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Doležálková-Kaštánková M, Dedukh D, Labajová V, Pustovalova E, Choleva L. Inheritance patterns of male asexuality in hybrid males of a water frog Pelophylax esculentus. Sci Rep 2024; 14:22221. [PMID: 39333615 DOI: 10.1038/s41598-024-73043-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 09/12/2024] [Indexed: 09/29/2024] Open
Abstract
Gametogenesis produces gametes as a piece of genetic information transmitted to the offspring. While during sexual reproduction, progeny inherits a mix of genetic material from both parents, asexually reproducing organisms transfer a copy of maternal or paternal DNA to the progeny clonally. Parthenogenetic, gynogenetic and hybridogenetic animals have developed various mechanisms of gametogenesis, however, their inheritance is not fully understood. Here, we focused on the inheritance of asexual gametogenesis in hybrid Pelophylax esculentus (RL), emerging after crosses of P. lessonae (LL) and P. ridibundus (RR). To understand the mechanisms of gametogenesis in hybrids, we performed three-generation experiments of sexual P. ridibundus females and hybrids from all-male hybrid populations. Using fluorescent in situ hybridization, micronuclei analysis, flow cytometry and genotyping, we found that most adult hybrid males simultaneously produced two types of clonal sperm. Also, most male tadpole progeny in two successive backcrossed generations simultaneously eliminated L and R parental genomes, while some progeny produced only one type of sperm. We hypothesize that the reproductive variability of males producing two kinds of sperm is an adaptive mechanism to reproduce in mixed populations with P. ridibundus and may explain the extensive distribution of the all-male lineage across the European River Basin.
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Affiliation(s)
- Marie Doležálková-Kaštánková
- Institute of Animal Physiology and Genetics, Laboratory of NonMendelian Evolution, The Czech Academy of Sciences, Liběchov, 277 21, Czech Republic.
| | - Dmitrij Dedukh
- Institute of Animal Physiology and Genetics, Laboratory of NonMendelian Evolution, The Czech Academy of Sciences, Liběchov, 277 21, Czech Republic.
| | - Veronika Labajová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, Ostrava, 710 00, Czech Republic
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Liběchov, 277 21, Czech Republic
| | - Eleonora Pustovalova
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Liběchov, 277 21, Czech Republic
- Laboratory of Amphibian Population Ecology, Department of Zoology and Animal Ecology, School of Biology, V. N. Karazin Kharkiv National University, Kharkiv, Ukraine
| | - Lukáš Choleva
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, Ostrava, 710 00, Czech Republic
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Liběchov, 277 21, Czech Republic
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Dedukh D, Maslova A, Al-Rikabi A, Padutsch N, Liehr T, Krasikova A. Karyotypes of water frogs from the Pelophylax esculentus complex: results of cross-species chromosomal painting. Chromosoma 2023; 132:329-342. [PMID: 38001396 DOI: 10.1007/s00412-023-00812-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023]
Abstract
Amphibian species have the largest genome size enriched with repetitive sequences and relatively similar karyotypes. Moreover, many amphibian species frequently hybridize causing nuclear and mitochondrial genome introgressions. In addition, hybridization in some amphibian species may lead to clonality and polyploidization. All such events were found in water frogs from the genus Pelophylax. Among the species within the genus Pelophylax, P. esculentus complex is the most widely distributed and well-studied. This complex includes two parental species, P. ridibundus and P. lessonae, and their hybrids, P. esculentus, reproducing hemiclonally. Parental species and their hybrids have similar but slightly polymorphic karyotypes, so their precise identification is still required. Here, we have developed a complete set of 13 chromosome painting probes for two parental species allowing the precise identification of all chromosomes. Applying chromosomal painting, we identified homologous chromosomes in both parental species and orthologous chromosomes in their diploid hemiclonal hybrids. Comparative painting did not reveal interchromosomal exchanges between the studied water frog species and their hybrids. Using cross-specific chromosome painting, we detected unequal distribution of the signals along chromosomes suggesting the presence of species-specific tandem repeats. Application of chromosomal paints to the karyotypes of hybrids revealed differences in the intensity of staining for P. ridibundus and P. lessonae chromosomes. Thus, both parental genomes have a divergence in unique sequences. Obtained chromosome probes may serve as a powerful tool to unravel chromosomal evolution in phylogenetically related species, identify individual chromosomes in different cell types, and investigate the elimination of chromosomes in hybrid water frogs.
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Affiliation(s)
- Dmitrij Dedukh
- Laboratory of Cell Nucleus Structure and Dynamics, Saint-Petersburg State University, Saint-Petersburg, Russia
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Antonina Maslova
- Laboratory of Cell Nucleus Structure and Dynamics, Saint-Petersburg State University, Saint-Petersburg, Russia
| | - Ahmed Al-Rikabi
- Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Jena, Germany
| | - Niklas Padutsch
- Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Jena, Germany
| | - Thomas Liehr
- Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Jena, Germany
| | - Alla Krasikova
- Laboratory of Cell Nucleus Structure and Dynamics, Saint-Petersburg State University, Saint-Petersburg, Russia.
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Moerman F, Fronhofer EA, Altermatt F, Wagner A. Selection on growth rate and local adaptation drive genomic adaptation during experimental range expansions in the protist Tetrahymena thermophila. J Anim Ecol 2021; 91:1088-1103. [PMID: 34582573 PMCID: PMC9291582 DOI: 10.1111/1365-2656.13598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/19/2021] [Indexed: 11/29/2022]
Abstract
Populations that expand their range can undergo rapid evolutionary adaptation of life‐history traits, dispersal behaviour and adaptation to the local environment. Such adaptation may be aided or hindered by sexual reproduction, depending on the context. However, few empirical and experimental studies have investigated the genetic basis of adaptive evolution during range expansions. Even less attention has been given to the question how sexual reproduction may modulate such adaptive evolution during range expansions. We here studied genomic adaptation during experimental range expansions of the protist Tetrahymena thermophila in landscapes with a uniform environment or a pH gradient. Specifically, we investigated two aspects of genomic adaptation during range expansion. First, we investigated adaptive genetic change in terms of the underlying numbers of allele frequency changes from standing genetic variation and de novo variants. We focused on how sexual reproduction may alter this adaptive genetic change. Second, we identified genes subject to selection caused by the expanding range itself, and directional selection due to the presence or absence of the pH gradient. We focused this analysis on alleles with large frequency changes that occurred in parallel in more than one population to identify the most likely candidate targets of selection. We found that sexual reproduction altered adaptive genetic change both in terms of de novo variants and standing genetic variation. However, sexual reproduction affected allele frequency changes in standing genetic variation only in the absence of long‐distance gene flow. Adaptation to the range expansion affected genes involved in cell divisions and DNA repair, whereas adaptation to the pH gradient additionally affected genes involved in ion balance and oxidoreductase reactions. These genetic changes may result from selection on growth and adaptation to low pH. In the absence of gene flow, sexual reproduction may have aided genetic adaptation. Gene flow may have swamped expanding populations with maladapted alleles, thus reducing the extent of evolutionary adaptation during range expansion. Sexual reproduction also altered the genetic basis of adaptation in our evolving populations via de novo variants, possibly by purging deleterious mutations or by revealing fitness benefits of rare genetic variants.
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Affiliation(s)
- Felix Moerman
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland.,Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge-Bâtiment Génopode, Lausanne, Switzerland.,ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | - Florian Altermatt
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland.,Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge-Bâtiment Génopode, Lausanne, Switzerland.,The Santa Fe Institute, Santa Fe, NM, USA.,Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
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Capture and return of sexual genomes by hybridogenetic frogs provide clonal genome enrichment in a sexual species. Sci Rep 2021; 11:1633. [PMID: 33452404 PMCID: PMC7810977 DOI: 10.1038/s41598-021-81240-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 01/04/2021] [Indexed: 01/29/2023] Open
Abstract
Hybridogenesis is a reproductive tool for sexual parasitism. Hybridogenetic hybrids use gametes from their sexual host for their own reproduction, but sexual species gain no benefit from such matings as their genome is later eliminated. Here, we examine the presence of sexual parasitism in water frogs through crossing experiments and genome-wide data. We specifically focus on the famous Central-European populations where Pelophylax esculentus males (hybrids of P. ridibundus and P. lessonae) live with P. ridibundus. We identified a system where the hybrids commonly produce two types of clonal gametes (hybrid amphispermy). The haploid lessonae genome is clonally inherited from generation to generation and assures the maintenance of hybrids through a process, in which lessonae sperm fertilize P. ridibundus eggs. The haploid ridibundus genome in hybrids received from P. ridibundus a generation ago, is perpetuated as clonal ridibundus sperm and used to fertilize P. ridibundus eggs, yielding female P. ridibundus progeny. These results imply animal reproduction in which hybridogenetic taxa are not only sexual parasites, but also participate in the formation of a sexual taxon in a remarkable way. This occurs through a process by which sexual gametes are being captured, converted to clones, and returned to sexual populations in one generation.
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Walters RJ, Berger D. Implications of existing local (mal)adaptations for ecological forecasting under environmental change. Evol Appl 2019; 12:1487-1502. [PMID: 31417629 PMCID: PMC6691230 DOI: 10.1111/eva.12840] [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: 08/03/2018] [Revised: 06/22/2019] [Accepted: 06/24/2019] [Indexed: 01/31/2023] Open
Abstract
Standing genetic variation represents a genetic load on population fitness but can also support a rapid response to short-term environmental change, and the greatest potential source of such standing genetic variation typically exists among locally adapted populations living along an environmental gradient. Here, we develop a spatially explicit simulation model to quantify the contribution of existing genetic variation arising from migration-mutation-selection-drift balance to time to extinction under environmental change. Simulations reveal that local adaptation across a species range associated with an underlying environmental gradient could extend time to extinction by nearly threefold irrespective of the rate of environmental change. The potential for preadapted alleles to increase the rate of adaptation changes the relative importance of established extinction risk factors; in particular, it reduced the importance of the breadth of environmental tolerance and it increased the relative importance of fecundity. Although migration of preadapted alleles generally increased persistence time, it decreased it at rates of environmental change close to the critical rate of change by creating a population bottleneck, which ultimately limited the rate at which de novo mutations could arise. An analysis of the extinction dynamics further revealed that one consequence of gene flow is the potential to maximize population growth rate in at least part of the species range, which is likely to have consequences for forecasting the consequences of ecological interactions. Our study shows that predictions of persistence time change fundamentally when existing local adaptations are explicitly taken into account, underscoring the need to preserve and manage genetic diversity.
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Affiliation(s)
- Richard J. Walters
- Centre for Environmental and Climate ResearchLund UniversityLundSweden
- School of Biological SciencesUniversity of ReadingReadingUK
| | - David Berger
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
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Schmeller DS, Weatherdon LV, Loyau A, Bondeau A, Brotons L, Brummitt N, Geijzendorffer IR, Haase P, Kuemmerlen M, Martin CS, Mihoub JB, Rocchini D, Saarenmaa H, Stoll S, Regan EC. A suite of essential biodiversity variables for detecting critical biodiversity change. Biol Rev Camb Philos Soc 2017; 93:55-71. [DOI: 10.1111/brv.12332] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 03/11/2017] [Accepted: 03/16/2017] [Indexed: 01/13/2023]
Affiliation(s)
- Dirk S. Schmeller
- Department of Conservation Biology; Helmholtz Center for Environmental Research - UFZ; 04318 Leipzig Germany
- ECOLAB; Université de Toulouse, CNRS, INPT, UPS; Toulouse France
| | - Lauren V. Weatherdon
- United Nations Environment World Conservation Monitoring Centre; Cambridge CB3 0DL U.K
| | - Adeline Loyau
- ECOLAB; Université de Toulouse, CNRS, INPT, UPS; Toulouse France
- Department of System Ecotoxicology; Helmholtz Center for Environmental Research - UFZ; 04318 Leipzig Germany
| | - Alberte Bondeau
- Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE); Aix Marseille Université, CNRS, IRD, Avignon Université, Technopôle Arbois-Méditerranée Bât; F-13545 Aix-en-Provence cedex 04 France
| | - Lluis Brotons
- Forest Sciences Centre of Catalonia (CEMFOR-CTFC); Catalonia Spain
- CREAF, Centre for Ecological Research and Forestry Applications; Autonomous University of Barcelona; Catalonia Spain
- CSIC, Cerdanyola del Vallés; Catalonia Spain
| | - Neil Brummitt
- Department of Life Sciences; Natural History Museum; London SW7 5BD U.K
| | - Ilse R. Geijzendorffer
- Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE); Aix Marseille Université, CNRS, IRD, Avignon Université, Technopôle Arbois-Méditerranée Bât; F-13545 Aix-en-Provence cedex 04 France
- Tour du Valat, Institut de recherche pour la conservation des zones humides méditerranéennes, Le Sambuc; Arles 13200 France
| | - Peter Haase
- Department of River Ecology and Conservation; Senckenberg Research Institute and Natural History Museum Frankfurt; D-63571 Gelnhausen Germany
- Faculty of Biology; University of Duisburg-Essen; 45141 Essen Germany
| | - Mathias Kuemmerlen
- Department of River Ecology and Conservation; Senckenberg Research Institute and Natural History Museum Frankfurt; D-63571 Gelnhausen Germany
- Department of Systems Analysis; Integrated Assessment and Modelling, Swiss Federal Institute of Aquatic Science and Technology - Eawag; Überlandstrasse 133 8600 Dübendorf Switzerland
| | - Corinne S. Martin
- United Nations Environment World Conservation Monitoring Centre; Cambridge CB3 0DL U.K
| | - Jean-Baptiste Mihoub
- Department of Conservation Biology; Helmholtz Center for Environmental Research - UFZ; 04318 Leipzig Germany
- Sorbonne Universités; UPMC Univ Paris 06, Muséum National d'Histoire Naturelle, CNRS, CESCO; UMR 7204, 75005 Paris France
| | - Duccio Rocchini
- Department of Biodiversity and Molecular Ecology; Fondazione Edmund Mach, Research and Innovation Centre; 38010 S. Micehle all'Adige (TN) Italy
| | | | - Stefan Stoll
- Department of River Ecology and Conservation; Senckenberg Research Institute and Natural History Museum Frankfurt; D-63571 Gelnhausen Germany
- Ecosystem Research Facility Eußerthal, Institute of Environmental Science; University of Koblenz-Landau; Koblenz-Landau Germany
| | - Eugenie C. Regan
- United Nations Environment World Conservation Monitoring Centre; Cambridge CB3 0DL U.K
- The Biodiversity Consultancy; Cambridge CB2 1SJ U.K
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Radojičić JM, Krizmanić I, Kasapidis P, Zouros E. Extensive mitochondrial heteroplasmy in hybrid water frog (Pelophylax spp.) populations from Southeast Europe. Ecol Evol 2015; 5:4529-41. [PMID: 26668720 PMCID: PMC4670067 DOI: 10.1002/ece3.1692] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/05/2015] [Accepted: 08/12/2015] [Indexed: 11/30/2022] Open
Abstract
Water frogs of the genus Pelophylax (previous Rana) species have been much studied in Europe for their outstanding reproductive mechanism in which sympatric hybridization between genetically distinct parental species produces diverse genetic forms of viable hybrid animals. The most common hybrid is P. esculentus that carries the genomes of both parental species, P. ridibundus and P. lessonae, but usually transfers the whole genome of only one parent to its offsprings (hybridogenesis). The evolutionary cost of transfer of the intact genome and hence the hemiclonal reproduction is the depletion of heterozygosity in the hybrid populations. Pelophylax esculentus presents an excellent example of the long‐term sustained hybridization and hemiclonal reproduction in which the effects of the low genetic diversity are balanced through the novel mutations and periodic recombinations. In this study, we analyzed the mitochondrial (mt) and microsatellites DNA variations in hybrid Pelophylax populations from southern parts of the Pannonian Basin and a north–south transect of the Balkan Peninsula, which are home for a variety of Pelophylax genetic lineages. The mtDNA haplotypes found in this study corresponded to P. ridibundus and P. epeiroticus of the Balkan – Anatolian lineage (ridibundus–bedriagae) and to P. lessonae and a divergent lessonae haplotype of the lessonae lineage. The mtDNA genomes showed considerable intraspecific variation and geographic differentiation. The Balkan wide distributed P. ridibundus was found in all studied populations and its nuclear genome, along with either the lessonae or the endemic epeiroticus genome, in all hybrids. An unexpected finding was that the hybrid populations were invariably heteroplasmic, that is, they contained the mtDNA of both parental species. We discussed the possibility that such extensive heteroplasmy is a result of hybridization and it comes from regular leakage of the paternal mtDNA from a sperm of one species that fertilizes eggs of another. In this case, the mechanisms that protect the egg from heterospecific fertilization and further from the presence of sperm mtDNA could become compromised due to their differences and divergence at both, mitochondrial and nuclear DNA. The heteroplasmy once retained in the fertilized egg could be transmitted by hybrid backcrossing to the progeny and maintained in a population over generations. The role of interspecies and heteroplasmic hybrid animals due to their genomic diversity and better fitness compare to the parental species might be of the special importance in adaptations to miscellaneous and isolated environments at the Balkan Peninsula.
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Affiliation(s)
- Jelena M Radojičić
- Hellenic Centre for Marine Research Institute of Marine Biology, Biotechnology and Aquaculture Heraklion Greece ; Department of Biology University of Crete Heraklion Greece
| | - Imre Krizmanić
- Faculty of Biology Institute of Zoology University of Belgrade Belgrade Serbia
| | - Panagiotis Kasapidis
- Hellenic Centre for Marine Research Institute of Marine Biology, Biotechnology and Aquaculture Heraklion Greece
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9
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Leuenberger J, Gander A, Schmidt BR, Perrin N. Are invasive marsh frogs (Pelophylax ridibundus) replacing the native P. lessonae/P. esculentus hybridogenetic complex in Western Europe? Genetic evidence from a field study. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0585-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Hoffmann A, Reyer HU. Genomic effects on advertisement call structure in diploid and triploid hybrid waterfrogs (Anura, Pelophylax esculentus). BMC Ecol 2013; 13:47. [PMID: 24304922 PMCID: PMC4235041 DOI: 10.1186/1472-6785-13-47] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 11/23/2013] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND In anurans, differences in male mating calls have intensively been studied with respect to taxonomic classification, phylogeographic comparisons among different populations and sexual selection. Although overall successful, there is often much unexplained variation in these studies. Potential causes for such variation include differences among genotypes and breeding systems, as well as differences between populations. We investigated how these three factors affect call properties in male water frogs of Pelophylax lessonae (genotype LL), P. ridibundus (RR) and their interspecific hybrid P. esculentus which comes in diploid (LR) and triploid types (LLR, LRR). RESULTS We investigated five call parameters that all showed a genomic dosage effect, i.e. they either decreased or increased with the L/R ratio in the order LL-LLR-LR-LRR-RR. Not all parameters differentiated equally well between the five genotypes, but combined they provided a good separation. Two of the five call parameters were also affected by the breeding system. Calls of diploid LR males varied, depending on whether these males mated with one or both of the parental species (diploid systems) or triploid hybrids (mixed ploidy systems). With the exception of the northernmost mixed-ploidy population, call differences were not related to the geographic location of the population and they were not correlated with genetic distances in the R and L genomes. CONCLUSIONS We found an influence of all three tested factors on call parameters, with the effect size decreasing from genotype through breeding system to geographic location of the population. Overall, results were in line with predictions from a dosage effect in L/R ratios, but in three call parameters all three hybrid types were more similar to one or the other parental species. Also calls of diploid hybrids varied between breeding systems in agreement with the sexual host required for successful reproduction. The lack of hybrid call differences in a mixed-ploidy population at the northern edge of the water frog distribution is likely to be associated with genetic particularities, including a) low genetic variability and/or b) a local loss of genes coding for genotype-dependent call differentiation under conditions where female discrimination between diploid and triploid males is not beneficial.
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Affiliation(s)
- Alexandra Hoffmann
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Heinz-Ulrich Reyer
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
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Drechsler A, Geller D, Freund K, Schmeller DS, Künzel S, Rupp O, Loyau A, Denoël M, Valbuena-Ureña E, Steinfartz S. What remains from a 454 run: estimation of success rates of microsatellite loci development in selected newt species (Calotriton asper, Lissotriton helveticus, and Triturus cristatus) and comparison with Illumina-based approaches. Ecol Evol 2013; 3:3947-57. [PMID: 24198952 PMCID: PMC3810887 DOI: 10.1002/ece3.764] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 08/07/2013] [Accepted: 08/12/2013] [Indexed: 11/24/2022] Open
Abstract
The development of microsatellite loci has become more efficient using next-generation sequencing (NGS) approaches, and many studies imply that the amount of applicable loci is large. However, few studies have sought to quantify the number of loci that are retained for use out of the thousands of sequence reads initially obtained. We analyzed the success rate of microsatellite loci development for three amphibian species using a 454 NGS approach on tetra-nucleotide motif-enriched species-specific libraries. The number of sequence reads obtained differed strongly between species and ranged from 19,562 for Triturus cristatus to 55,626 for Lissotriton helveticus, with 52,075 reads obtained for Calotriton asper. PHOBOS was used to identify sequences with tetra-nucleotide repeat motifs with a minimum repeat number of ten and high quality primer binding sites. Of 107 sequences for T. cristatus, 316 for C. asper and 319 for L. helveticus, we tested the amplification success, polymorphism, and degree of heterozygosity for 41 primer combinations each for C. asper and T. cristatus, and 22 for L. helveticus. We found 11 polymorphic loci for T. cristatus, 20 loci for C. asper, and 15 loci for L. helveticus. Extrapolated, the number of potentially amplifiable loci (PALs) resulted in estimated species-specific success rates of 0.15% (T. cristatus), 0.30% (C. asper), and 0.39% (L. helveticus). Compared with representative Illumina NGS approaches, our applied 454-sequencing approach on specifically enriched sublibraries proved to be quite competitive in terms of success rates and number of finally applicable loci.
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Affiliation(s)
- Axel Drechsler
- Department of Behavioral Biology, Unit of Molecular Ecology and Behavior, University of Bielefeld Morgenbreede 45, D-33619, Bielefeld, Germany
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Bogart JP, Bi K. Genetic and genomic interactions of animals with different ploidy levels. Cytogenet Genome Res 2013; 140:117-36. [PMID: 23751376 DOI: 10.1159/000351593] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Polyploid animals have independently evolved from diploids in diverse taxa across the tree of life. We review a few polyploid animal species or biotypes where recently developed molecular and cytogenetic methods have significantly improved our understanding of their genetics, reproduction and evolution. Mitochondrial sequences that target the maternal ancestor of a polyploid show that polyploids may have single (e.g. unisexual salamanders in the genus Ambystoma) or multiple (e.g. parthenogenetic polyploid lizards in the genus Aspidoscelis) origins. Microsatellites are nuclear markers that can be used to analyze genetic recombinations, reproductive modes (e.g. Ambystoma) and recombination events (e.g. polyploid frogs such as Pelophylax esculentus). Hom(e)ologous chromosomes and rare intergenomic exchanges in allopolyploids have been distinguished by applying genome-specific fluorescent probes to chromosome spreads. Polyploids arise, and are maintained, through perturbations of the 'normal' meiotic program that would include pre-meiotic chromosome replication and genomic integrity of homologs. When possible, asexual, unisexual and bisexual polyploid species or biotypes interact with diploid relatives, and genes are passed from diploid to polyploid gene pools, which increase genetic diversity and ultimately evolutionary flexibility in the polyploid. When diploid relatives do not exist, polyploids can interact with another polyploid (e.g. species of African Clawed Frogs in the genus Xenopus). Some polyploid fish (e.g. salmonids) and frogs (Xenopus) represent independent lineages whose ancestors experienced whole genome duplication events. Some tetraploid frogs (P. esculentus) and fish (Squaliusalburnoides) may be in the process of becoming independent species, but diploid and triploid forms of these 'species' continue to genetically interact with the comparatively few tetraploid populations. Genetic and genomic interaction between polyploids and diploids is a complex and dynamic process that likely plays a crucial role for the evolution and persistence of polyploid animals. See also other articles in this themed issue.
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Affiliation(s)
- J P Bogart
- Department of Integrative Biology, University of Guelph, Guelph, Ont., Canada. jbogart @ uoguelph.ca
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Multi-event models reveal the absence of interaction between an invasive frog and a native endangered amphibian. Biol Invasions 2013. [DOI: 10.1007/s10530-013-0427-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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SCHULTE ULRICH, VEITH MICHAEL, HOCHKIRCH AXEL. Rapid genetic assimilation of native wall lizard populations (Podarcis muralis) through extensive hybridization with introduced lineages. Mol Ecol 2012; 21:4313-26. [DOI: 10.1111/j.1365-294x.2012.05693.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Unisexual vertebrates are model systems for understanding the evolution of sex. Many predominantly clonal lineages allow occasional genetic recombination, which may be sufficient to avoid the accumulation of deleterious mutations and parasites. Introgression of paternal DNA into an all-female lineage represents a one-way flow of genetic material. Over many generations, this could result in complete replacement of the unisexual genomes by those of the donor species. The process of genome replacement may be counteracted by contemporary dispersal or by positive selection on hybrid nuclear genomes in ecotones. I present a conceptual model that relates nuclear genome replacement, positive selection on hybrids and biogeography in unisexual systems. I execute an individual-based simulation of the fate of hybrid genotypes in contact with a single host species. I parameterize these models for unisexual salamanders in the Ambystoma genus, for which the frequency of genome replacement has been a source of ongoing debate. I find that, if genome replacement occurs at a rate greater than 1/10,000 in Ambystoma, then there must be compensating positive selection in order to maintain observed levels of hybrid nuclei. Future researchers studying unisexual systems may use this framework as a guide to evaluating the hybrid superiority hypothesis.
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Affiliation(s)
- Noah D Charney
- Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003-9297, USA.
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16
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Luquet E, Vorburger C, Hervant F, Joly P, Kaufmann B, Schmeller DS, Léna JP, Grolet O, Konecny L, Plénet S. Invasiveness of an introduced species: the role of hybridization and ecological constraints. Biol Invasions 2011. [DOI: 10.1007/s10530-011-0010-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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17
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Zaleśna A, Choleva L, Ogielska M, Rábová M, Marec F, Ráb P. Evidence for integrity of parental genomes in the diploid hybridogenetic water frog Pelophylax esculentus by genomic in situ hybridization. Cytogenet Genome Res 2011; 134:206-12. [PMID: 21555873 DOI: 10.1159/000327716] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2011] [Indexed: 11/19/2022] Open
Abstract
The Western Palearctic water frogs Pelophylax ridibundus and P. lessonae were identified as parental (sexual) species and P. esculentus as their interspecific, hybridogenetically reproducing hybrid with hemiclonal heredity. We used genomic in situ hybridization (GISH) to identify parental chromosomes of P.lessonae and P.ridibundus in diploid P. esculentus karyotypes (2n = 26). GISH probes were made by fluorochrome labeling of total genomic DNA extracted from the sexual progenitors. The labeled probe from one species was hybridized to chromosomes of P. esculentus in the presence of excess of unlabeled genomic DNA from the other species. Thus, the P. lessonae probe was blocked by P. ridibundus unlabeled DNA, and vice versa. We successfully discriminated each of the 13 respective parental chromosomes in metaphase complements of the hybrids according to species-specific hybridization signals. GISH enabled us to confirm additional differences between parental chromosomes in size (smaller chromosomes belong to P. lessonae) and in the presence of DAPI-positive centromeric heterochromatin (detected in chromosomes of P. ridibundus, but not in P. lessonae). The fact that no visible intergenomic exchanges were found in metaphase chromosomes of diploid P. esculentus provides important information on the genomic integrity of hemiclonal transmission and supports hybridogenesis as a reproductive mode at the chromosome level for the specimens examined.
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Affiliation(s)
- A Zaleśna
- Department of Biology and Conservation of Vertebrates, Zoological Institute, University of Wroclaw, Wroclaw, Poland
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18
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Holsbeek G, Jooris R. Potential impact of genome exclusion by alien species in the hybridogenetic water frogs (Pelophylax esculentus complex). Biol Invasions 2009. [DOI: 10.1007/s10530-009-9427-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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19
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Grant BR, Grant PR. Fission and fusion of Darwin's finches populations. Philos Trans R Soc Lond B Biol Sci 2008; 363:2821-9. [PMID: 18508750 DOI: 10.1098/rstb.2008.0051] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This study addresses the causes and evolutionary consequences of introgressive hybridization in the sympatric species of Darwin's ground finches (Geospiza) on the small island of Daphne Major in the Galápagos archipelago. Hybridization occurs rarely (less than 2% of breeding pairs) but persistently across years, usually as a result of imprinting on the song of another species. Hybrids survive well under some ecological conditions, but not others. Hybrids mate according to song type. The resulting introgression increases phenotypic and genetic variation in the backcrossed populations. Effects of introgression on beak shape are determined by the underlying developmental genetic pathways. Introgressive hybridization has been widespread throughout the archipelago in the recent past, and may have been a persistent feature throughout the early history of the radiation, episodically affecting both the speed and direction of evolution. We discuss how fission through selection and fusion through introgression in contemporary Darwin's finch populations may be a reflection of processes occurring in other young radiations. We propose that introgression has the largest effect on the evolution of interbreeding species after they have diverged in morphology, but before the point is reached when genetic incompatibilities incur a severe fitness cost.
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Affiliation(s)
- B Rosemary Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
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20
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Pagano A, Lesbarreres D, O’Hara R, Crivelli A, Veith M, Lode T, Schmeller DS. Geographical and ecological distributions of frog hemiclones suggest occurrence of both ‘General-Purpose Genotype’ and ‘Frozen Niche Variation’ clones. J ZOOL SYST EVOL RES 2008. [DOI: 10.1111/j.1439-0469.2007.00439.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Schmeller DS, Pagano A, Plénet S, Veith M. Introducing water frogs – Is there a risk for indigenous species in France? C R Biol 2007; 330:684-90. [PMID: 17720585 DOI: 10.1016/j.crvi.2007.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2005] [Revised: 04/13/2007] [Accepted: 04/17/2007] [Indexed: 10/23/2022]
Abstract
The ecological success of introduced species in their new environments is difficult to predict. Recently, the water frog species Rana ridibunda has raised interest, as different genetic lineages were introduced to various European countries. The aim of the present study was to analyze the potential invasiveness of R. ridibunda and assess the risk of replacement for indigenous water frog species. The investigation of over 700 water frogs from 22 locations in southern France and four locations in Spain shows that the competition with indigenous species is mainly limited to a particular habitat type, characterized by high-oxygen and low-salinity freshwater. The competitive strength of R. ridibunda may be related to a higher growth rate and longevity as compared to the indigenous species R. grafi and R. perezi. Our data suggest that R. ridibunda is a risk to the diversity of indigenous water frog assemblages in France. Future monitoring needs to clarify the distribution of R. ridibunda, its ecological niche, and the risk status for indigenous water frog species.
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Affiliation(s)
- Dirk S Schmeller
- Institute of Zoology, Department of Population Biology, Johannes Gutenberg-University Mainz, Saarstrasse 21, 55099 Mainz, Germany.
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22
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Schmeller DS, Schregel J, Veith M. The importance of heterozygosity in a frog's life. Naturwissenschaften 2007; 94:360-6. [PMID: 17242953 DOI: 10.1007/s00114-006-0205-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2005] [Revised: 11/13/2006] [Accepted: 11/15/2006] [Indexed: 10/23/2022]
Abstract
High genetic variability may increase metabolic efficiency and thus allows responding to environmental challenges as limits to adaptation are approached. Therefore, it has been suggested that high genetic variability contributes strongly to the fitness of an individual. Survival to high age may thus depend on high genetic variability, and genetically variable individuals may have a higher survival rate to high ages in comparison to less variable sympatric conspecifics. Such a heterozygosity x age relationship might be more readily detectable in stressful as compared to benign environments. For testing the relationship between age and heterozygosity, we genetically analyzed 71 individuals of the frog species Rana perezi from a total of seven populations at 13 allozyme loci. The age of the individuals was determined by skeletochronology. We found effects on age of both environment and allozyme heterozygosity, especially in populations with high stress regimes. A significant heterozygosity x age relationship has so far rarely been shown in natural populations. The result of our analysis suggests that more heterozygous individuals have a higher longevity and may be an important source of genetic variability of a population, likely contributing to a stabilization of the effective population size.
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Affiliation(s)
- Dirk S Schmeller
- Department of Ecology, Institute of Zoology, Johannes Gutenberg-University Mainz, Saarstrasse 21, Mainz, Germany.
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23
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Kvell K, Cooper EL, Engelmann P, Bovari J, Nemeth P. Blurring borders: innate immunity with adaptive features. Clin Dev Immunol 2007; 2007:83671. [PMID: 18317532 PMCID: PMC2248247 DOI: 10.1155/2007/83671] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2007] [Accepted: 11/05/2007] [Indexed: 02/04/2023]
Abstract
Adaptive immunity has often been considered the penultimate of immune capacities. That system is now being deconstructed to encompass less stringent rules that govern its initiation, actual effector activity, and ambivalent results. Expanding the repertoire of innate immunity found in all invertebrates has greatly facilitated the relaxation of convictions concerning what actually constitutes innate and adaptive immunity. Two animal models, incidentally not on the line of chordate evolution (C. elegans and Drosophila), have contributed enormously to defining homology. The characteristics of specificity and memory and whether the antigen is pathogenic or nonpathogenic reveal considerable information on homology, thus deconstructing the more fundamentalist view. Senescence, cancer, and immunosuppression often associated with mammals that possess both innate and adaptive immunity also exist in invertebrates that only possess innate immunity. Strict definitions become blurred casting skepticism on the utility of creating rigid definitions of what innate and adaptive immunity are without considering overlaps.
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Affiliation(s)
- K. Kvell
- Department of Immunology and Biotechnology,
Faculty of Medicine,
University of Pécs,
7624 Pécs,
Hungary
| | - EL. Cooper
- Laboratory of Comparative Neuroimmunology,
Department of Neurobiology,
David Geffen School of Medicine at UCLA,
University of California,
Los Angeles, CA 90095-1763, USA
| | - P. Engelmann
- Department of Immunology and Biotechnology,
Faculty of Medicine,
University of Pécs,
7624 Pécs,
Hungary
| | - J. Bovari
- Department of Immunology and Biotechnology,
Faculty of Medicine,
University of Pécs,
7624 Pécs,
Hungary
| | - P. Nemeth
- Department of Immunology and Biotechnology,
Faculty of Medicine,
University of Pécs,
7624 Pécs,
Hungary
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24
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Abstract
An increasing number of studies describe moving hybrid zones. This raises the issue of their actual frequency and emphasizes the need for methods that enable the detection of zone movements without historical records. Asymmetric introgression, usually considered as a signature of geographical shift, might be misleading when applied to mitochondrial or potentially non-neutral markers. We investigated mitochondrial and genomic introgression, using 30 AFLP derived markers, in a well-documented moving avian contact zone between two warblers. We found no instances of cross-species transmission of mitochondrial DNA but we detected nuclear introgression. Introgression levels were higher in the expanding species. Highest introgression was observed in populations that recently became allopatric than in current sympatric populations, which suggests that alien genetic material mainly spread at the time just before the receding species became extinct. We propose that either local recruitment or positive selection on some loci contribute to this pattern. Furthermore, we propose that, when the rarefaction of sexual partners drive the hybridization process, movement could be revealed by introgression peaking on the rear edge of the moving zone, or in its close vicinity.
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Affiliation(s)
- Jean Secondi
- UMR MA105 Paysages et biodiversité, Université d"Angers Belle-Beille, 2 bd Lavoisier, 49045 Angers cedex, France.
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