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Caeiro-Dias G, Brelsford A, Meneses-Ribeiro M, Crochet PA, Pinho C. Hybridization in late stages of speciation: Strong but incomplete genome-wide reproductive isolation and 'large Z-effect' in a moving hybrid zone. Mol Ecol 2023. [PMID: 37316984 DOI: 10.1111/mec.17035] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/27/2023] [Accepted: 05/12/2023] [Indexed: 06/16/2023]
Abstract
In organisms reproducing sexually, speciation occurs when increasing divergence results in pre- or post-zygotic reproductive isolation between lineages. Studies focusing on reproductive isolation origin in early stages of speciation are common and many rely on genomic scans to infer introgression providing limited information on the genomic architecture of reproductive isolation long-term maintenance. This study analyses a natural hybrid zone between two species in a late stage of speciation. We used ddRADseq genotyping in the contact between Podarcis bocagei and P. carbonelli to examine admixture extent, analyse hybrid zone stability and assess genome-wide variation in selection against introgression. We confirmed strong but incomplete reproductive isolation in a bimodal hybrid zone. New findings revealed population genetic structure within P. carbonelli in the contact zone; geographical and genomic clines analysis suggested strong selection against gene flow, but a relatively small proportion of the loci can introgress, mostly within the narrow contact zone. However, geographical clines revealed that a few introgressed loci show signs of potential positive selection, particularly into P. bocagei. Geographical clines also detected a signal of hybrid zone movement towards P. bocagei distribution. Genomic cline analysis revealed heterogeneous patterns of introgression among loci within the syntopy zone, but the majority maintain a strong association with the genomic background of origin. However, incongruences between both cline approaches were found, potentially driven by confounding effects on genomic clines. Last, an important role of the Z chromosome in reproductive isolation is suggested. Importantly, overall patterns of restricted introgression seem to result from numerous strong intrinsic barriers across the genome.
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Affiliation(s)
- Guilherme Caeiro-Dias
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France
| | - Alan Brelsford
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Biology Department, University of California Riverside, Riverside, California, USA
| | - Mariana Meneses-Ribeiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Pierre-André Crochet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Catarina Pinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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2
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Mao J, Liang Y, Wang X, Zhang D. Comparison of plastid genomes and ITS of two sister species in Gentiana and a discussion on potential threats for the endangered species from hybridization. BMC PLANT BIOLOGY 2023; 23:101. [PMID: 36800941 PMCID: PMC9940437 DOI: 10.1186/s12870-023-04088-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Gentiana rigescens Franchet is an endangered medicinal herb from the family Gentianaceae with medicinal values. Gentiana cephalantha Franchet is a sister species to G. rigescens possessing similar morphology and wider distribution. To explore the phylogeny of the two species and reveal potential hybridization, we adopted next-generation sequencing technology to acquire their complete chloroplast genomes from sympatric and allopatric distributions, as along with Sanger sequencing to produce the nrDNA ITS sequences. RESULTS The plastid genomes were highly similar between G. rigescens and G. cephalantha. The lengths of the genomes ranged from 146,795 to 147,001 bp in G. rigescens and from 146,856 to 147,016 bp in G. cephalantha. All genomes consisted of 116 genes, including 78 protein-coding genes, 30 tRNA genes, four rRNA genes and four pseudogenes. The total length of the ITS sequence was 626 bp, including six informative sites. Heterozygotes occurred intensively in individuals from sympatric distribution. Phylogenetic analysis was performed based on chloroplast genomes, coding sequences (CDS), hypervariable sequences (HVR), and nrDNA ITS. Analysis based on all the datasets showed that G. rigescens and G. cephalantha formed a monophyly. The two species were well separated in phylogenetic trees using ITS, except for potential hybrids, but were mixed based on plastid genomes. This study supports that G. rigescens and G. cephalantha are closely related, but independent species. However, hybridization was confirmed to occur frequently between G. rigescens and G. cephalantha in sympatric distribution owing to the lack of stable reproductive barriers. Asymmetric introgression, along with hybridization and backcrossing, may probably lead to genetic swamping and even extinction of G. rigescens. CONCLUSION G. rigescens and G. cephalantha are recently diverged species which might not have undergone stable post-zygotic isolation. Though plastid genome shows obvious advantage in exploring phylogenetic relationships of some complicated genera, the intrinsic phylogeny was not revealed because of matrilineal inheritance here; nuclear genomes or regions are hence crucial for uncovering the truth. As an endangered species, G. rigescens faces serious threats from both natural hybridization and human activities; therefore, a balance between conservation and utilization of the species is extremely critical in formulating conservation strategies.
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Affiliation(s)
- Jiuyang Mao
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China
| | - Yuze Liang
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China
| | - Xue Wang
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China
| | - Dequan Zhang
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China.
- Yunnan Key Laboratory of Screening and Research on Anti-pathogenic Plant Resources from Western Yunnan (Cultivation), Dali, 671000, Yunnan, China.
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3
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Pinho C, Kaliontzopoulou A, Ferreira CA, Gama J. Identification of morphologically cryptic species with computer vision models: wall lizards (Squamata: Lacertidae: Podarcis) as a case study. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Automated image classification is a thriving field of machine learning, and various successful applications dealing with biological images have recently emerged. In this work, we address the ability of these methods to identify species that are difficult to tell apart by humans due to their morphological similarity. We focus on distinguishing species of wall lizards, namely those belonging to the Podarcis hispanicus species complex, which constitutes a well-known example of cryptic morphological variation. We address two classification experiments: (1) assignment of images of the morphologically relatively distinct P. bocagei and P. lusitanicus; and (2) distinction between the overall more cryptic nine taxa that compose this complex. We used four datasets (two image perspectives and individuals of the two sexes) and three deep-learning models to address each problem. Our results suggest a high ability of the models to identify the correct species, especially when combining predictions from different perspectives and models (accuracy of 95.9% and 97.1% for females and males, respectively, in the two-class case; and of 91.2% to 93.5% for females and males, respectively, in the nine-class case). Overall, these results establish deep-learning models as an important tool for field identification and monitoring of cryptic species complexes, alleviating the burden of expert or genetic identification.
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Affiliation(s)
- Catarina Pinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto , 4485-661 Vairão , Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO , Campus de Vairão, 4485-661 Vairão , Portugal
| | - Antigoni Kaliontzopoulou
- Department of Evolutionary Biology, Ecology and Environmental Sciences, and Biodiversity Research Institute (IRBio), Universitat de Barcelona , E-08028 Barcelona, Catalonia , Spain
| | | | - João Gama
- INESC TEC , Rua Dr. Roberto Frias, 4200-465 Porto , Portugal
- FEP - University of Porto , Rua Dr. Roberto Frias, 4200-464 Porto , Portugal
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4
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Freitas S, Westram AM, Schwander T, Arakelyan M, Ilgaz Ç, Kumlutas Y, Harris DJ, Carretero MA, Butlin RK. Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. Evolution 2022; 76:899-914. [PMID: 35323995 PMCID: PMC9324800 DOI: 10.1111/evo.14462] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Hybridization is a common evolutionary process with multiple possible outcomes. In vertebrates, interspecific hybridization has repeatedly generated parthenogenetic hybrid species. However, it is unknown whether the generation of parthenogenetic hybrids is a rare outcome of frequent hybridization between sexual species within a genus or the typical outcome of rare hybridization events. Darevskia is a genus of rock lizards with both hybrid parthenogenetic and sexual species. Using capture sequencing, we estimate phylogenetic relationships and gene flow among the sexual species, to determine how introgressive hybridization relates to the origins of parthenogenetic hybrids. We find evidence for widespread hybridization with gene flow, both between recently diverged species and deep branches. Surprisingly, we find no signal of gene flow between parental species of the parthenogenetic hybrids, suggesting that the parental pairs were either reproductively or geographically isolated early in their divergence. The generation of parthenogenetic hybrids in Darevskia is, then, a rare outcome of the total occurrence of hybridization within the genus, but the typical outcome when specific species pairs hybridize. Our results question the conventional view that parthenogenetic lineages are generated by hybridization in a window of divergence. Instead, they suggest that some lineages possess specific properties that underpin successful parthenogenetic reproduction.
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Affiliation(s)
- Susana Freitas
- Department of Ecology and EvolutionUniversity of LausanneLausanneCH‐1015Switzerland
| | - Anja Marie Westram
- IST AustriaKlosterneuburg3400Austria,Faculty of Biosciences and AquacultureNord UniversityBodøN‐8049Norway
| | - Tanja Schwander
- Department of Ecology and EvolutionUniversity of LausanneLausanneCH‐1015Switzerland
| | | | - Çetin Ilgaz
- Department of Biology, Faculty of ScienceDokuz Eylül Universityİzmir35400Turkey,Fauna and Flora Research CentreDokuz Eylül Universityİzmir35610Turkey
| | - Yusuf Kumlutas
- Department of Biology, Faculty of ScienceDokuz Eylül Universityİzmir35400Turkey,Fauna and Flora Research CentreDokuz Eylül Universityİzmir35610Turkey
| | - David James Harris
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIOUniversidade do PortoCampus de VairãoVairão4485–661Portugal
| | - Miguel A. Carretero
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIOUniversidade do PortoCampus de VairãoVairão4485–661Portugal,Departamento de Biologia, Faculdade de CiênciasUniversidade do PortoPorto4169‐007Portugal
| | - Roger K. Butlin
- Department of Animal and Plant SciencesThe University of SheffieldSheffieldS10 2TNUnited Kingdom,Department of Marine SciencesUniversity of GothenburgGothenburgSE‐40530Sweden
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5
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Aguilar P, Andrade P, Afonso S, Carretero MÁ, Pérez i de Lanuza G, Pinho C. No genomic repercussions of assortative pairing in a colour polymorphic lizard. J Evol Biol 2022; 35:648-656. [DOI: 10.1111/jeb.13990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 02/01/2022] [Accepted: 02/09/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Prem Aguilar
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Universidade do Porto Porto Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning CIBIO Campus de Vairão Vairão Portugal
- Departamento de Biologia Faculdade de Ciências da Universidade do Porto Porto Portugal
| | - Pedro Andrade
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Universidade do Porto Porto Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning CIBIO Campus de Vairão Vairão Portugal
| | - Sandra Afonso
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Universidade do Porto Porto Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning CIBIO Campus de Vairão Vairão Portugal
| | - Miguel Á. Carretero
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Universidade do Porto Porto Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning CIBIO Campus de Vairão Vairão Portugal
- Departamento de Biologia Faculdade de Ciências da Universidade do Porto Porto Portugal
| | - Guillem Pérez i de Lanuza
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Universidade do Porto Porto Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning CIBIO Campus de Vairão Vairão Portugal
- Ethology Lab Institut Cavanilles de Biodiversitat i Biologia Evolutiva Universitat de València València Spain
| | - Catarina Pinho
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Universidade do Porto Porto Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning CIBIO Campus de Vairão Vairão Portugal
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6
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Yang W, Feiner N, Salvi D, Laakkonen H, Jablonski D, Pinho C, Carretero MA, Sacchi R, Zuffi MAL, Scali S, Plavos K, Pafilis P, Poulakakis N, Lymberakis P, Jandzik D, Schulte U, Aubret F, Badiane A, Perez I de Lanuza G, Abalos J, While GM, Uller T. Population genomics of wall lizards reflects the dynamic history of the Mediterranean Basin. Mol Biol Evol 2021; 39:6413643. [PMID: 34718699 PMCID: PMC8760935 DOI: 10.1093/molbev/msab311] [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] [Indexed: 11/15/2022] Open
Abstract
The Mediterranean Basin has experienced extensive change in geology and climate over the past six million years. Yet, the relative importance of key geological events for the distribution and genetic structure of the Mediterranean fauna remains poorly understood. Here, we use population genomic and phylogenomic analyses to establish the evolutionary history and genetic structure of common wall lizards (Podarcis muralis). This species is particularly informative because, in contrast to other Mediterranean lizards, it is widespread across the Iberian, Italian, and Balkan Peninsulas, and in extra-Mediterranean regions. We found strong support for six major lineages within P. muralis, which were largely discordant with the phylogenetic relationship of mitochondrial DNA. The most recent common ancestor of extant P. muralis was likely distributed in the Italian Peninsula, and experienced an “Out-of-Italy” expansion following the Messinian salinity crisis (∼5 Mya), resulting in the differentiation into the extant lineages on the Iberian, Italian, and Balkan Peninsulas. Introgression analysis revealed that both inter- and intraspecific gene flows have been pervasive throughout the evolutionary history of P. muralis. For example, the Southern Italy lineage has a hybrid origin, formed through admixture between the Central Italy lineage and an ancient lineage that was the sister to all other P. muralis. More recent genetic differentiation is associated with the onset of the Quaternary glaciations, which influenced population dynamics and genetic diversity of contemporary lineages. These results demonstrate the pervasive role of Mediterranean geology and climate for the evolutionary history and population genetic structure of extant species.
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Affiliation(s)
- Weizhao Yang
- Department of Biology, Lund University, Lund, 223 62, Sweden
| | - Nathalie Feiner
- Department of Biology, Lund University, Lund, 223 62, Sweden
| | - Daniele Salvi
- Department of Health, Life and Environmental Sciences, University of L'Aquila, 67100, Italy Coppito L'Aquila
| | - Hanna Laakkonen
- Department of Biology, Lund University, Lund, 223 62, Sweden
| | - Daniel Jablonski
- Department of Zoology, Comenius University, Ilkovičova 6, 842 15, Slovakia in Bratislava, Bratislava
| | - Catarina Pinho
- CIBIO/InBIO Research Centre in Biodiversity and Genetic Resources, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Miguel A Carretero
- CIBIO/InBIO Research Centre in Biodiversity and Genetic Resources, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, R. Campo Alegre, s/n, Porto, 4169 - 007, Portugal
| | - Roberto Sacchi
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, 27100, Italy
| | - Marco A L Zuffi
- Museum Natural History, University of Pisa, Pisa, 56011, Italy
| | - Stefano Scali
- Museum of Natural History of Milan, Milano, 20121, Italy
| | | | - Panayiotis Pafilis
- National & Kapodistrian University of Athens, School of Science, Faculty of Biology, Panepistimiopolis 15701, Athens, Greece
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion, 71409, Greece.,Biology Department, School of Sciences and Engineering, University of Crete, Voutes University Campus, Heraklion, 70013, Greece.,Institute of Molecular Biology and Biotechnology (IMBB), Heraklion, 70013, GreeceFoundation for Research and Technology-Hellas (FORTH)
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion, 71409, Greece
| | - David Jandzik
- Department of Zoology, Comenius University, Ilkovičova 6, 842 15, Slovakia in Bratislava, Bratislava
| | - Ulrich Schulte
- Büro für Faunistische Gutachten-Dr. Ulrich Schulte, Kaiserstraße 2, Borgholzhausen, 33829, Germany
| | - Fabien Aubret
- Station d'Ecologie Théorique et Expérimentale, CNRS, 09200, Moulis, France.,School of Molecular and Life Sciences, Curtin University, WA, 6102, Australia
| | - Arnaud Badiane
- IMBE, Aix-Marseille Université, Avignon Université, CNRS, IRD, Marseille, France
| | - Guillem Perez I de Lanuza
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Valencia, APT. 22085, 46071, Spain
| | - Javier Abalos
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Valencia, APT. 22085, 46071, Spain
| | - Geoffrey M While
- School of Natural Sciences, University of Tasmania, Sandy Bay, Tasmania, 7005, Australia
| | - Tobias Uller
- Department of Biology, Lund University, Lund, 223 62, Sweden
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7
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Mangiacotti M, Baeckens S, Scali S, Martín J, Van Damme R, Sacchi R. Evolutionary and biogeographical support for species-specific proteins in lizard chemical signals. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The species-specific components of animal signals can facilitate species recognition and reduce the risks of mismatching and interbreeding. Nonetheless, empirical evidence for species-specific components in chemical signals is scarce and mostly limited to insect pheromones. Based on the proteinaceous femoral gland secretions of 36 lizard species (Lacertidae), we examine the species-specific component potential of proteins in lizard chemical signals. By quantitative comparison of the one-dimensional electrophoretic patterns of the protein fraction from femoral gland secretions, we first reveal that the protein composition is species specific, accounting for a large part of the observed raw variation and allowing us to discriminate species on this basis. Secondly, we find increased protein pattern divergence in sympatric, closely related species. Thirdly, lizard protein profiles show a low phylogenetic signal, a recent and steep increase in relative disparity and a high rate of evolutionary change compared with non-specifically signal traits (i.e. body size and shape). Together, these findings provide support for the species specificity of proteins in the chemical signals of a vertebrate lineage.
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Affiliation(s)
- Marco Mangiacotti
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
- Museo di Storia Naturale di Milano, Milano, Italy
| | - Simon Baeckens
- Laboratory for Functional Morphology, Department of Biology, University of Antwerp, Wilrijk, Belgium
| | | | - José Martín
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Raoul Van Damme
- Laboratory for Functional Morphology, Department of Biology, University of Antwerp, Wilrijk, Belgium
| | - Roberto Sacchi
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
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