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Beninde J, Möst M, Meyer A. Optimized and affordable high-throughput sequencing workflow for preserved and nonpreserved small zooplankton specimens. Mol Ecol Resour 2020; 20:1632-1646. [PMID: 32677266 DOI: 10.1111/1755-0998.13228] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 12/12/2022]
Abstract
Genomic analysis of hundreds of individuals is increasingly becoming standard in evolutionary and ecological research. Individual-based sequencing generates large amounts of valuable data from experimental and field studies, while using preserved samples is an invaluable resource for studying biodiversity in remote areas or across time. Yet, small-bodied individuals or specimens from collections are often of limited use for genomic analyses due to a lack of suitable extraction and library preparation protocols for preserved or small amounts of tissues. Currently, high-throughput sequencing in zooplankton is mostly restricted to clonal species, that can be maintained in live cultures to obtain sufficient amounts of tissue, or relies on a whole-genome amplification step that comes with several biases and high costs. Here, we present a workflow for high-throughput sequencing of single small individuals omitting the need for prior whole-genome amplification or live cultures. We establish and demonstrate this method using 27 species of the genus Daphnia, aquatic keystone organisms, and validate it with small-bodied ostracods. Our workflow is applicable to both live and preserved samples at low costs per sample. We first show that a silica-column based DNA extraction method resulted in the highest DNA yields for nonpreserved samples while a precipitation-based technique gave the highest yield for ethanol-preserved samples and provided the longest DNA fragments. We then successfully performed short-read whole genome sequencing from single Daphnia specimens and ostracods. Moreover, we assembled a draft reference genome from a single Daphnia individual (>50× coverage) highlighting the value of the workflow for non-model organisms.
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Affiliation(s)
- Jannik Beninde
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Markus Möst
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
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2
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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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3
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Morgan-Richards M, Langton-Myers SS, Trewick SA. Loss and gain of sexual reproduction in the same stick insect. Mol Ecol 2019; 28:3929-3941. [PMID: 31386772 PMCID: PMC6852293 DOI: 10.1111/mec.15203] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 06/17/2019] [Accepted: 07/30/2019] [Indexed: 01/10/2023]
Abstract
The outcome of competition between different reproductive strategies within a single species can be used to infer selective advantage of the winning strategy. Where multiple populations have independently lost or gained sexual reproduction it is possible to investigate whether the advantage is contingent on local conditions. In the New Zealand stick insect Clitarchus hookeri, three populations are distinguished by recent change in reproductive strategy and we determine their likely origins. One parthenogenetic population has established in the United Kingdom and we provide evidence that sexual reproduction has been lost in this population. We identify the sexual population from which the parthenogenetic population was derived, but show that the UK females have a post‐mating barrier to fertilisation. We also demonstrate that two sexual populations have recently arisen in New Zealand within the natural range of the mtDNA lineage that otherwise characterizes parthenogenesis in this species. We infer independent origins of males at these two locations using microsatellite genotypes. In one population, a mixture of local and nonlocal alleles suggested males were the result of invasion. Males in another population were most probably the result of loss of an X chromosome that produced a male phenotype in situ. Two successful switches in reproductive strategy suggest local competitive advantage for outcrossing over parthenogenetic reproduction. Clitarchus hookeri provides remarkable evidence of repeated and rapid changes in reproductive strategy, with competitive outcomes dependent on local conditions.
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Affiliation(s)
| | | | - Steven A Trewick
- Wildlife & Ecology, Massey University, Palmerston North, New Zealand
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Neiman M, Meirmans PG, Schwander T, Meirmans S. Sex in the wild: How and why field-based studies contribute to solving the problem of sex. Evolution 2018; 72:1194-1203. [PMID: 29645091 DOI: 10.1111/evo.13485] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/27/2018] [Indexed: 02/06/2023]
Abstract
Why and how sexual reproduction is maintained in natural populations, the so-called "queen of problems," is a key unanswered question in evolutionary biology. Recent efforts to solve the problem of sex have often emphasized results generated from laboratory settings. Here, we use a survey of representative "sex in the wild" literature to review and synthesize the outcomes of empirical studies focused on natural populations. Especially notable results included relatively strong support for mechanisms involving niche differentiation and a near absence of attention to adaptive evolution. Support for a major role of parasites is largely confined to a single study system, and only three systems contribute most of the support for mutation accumulation hypotheses. This evidence for taxon specificity suggests that outcomes of particular studies should not be more broadly extrapolated without extreme caution. We conclude by suggesting steps forward, highlighting tests of niche differentiation mechanisms in both laboratory and nature, and empirical evaluation of adaptive evolution-focused hypotheses in the wild. We also emphasize the value of leveraging the growing body of genomic resources for nonmodel taxa to address whether the clearance of harmful mutations and spread of beneficial variants in natural populations proceeds as expected under various hypotheses for sex.
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Affiliation(s)
- Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Patrick G Meirmans
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94248, 1090GE Amsterdam, The Netherlands
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Stephanie Meirmans
- Academic Medical Center (AMC), University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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5
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Amat I, van Alphen JJ, Kacelnik A, Desouhant E, Bernstein C. Adaptations to different habitats in sexual and asexual populations of parasitoid wasps: a meta-analysis. PeerJ 2017; 5:e3699. [PMID: 28924495 PMCID: PMC5600175 DOI: 10.7717/peerj.3699] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/26/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Coexistence of sexual and asexual populations remains a key question in evolutionary ecology. We address the question how an asexual and a sexual form of the parasitoid Venturia canescens can coexist in southern Europe. We test the hypothesis that both forms are adapted to different habitats within their area of distribution. Sexuals inhabit natural environments that are highly unpredictable, and where density of wasps and their hosts is low and patchily distributed. Asexuals instead are common in anthropic environments (e.g., grain stores) where host outbreaks offer periods when egg-load is the main constraint on reproductive output. METHODS We present a meta-analysis of known adaptations to these habitats. Differences in behavior, physiology and life-history traits between sexual and asexual wasps were standardized in term of effect size (Cohen's d value; Cohen, 1988). RESULTS Seeking consilience from the differences between multiple traits, we found that sexuals invest more in longevity at the expense of egg-load, are more mobile, and display higher plasticity in response to thermal variability than asexual counterparts. DISCUSSION Thus, each form has consistent multiple adaptations to the ecological circumstances in the contrasting environments.
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Affiliation(s)
- Isabelle Amat
- UMR CNRS 5558 Biométrie et Biologie Evolutive, Univ Lyon; Université Claude Bernard (Lyon I), Villeurbanne, France
| | | | - Alex Kacelnik
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Emmanuel Desouhant
- UMR CNRS 5558 Biométrie et Biologie Evolutive, Univ Lyon; Université Claude Bernard (Lyon I), Villeurbanne, France
| | - Carlos Bernstein
- UMR CNRS 5558 Biométrie et Biologie Evolutive, Univ Lyon; Université Claude Bernard (Lyon I), Villeurbanne, France
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Zhang YN, Zhu XY, Wang WP, Wang Y, Wang L, Xu XX, Zhang K, Deng DG. Reproductive switching analysis of Daphnia similoides between sexual female and parthenogenetic female by transcriptome comparison. Sci Rep 2016; 6:34241. [PMID: 27671106 PMCID: PMC5037449 DOI: 10.1038/srep34241] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 09/06/2016] [Indexed: 11/09/2022] Open
Abstract
The water flea Daphnia are planktonic crustaceans commonly found in freshwater environment that can switch their reproduction mode from parthenogenesis to sexual reproduction to adapt to the external environment. As such, Daphnia are great model organisms to study the mechanism of reproductive switching, the underlying mechanism of reproduction and development in cladocerans and other animals. However, little is known about the Daphnia's reproductive behaviour at a molecular level. We constructed a genetic database of the genes expressed in a sexual female (SF) and a parthenogenetic female (PF) of D. similoides using Illumina HiSeq 2500. A total of 1,763 differentially expressed genes (865 up- and 898 down-regulated) were detected in SF. Of the top 30 up-regulated SF unigenes, the top 4 unigenes belonged to the Chitin_bind_4 family. In contrast, of the top down-regulated SF unigenes, the top 3 unigenes belonged to the Vitellogenin_N family. This is the first study to indicate genes that may have a crucial role in reproductive switching of D. similoides, which could be used as candidate genes for further functional studies. Thus, this study provides a rich resource for investigation and elucidation of reproductive switching in D. similoides.
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Affiliation(s)
- Ya-Nan Zhang
- College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Xiu-Yun Zhu
- College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Wen-Ping Wang
- College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Yi Wang
- College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Lu Wang
- College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Xiao-Xue Xu
- College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Kun Zhang
- College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Dao-Gui Deng
- College of Life Sciences, Huaibei Normal University, Huaibei, China
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7
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Hillis JJ, Garvey JE, Lydy MJ. Contaminants reduce male contribution to reproduction at the population scale. Ecosphere 2015. [DOI: 10.1890/es14-00391.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jeffrey J. Hillis
- Department of Zoology, Center for Fisheries, Aquaculture, and Aquatic Sciences, Center for Ecology, Southern Illinois University, Carbondale, Illinois 62901 USA
| | - James E. Garvey
- Department of Zoology, Center for Fisheries, Aquaculture, and Aquatic Sciences, Center for Ecology, Southern Illinois University, Carbondale, Illinois 62901 USA
| | - Michael J. Lydy
- Department of Zoology, Center for Fisheries, Aquaculture, and Aquatic Sciences, Center for Ecology, Southern Illinois University, Carbondale, Illinois 62901 USA
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Varó I, Redón S, Garcia-Roger EM, Amat F, Guinot D, Serrano R, Navarro JC. Aquatic pollution may favor the success of the invasive species A. franciscana. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2015; 161:208-20. [PMID: 25723047 DOI: 10.1016/j.aquatox.2015.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 02/11/2015] [Accepted: 02/17/2015] [Indexed: 05/06/2023]
Abstract
The genus Artemia consists of several bisexual and parthenogenetic sibling species. One of them, A. franciscana, originally restricted to the New World, becomes invasive when introduced into ecosystems out of its natural range of distribution. Invasiveness is anthropically favored by the use of cryptobiotic eggs in the aquaculture and pet trade. The mechanisms of out-competition of the autochthonous Artemia by the invader are still poorly understood. Ecological fitness may play a pivotal role, but other underlying biotic and abiotic factors may contribute. Since the presence of toxicants in hypersaline aquatic ecosystems has been documented, our aim here is to study the potential role of an organophosphate pesticide, chlorpyrifos, in a congeneric mechanism of competition between the bisexual A. franciscana (AF), and one of the Old World parthenogenetic siblings, A. parthenogenetica (PD). For this purpose we carried out life table experiments with both species, under different concentrations of the toxicant (0.1, 1 and 5μg/l), and analyzed the cholinesterase inhibition at different developmental stages. The results evidence that both, AF and PD, showed an elevated tolerance to high ranges of chlorpyrifos, but AF survived better and its fecundity was less affected by the exposure to the pesticide than that of PD. The higher fecundity of AF is a selective advantage in colonization processes leading to its establishment as NIS. Besides, under the potential selective pressure of abiotic factors, such as the presence of toxicants, its higher resistance in terms of survival and biological fitness also indicates out-competitive advantages.
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Affiliation(s)
- I Varó
- Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Ribera de Cabanes, Castellón 12595 Spain.
| | - S Redón
- Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Ribera de Cabanes, Castellón 12595 Spain
| | - E M Garcia-Roger
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Burjassot, Spain
| | - F Amat
- Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Ribera de Cabanes, Castellón 12595 Spain
| | - D Guinot
- Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Ribera de Cabanes, Castellón 12595 Spain
| | - R Serrano
- Research Institute for Pesticides and Water (IUPA), Avda. Sos Baynat, s/n. University Jaume I, Castellón 12071, Spain
| | - J C Navarro
- Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Ribera de Cabanes, Castellón 12595 Spain
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