies do not find the patterns predicted by theory. Here, to shine light on this conundrum, we investigate one such case of an asexual advantage in the presence of parasites. We follow the frequency dynamics of sexual and asexual Daphnia pulex in a natural pond that was initially dominated by sexuals. Coinciding with an epidemic of a microsporidian parasite infecting both sexuals and asexuals, the pond was rapidly taken over by the initially rare asexuals. With experiments comparing multiple sexual and asexual clones from across the local metapopulation, we confirm that asexuals are less susceptible and also suffer less from the parasite once infected. These results are consistent with the parasite-driven, ecological replacement of dominant sexuals by closely related, but more resistant asexuals, ultimately leading to the extinction of the formerly superior sexual competitor. Our study is one of the clearest examples from nature, backed up by experimental verification, showing a parasite-mediated reversal of competition dynamics. The experiments show that, across the metapopulation, asexuals have an advantage in the presence of parasites. In this metapopulation, asexuals are relatively rare, likely due to their recent invasion. While we cannot rule out other reasons for the observed patterns, the results are consistent with a temporary parasite-mediated advantage of asexuals due to the fact that they are rare, which is an underappreciated aspect of the Red Queen Hypothesis.
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Affiliation(s)
- Jennifer N Lohr
- Department of Biology, Ecology and Evolution, University of Fribourg, Chemin du Musée 10, 1700, Fribourg, Switzerland.,Tvärminne Zoological Station, J.A. Palménin tie 260, 10900, Hanko, Finland.,Department of Genetics, Evolution and Environment, University College London, Institute of Healthy Ageing, Darwin Building, Gower Street, London, WC1E 6BT, United Kingdom
| | - Christoph R Haag
- Department of Biology, Ecology and Evolution, University of Fribourg, Chemin du Musée 10, 1700, Fribourg, Switzerland.,Tvärminne Zoological Station, J.A. Palménin tie 260, 10900, Hanko, Finland.,CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, 1919, route de Mende, 34293, Montpellier Cedex 5, France
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9
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Luu DHK, Vo HP, Xu S. An efficient method for hatching diapausing embryos of Daphnia pulex species complex (Crustacea, Anomopoda). JOURNAL OF EXPERIMENTAL ZOOLOGY PART 2019; 333:111-117. [PMID: 31709765 DOI: 10.1002/jez.2331] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 11/12/2022]
Abstract
A general method for efficiently hatching sexually produced diapausing embryos of the microcrustacean Daphnia is valuable for establishing Daphnia as a genetic model system. In this study, we examine the effect of ultraviolet light and different amounts of storage time in darkness on the hatching efficiency in two species of the Daphnia pulex species complex, D. pulex and Daphnia pulicaria. We identified a set of lighting conditions that can trigger 80% to ~100% hatching rate for embryos produced through selfing, outcrossing, and obligate parthenogenesis. Furthermore, we found that a storage time of at least 2 weeks in the dark before exposing embryos to ultraviolet light is critical for achieving high hatching rate. The identification of these key factors for hatching diapausing embryos can greatly facilitate future Daphnia research involving complex breeding designs as well as investigating the genetic switch that activates the hatching of diapausing embryos.
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Affiliation(s)
- Dustin H-K Luu
- Department of Biology, University of Texas at Arlington, Arlington, Texas
| | - Hillary P Vo
- Department of Biology, University of Texas at Arlington, Arlington, Texas
| | - Sen Xu
- Department of Biology, University of Texas at Arlington, Arlington, Texas
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10
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Abstract
The absence of a paternal contribution in an unfertilized ovum presents two developmental constraints against the evolution of parthenogenesis. We discuss the constraint caused by the absence of a centrosome and the one caused by the missing set of chromosomes and how they have been broken in specific taxa. They are examples of only a few well-underpinned examples of developmental constraints acting at macro-evolutionary scales in animals. Breaking of the constraint of the missing chromosomes is the best understood and generally involves rare occasions of drastic changes of meiosis. These drastic changes can be best explained by having been induced, or at least facilitated, by sudden cytological events (e.g., repeated rounds of hybridization, endosymbiont infections, and contagious infections). Once the genetic and developmental machinery is in place for regular or obligate parthenogenesis, shifts to other types of parthenogenesis can apparently rather easily evolve, for example, from facultative to obligate parthenogenesis, or from pseudoarrhenotoky to haplodiploidy. We argue that the combination of the two developmental constraints forms a near-absolute barrier against the gradual evolution from sporadic to obligate or regular facultative parthenogenesis, which can probably explain why the occurrence of the highly advantageous mode of regular facultative parthenogenesis is so rare and entirely absent in vertebrates.
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11
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Dedryver CA, Bonhomme J, Le Gallic JF, Simon JC. Differences in egg hatching time between cyclical and obligate parthenogenetic lineages of aphids. INSECT SCIENCE 2019; 26:135-141. [PMID: 28608995 DOI: 10.1111/1744-7917.12493] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/23/2017] [Accepted: 05/31/2017] [Indexed: 06/07/2023]
Abstract
Many aphid species exhibit a variation in reproductive mode which is influenced by winter climate regimes, with cyclical parthenogenetic (CP) lines dominating in cold winter areas (because they produce cold-resistant eggs) and obligate parthenogenetic (OP) ones in mild winter regions (because of their parthenogenetic overwintering). Genetic studies on several aphid species have shown that the OP trait can be transmitted during sexual events involving the 2 types of lines. This genetic system could be considered as a local safeguarding mechanism for OP alleles in case severe frost would have killed all parthenogenetically overwintering individuals. However, this strategy would only be efficient in restoring local polymorphism in breeding systems if the newly hatched OP recombinants remain competitive over their CP counterparts. In this study we compared egg hatching sequences of CP and OP F1 clones from several crosses obtained for 2 cereal aphid species, Sitobion avenae (constant 5 °C, 8 h of light) and Rhopalosiphum padi (winter outdoor conditions). For S. avenae, we obtained F1 offspring from 6 crosses, involving 4 clones while in R. padi F1 were obtained from 11 crosses involving 14 clones. We showed that in both species proportions of OP clones were higher in the first half of the progeny relative to the second half. In addition, F1 OP clones hatched in the mean about a week earlier than their CP sibs, which gives them a demographic advantage at the start of the growth season. We then discussed the consequences of this fitness advantage for the maintenance and spread of the OP trait in aphid populations.
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Affiliation(s)
- Charles-Antoine Dedryver
- Unité Mixte de Recherche IGEPP 1349, INRA/Agrocampus Ouest/Université Rennes 1, Le Rheu cedex, France
| | - Joël Bonhomme
- Unité Mixte de Recherche IGEPP 1349, INRA/Agrocampus Ouest/Université Rennes 1, Le Rheu cedex, France
| | - Jean-François Le Gallic
- Unité Mixte de Recherche IGEPP 1349, INRA/Agrocampus Ouest/Université Rennes 1, Le Rheu cedex, France
| | - Jean-Christophe Simon
- Unité Mixte de Recherche IGEPP 1349, INRA/Agrocampus Ouest/Université Rennes 1, Le Rheu cedex, France
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12
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Parker DJ, Bast J, Jalvingh K, Dumas Z, Robinson-Rechavi M, Schwander T. Repeated Evolution of Asexuality Involves Convergent Gene Expression Changes. Mol Biol Evol 2019; 36:350-364. [PMID: 30445505 PMCID: PMC6404633 DOI: 10.1093/molbev/msy217] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Asexual reproduction has evolved repeatedly from sexual ancestors across a wide range of taxa. Whereas the costs and benefits associated with asexuality have received considerable attention, the molecular changes underpinning the evolution of asexual reproduction remain relatively unexplored. In particular, it is completely unknown whether the repeated evolution of asexual phenotypes involves similar molecular changes, as previous studies have focused on changes occurring in single lineages. Here, we investigate the extent of convergent gene expression changes across five independent transitions to asexuality in stick insects. We compared gene expression of asexual females to females of close sexual relatives in whole-bodies, reproductive tracts, and legs. We identified a striking amount of convergent gene expression change (up to 8% of genes), greatly exceeding that expected by chance. Convergent changes were also tissue-specific, and most likely driven by selection for functional changes. Genes showing convergent changes in the reproductive tract were associated with meiotic spindle formation and centrosome organization. These genes are particularly interesting as they can influence the production of unreduced eggs, a key barrier to asexual reproduction. Changes in legs and whole-bodies were likely involved in female sexual trait decay, with enrichment in terms such as sperm-storage and pigmentation. By identifying changes occurring across multiple independent transitions to asexuality, our results provide a rare insight into the molecular basis of asexual phenotypes and suggest that the evolutionary path to asexuality is highly constrained, requiring repeated changes to the same key genes.
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Affiliation(s)
- Darren J Parker
- 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
| | - Kirsten Jalvingh
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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13
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Haag CR, Theodosiou L, Zahab R, Lenormand T. Low recombination rates in sexual species and sex-asex transitions. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160461. [PMID: 29109224 PMCID: PMC5698623 DOI: 10.1098/rstb.2016.0461] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2017] [Indexed: 12/11/2022] Open
Abstract
In most sexual, diploid eukaryotes, at least one crossover occurs between each pair of homologous chromosomes during meiosis, presumably in order to ensure proper segregation. Well-known exceptions to this rule are species in which one sex does not recombine and specific chromosomes lacking crossover. We review other possible exceptions, including species with chromosome maps of less than 50 cM in one or both sexes. We discuss the idea that low recombination rates may favour sex-asex transitions, or, alternatively may be a consequence of it. We then show that a yet undescribed species of brine shrimp Artemia from Kazakhstan (A sp. Kazakhstan), the closest known relative of the asexual Artemia parthenogenetica, has one of the shortest genetic linkage maps known. Based on a family of 42 individuals and 589 RAD markers, we find that many linkage groups are considerably shorter than 50 cM, suggesting either no obligate crossover or crossovers concentrated at terminal positions with little effect on recombination. We contrast these findings with the published map of the more distantly related sexual congener, A. franciscana, and conclude that the study of recombination in non-model systems is important to understand the evolutionary causes and consequences of recombination.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'.
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Affiliation(s)
- Christoph R Haag
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE)-Unité Mixte de Recherche 5175, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier-Université Paul-Valéry Montpellier-École Pratique des Hautes Études, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
| | - Loukas Theodosiou
- Research Group for Community Dynamics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany
| | - Roula Zahab
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE)-Unité Mixte de Recherche 5175, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier-Université Paul-Valéry Montpellier-École Pratique des Hautes Études, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
| | - Thomas Lenormand
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE)-Unité Mixte de Recherche 5175, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier-Université Paul-Valéry Montpellier-École Pratique des Hautes Études, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
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14
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Jiang X, Tang H, Ye Z, Lynch M. Insertion Polymorphisms of Mobile Genetic Elements in Sexual and Asexual Populations of Daphnia pulex. Genome Biol Evol 2017; 9:362-374. [PMID: 28057730 PMCID: PMC5381639 DOI: 10.1093/gbe/evw302] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2016] [Indexed: 12/20/2022] Open
Abstract
Transposable elements (TEs) constitute a substantial portion of many eukaryotic genomes, and can in principle contribute to evolutionary innovation as well as genomic deterioration. Daphnia pulex serves as a useful model for studying TE dynamics as a potential cause and/or consequence of asexuality. We analyzed insertion polymorphisms of TEs in 20 sexual and 20 asexual isolates of D. pulex across North American from their available whole-genome sequencing data. Our results show that the total fraction of the derived sequences of TEs is not substantially different between asexual and sexual D. pulex isolates. However, in general, sexual clones contain fewer fixed TE insertions but more total insertion polymorphisms than asexual clones, supporting the hypothesis that sexual reproduction facilitates the spread and elimination of TEs. We identified nine asexual-specific fixed TE insertions, eight long terminal repeat retrotransposons, and one DNA transposon. By comparison, no sexual-specific fixed TE insertions were observed in our analysis. Furthermore, except one TE insertion located on a contig from chromosome 7, the other eight asexual-specific insertion sites are located on contigs from chromosome 9 that is known to be associated with obligate asexuality in D. pulex. We found that all nine asexual-specific fixed TE insertions can also be detected in some Daphnia pulicaria isolates, indicating that a substantial number of TE insertions in asexual D. pulex have been directly inherited from D. pulicaria during the origin of obligate asexuals.
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Affiliation(s)
- Xiaoqian Jiang
- Department of Biology, Indiana University, Bloomington, Indiana
| | - Haixu Tang
- School of Informatics and Computing, Indiana University, Bloomington, Indiana
| | - Zhiqiang Ye
- Department of Biology, Indiana University, Bloomington, Indiana
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, Indiana
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15
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Marco HG, Verlinden H, Vanden Broeck J, Gäde G. Characterisation and pharmacological analysis of a crustacean G protein-coupled receptor: the red pigment-concentrating hormone receptor of Daphnia pulex. Sci Rep 2017; 7:6851. [PMID: 28761110 PMCID: PMC5537346 DOI: 10.1038/s41598-017-06805-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 06/16/2017] [Indexed: 02/06/2023] Open
Abstract
This is the first pharmacological characterisation of a neuropeptide G protein-coupled receptor (GPCR) in a crustacean. We cloned the ORF of the red pigment-concentrating hormone from a German strain of Daphnia pulex (Dappu-RPCH), as well as that of the cognate receptor (Dappu-RPCHR). Dappu-RPCHR has the hallmarks of the rhodopsin superfamily of GPCRs, and is more similar to insect adipokinetic hormone (AKH) receptor sequences than to receptor sequences for AKH/corazonin-like peptide or corazonin. We provide experimental evidence that Dappu-RPCH specifically activates the receptor (EC50 value of 65 pM) in a mammalian cell-based bioluminescence assay. We further characterised the properties of the ligands for the Dappu-RPCHR by investigating the activities of a variety of naturally-occurring peptides (insect AKH and crustacean RPCH peptides). The insect AKHs had lower EC50 values than the crustacean RPCHs. In addition, we tested a series of Dappu-RPCH analogues, where one residue at a time is systematically replaced by an alanine to learn about the relative importance of the termini and side chains for activation. Mainly amino acids in positions 1 to 4 and 8 of Dappu-RPCH appear responsible for effective activation of Dappu-RPCHR. The substitution of Phe4 in Dappu-RPCH had the most damaging effect on its agonistic activity.
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Affiliation(s)
- Heather G Marco
- Department of Biological Sciences, University of Cape Town, Rondebosch, South Africa.
| | - Heleen Verlinden
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59, P.O. Box 02465, B-3000, Leuven, Belgium
| | - Jozef Vanden Broeck
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59, P.O. Box 02465, B-3000, Leuven, Belgium
| | - Gerd Gäde
- Department of Biological Sciences, University of Cape Town, Rondebosch, South Africa
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16
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Foighil DÓ, Smith MJ. EVOLUTION OF ASEXUALITY IN THE COSMOPOLITAN MARINE CLAM LASAEA. Evolution 2017; 49:140-150. [PMID: 28593668 DOI: 10.1111/j.1558-5646.1995.tb05966.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/1992] [Accepted: 06/29/1993] [Indexed: 11/27/2022]
Abstract
The marine clam genus Lasaea is unique among marine bivalves in that it contains both sexual and asexual lineages. We employed molecular tools to infer intrageneric relationships of geographically restricted sexual versus cosmopolitan asexual forms. Polymerase chain reaction primers were used to amplify and sequence homologous 624 nucleotide fragments of COIII from polyploid, asexual, direct-developing individuals representing northeastern Pacific, northeastern Atlantic, Mediterranean, southern Indian Ocean, and Australian populations. DNA sequences also were obtained from the two known diploid congeners, the Australian sexual, indirect developer, Lasaea australis, and an undescribed meiotic Australian direct developer. Estimated tree topologies did not support monophyly for polyploid asexual Lasaea lineages. A robust dichotomy was evident in all phylogenetic trees and each of the two main branches included one of the diploid meitoic Australian congeners. Lasaea australis clustered with two of the direct-developing, polyploid asexual haplotypes, one from Australia, the other from the northeastern Atlantic. Monophyly is supported for the diploid Australian direct-developing lineage together with the remaining polyploid asexual lineages from the northeastern Pacific, northeastern Atlantic, Mediterranean, and southern Indian Ocean. These results indicate that asexual Lasaea lineages are polyphyletic and may have resulted from multiple hybridization events. The high degree of genetic divergence of asexual lineages from co-clustering meiotic congeners (16%-22%) and among geographically restricted monophyletic clones (9%-11%) suggests that asexual Lasaea lineages may be exceptionally long lived.
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Affiliation(s)
- Diarmaid Ó Foighil
- Institute of Molecular Biology and Biochemistry, Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada, V5A 1S6
| | - Michael J Smith
- Institute of Molecular Biology and Biochemistry, Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada, V5A 1S6
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17
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Moritz C, Wright JW, Brown WM. MITOCHONDRIAL DNA ANALYSES AND THE ORIGIN AND RELATIVE AGE OF PARTHENOGENETIC CNEMIDOPHORUS: PHYLOGENETIC CONSTRAINTS ON HYBRID ORIGINS. Evolution 2017; 46:184-192. [PMID: 28564972 DOI: 10.1111/j.1558-5646.1992.tb01993.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/1989] [Accepted: 06/28/1991] [Indexed: 11/30/2022]
Abstract
Within the genus Cnemidophorus, parthenogenesis has arisen by hybridization several times. This provides the opportunity to investigate general features of hybridization events that result in the formation of parthenogenetic lineages. The relationships of mtDNA from all bisexual species of Cnemidophorus known to be parents of parthenogens were investigated to evaluate phylogenetic constraints on the hybrid-origin of parthenogenesis. No phylogenetic clustering of the parental species, either maternal or paternal, was apparent. However, the combination of bisexual species that have resulted in parthenogenetic lineages are generally distantly related or genetically divergent. This contrasts with the expectation if parthenogenesis in hybrids is due to the action of a single rare allele, but is consistent with the hypothesis that some minimal level of divergence is necessary to stimulate parthenogenetic reproduction in hybrids.
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Affiliation(s)
- C Moritz
- Laboratory of Molecular systematics, Museum of Zoology and Department of Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - J W Wright
- Section of Herpetology, Natural History Museum of Los Angeles County, Los Angeles, CA, 90007, USA
| | - W M Brown
- Laboratory of Molecular systematics, Museum of Zoology and Department of Biology, University of Michigan, Ann Arbor, MI, 48109, USA
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18
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Lynch M, Spitze K, Crease T. THE DISTRIBUTION OF LIFE‐HISTORY VARIATION IN THE
DAPHNIA PULEX
COMPLEX. Evolution 2017; 43:1724-1736. [DOI: 10.1111/j.1558-5646.1989.tb02622.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/1988] [Accepted: 05/04/1989] [Indexed: 12/01/2022]
Affiliation(s)
- Michael Lynch
- Department of Ecology, Ethology, and Evolution, Shelford Vivarium University of Illinois 606 East Healey Street Champaign IL 61820
| | - Ken Spitze
- Department of Ecology, Ethology, and Evolution, Shelford Vivarium University of Illinois 606 East Healey Street Champaign IL 61820
| | - Teresa Crease
- Department of Ecology, Ethology, and Evolution, Shelford Vivarium University of Illinois 606 East Healey Street Champaign IL 61820
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19
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Johnson SG, Bragg E. AGE AND POLYPHYLETIC ORIGINS OF HYBRID AND SPONTANEOUS PARTHENOGENETIC
CAMPELOMA
(GASTROPODA: VIVIPARIDAE) FROM THE SOUTHEASTERN UNITED STATES. Evolution 2017; 53:1769-1781. [DOI: 10.1111/j.1558-5646.1999.tb04561.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/1998] [Accepted: 06/10/1999] [Indexed: 11/30/2022]
Affiliation(s)
- Steven G. Johnson
- Department of Biological Sciences University of New Orleans New Orleans Louisiana 70148
| | - Eric Bragg
- Department of Biological Sciences University of New Orleans New Orleans Louisiana 70148
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20
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Riparbelli MG, Gottardo M, Callaini G. Parthenogenesis in Insects: The Centriole Renaissance. Results Probl Cell Differ 2017; 63:435-479. [PMID: 28779329 DOI: 10.1007/978-3-319-60855-6_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Building a new organism usually requires the contribution of two differently shaped haploid cells, the male and female gametes, each providing its genetic material to restore diploidy of the new born zygote. The successful execution of this process requires defined sequential steps that must be completed in space and time. Otherwise, development fails. Relevant among the earlier steps are pronuclear migration and formation of the first mitotic spindle that promote the mixing of parental chromosomes and the formation of the zygotic nucleus. A complex microtubule network ensures the proper execution of these processes. Instrumental to microtubule organization and bipolar spindle assembly is a distinct non-membranous organelle, the centrosome. Centrosome inheritance during fertilization is biparental, since both gametes provide essential components to build a functional centrosome. This model does not explain, however, centrosome formation during parthenogenetic development, a special mode of sexual reproduction in which the unfertilized egg develops without the contribution of the male gamete. Moreover, whereas fertilization is a relevant example in which the cells actively check the presence of only one centrosome, to avoid multipolar spindle formation, the development of parthenogenetic eggs is ensured, at least in insects, by the de novo assembly of multiple centrosomes.Here, we will focus our attention on the assembly of functional centrosomes following fertilization and during parthenogenetic development in insects. Parthenogenetic development in which unfertilized eggs are naturally depleted of centrosomes would provide a useful experimental system to investigate centriole assembly and duplication together with centrosome formation and maturation.
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Affiliation(s)
| | - Marco Gottardo
- Department of Life Sciences, University of Siena, Via A. Moro 2, 53100, Siena, Italy
| | - Giuliano Callaini
- Department of Life Sciences, University of Siena, Via A. Moro 2, 53100, Siena, Italy.
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21
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Keith N, Tucker AE, Jackson CE, Sung W, Lucas Lledó JI, Schrider DR, Schaack S, Dudycha JL, Ackerman M, Younge AJ, Shaw JR, Lynch M. High mutational rates of large-scale duplication and deletion in Daphnia pulex. Genome Res 2016; 26:60-9. [PMID: 26518480 PMCID: PMC4691751 DOI: 10.1101/gr.191338.115] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 10/13/2015] [Indexed: 02/06/2023]
Abstract
Knowledge of the genome-wide rate and spectrum of mutations is necessary to understand the origin of disease and the genetic variation driving all evolutionary processes. Here, we provide a genome-wide analysis of the rate and spectrum of mutations obtained in two Daphnia pulex genotypes via separate mutation-accumulation (MA) experiments. Unlike most MA studies that utilize haploid, homozygous, or self-fertilizing lines, D. pulex can be propagated ameiotically while maintaining a naturally heterozygous, diploid genome, allowing the capture of the full spectrum of genomic changes that arise in a heterozygous state. While base-substitution mutation rates are similar to those in other multicellular eukaryotes (about 4 × 10(-9) per site per generation), we find that the rates of large-scale (>100 kb) de novo copy-number variants (CNVs) are significantly elevated relative to those seen in previous MA studies. The heterozygosity maintained in this experiment allowed for estimates of gene-conversion processes. While most of the conversion tract lengths we report are similar to those generated by meiotic processes, we also find larger tract lengths that are indicative of mitotic processes. Comparison of MA lines to natural isolates reveals that a majority of large-scale CNVs in natural populations are removed by purifying selection. The mutations observed here share similarities with disease-causing, complex, large-scale CNVs, thereby demonstrating that MA studies in D. pulex serve as a system for studying the processes leading to such alterations.
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Affiliation(s)
- Nathan Keith
- School of Public and Environmental Affairs, Indiana University, Bloomington, Indiana 47405, USA
| | - Abraham E Tucker
- Biology Department, Southern Arkansas University, Magnolia, Arkansas 71753, USA
| | - Craig E Jackson
- School of Public and Environmental Affairs, Indiana University, Bloomington, Indiana 47405, USA
| | - Way Sung
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | | | - Daniel R Schrider
- Department of Genetics, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Sarah Schaack
- Biology Department, Reed College, Portland, Oregon 97202, USA
| | - Jeffry L Dudycha
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Matthew Ackerman
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Andrew J Younge
- School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405, USA
| | - Joseph R Shaw
- School of Public and Environmental Affairs, Indiana University, Bloomington, Indiana 47405, USA; School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
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22
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Xu S, Spitze K, Ackerman MS, Ye Z, Bright L, Keith N, Jackson CE, Shaw JR, Lynch M. Hybridization and the Origin of Contagious Asexuality in Daphnia pulex. Mol Biol Evol 2015; 32:3215-25. [PMID: 26351296 PMCID: PMC4840848 DOI: 10.1093/molbev/msv190] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Hybridization plays a potentially important role in the origin of obligate parthenogenesis (OP) in many organisms. However, it remains controversial whether hybridization directly triggers the transition from sexual reproduction to obligate asexuality or a hybrid genetic background enables asexual species to persist. Furthermore, we know little about the specific genetic elements from the divergent, yet still hybridizing lineages responsible for this transition and how these elements are further spread to create other OP lineages. In this study, we address these questions in Daphnia pulex, where cyclically parthenogenetic (CP) and OP lineages coexist. Ancestry estimates and whole-genome association mapping using 32 OP isolates suggest that a complex hybridization history between the parental species D. pulex and D. pulicaria is responsible for the introgression of a set of 647 D. pulicaria single nucleotide polymorphism alleles that show perfect association with OP. Crossing experiments using males of OP lineages and females of CP lineages strongly support a polygenic basis for OP. Single-sperm analyses show that although normal meiotic recombination occurs in the production of haploid sperm by males of OP lineages, a significant proportion of such sperm are polyploid, suggesting that the spread of asexual elements through these males (i.e., contagious asexuality) is much less efficient than previously envisioned. Although the current Daphnia genome annotation does not provide mechanistic insight into the nature of the asexuality-associated alleles, these alleles should be considered as candidates for future investigations on the genetic underpinnings of OP.
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Affiliation(s)
- Sen Xu
- Department of Biology, Indiana University, Bloomington
| | - Ken Spitze
- Department of Biology, Indiana University, Bloomington
| | | | - Zhiqiang Ye
- Department of Biology, Indiana University, Bloomington
| | - Lydia Bright
- Department of Biology, Indiana University, Bloomington
| | - Nathan Keith
- School of Public and Environmental Affairs, Indiana University, Bloomington
| | - Craig E Jackson
- School of Public and Environmental Affairs, Indiana University, Bloomington
| | - Joseph R Shaw
- School of Public and Environmental Affairs, Indiana University, Bloomington School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington
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23
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Detection of Gene Flow from Sexual to Asexual Lineages in Thrips tabaci (Thysanoptera: Thripidae). PLoS One 2015; 10:e0138353. [PMID: 26375283 PMCID: PMC4573522 DOI: 10.1371/journal.pone.0138353] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 08/28/2015] [Indexed: 11/19/2022] Open
Abstract
Populations of Thrips tabaci are known to have two sympatric but genetically isolated reproductive modes, arrhenotoky (sexual reproduction) and thelytoky (asexual reproduction). Herein, we report behavioral, ecological and genetic studies to determine whether there is gene flow between arrhenotokous and thelytokous T. tabaci. We did not detect significant preference by arrhenotokous males to mate with females of a particular reproductive mode, nor did we detect significant behavioral differences between arrhenotokous males mated with arrhenotokous or thelytokous females in their pre-copulation, copulation duration and mating frequency. Productive gene transfer resulting from the mating between the two modes was experimentally confirmed. Gene transfer from arrhenotokous T. tabaci to thelytokous T. tabaci was further validated by confirmation of the passage of the arrhenotokous male-originated nuclear gene (histone H3 gene) allele to the F2 generation. These behavioral, ecological and genetic studies confirmed gene transfer from the sexual arrhenotokous mode to the asexual thelytokous mode of T. tabaci in the laboratory. These results demonstrate that asexual T. tabaci populations may acquire genetic variability from sexual populations, which could offset the long-term disadvantage of asexual reproduction.
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24
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Nokkala C, Kuznetsova VG, Nokkala S. Rare diploid females coexist with rare males: a novel finding in triploid parthenogenetic populations in the psyllid Cacopsylla myrtilli (W. Wagner, 1947) (Hemiptera, Psylloidea) in northern Europe. Genetica 2015. [PMID: 26208490 DOI: 10.1007/s10709-015-9858-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Using a cytological approach, diploid females were found coexisting with rare males in triploid apomictic parthenogenetic populations of the psyllid Cacopsylla myrtilli (W. Wagner, 1947) in Norway, Sweden, Finland and northwest Russia. Diploid females were easily distinguished from triploid apomictic females by the presence of 13 chiasmate bivalents instead of 39 univalent chromosomes at metaphase I. Abundance equaled that of males, but the proportion of males and diploid females was significantly greater in high altitude compared with low altitude populations. Males mated with females but showed no mating preference for diploid females. Lack of genuine bisexual reproduction owing to either asynaptic meiosis in males, or rarity of males with normal meiosis, suggests that diploids are produced in every generation by parthenogenetic females as reversals from triploidy, with their production being enhanced by environmental factor(s) associated with high altitude. This is further supported by the observation that within a population the COI haplotype found in rare males was the same as that in parthenogenetic triploid females. Thus, in northern Europe parthenogenesis in C. myrtilli is obligate, geographic parthenogenesis. Bisexual populations of C. myrtilli should be looked for in Central and Southern Europe. From the evolutionary point of view, the presence of males and diploid females with normal meiosis in parthenogenetic populations could be significant as they exhibit the potential to re-evolve either a new sexual species of parthenogenetic ancestry or a new parthenogenetic species by contagious parthenogenesis.
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Affiliation(s)
- C Nokkala
- Laboratory of Genetics, Department of Biology, University of Turku, 20014, Turku, Finland,
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25
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Innes DJ, Ginn M. A population of sexual Daphnia pulex resists invasion by asexual clones. Proc Biol Sci 2015; 281:20140564. [PMID: 24943366 DOI: 10.1098/rspb.2014.0564] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Asexual reproduction avoids the costs associated with sex, predicting that invading asexual clones can quickly replace sexual populations. Daphnia pulex populations in the Great Lakes area are predominately asexual, but the elimination of sexual populations by invading clones is poorly understood. Asexual clones were detected at low frequency in one rare sexual population in 1995, with some increase in frequency during 2003 and 2004. However, these clones remained at low frequency during further yearly sampling (2005-2013) with no evidence that the resident sexual population was in danger of elimination. There was evidence for hybridization between rare males produced by asexual clones and sexual females with the potential to produce new asexual genotypes and spread the genetic factors for asexuality. In a short-term laboratory competition experiment, the two most common asexual clones did not increase in frequency relative to a genetically diverse sexual population due in part to a greater investment in diapausing eggs that trades-off current population growth for increased contribution to the egg bank. Our results suggest that a successful invasion can be prolonged, requiring a combination of clonal genotypes with high fitness, persistence of clones in the egg bank and negative factors affecting the sexual population such as inbreeding depression resulting from population bottlenecks.
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Affiliation(s)
- David J Innes
- Department of Biology, Memorial University, St John's, Newfoundland and Labrador, Canada A1B 3X9
| | - Michael Ginn
- Department of Biology, Memorial University, St John's, Newfoundland and Labrador, Canada A1B 3X9
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26
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Abstract
A key part of the life cycle of an organism is reproduction. For a number of important protist parasites that cause human and animal disease, their sexuality has been a topic of debate for many years. Traditionally, protists were considered to be primitive relatives of the ‘higher’ eukaryotes, which may have diverged prior to the evolution of sex and to reproduce by binary fission. More recent views of eukaryotic evolution suggest that sex, and meiosis, evolved early, possibly in the common ancestor of all eukaryotes. However, detecting sex in these parasites is not straightforward. Recent advances, particularly in genome sequencing technology, have allowed new insights into parasite reproduction. Here, we review the evidence on reproduction in parasitic protists. We discuss protist reproduction in the light of parasitic life cycles and routes of transmission among hosts.
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Maccari M, Amat F, Hontoria F, Gómez A. Laboratory generation of new parthenogenetic lineages supports contagious parthenogenesis in Artemia. PeerJ 2014; 2:e439. [PMID: 25024909 PMCID: PMC4081286 DOI: 10.7717/peerj.439] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 05/31/2014] [Indexed: 11/23/2022] Open
Abstract
Contagious parthenogenesis—a process involving rare functional males produced by a parthenogenetic lineage which mate with coexisting sexual females resulting in fertile parthenogenetic offspring—is one of the most striking mechanisms responsible for the generation of new parthenogenetic lineages. Populations of the parthenogenetic diploid brine shrimp Artemia produce fully functional males in low proportions. The evolutionary role of these so-called Artemia rare males is, however, unknown. Here we investigate whether new parthenogenetic clones could be obtained in the laboratory by mating these rare males with sexual females. We assessed the survival and sex ratio of the hybrid ovoviviparous offspring from previous crosses between rare males and females from all Asiatic sexual species, carried out cross-mating experiments between F1 hybrid individuals to assess their fertility, and estimated the viability and the reproductive mode of the resulting F2 offspring. Molecular analysis confirmed the parentage of hybrid parthenogenetic F2. Our study documents the first laboratory synthesis of new parthenogenetic lineages in Artemia and supports a model for the contagious spread of parthenogenesis. Our results suggest recessive inheritance but further experiments are required to confirm the likelihood of the contagious parthenogenesis model.
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Affiliation(s)
- Marta Maccari
- Instituto de Acuicultura de Torre de la Sal (Consejo Superior de Investigaciones Científicas) , Ribera de Cabanes (Castellón) , Spain ; School of Biological, Biomedical and Environmental Sciences, University of Hull , Hull , United Kingdom
| | - Francisco Amat
- Instituto de Acuicultura de Torre de la Sal (Consejo Superior de Investigaciones Científicas) , Ribera de Cabanes (Castellón) , Spain
| | - Francisco Hontoria
- Instituto de Acuicultura de Torre de la Sal (Consejo Superior de Investigaciones Científicas) , Ribera de Cabanes (Castellón) , Spain
| | - Africa Gómez
- School of Biological, Biomedical and Environmental Sciences, University of Hull , Hull , United Kingdom
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Neiman M, Sharbel TF, Schwander T. Genetic causes of transitions from sexual reproduction to asexuality in plants and animals. J Evol Biol 2014; 27:1346-59. [DOI: 10.1111/jeb.12357] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 02/17/2014] [Accepted: 02/18/2014] [Indexed: 11/30/2022]
Affiliation(s)
- M. Neiman
- Department of Biology; University of Iowa; Iowa City IA USA
| | - T. F. Sharbel
- Apomixis Research Group; Leibniz Institute of Plant Genetics and Crop Plant Research (IPK); Gatersleben Germany
| | - T. Schwander
- Department of Ecology and Evolution; University of Lausanne; Lausanne Switzerland
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Roze D. Selection for sex in finite populations. J Evol Biol 2014; 27:1304-22. [DOI: 10.1111/jeb.12344] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 01/07/2014] [Accepted: 01/20/2014] [Indexed: 11/28/2022]
Affiliation(s)
- D. Roze
- CNRS; UMI 3614; Evolutionary Biology and Ecology of Algae; Roscoff France
- Sorbonne Universités; UPMC Université Paris VI; Roscoff France
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Vergilino R, Eagle SH, Crease TJ, Dufresne F. Impact of ploidy level on the distribution of Pokey element insertions in the Daphnia pulex complex. Mob DNA 2014; 5:1. [PMID: 24382139 PMCID: PMC3882798 DOI: 10.1186/1759-8753-5-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 11/20/2013] [Indexed: 11/22/2022] Open
Abstract
Background Transposable elements (TEs) play a major role in genome evolution. Their capacity to move and/or multiply in the genome of their host may have profound impacts on phenotypes and dramatic consequences on genome structure. The population dynamics and distribution of TEs are influenced by their mode of transposition, the availability of niches in host genomes, and host population dynamics. Theories predict an increase in the number of TE insertions following hybridization or polyploidization. Evolution of TEs in hybrids and polyploids has mostly been studied in plants; few studies have examined the impacts of hybridization and/or polyploidization on TEs in animals. Hybrids and polyploids have arisen multiple times in the Daphnia pulex complex and are thought to reproduce by obligate parthenogenesis. Our study examines the effects of ploidy level on polymorphism and number of Pokey element insertions in diploid and polyploid hybrid isolates from the Daphnia pulex complex. Results The polymorphism of Pokey insertion sites did not depend solely on either the ploidy level or the genetic background of their host; therefore, it may be the result of interactions between these parameters and other parameters such as Pokey activity, selection and/or drift. No significant effect of ploidy level was found on the number of Pokey insertions using TE display and qPCR. However, the load of Pokey insertion sites and the number of unique insertion sites were slightly (but not significantly) higher in polyploids than in diploids. Conclusions These results suggest a lack of increase in the number of Pokey insertions following polyploidization but higher availability of Pokey insertion sites in polyploids than in diploids. Compared to previous TE display and qPCR results, the load of Pokey insertions in hybrid diploids was higher than in non-hybrid sexual and asexual diploids, which suggests an increase in the density of Pokey insertions following hybridization.
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Affiliation(s)
- Roland Vergilino
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, Rimouski, Québec G5L 3A1, Canada.
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Origin and genetic diversity of diploid parthenogenetic Artemia in Eurasia. PLoS One 2013; 8:e83348. [PMID: 24376692 PMCID: PMC3869768 DOI: 10.1371/journal.pone.0083348] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 11/04/2013] [Indexed: 11/19/2022] Open
Abstract
There is wide interest in understanding how genetic diversity is generated and maintained in parthenogenetic lineages, as it will help clarify the debate of the evolution and maintenance of sexual reproduction. There are three mechanisms that can be responsible for the generation of genetic diversity of parthenogenetic lineages: contagious parthenogenesis, repeated hybridization and microorganism infections (e.g. Wolbachia). Brine shrimps of the genus Artemia (Crustacea, Branchiopoda, Anostraca) are a good model system to investigate evolutionary transitions between reproductive systems as they include sexual species and lineages of obligate parthenogenetic populations of different ploidy level, which often co-occur. Diploid parthenogenetic lineages produce occasional fully functional rare males, interspecific hybridization is known to occur, but the mechanisms of origin of asexual lineages are not completely understood. Here we sequenced and analysed fragments of one mitochondrial and two nuclear genes from an extensive set of populations of diploid parthenogenetic Artemia and sexual species from Central and East Asia to investigate the evolutionary origin of diploid parthenogenetic Artemia, and geographic origin of the parental taxa. Our results indicate that there are at least two, possibly three independent and recent maternal origins of parthenogenetic lineages, related to A. urmiana and Artemia sp. from Kazakhstan, but that the nuclear genes are very closely related in all the sexual species and parthenogegetic lineages except for A. sinica, who presumable took no part on the origin of diploid parthenogenetic strains. Our data cannot rule out either hybridization between any of the very closely related Asiatic sexual species or rare events of contagious parthenogenesis via rare males as the contributing mechanisms to the generation of genetic diversity in diploid parthenogenetic Artemia lineages.
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Tucker AE, Ackerman MS, Eads BD, Xu S, Lynch M. Population-genomic insights into the evolutionary origin and fate of obligately asexual Daphnia pulex. Proc Natl Acad Sci U S A 2013; 110:15740-5. [PMID: 23959868 PMCID: PMC3785735 DOI: 10.1073/pnas.1313388110] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Despite much theoretical work, the molecular-genetic causes and evolutionary consequences of asexuality remain largely undetermined. Asexual animal species are rare, evolutionarily short-lived, and thought to suffer mutational meltdown as a result of lack of recombination. Whole-genome analysis of 11 sexual and 11 asexual genotypes of Daphnia pulex indicates that current asexual lineages are in fact very young, exhibit no signs of purifying selection against accumulating mutations, and have extremely high rates of gene conversion and deletion. The reconstruction of chromosomal haplotypes in regions containing SNP markers associated with asexuality (chromosomes VIII and IX) indicates that introgression from a sister species, Daphnia pulicaria, underlies the origin of the asexual phenotype. Silent-site divergence of the shared chromosomal haplotypes of asexuals indicates that the spread of asexuality is as recent as 1,250 y, although the origin of the meiosis-suppressing element or elements could be substantially older. In addition, using previous estimates of the gene conversion rate from Daphnia mutation accumulation lines, we are able to age each asexual lineage. Although asexual lineages originate from wide crosses that introduce elevated individual heterozygosities on clone foundation, they also appear to be constrained by the inbreeding-like effect of loss of heterozygosity that accrues as gene conversion and hemizygous deletion expose preexisting recessive deleterious alleles of asexuals, limiting their evolutionary longevity. Our study implies that the buildup of newly introduced deleterious mutations (i.e., Muller's ratchet) may not be the dominant force imperiling nonrecombining populations of D. pulex, as previously proposed.
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Affiliation(s)
| | | | - Brian D. Eads
- Department of Biology, Indiana University, Bloomington, IN 47405
| | - Sen Xu
- Department of Biology, Indiana University, Bloomington, IN 47405
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, IN 47405
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Xu S, Innes DJ, Lynch M, Cristescu ME. The role of hybridization in the origin and spread of asexuality in Daphnia. Mol Ecol 2013; 22:4549-61. [PMID: 23879327 DOI: 10.1111/mec.12407] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 05/16/2013] [Accepted: 05/26/2013] [Indexed: 11/27/2022]
Abstract
The molecular mechanisms leading to asexuality remain little understood despite their substantial bearing on why sexual reproduction is dominant in nature. Here, we examine the role of hybridization in the origin and spread of obligate asexuality in Daphnia pulex, arguably the best-documented case of contagious asexuality. Obligately parthenogenetic (OP) clones of D. pulex have traditionally been separated into 'hybrid' (Ldh SF) and 'nonhybrid' (Ldh SS) forms because the lactase dehydrogenase (Ldh) locus distinguishes the cyclically parthenogenetic (CP) lake dwelling Daphnia pulicaria (Ldh FF) from its ephemeral pond dwelling sister species D. pulex (Ldh SS). The results of our population genetic analyses based on microsatellite loci suggest that both Ldh SS and SF OP individuals can originate from the crossing of CP female F1 (D. pulex × D. pulicaria) and backcross with males from OP lineages carrying genes that suppress meiosis specifically in female offspring. In previous studies, a suite of diagnostic markers was found to be associated with OP in Ldh SS D. pulex lineages. Our association mapping supports a similar genetic mechanism for the spread of obligate parthenogenesis in Ldh SF OP individuals. Interestingly, our study shows that CP D. pulicaria carry many of the diagnostic microsatellite alleles associated with obligate parthenogenesis. We argue that the assemblage of mutations that suppress meiosis and underlie obligate parthenogenesis in D. pulex originated due to a unique historical hybridization and introgression event between D. pulex and D. pulicaria.
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Affiliation(s)
- Sen Xu
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada N9B 3P4.
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Maccari M, Gómez A, Hontoria F, Amat F. Functional rare males in diploid parthenogenetic Artemia. J Evol Biol 2013; 26:1934-48. [PMID: 23837914 DOI: 10.1111/jeb.12191] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 04/05/2013] [Accepted: 04/29/2013] [Indexed: 10/26/2022]
Abstract
Functional males that are produced occasionally in some asexual taxa - called 'rare males' - raise considerable evolutionary interest, as they might be involved in the origin of new parthenogenetic lineages. Diploid parthenogenetic Artemia produce rare males, which may retain the ability to mate with females of related sexual lineages. Here, we (i) describe the frequency of male progeny in populations of diploid parthenogenetic Artemia, (ii) characterize rare males morphologically, (iii) assess their reproductive role, using cross-mating experiments with sexual females of related species from Central Asia and characterize the F1 hybrid offspring viability and (iv) confirm genetically both the identity and functionality of rare males using DNA barcoding and microsatellite loci. Our result suggests that these males may have an evolutionary role through genetic exchange with related sexual species and that diploid parthenogenetic Artemia is a good model system to investigate the evolutionary transitions between sexual species and parthenogenetic strains.
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Affiliation(s)
- M Maccari
- Instituto de Acuicultura de Torre de la Sal Consejo Superior de Investigaciones Científicas, Ribera de Cabanes Castellón, Spain.
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35
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Vergilino R, Elliott TA, Desjardins-Proulx P, Crease TJ, Dufresne F. Evolution of a transposon in Daphnia hybrid genomes. Mob DNA 2013; 4:7. [PMID: 23384095 PMCID: PMC3575242 DOI: 10.1186/1759-8753-4-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 11/06/2012] [Indexed: 11/17/2022] Open
Abstract
Background Transposable elements play a major role in genome evolution. Their capacity to move and/or multiply in the genome of their host may have profound impacts on phenotypes, and may have dramatic consequences on genome structure. Hybrid and polyploid clones have arisen multiple times in the Daphnia pulex complex and are thought to reproduce by obligate parthenogenesis. Our study examines the evolution of a DNA transposable element named Pokey in the D. pulex complex. Results Portions of Pokey elements inserted in the 28S rRNA genes from various Daphnia hybrids (diploids and polyploids) were sequenced and compared to sequences from a previous study to understand the evolutionary history of the elements. Pokey sequences show a complex phylogenetic pattern. We found evidence of recombination events in numerous Pokey alleles from diploid and polyploid hybrids and also from non-hybrid diploids. The recombination rate in Pokey elements is comparable to recombination rates previously estimated for 28S rRNA genes in the congener, Daphnia obtusa. Some recombinant Pokey alleles were encountered in Daphnia isolates from multiple locations and habitats. Conclusions Phylogenetic and recombination analyses showed that recombination is a major force that shapes Pokey evolution. Based on Pokey phylogenies, reticulation has played and still plays an important role in shaping the diversity of the D. pulex complex. Horizontal transfer of Pokey seems to be rare and hybrids often possess Pokey elements derived from recombination among alleles encountered in the putative parental species. The insertion of Pokey in hotspots of recombination may have important impacts on the diversity and fitness of this transposable element.
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Affiliation(s)
- Roland Vergilino
- Department of Integrative Biology, University of Guelph, Science complex, N1G 2 W1, Guelph, ON, Canada.
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Dedryver CA, Le Gallic JF, Mahéo F, Simon JC, Dedryver F. The genetics of obligate parthenogenesis in an aphid species and its consequences for the maintenance of alternative reproductive modes. Heredity (Edinb) 2012; 110:39-45. [PMID: 22990313 DOI: 10.1038/hdy.2012.57] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Although loss of sex is widespread among metazoans, the genetic mechanisms underlying the transition to asexuality are poorly understood. Aphids are good models to address this issue because they frequently show reproductive-mode variation at the species level, involving cyclical parthenogens (CP) that reproduce sexually once a year and obligate parthenogens (OP) that reproduce asexually all year round. Here, we explore the genetic basis of OP in the cereal aphid Sitobion avenae by crossing several genotypes with contrasting reproductive modes and then characterising the reproductive phenotypes of F1 and F2 offspring. The analysis of phenotypic variation in F1 and F2 progenies suggests that at least two autosomal loci control OP in S. avenae. First, the transition to asexuality seems to depend on a single recessive locus, because the offspring from self-crossed cyclical parthenogenetic genotypes contain either 0 or 25% OP. Second, as we observed OP in the F1 progenies from crosses between CP and OP, and some CP in the offspring from outcrossed OP, a dominant 'suppressor' gene may also be involved, being inactive when in a recessive homozygous state in CP; this is the most parsimonious explanation for these results. This oligogenic inheritance of OP in S. avenae appears to be an efficient genetic system to generate new OP genotypes continually. It also allows asexuality-inducing alleles to be protected locally during harsh winters when extreme frost kills most OP, and then to spread very quickly after winter.
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Affiliation(s)
- C-A Dedryver
- INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, Domaine de la Motte-35653, Le Rheu, France.
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The spread of a transposon insertion in Rec8 is associated with obligate asexuality in Daphnia. Proc Natl Acad Sci U S A 2012; 109:858-63. [PMID: 22215604 DOI: 10.1073/pnas.1119667109] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Although transitions from sexual to asexual reproduction are thought to have important evolutionary consequences, little is known about the mechanistic underpinnings of these changes. The cyclical parthenogen Daphnia pulex is a powerful model in which to address these issues because female-limited meiosis suppression can be transmitted to sexual individuals via males, providing the opportunity for genetic dissection of the trait. A previous study identified genomic regions differentiating obligately asexual females from their sexual counterparts, and a candidate gene within one such region, encoding the meiotic cohesin Rec8, is the subject of this investigation. The D. pulex genome contains three Rec8 loci, all of which are quite polymorphic. However, at one of the loci, all obligately asexual clones carry an allele containing an identical upstream insertion of a transposable element as well as a frameshift mutation, both of which are completely absent from sexual lineages. The low level of variation within the insertion allele across all asexual lineages suggests that this element may be in the process of spreading through the species, and abrogation or modification of Rec8 function is possibly responsible for converting meiotically reproducing lineages into obligate asexuals.
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Sandrock C, Schirrmeister BE, Vorburger C. Evolution of reproductive mode variation and host associations in a sexual-asexual complex of aphid parasitoids. BMC Evol Biol 2011; 11:348. [PMID: 22132834 PMCID: PMC3259107 DOI: 10.1186/1471-2148-11-348] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 12/01/2011] [Indexed: 11/10/2022] Open
Abstract
Background The Lysiphlebus fabarum group is a taxonomically poorly resolved complex of aphid parasitoids, presently split into three described species that comprise sexual (arrhenotokous) and asexual (thelytokous) lineages of unknown relationship. Specifically, it is unclear how asexuals evolved from sexuals in this system, to what extent reproductive modes are still connected by genetic exchange, how much the complex is structured by geography or by host-associated differentiation, and whether species designations are valid. Using a combination of population genetic and phylogenetic approaches, we addressed these issues in a comprehensive sample of parasitoid wasps from across Europe. Results Asexual reproduction predominated in parasitoids of the L. fabarum group, with asexual populations exhibiting high genotypic diversity. Sexual populations were only common in southern France; elsewhere sexual reproduction was restricted to specific aphid hosts. Although reproductive modes were aggregated on the mitochondrial genealogy and significantly differentiated at nuclear microsatellite loci, there was clear evidence for genetic exchange, especially on hosts attacked by sexual and asexual parasitoids. The microsatellite data further revealed that parasitoids collected from certain host aphids were significantly differentiated, yet the mitochondrial sequence variation across the entire L. fabarum group did not exceed 1.32% and exhibited a very shallow topology. Morphological characters used for delineation of described species were found to be phylogenetically non-conservative. Conclusions Our results suggest that the sexual-asexual L. fabarum group represents a young complex of lineages with incomplete isolation between reproductive modes. We propose three mechanisms of genetic exchange that may jointly explain the high genotypic diversity observed in asexual parasitoids: (i) the formation of new asexual lineages via 'contagious parthenogenesis', (ii) introgression from sexual lineages through matings between sexual males and thelytokous females, and (iii) 'cryptic sex' within asexuals, mediated by rare males that thelytokous lines are known to produce spontaneously. The partially strong differentiation among wasps collected from different aphids suggests that host specialization can evolve readily in these parasitoids. Finally, we conclude that in the light of our data, the current taxonomic division of the L. fabarum group into three species cannot be upheld.
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Affiliation(s)
- Christoph Sandrock
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
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Dufresne F, Marková S, Vergilino R, Ventura M, Kotlík P. Diversity in the reproductive modes of European Daphnia pulicaria deviates from the geographical parthenogenesis. PLoS One 2011; 6:e20049. [PMID: 21655327 PMCID: PMC3104988 DOI: 10.1371/journal.pone.0020049] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Accepted: 04/23/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Multiple transitions to obligate parthenogenesis have occurred in the Daphnia pulex complex in North America. These newly formed asexual lineages are differentially distributed being found predominantly at high latitudes. This conforms to the rule of geographical parthenogenesis postulating prevalence of asexuals at high latitudes and altitudes. While the reproductive mode of high-latitude populations is relatively well studied, little is known about the reproduction mode in high altitudes. This study aimed to assess the reproductive mode of Daphnia pulicaria, a species of the D. pulex complex, from high altitude lakes in Europe. METHODOLOGY/PRINCIPAL FINDINGS Variation at eight microsatellite loci revealed that D. pulicaria from the High Tatra Mountains (HTM) had low genotype richness and showed excess of heterozygotes and significant deviations from Hardy-Weinberg expectations, and was thus congruent with reproduction by obligate parthenogenesis. By contrast, populations from the Pyrenees (Pyr) were generally in Hardy-Weinberg equilibrium and had higher genotypic richness, suggesting that they are cyclic parthenogens. Four lakes from lowland areas (LLaP) had populations with an uncertain or mixed breeding mode. All D. pulicaria had mtDNA ND5 haplotypes of the European D. pulicaria lineage. Pyr were distinct from LLaP and HTM at the ND5 gene. By contrast, HTM shared two haplotypes with LLaP and one with Pyr. Principal Coordinate Analysis of the microsatellite data revealed clear genetic differentiation into three groups. HTM isolates were intermediate to Pyr and LLaP, congruent with a hybrid origin. CONCLUSION/SIGNIFICANCE Inferred transitions to obligate parthenogenesis have occurred only in HTM, most likely as a result of hybridizations. In contrast to North American populations, these transitions do not appear to involve meiosis suppressor genes and have not been accompanied by polyploidy. The absence of obligate parthenogenesis in Pyr, an environment highly similar to the HTM, may be due to the lack of opportunities for hybridization.
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Affiliation(s)
- France Dufresne
- Département de Biologie, Centre d'Études Nordiques, Université du Québec à Rimouski, Rimouski, Québec, Canada.
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Stelzer CP, Schmidt J, Wiedlroither A, Riss S. Loss of sexual reproduction and dwarfing in a small metazoan. PLoS One 2010; 5. [PMID: 20862222 PMCID: PMC2942836 DOI: 10.1371/journal.pone.0012854] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 08/27/2010] [Indexed: 11/22/2022] Open
Abstract
Background Asexuality has major theoretical advantages over sexual reproduction, yet newly formed asexual lineages rarely endure. The success, or failure, of such lineages is affected by their mechanism of origin, because it determines their initial genetic makeup and variability. Most previously described mechanisms imply that asexual lineages are randomly frozen subsamples of a sexual population. Methodology/Principal Findings We found that transitions to obligate parthenogenesis (OP) in the rotifer Brachionus calyciflorus, a small freshwater invertebrate which normally reproduces by cyclical parthenogenesis, were controlled by a simple Mendelian inheritance. Pedigree analysis suggested that obligate parthenogens were homozygous for a recessive allele, which caused inability to respond to the chemical signals that normally induce sexual reproduction in this species. Alternative mechanisms, such as ploidy changes, could be ruled out on the basis of flow cytometric measurements and genetic marker analysis. Interestingly, obligate parthenogens were also dwarfs (approximately 50% smaller than cyclical parthenogens), indicating pleiotropy or linkage with genes that strongly affect body size. We found no adverse effects of OP on survival or fecundity. Conclusions/Significance This mechanism of inheritance implies that genes causing OP may evolve within sexual populations and remain undetected in the heterozygous state long before they get frequent enough to actually cause a transition to asexual reproduction. In this process, genetic variation at other loci might become linked to OP genes, leading to non-random associations between asexuality and other phenotypic traits.
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Neiman M, Meirmans S, Meirmans PG. What Can Asexual Lineage Age Tell Us about the Maintenance of Sex? Ann N Y Acad Sci 2009; 1168:185-200. [DOI: 10.1111/j.1749-6632.2009.04572.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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VERGILINO ROLAND, BELZILE CLAUDE, DUFRESNE FRANCE. Genome size evolution and polyploidy in the Daphnia pulex complex (Cladocera: Daphniidae). Biol J Linn Soc Lond 2009. [DOI: 10.1111/j.1095-8312.2008.01185.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Schwander T, Crespi BJ. MULTIPLE DIRECT TRANSITIONS FROM SEXUAL REPRODUCTION TO APOMICTIC PARTHENOGENESIS INTIMEMASTICK INSECTS. Evolution 2009; 63:84-103. [DOI: 10.1111/j.1558-5646.2008.00524.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Although approximately 1 in 10,000 animal species is capable of parthenogenetic reproduction, the evolutionary causes and consequences of such transitions remain uncertain. The microcrustacean Daphnia pulex provides a potentially powerful tool for investigating these issues because lineages that are obligately asexual in terms of female function can nevertheless transmit meiosis-suppressing genes to sexual populations via haploid sperm produced by environmentally induced males. The application of association mapping to a wide geographic collection of D. pulex clones suggests that sex-limited meiosis suppression in D. pulex has spread westward from a northeastern glacial refugium, conveyed by a dominant epistatic interaction among the products of at least four unlinked loci, with one entire chromosome being inherited through males in a nearly nonrecombining fashion. With the enormous set of genomic tools now available for D. pulex, these results set the stage for the determination of the functional underpinnings of the conversion of meiosis to a mitotic-like mode of inheritance.
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Wolinska J, Lively CM. The cost of males in Daphnia pulex. OIKOS 2008. [DOI: 10.1111/j.0030-1299.2008.16760.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Schurko AM, Logsdon JM. Using a meiosis detection toolkit to investigate ancient asexual "scandals" and the evolution of sex. Bioessays 2008; 30:579-89. [PMID: 18478537 DOI: 10.1002/bies.20764] [Citation(s) in RCA: 167] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Sexual reproduction is the dominant reproductive mode in eukaryotes but, in many taxa, it has never been observed. Molecular methods that detect evidence of sex are largely based on the genetic consequences of sexual reproduction. Here we describe a powerful new approach to directly search genomes for genes that function in meiosis. We describe a "meiosis detection toolkit", a set of meiotic genes that represent the best markers for the presence of meiosis. These genes are widely present in eukaryotes, function only in meiosis and can be isolated by degenerate PCR. The presence of most, or all, of these genes in a genome would suggest they have been maintained for meiosis and, implicitly, sexual reproduction. In contrast, their absence would be consistent with the loss of meiosis and asexuality. This approach will help to understand both meiotic gene evolution and the capacity for meiosis and sex in putative obligate asexuals.
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Affiliation(s)
- Andrew M Schurko
- Department of Biology and Roy J. Carver Center for Comparative Genomics, University of Iowa, IA 52242, USA
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MERGEAY JOACHIM, AGUILERA XIMENA, DECLERCK STEVEN, PETRUSEK ADAM, HUYSE TINE, DE MEESTER LUC. The genetic legacy of polyploid BolivianDaphnia: the tropical Andes as a source for the North and South AmericanD. pulicariacomplex. Mol Ecol 2008; 17:1789-800. [DOI: 10.1111/j.1365-294x.2007.03679.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Eads BD, Colbourne JK, Bohuski E, Andrews J. Profiling sex-biased gene expression during parthenogenetic reproduction in Daphnia pulex. BMC Genomics 2007; 8:464. [PMID: 18088424 PMCID: PMC2245944 DOI: 10.1186/1471-2164-8-464] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2007] [Accepted: 12/18/2007] [Indexed: 11/28/2022] Open
Abstract
Background Sexual reproduction is a core biological function that is conserved throughout eukaryotic evolution, yet breeding systems are extremely variable. Genome-wide comparative studies can be effectively used to identify genes and regulatory patterns that are constrained to preserve core functions from those that may help to account for the diversity of animal reproductive strategies. We use a custom microarray to investigate gene expression in males and two reproductive stages of females in the crustacean Daphnia pulex. Most Daphnia species reproduce by cyclical parthenogenesis, alternating between sexual and clonal reproduction. Both sex determination and the switch in their mode of reproduction is environmentally induced, making Daphnia an interesting comparative system for the study of sex-biased and reproductive genes. Results Patterns of gene expression in females and males reveal that 50% of assayed transcripts show some degree of sex-bias. Female-biased transcription is enriched for translation, metabolic and regulatory genes associated with development. Male-biased expression is enriched for cuticle and protease function. Comparison with well studied arthropods such as Drosophila melanogaster and Anopheles gambiae suggests that female-biased patterns tend to be conserved, whereas male-biased genes are evolving faster in D. pulex. These findings are based on the proportion of female-biased, male-biased, and unbiased genes that share sequence similarity with proteins in other animal genomes. Conclusion Some transcriptional differences between males and females appear to be conserved across Arthropoda, including the rapid evolution of male-biased genes which is observed in insects and now in a crustacean. Yet, novel patterns of male-biased gene expression are also uncovered. This study is an important first step towards a detailed understanding of the genetic basis and evolution of parthenogenesis, environmental sex determination, and adaptation to aquatic environments.
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Affiliation(s)
- Brian D Eads
- The Center for Genomics and Bioinformatics and Department of Biology, Indiana University Bloomington, Indiana 47405, USA.
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Stone GN, Atkinson RJ, Rokas A, Aldrey JLN, Melika G, Acs Z, Csóka G, Hayward A, Bailey R, Buckee C, McVean GAT. Evidence for widespread cryptic sexual generations in apparently purely asexual Andricus gallwasps. Mol Ecol 2007; 17:652-65. [PMID: 18086197 DOI: 10.1111/j.1365-294x.2007.03573.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oak gallwasps (Hymenoptera, Cynipidae, Cynipini) are one of seven major animal taxa that commonly reproduce by cyclical parthenogenesis (CP). A major question in research on CP taxa is the frequency with which lineages lose their sexual generations, and diversify as purely asexual radiations. Most oak gallwasp species are only known from an asexual generation, and secondary loss of sex has been conclusively demonstrated in several species, particularly members of the holarctic genus Andricus. This raises the possibility of widespread secondary loss of sex in the Cynipini, and of diversification within purely parthenogenetic lineages. We use two approaches based on analyses of allele frequency data to test for cryptic sexual generations in eight apparently asexual European species distributed through a major western palaearctic lineage of the gallwasp genus Andricus. All species showing adequate levels of polymorphism (7/8) showed signatures of sex compatible with cyclical parthenogenesis. We also use DNA sequence data to test the hypothesis that ignorance of these sexual generations (despite extensive study on this group) results from failure to discriminate among known but morphologically indistinguishable sexual generations. This hypothesis is supported: 35 sequences attributed by leading cynipid taxonomists to a single sexual adult morphospecies, Andricus burgundus, were found to represent the sexual generations of at least six Andricus species. We confirm cryptic sexual generations in a total of 11 Andricus species, suggesting that secondary loss of sex is rare in Andricus.
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Affiliation(s)
- Graham N Stone
- Institute of Evolutionary Biology, School of Biology, The King's Buildings, West Mains Road, Edinburgh EH9 3JT, UK.
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