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Blanc C, Saclier N, Le Faou E, Marie-Orleach L, Wenger E, Diblasi C, Glemin S, Galtier N, Delattre M. Cosegregation of recombinant chromatids maintains genome-wide heterozygosity in an asexual nematode. SCIENCE ADVANCES 2023; 9:eadi2804. [PMID: 37624896 PMCID: PMC10456839 DOI: 10.1126/sciadv.adi2804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023]
Abstract
In asexual animals, female meiosis is modified to produce diploid oocytes. If meiosis still involves recombination, this is expected to lead to a rapid loss of heterozygosity, with adverse effects on fitness. Many asexuals, however, have a heterozygous genome, the underlying mechanisms being most often unknown. Cytological and population genomic analyses in the nematode Mesorhabditis belari revealed another case of recombining asexual being highly heterozygous genome-wide. We demonstrated that heterozygosity is maintained despite recombination because the recombinant chromatids of each chromosome pair cosegregate during the unique meiotic division. A theoretical model confirmed that this segregation bias is necessary to account for the observed pattern and likely to evolve under a wide range of conditions. Our study uncovers an unexpected type of non-Mendelian genetic inheritance involving cosegregation of recombinant chromatids.
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Affiliation(s)
- Caroline Blanc
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR 5239, Inserm U1293, University Claude Bernard Lyon 1, Lyon, France
| | - Nathanaelle Saclier
- Institut des Sciences de l'Evolution, Université Montpellier, Institut de Recherche pour le Développement, 34090 Montpellier, France
| | - Ehouarn Le Faou
- University of Rennes, CNRS, ECOBIO (Ecologie, Biodiversité, Evolution)–UMR 6553, F-35000 Rennes, France
| | - Lucas Marie-Orleach
- University of Rennes, CNRS, ECOBIO (Ecologie, Biodiversité, Evolution)–UMR 6553, F-35000 Rennes, France
| | - Eva Wenger
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR 5239, Inserm U1293, University Claude Bernard Lyon 1, Lyon, France
| | - Celian Diblasi
- Institut des Sciences de l'Evolution, Université Montpellier, Institut de Recherche pour le Développement, 34090 Montpellier, France
| | - Sylvain Glemin
- University of Rennes, CNRS, ECOBIO (Ecologie, Biodiversité, Evolution)–UMR 6553, F-35000 Rennes, France
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Nicolas Galtier
- Institut des Sciences de l'Evolution, Université Montpellier, Institut de Recherche pour le Développement, 34090 Montpellier, France
| | - Marie Delattre
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR 5239, Inserm U1293, University Claude Bernard Lyon 1, Lyon, France
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2
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Feiner N, Radersma R, Vasquez L, Ringnér M, Nystedt B, Raine A, Tobi EW, Heijmans BT, Uller T. Environmentally induced DNA methylation is inherited across generations in an aquatic keystone species. iScience 2022; 25:104303. [PMID: 35573201 PMCID: PMC9097707 DOI: 10.1016/j.isci.2022.104303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/02/2022] [Accepted: 04/21/2022] [Indexed: 11/16/2022] Open
Abstract
Transgenerational inheritance of environmentally induced epigenetic marks can have significant impacts on eco-evolutionary dynamics, but the phenomenon remains controversial in ecological model systems. We used whole-genome bisulfite sequencing of individual water fleas (Daphnia magna) to assess whether environmentally induced DNA methylation is transgenerationally inherited. Genetically identical females were exposed to one of three natural stressors, or a de-methylating drug, and their offspring were propagated clonally for four generations under control conditions. We identified between 70 and 225 differentially methylated CpG positions (DMPs) in F1 individuals whose mothers were exposed to a natural stressor. Roughly half of these environmentally induced DMPs persisted until generation F4. In contrast, treatment with the drug demonstrated that pervasive hypomethylation upon exposure is reset almost completely after one generation. These results suggest that environmentally induced DNA methylation is non-random and stably inherited across generations in Daphnia, making epigenetic inheritance a putative factor in the eco-evolutionary dynamics of freshwater communities. Naturally induced DNA-methylation persists until generation F4 in Daphnia Drug-induced de-methylation is reset after one generation Methylation is enriched in exons suggesting a gene regulatory function Epigenetic inheritance may influence eco-evolutionary dynamics
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Affiliation(s)
| | - Reinder Radersma
- Department of Biology, Lund University, Lund, Sweden
- Centrum Wiskunde & Informatica, Amsterdam, The Netherlands
| | - Louella Vasquez
- Department of Laboratory Medicine, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Markus Ringnér
- Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Amanda Raine
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Elmar W Tobi
- Periconceptional Epidemiology, Department of Obstetrics and Gynaecology, Division of Obstetrics and Prenatal Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Division of Human Nutrition and Health, Department of Agrotechnology and Food Science, Wageningen University & Research, Wageningen, The Netherlands
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Tobias Uller
- Department of Biology, Lund University, Lund, Sweden
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3
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Pfenninger M, Doria HB, Nickel J, Thielsch A, Schwenk K, Cordellier M. Spontaneous rate of clonal single nucleotide mutations in Daphnia galeata. PLoS One 2022; 17:e0265632. [PMID: 35363773 PMCID: PMC8975155 DOI: 10.1371/journal.pone.0265632] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 03/05/2022] [Indexed: 11/30/2022] Open
Abstract
Mutations are the ultimate source of heritable variation and therefore the fuel for evolution, but direct estimates of mutation rates exist only for few species. We estimated the spontaneous single nucleotide mutation rate among clonal generations in the waterflea Daphnia galeata with a short-term mutation accumulation approach. Individuals from eighteen mutation accumulation lines over five generations were deep sequenced to count de novo mutations that were not present in a pool of F1 individuals, representing the parental genotype. We identified 12 new nucleotide mutations in 90 clonal generational passages. This resulted in an estimated single nucleotide mutation rate of 0.745 x 10-9 (95% c.f. 0.39 x 10-9-1.26 x 10-9), which is slightly lower than recent estimates for other Daphnia species. We discuss the implications for the population genetics of Cladocerans.
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Affiliation(s)
- Markus Pfenninger
- Department Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Mainz, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Halina Binde Doria
- Department Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Jana Nickel
- Institut für Zoologie, Fakultät für Mathematik, Informatik und Naturwissenschaften, Universität Hamburg, Hamburg, Germany
| | - Anne Thielsch
- Institute for Environmental Sciences, Universität Koblenz-Landau, Landau, Germany
| | - Klaus Schwenk
- Institute for Environmental Sciences, Universität Koblenz-Landau, Landau, Germany
| | - Mathilde Cordellier
- Institut für Zoologie, Fakultät für Mathematik, Informatik und Naturwissenschaften, Universität Hamburg, Hamburg, Germany
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4
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Janko K, Bartoš O, Kočí J, Roslein J, Drdová EJ, Kotusz J, Eisner J, Mokrejš M, Štefková-Kašparová E. Genome Fractionation and Loss of Heterozygosity in Hybrids and Polyploids: Mechanisms, Consequences for Selection, and Link to Gene Function. Mol Biol Evol 2021; 38:5255-5274. [PMID: 34410426 PMCID: PMC8662595 DOI: 10.1093/molbev/msab249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Hybridization and genome duplication have played crucial roles in the evolution of many animal and plant taxa. The subgenomes of parental species undergo considerable changes in hybrids and polyploids, which often selectively eliminate segments of one subgenome. However, the mechanisms underlying these changes are not well understood, particularly when the hybridization is linked with asexual reproduction that opens up unexpected evolutionary pathways. To elucidate this problem, we compared published cytogenetic and RNAseq data with exome sequences of asexual diploid and polyploid hybrids between three fish species; Cobitis elongatoides, C. taenia, and C. tanaitica. Clonal genomes remained generally static at chromosome-scale levels but their heterozygosity gradually deteriorated at the level of individual genes owing to allelic deletions and conversions. Interestingly, the impact of both processes varies among animals and genomic regions depending on ploidy level and the properties of affected genes. Namely, polyploids were more tolerant to deletions than diploid asexuals where conversions prevailed, and genomic restructuring events accumulated preferentially in genes characterized by high transcription levels and GC-content, strong purifying selection and specific functions like interacting with intracellular membranes. Although hybrids were phenotypically more similar to C. taenia, we found that they preferentially retained C. elongatoides alleles. This demonstrates that favored subgenome is not necessarily the transcriptionally dominant one. This study demonstrated that subgenomes in asexual hybrids and polyploids evolve under a complex interplay of selection and several molecular mechanisms whose efficiency depends on the organism's ploidy level, as well as functional properties and parental ancestry of the genomic region.
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Affiliation(s)
- Karel Janko
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Oldřich Bartoš
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Kočí
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jan Roslein
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Edita Janková Drdová
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jan Kotusz
- Museum of Natural History, University of Wroclaw, Wroclaw, Poland
| | - Jan Eisner
- Department of Mathematics, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
| | - Martin Mokrejš
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- IT4Innovations, VŠB—Technical University of Ostrava, Ostrava-Poruba, Czech Republic
| | - Eva Štefková-Kašparová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Genetics and Breeding, FAFNR, Czech University of Life Sciences Prague, Czech Republic
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Lemmen KD, Verhoeven KJF, Declerck SAJ. Experimental evidence of rapid heritable adaptation in the absence of initial standing genetic variation. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13943] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kimberley D. Lemmen
- Department of Aquatic Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
| | - Koen J. F. Verhoeven
- Department of Terrestrial Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
| | - Steven A. J. Declerck
- Department of Aquatic Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
- Department of Biology Laboratory of Aquatic Ecology, Evolution and Conservation KULeuven Leuven Belgium
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Morozov-Leonov SY. Evolutionary Potential of the Hybrid Form Pelophylax esculentus-ridibundus (Amphibia, Ranidae) within Dnieper and Desna Drainages: Its Loss Caused by the Hemiclonal Inheritance and the Compensatory Role of Parental Genomes’ Recombination. CYTOL GENET+ 2021. [DOI: 10.3103/s0095452721030063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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7
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Boyer L, Jabbour-Zahab R, Mosna M, Haag CR, Lenormand T. Not so clonal asexuals: Unraveling the secret sex life of Artemia parthenogenetica. Evol Lett 2021; 5:164-174. [PMID: 33868712 PMCID: PMC8045904 DOI: 10.1002/evl3.216] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 01/08/2021] [Accepted: 01/15/2021] [Indexed: 12/11/2022] Open
Abstract
The maintenance of sex is paradoxical as sexual species pay the “twofold cost of males” and should thus quickly be replaced by asexual mutants reproducing clonally. However, asexuals may not be strictly clonal and engage in “cryptic sex,” challenging this simple scenario. We study the cryptic sex life of the brine shrimp Artemia parthenogenetica, which has once been termed an “ancient asexual” and where no genetic differences have ever been observed between parents and offspring. This asexual species rarely produces males, which can hybridize with sexual females of closely related species and transmit asexuality to their offspring. Using such hybrids, we show that recombination occurs in asexual lineages, causing loss‐of‐heterozygosity and parent‐offspring differences. These differences cannot generally be observed in field‐sampled asexuals because once heterozygosity is lost, subsequent recombination leaves no footprint. Furthermore, using extensive paternity tests, we show that hybrid females can reproduce both sexually and asexually, and transmit asexuality to both sexually and asexually produced offspring in a dominant fashion. Finally, we show that, contrary to previous reports, field‐sampled asexual females also rarely reproduce sexually (rate ∼2‰). Overall, most previously known facts about Artemia asexuality turned out to be erroneous. More generally, our findings suggest that the evidence for strictly clonal reproduction of asexual species needs to be reconsidered, and that rare sex and consequences of nonclonal asexuality, such as gene flow within asexuals, need to be more widely taken into account in more realistic models for the maintenance of sex and the persistence of asexual lineages.
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Affiliation(s)
- Loreleï Boyer
- CEFE Univ Montpellier, CNRS, Univ Paul Valéry Montpellier 3, EPHE, IRD Montpellier France
| | - Roula Jabbour-Zahab
- CEFE Univ Montpellier, CNRS, Univ Paul Valéry Montpellier 3, EPHE, IRD Montpellier France
| | - Marta Mosna
- CEFE Univ Montpellier, CNRS, Univ Paul Valéry Montpellier 3, EPHE, IRD Montpellier France
| | - Christoph R Haag
- CEFE Univ Montpellier, CNRS, Univ Paul Valéry Montpellier 3, EPHE, IRD Montpellier France
| | - Thomas Lenormand
- CEFE Univ Montpellier, CNRS, Univ Paul Valéry Montpellier 3, EPHE, IRD Montpellier France
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8
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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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9
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Dukić M, Berner D, Haag CR, Ebert D. How clonal are clones? A quest for loss of heterozygosity during asexual reproduction in Daphnia magna. J Evol Biol 2019; 32:619-628. [PMID: 30888725 PMCID: PMC6850383 DOI: 10.1111/jeb.13443] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 03/04/2019] [Indexed: 12/25/2022]
Abstract
Due to the lack of recombination, asexual organisms are predicted to accumulate mutations and show high levels of within‐individual allelic divergence (heterozygosity); however, empirical evidence for this prediction is largely missing. Instead, evidence of genome homogenization during asexual reproduction is accumulating. Ameiotic crossover recombination is a mechanism that could lead to long genomic stretches of loss of heterozygosity (LOH) and unmasking of mutations that have little or no effect in heterozygous state. Therefore, LOH might be an important force for inducing variation among asexual offspring and may contribute to the limited longevity of asexual lineages. To investigate the genetic consequences of asexuality, here we used high‐throughput sequencing of Daphnia magna for assessing the rate of LOH over a single generation of asexual reproduction. Comparing parthenogenetic daughters with their mothers at several thousand genetic markers generated by restriction site‐associated DNA (RAD) sequencing resulted in high LOH rate estimation that largely overlapped with our estimates for the error rate. To distinguish these two, we Sanger re‐sequenced the top 17 candidate RAD‐loci for LOH, and all of them proved to be false positives. Hence, even though we cannot exclude the possibility that short stretches of LOH occur in genomic regions not covered by our markers, we conclude that LOH does not occur frequently during asexual reproduction in D. magna and ameiotic crossovers are very rare or absent. This finding suggests that clonal lineages of D. magna will remain genetically homogeneous at least over time periods typically relevant for experimental work.
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Affiliation(s)
- Marinela Dukić
- Zoological Institute, University of Basel, Basel, Switzerland.,Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Daniel Berner
- Zoological Institute, University of Basel, Basel, Switzerland
| | - Christoph R Haag
- Centre d'Ecologie Fonctionnelle et Evolutive-CEFE UMR 5175, CNRS-Université de Montpellier-Université Paul-Valéry Montpellier-EPHE, campus CNRS, Montpellier, France.,Department of Biology, Ecology and Evolution, University of Fribourg, Fribourg, Switzerland
| | - Dieter Ebert
- Zoological Institute, University of Basel, Basel, Switzerland
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