1
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Herczeg D, Palomar G, Zieliński P, van Riemsdijk I, Babik W, Dankovics R, Halpern B, Cvijanović M, Vörös J. Genomic analysis reveals complex population structure within the smooth newt, Lissotriton vulgaris, in Central Europe. Ecol Evol 2023; 13:e10478. [PMID: 37664508 PMCID: PMC10469019 DOI: 10.1002/ece3.10478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 08/01/2023] [Accepted: 08/08/2023] [Indexed: 09/05/2023] Open
Abstract
Species with wide-range distributions usually display high genetic variation. This variation can be partly explained by historical lineages that were temporally isolated from each other and are back into secondary reproductive contact, and partly by local adaptations. The smooth newt (Lissotriton vulgaris) is one of the most widely distributed amphibians species across Eurasia and forms a species complex with a partially overlapping distribution and morphology. In the present study, we explored the population genomic structure of smooth newt lineages in the Carpathian Basin (CB) relying on single-nucleotide polymorphisms. Our dataset included new and previously published data to study the secondary contact zone between lineages in the CB and also tested for the barrier effect of rivers to gene flow between these lineages. We confirmed the presence of the South L. v. vulgaris Lineage distributed in Transdanubia and we provided new distribution records of L. v. ampelensis inhabiting the eastern territories of the CB. High genetic diversity of smooth newts was observed, especially in the North Hungarian Mountains and at the interfluves of the main rivers in the South with four distinct lineages of L. v. vulgaris and one lineage of L. v. ampelensis showing a low level of admixture with the spatially closest L. v. vulgaris lineage. Moreover, admixture detected at the interfluve of the main rivers (i.e. Danube and Tisza) suggested a secondary contact zone in the area. Finally, we found that the river Danube has a very weak effect on population divergence, while the river Tisza is a geographical barrier limiting gene flow between smooth newt lineages. As the range boundaries of L. v. vulgaris and L. v. ampelensis in the CB coincide with the river Tisza, our study underpins the influence of rivers in lineage diversification.
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Affiliation(s)
- Dávid Herczeg
- ELKH‐ELTE‐MTM Integrative Ecology Research GroupBudapestHungary
- Department of Systematic Zoology and Ecology, Institute of BiologyELTE Eötvös Loránd UniversityBudapestHungary
| | - Gemma Palomar
- Department of Genetics, Physiology, and Microbiology, Faculty of Biological SciencesComplutense University of MadridMadridSpain
- Institute of Environmental SciencesFaculty of Biology, Jagiellonian UniversityKrakówPoland
| | - Piotr Zieliński
- Institute of Environmental SciencesFaculty of Biology, Jagiellonian UniversityKrakówPoland
| | | | - Wiesław Babik
- Institute of Environmental SciencesFaculty of Biology, Jagiellonian UniversityKrakówPoland
| | | | - Bálint Halpern
- ELKH‐ELTE‐MTM Integrative Ecology Research GroupBudapestHungary
- Department of Systematic Zoology and Ecology, Institute of BiologyELTE Eötvös Loránd UniversityBudapestHungary
- MME Birdlife HungaryBudapestHungary
| | - Milena Cvijanović
- Institute for Biological Research “Siniša Stanković”, National Institute of the Republic of SerbiaUniversity of BelgradeBelgradeSerbia
| | - Judit Vörös
- Department of ZoologyHungarian Natural History MuseumBudapestHungary
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2
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Antunes B, Figueiredo-Vázquez C, Dudek K, Liana M, Pabijan M, Zieliński P, Babik W. Landscape genetics reveals contrasting patterns of connectivity in two newt species (Lissotriton montandoni and L. vulgaris). Mol Ecol 2023; 32:4515-4530. [PMID: 35593303 DOI: 10.1111/mec.16543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 03/28/2022] [Accepted: 04/04/2022] [Indexed: 11/30/2022]
Abstract
Ecologically distinct species may respond to landscape changes in different ways. In addition to basic ecological data, the extent of the geographic range has been successfully used as an indicator of species sensitivity to anthropogenic landscapes, with widespread species usually found to be less sensitive compared to range-restricted species. In this study, we investigate connectivity patterns of two closely related but ecologically distinct newt species - the range-restricted, Lissotriton montandoni and the widespread, L. vulgaris - using genomic data, a highly replicated setting (six geographic regions per species), and tools from landscape genetics. Our results show the importance of forest for connectivity in both species, but at the same time suggest differential use of forested habitat, with L. montandoni and L. vulgaris showing the highest connectivity at forest-core and forest-edges, respectively. Anthropogenic landscapes (i.e., higher crop- or urban-cover) increased resistance in both species, but the effect was one to three orders of magnitude stronger in L. montandoni than in L. vulgaris. This result is consistent with a view of L. vulgaris as an ecological generalist. Even so, currently, the negative impact of anthropogenic landscapes is mainly seen in connectivity among L. vulgaris populations, which show significantly stronger isolation and lower effective sizes relative to L. montandoni. Overall, this study emphasizes how habitat destruction is compromising genetic connectivity not only in endemic, range-restricted species of conservation concern but also in widespread generalist species, despite their comparatively lower sensitivity to anthropogenic landscape changes.
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Affiliation(s)
- Bernardo Antunes
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Clara Figueiredo-Vázquez
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | | | - Maciej Pabijan
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Piotr Zieliński
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Wiesław Babik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
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3
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Portinha B, Avril A, Bernasconi C, Helanterä H, Monaghan J, Seifert B, Sousa VC, Kulmuni J, Nouhaud P. Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European ranges. Mol Ecol 2022; 31:3416-3431. [PMID: 35460311 PMCID: PMC9320829 DOI: 10.1111/mec.16481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 11/30/2022]
Abstract
The application of demographic history modelling and inference to the study of divergence between species has become a cornerstone of speciation genomics. Speciation histories are usually reconstructed by analysing single populations from each species, assuming that the inferred population history represents the actual speciation history. However, this assumption may not be met when species diverge with gene flow, for example, when secondary contact may be confined to specific geographic regions. Here, we tested whether divergence histories inferred from heterospecific populations may vary depending on their geographic locations, using the two wood ant species Formica polyctena and F. aquilonia. We performed whole‐genome resequencing of 20 individuals sampled in multiple locations across the European ranges of both species. Then, we reconstructed the histories of distinct heterospecific population pairs using a coalescent‐based approach. Our analyses always supported a scenario of divergence with gene flow, suggesting that divergence started in the Pleistocene (c. 500 kya) and occurred with continuous asymmetrical gene flow from F. aquilonia to F. polyctena until a recent time, when migration became negligible (2–19 kya). However, we found support for contemporary gene flow in a sympatric pair from Finland, where the species hybridise, but no signature of recent bidirectional gene flow elsewhere. Overall, our results suggest that divergence histories reconstructed from a few individuals may be applicable at the species level. Nonetheless, the geographical context of populations chosen to represent their species should be taken into account, as it may affect estimates of migration rates between species when gene flow is spatially heterogeneous.
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Affiliation(s)
- Beatriz Portinha
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,cE3c, Centre for Ecology, Evolution and Environmental changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Edifício C2, 1749-016, Lisboa, Portugal
| | - Amaury Avril
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | | | - Heikki Helanterä
- Ecology and Genetics research unit, University of Oulu, PO Box 3000, 90014, Oulu, Finland
| | | | | | - Vitor C Sousa
- cE3c, Centre for Ecology, Evolution and Environmental changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Edifício C2, 1749-016, Lisboa, Portugal
| | - Jonna Kulmuni
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
| | - Pierre Nouhaud
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
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4
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Nadachowska‐Brzyska K, Konczal M, Babik W. Navigating the temporal continuum of effective population size. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13740] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | | | - Wieslaw Babik
- Jagiellonian University in Kraków Faculty of Biology Institute of Environmental Sciences Kraków Poland
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5
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Sequeira F, Bessa-Silva A, Tarroso P, Sousa-Neves T, Vallinoto M, Gonçalves H, Martínez-Solano I. Discordant patterns of introgression across a narrow hybrid zone between two cryptic lineages of an Iberian endemic newt. J Evol Biol 2019; 33:202-216. [PMID: 31677317 DOI: 10.1111/jeb.13562] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 10/15/2019] [Accepted: 10/25/2019] [Indexed: 11/30/2022]
Abstract
The study of natural hybrid zones can illuminate aspects of lineage divergence and speciation in morphologically cryptic taxa. We studied a hybrid zone between two highly divergent but morphologically similar lineages (south-western and south-eastern) of the Iberian endemic Bosca's newt (Lissotriton boscai) in SW Iberia with a multilocus dataset (microsatellites, nuclear and mitochondrial genes). STRUCTURE and NEWHYBRIDS analyses retrieved few admixed individuals, which classified as backcrosses involving parental individuals of the south-western lineage. Our results show asymmetric introgression of mtDNA beyond the contact from this lineage into the south-eastern lineage. Analysis of nongeographic introgression patterns revealed asymmetries in the direction of introgression, but except for mtDNA, we did not find evidence for nonconcordant introgression patterns across nuclear loci. Analysis of a 150-km transect across the hybrid zone showed broadly coincident cline widths (ca. 3.2-27.9 km), and concordant cline centres across all markers, except for mtDNA that is displaced ca. 60 km northward. Results from ecological niche modelling show that the hybrid zone is in a climatically homogenous area with suitable habitat for the species, suggesting that contact between the two lineages is unlikely to occur further south as their distributions are currently separated by an extensive area of unfavourable habitat. Taken together, our findings suggest the genetic structure of this hybrid zone results from the interplay of historical (biogeographic) and population-level processes. The narrowness and coincidence of genetic clines can be explained by weak selection against hybrids and reflect a degree of reproductive isolation that is consistent with cryptic speciation.
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Affiliation(s)
- Fernando Sequeira
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal
| | - Adam Bessa-Silva
- Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Pará, Brasil
| | - Pedro Tarroso
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal
| | - Tiago Sousa-Neves
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal.,Museu Paraense Emílio Goeldi, Coordenação de Zoologia, Pará, Brasil
| | - Marcelo Vallinoto
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal.,Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Pará, Brasil
| | - Helena Gonçalves
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal.,Museu de História Natural e da Ciência, Universidade do Porto, Porto, Portugal
| | - Iñigo Martínez-Solano
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC (MNCN-CSIC), Madrid, Spain
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6
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Dudek K, Gaczorek TS, Zieliński P, Babik W. Massive introgression of major histocompatibility complex (MHC) genes in newt hybrid zones. Mol Ecol 2019; 28:4798-4810. [PMID: 31574568 DOI: 10.1111/mec.15254] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/25/2019] [Accepted: 09/26/2019] [Indexed: 12/22/2022]
Abstract
Variation in the vertebrate major histocompatibility complex (MHC) genes is crucial for fighting pathogen assault. Because new alleles confer a selective advantage, MHC should readily introgress between species, even under limited hybridization. Using replicated transects through two hybrid zones between strongly reproductively isolated European newts, Lissotriton montandoni and L. vulgaris, we demonstrated recent and ongoing MHC class I and II introgression in the Carpathian region. The extent of introgression correlated with the age of contact. In the older zone, MHC similarity between species within transects exceeded similarity between transects within species, implying pervasive introgression - a massive exchange of MHC genes, not limited to specific variants. In simulations, the observed pattern emerged under the combined action of balancing selection and hybridization, but not when these processes acted separately. Thus, massive introgression at advanced stages of divergence can introduce novel and restore previously lost MHC variation, boosting the adaptive potential of hybridizing taxa. In consequence, MHC genes may be the last to stop introgressing between incipient species.
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Affiliation(s)
- Katarzyna Dudek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Tomasz S Gaczorek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Piotr Zieliński
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Wiesław Babik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
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7
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Zieliński P, Dudek K, Arntzen JW, Palomar G, Niedzicka M, Fijarczyk A, Liana M, Cogǎlniceanu D, Babik W. Differential introgression across newt hybrid zones: Evidence from replicated transects. Mol Ecol 2019; 28:4811-4824. [DOI: 10.1111/mec.15251] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/16/2019] [Accepted: 09/19/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Piotr Zieliński
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
| | | | - Gemma Palomar
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
| | - Marta Niedzicka
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
| | - Anna Fijarczyk
- Département de Biologie Faculté des Sciences et de génie Université Laval Québec QC Canada
| | | | - Dan Cogǎlniceanu
- Faculty of Natural Sciences and Agricultural Sciences University Ovidius Constanţa Constanţa Romania
| | - Wiesław Babik
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
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8
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Fijarczyk A, Dudek K, Niedzicka M, Babik W. Balancing selection and introgression of newt immune-response genes. Proc Biol Sci 2018; 285:20180819. [PMID: 30111606 PMCID: PMC6111169 DOI: 10.1098/rspb.2018.0819] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 07/18/2018] [Indexed: 12/20/2022] Open
Abstract
The importance of interspecific introgression as a source of adaptive variation is increasingly recognized. Theory predicts that beneficial genetic variants cross species boundaries easily even when interspecific hybridization is rare and gene flow is strongly constrained throughout the genome. However, it remains unclear whether certain classes of genes are particularly prone to adaptive introgression. Genes affected by balancing selection (BS) may constitute such a class, because forms of BS that favour novel, initially rare alleles, should facilitate introgression. We tested this hypothesis in hybridizing newts by comparing 13 genes with signatures of BS, in particular an excess of common non-synonymous polymorphisms, to the genomic background (154 genes). Parapatric hybridizing taxa were less differentiated in BS candidate genes than more closely related allopatric lineages, while the opposite was observed in the control genes. Coalescent and forward simulations that explored neutral and BS scenarios under isolation and migration showed that processes other than differential gene flow are unlikely to account for this pattern. We conclude that BS, probably involving a form of novel allele advantage, promotes introgression. This mechanism may be a source of adaptively relevant variation in hybridizing species over prolonged periods.
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Affiliation(s)
- Anna Fijarczyk
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
- Institut de Biologie Intégrative et des Systèmes, Département de Biologie, Université Laval, 1030, Avenue de la Médecine, Québec, Canada G1V 0A6
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Marta Niedzicka
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
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9
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Wielstra B, Canestrelli D, Cvijanović M, Denoël M, Fijarczyk A, Jablonski D, Liana M, Naumov B, Olgun K, Pabijan M, Pezzarossa A, Popgeorgiev G, Salvi D, Si Y, Sillero N, Sotiropoulos K, Zieliński P, Babik W. The distributions of the six species constituting the smooth newt species complex (Lissotriton vulgaris sensu lato and L. montandoni) – an addition to the New Atlas of Amphibians and Reptiles of Europe. AMPHIBIA-REPTILIA 2018. [DOI: 10.1163/15685381-17000128] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Abstract
The ‘smooth newt’, the taxon traditionally referred to as Lissotriton vulgaris, consists of multiple morphologically distinct taxa. Given the uncertainty concerning the validity and rank of these taxa, L. vulgaris sensu lato has often been treated as a single, polytypic species. A recent study, driven by genetic data, proposed to recognize five species, L. graecus, L. kosswigi, L. lantzi, L. schmidtleri and a more restricted L. vulgaris. The Carpathian newt L. montandoni was confirmed to be a closely related sister species. We propose to refer to this collective of six Lissotriton species as the smooth newt or Lissotriton vulgaris species complex. Guided by comprehensive genomic data from throughout the range of the smooth newt species complex we 1) delineate the distribution ranges, 2) provide a distribution database, and 3) produce distribution maps according to the format of the New Atlas of Amphibians and Reptiles of Europe, for the six constituent species. This allows us to 4) highlight regions where more research is needed to determine the position of contact zones.
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Affiliation(s)
- Ben Wielstra
- 1Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- 2Department of Animal and Plant Sciences, University of Sheffield, S10 2TN Sheffield, UK
- 3Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
| | - Daniele Canestrelli
- 4Department of Ecological and Biological Science, Tuscia University, 01100 Viterbo, Italy
| | - Milena Cvijanović
- 5Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković”, University of Belgrade, Bul. Despota Stefana 142, 11060 Belgrade, Serbia
| | - Mathieu Denoël
- 6Laboratory of Fish and Amphibian Ethology, Behavioural Biology Unit, Freshwater and OCeanic science Unit of reSearch (FOCUS), University of Liège, Liège, Belgium
| | - Anna Fijarczyk
- 7Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
- 8Institut de Biologie Intégrative et des Systèmes, Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, Québec, QC, Canada
| | - Daniel Jablonski
- 9Department of Zoology, Comenius University in Bratislava Mlynská dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | | | - Borislav Naumov
- 11Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Gagarin Street, 1113 Sofia, Bulgaria
| | - Kurtuluş Olgun
- 12Department of Biology, Faculty of Arts and Sciences, Adnan Menderes University, 09010 Aydın, Turkey
| | - Maciej Pabijan
- 13Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, ul. Gronostajowa 9, 30-387 Kraków, Poland
| | - Alice Pezzarossa
- 4Department of Ecological and Biological Science, Tuscia University, 01100 Viterbo, Italy
| | - Georgi Popgeorgiev
- 14National Museum of Natural History, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd, 1000 Sofia, Bulgaria
| | - Daniele Salvi
- 15Department of Health, Life and Environmental Sciences, University of L’Aquila, Via Vetoio, 67100 Coppito, L’Aquila, Italy
- 16CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Yali Si
- 17Ministry of Education Key Laboratory for Earth System Modeling, and Department of Earth System Science, Tsinghua University, Beijing, China
- 18Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, 621 Charles E. Yong Drive South, Los Angeles, CA 90095, USA
| | - Neftalí Sillero
- 19CICGE – Centro de Investigação em Ciências Geo-Espaciais, Observatório Astronómico Prof. Manuel de Barros, Alameda do Monte da Virgem, 4430-146 Vila Nova de Gaia, Portugal
| | - Konstantinos Sotiropoulos
- 20Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Greece
| | - Piotr Zieliński
- 7Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Wiesław Babik
- 7Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
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10
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Surmounting the Large-Genome “Problem” for Genomic Data Generation in Salamanders. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_36] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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11
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Pabijan M, Zieliński P, Dudek K, Stuglik M, Babik W. Isolation and gene flow in a speciation continuum in newts. Mol Phylogenet Evol 2017; 116:1-12. [PMID: 28797693 DOI: 10.1016/j.ympev.2017.08.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/04/2017] [Accepted: 08/06/2017] [Indexed: 02/06/2023]
Abstract
Because reproductive isolation often evolves gradually, differentiating lineages may retain the potential for genetic exchange for prolonged periods, providing an opportunity to quantify and to understand the fundamental role of gene flow during speciation. Here we delimit evolutionary lineages, reconstruct the phylogeny and infer gene flow in newts of the Lissotriton vulgaris species complex based on 74 nuclear markers sampled from 127 localities. We demonstrate that distinct lineages along the speciation continuum in newts exchange nontrivial amounts of genes, affecting their evolutionary trajectories. By integrating a wide array of methods, we delimit nine evolutionary lineages and show that two principal factors have driven their genetic differentiation: time since the last common ancestor determining levels of shared ancestral polymorphism, and shifts in geographic distributions determining the extent of secondary contact. Post-divergence gene flow, indicative of evolutionary non-independence, has been most extensive in Central Europe, while four southern European lineages have acquired the population-genetic hallmarks of independent species (L. graecus, L. kosswigi, L. lantzi, L. schmidtleri). We obtained strong statistical support for widespread mtDNA introgression following secondary contact, previously suggested by discordance between mtDNA phylogeny and morphology. Our study reveals long-term evolutionary persistence of evolutionary lineages that may periodically exchange genes with one another: although some of these lineages may become extinct or fuse, others will acquire complete reproductive isolation and will carry signatures of this complex history in their genomes.
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Affiliation(s)
- Maciej Pabijan
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland.
| | - Piotr Zieliński
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland.
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland.
| | - Michał Stuglik
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland; Scotland's Rural College, Integrative Animal Sciences, Easter Bush Campus, Midlothian EH25 9RG, Scotland, UK.
| | - Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland.
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12
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Wielstra B, ZieliŃski P, Babik W. The Carpathians hosted extra-Mediterranean refugia-within-refugia during the Pleistocene Ice Age: genomic evidence from two newt genera. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx087] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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13
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Linkage Map of Lissotriton Newts Provides Insight into the Genetic Basis of Reproductive Isolation. G3-GENES GENOMES GENETICS 2017; 7:2115-2124. [PMID: 28500054 PMCID: PMC5499121 DOI: 10.1534/g3.117.041178] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Linkage maps are widely used to investigate structure, function, and evolution of genomes. In speciation research, maps facilitate the study of the genetic architecture of reproductive isolation by allowing identification of genomic regions underlying reduced fitness of hybrids. Here we present a linkage map for European newts of the Lissotriton vulgaris species complex, constructed using two families of F2 L. montandoni × L. vulgaris hybrids. The map consists of 1146 protein-coding genes on 12 linkage groups, equal to the haploid chromosome number, with a total length of 1484 cM (1.29 cM per marker). It is notably shorter than two other maps available for salamanders, but the differences in map length are consistent with cytogenetic estimates of the number of chiasmata per chromosomal arm. Thus, large salamander genomes do not necessarily translate into long linkage maps, as previously suggested. Consequently, salamanders are an excellent model to study evolutionary consequences of recombination rate variation in taxa with large genomes and a similar number of chromosomes. A complex pattern of transmission ratio distortion (TRD) was detected: TRD occurred mostly in one family, in one breeding season, and was clustered in two genomic segments. This is consistent with environment-dependent mortality of individuals carrying L. montandoni alleles in these two segments and suggests a role of TRD blocks in reproductive isolation. The reported linkage map will empower studies on the genomic architecture of divergence and interactions between the genomes of hybridizing newts.
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Fijarczyk A, Dudek K, Babik W. Selective Landscapes in newt Immune Genes Inferred from Patterns of Nucleotide Variation. Genome Biol Evol 2016; 8:3417-3432. [PMID: 27702815 PMCID: PMC5203778 DOI: 10.1093/gbe/evw236] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Host–pathogen interactions may result in either directional selection or in pressure for the maintenance of polymorphism at the molecular level. Hence signatures of both positive and balancing selection are expected in immune genes. Because both overall selective pressure and specific targets may differ between species, large-scale population genomic studies are useful in detecting functionally important immune genes and comparing selective landscapes between taxa. Such studies are of particular interest in amphibians, a group threatened worldwide by emerging infectious diseases. Here, we present an analysis of polymorphism and divergence of 634 immune genes in two lineages of Lissotriton newts: L. montandoni and L. vulgaris graecus. Variation in newt immune genes has been shaped predominantly by widespread purifying selection and strong evolutionary constraint, implying long-term importance of these genes for functioning of the immune system. The two evolutionary lineages differ in the overall strength of purifying selection which can partially be explained by demographic history but may also signal differences in long-term pathogen pressure. The prevalent constraint notwithstanding, 23 putative targets of positive selection and 11 putative targets of balancing selection were identified. The latter were detected by composite tests involving the demographic model and further validated in independent population samples. Putative targets of balancing selection encode proteins which may interact closely with pathogens but include also regulators of immune response. The identified candidates will be useful for testing whether genes affected by balancing selection are more prone to interspecific introgression than other genes in the genome.
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Affiliation(s)
- Anna Fijarczyk
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Wieslaw Babik
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
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Stuglik MT, Babik W. Genomic heterogeneity of historical gene flow between two species of newts inferred from transcriptome data. Ecol Evol 2016; 6:4513-25. [PMID: 27386093 PMCID: PMC4930998 DOI: 10.1002/ece3.2152] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 04/02/2016] [Accepted: 04/04/2016] [Indexed: 01/31/2023] Open
Abstract
The role of gene flow in species formation is a major unresolved issue in speciation biology. Progress in this area requires information on the long-term patterns of gene flow between diverging species. Here, we used thousands of single-nucleotide polymorphisms derived from transcriptome resequencing and a method modeling the joint frequency spectrum of these polymorphisms to reconstruct patterns of historical gene flow between two Lissotriton newts: L. vulgaris (Lv) and L. montandoni (Lm). We tested several models of divergence including complete isolation and various scenarios of historical gene flow. The model of secondary contact received the highest support. According to this model, the species split from their common ancestor ca. 5.5 million years (MY) ago, evolved in isolation for ca. 2 MY, and have been exchanging genes for the last 3.5 MY Demographic changes have been inferred in both species, with the current effective population size of ca. 0.7 million in Lv and 0.2 million in Lm. The postdivergence gene flow resulted in two-directional introgression which affected the genomes of both species, but was more pronounced from Lv to Lm. Interestingly, we found evidence for genomic heterogeneity of interspecific gene flow. This study demonstrates the complexity of long-term gene flow between distinct but incompletely reproductively isolated taxa which divergence was initiated millions of years ago.
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Affiliation(s)
- Michał T. Stuglik
- Institute of Environmental SciencesJagiellonian UniversityGronostajowa 730387KrakowPoland
| | - Wiesław Babik
- Institute of Environmental SciencesJagiellonian UniversityGronostajowa 730387KrakowPoland
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