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Pang XX, Zhang DY. Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information. Syst Biol 2024; 73:207-222. [PMID: 38224495 PMCID: PMC11129598 DOI: 10.1093/sysbio/syad077] [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: 05/01/2023] [Revised: 12/17/2023] [Accepted: 12/27/2023] [Indexed: 01/17/2024] Open
Abstract
In recent years, the study of hybridization and introgression has made significant progress, with ghost introgression-the transfer of genetic material from extinct or unsampled lineages to extant species-emerging as a key area for research. Accurately identifying ghost introgression, however, presents a challenge. To address this issue, we focused on simple cases involving 3 species with a known phylogenetic tree. Using mathematical analyses and simulations, we evaluated the performance of popular phylogenetic methods, including HyDe and PhyloNet/MPL, and the full-likelihood method, Bayesian Phylogenetics and Phylogeography (BPP), in detecting ghost introgression. Our findings suggest that heuristic approaches relying on site-pattern counts or gene-tree topologies struggle to differentiate ghost introgression from introgression between sampled non-sister species, frequently leading to incorrect identification of donor and recipient species. The full-likelihood method BPP uses multilocus sequence alignments directly-hence taking into account both gene-tree topologies and branch lengths, by contrast, is capable of detecting ghost introgression in phylogenomic datasets. We analyzed a real-world phylogenomic dataset of 14 species of Jaltomata (Solanaceae) to showcase the potential of full-likelihood methods for accurate inference of introgression.
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Affiliation(s)
- Xiao-Xu Pang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Da-Yong Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
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2
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Otalora K, Riera JL, Tavecchia G, Rotger A, Igual JM, Trotta JP, Baldo L. Population genetics and phylogeographic history of the insular lizard Podarcis lilfordi (Gunther, 1874) from the Balearic Islands based on genome-wide polymorphic data. Ecol Evol 2024; 14:e11407. [PMID: 38799398 PMCID: PMC11116764 DOI: 10.1002/ece3.11407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/12/2024] [Accepted: 04/30/2024] [Indexed: 05/29/2024] Open
Abstract
Islands provide a great system to explore the processes that maintain genetic diversity and promote local adaptation. We explored the genomic diversity of the Balearic lizard Podarcis lilfordi, an endemic species characterized by numerous small insular populations with large phenotypic diversity. Using the newly available genome for this species, we characterized more than 300,000 SNPs, merging genotyping-by-sequencing (GBS) data with previously published restriction site-associated DNA sequencing (RAD-Seq) data, providing a dataset of 16 island populations (191 individuals) across the range of species distribution (Menorca, Mallorca, and Cabrera). Results indicate that each islet hosts a well-differentiated population (F ST = 0.247 ± 0.09), with no recent immigration/translocation events. Contrary to expectations, most populations harbor a considerable genetic diversity (mean nucleotide diversity, P i = 0.144 ± 0.021), characterized by overall low inbreeding values (F IS < 0.1). While the genetic diversity significantly decreased with decreasing islet surface, maintenance of substantial genetic diversity even in tiny islets suggests variable selection or other mechanisms that buffer genetic drift. Maximum-likelihood tree based on concatenated SNP data confirmed the existence of the two major independent lineages of Menorca and Mallorca/Cabrera. Multiple lines of evidence, including admixture and root testing, robustly placed the origin of the species in the Mallorca Island, rather than in Menorca. Outlier analysis mainly retrieved a strong signature of genome differentiation between the two major archipelagos, especially in the sexual chromosome Z. A set of proteins were target of multiple outliers and primarily associated with binding and catalytic activity, providing interesting candidates for future selection studies. This study provides the framework to explore crucial aspects of the genetic basis of phenotypic divergence and insular adaptation.
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Affiliation(s)
- Katherin Otalora
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Biology FacultyUniversity of Barcelona (UB)BarcelonaSpain
- Fundación FUNMAJO, EBA, RAIEC, Biodiversity BranchTunjaBoyacáColombia
| | - Joan Lluís Riera
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Biology FacultyUniversity of Barcelona (UB)BarcelonaSpain
| | - Giacomo Tavecchia
- Animal Demography and Ecology Unit (GEDA‐IMEDEA, CSIC‐UIB)EsporlesSpain
| | - Andreu Rotger
- Animal Demography and Ecology Unit (GEDA‐IMEDEA, CSIC‐UIB)EsporlesSpain
| | - José Manuel Igual
- Animal Demography and Ecology Unit (GEDA‐IMEDEA, CSIC‐UIB)EsporlesSpain
| | - Jean‐Remi Paul Trotta
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
| | - Laura Baldo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Biology FacultyUniversity of Barcelona (UB)BarcelonaSpain
- Institute for Research on Biodiversity (IRBio)University of Barcelona (UB)BarcelonaSpain
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3
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Escoriza D. Environmental colour pattern variation in Mediterranean Podarcis. BMC Ecol Evol 2024; 24:53. [PMID: 38658833 PMCID: PMC11044340 DOI: 10.1186/s12862-024-02242-1] [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: 01/11/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Lizards of the genus Podarcis are widespread in the Mediterranean region, including islands and island archipelagos. These small-bodied lizards have a predominantly protective green-brown colouration. However, some populations display unusual patterns, in which the colouration is predominantly blue or uniformly black. This study explores the factors that influence this chromatic variation, whether environmental (climate and island conditions) or evolutionary (phylogenetic trait conservatism). The colouration of 1400 individuals (27 species) was analysed in the CIELAB colour space. RESULTS Pagel's λ indicated that colouration is weakly conserved within phylogenetic lineages. Although the island surface plays a key role in the chromatic variability of these lacertids, geographic isolation and climate hold less influence. The colouration of some small island populations tends to be uniform and dark, possibly due to intense intraspecific competition and lower predatory pressure. CONCLUSIONS This study highlights the importance of island populations in understanding the processes that favour the emergence of extreme phenotypes in small ectothermic vertebrates.
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Affiliation(s)
- Daniel Escoriza
- GRECO, University of Girona, Campus de Montilivi, 17071, Girona, Spain.
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4
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Sherpa S, Paris JR, Silva‐Rocha I, Di Canio V, Carretero MA, Ficetola GF, Salvi D. Genetic depletion does not prevent rapid evolution in island-introduced lizards. Ecol Evol 2023; 13:e10721. [PMID: 38034325 PMCID: PMC10682264 DOI: 10.1002/ece3.10721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/02/2023] [Accepted: 10/23/2023] [Indexed: 12/02/2023] Open
Abstract
Experimental introductions of species have provided some of the most tractable examples of rapid phenotypic changes, which may reflect plasticity, the impact of stochastic processes, or the action of natural selection. Yet to date, very few studies have investigated the neutral and potentially adaptive genetic impacts of experimental introductions. We dissect the role of these processes in shaping the population differentiation of wall lizards in three Croatian islands (Sušac, Pod Kopište, and Pod Mrčaru), including the islet of Pod Mrčaru, where experimentally introduced lizards underwent rapid (~30 generations) phenotypic changes associated with a shift from an insectivorous to a plant-based diet. Using a genomic approach (~82,000 ddRAD loci), we confirmed a founder effect during introduction and very low neutral genetic differentiation between the introduced population and its source. However, genetic depletion did not prevent rapid population growth, as the introduced lizards exhibited population genetic signals of expansion and are known to have reached a high density. Our genome-scan analysis identified just a handful of loci showing large allelic shifts between ecologically divergent populations. This low overall signal of selection suggests that the extreme phenotypic differences observed among populations are determined by a small number of large-effect loci and/or that phenotypic plasticity plays a major role in phenotypic changes. Nonetheless, functional annotation of the outlier loci revealed some candidate genes relevant to diet-induced adaptation, in agreement with the hypothesis of directional selection. Our study provides important insights on the evolutionary potential of bottlenecked populations in response to new selective pressures on short ecological timescales.
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Affiliation(s)
- Stéphanie Sherpa
- Dipartimento di Scienze e Politiche AmbientaliUniversità degli Studi di MilanoMilanoItaly
| | - Josephine R. Paris
- Dipartimento di Medicina Clinica, Sanità Pubblica, Scienze della Vita e dell'AmbienteUniversità degli Studi dell'AquilaL'Aquila‐CoppitoItaly
| | - Iolanda Silva‐Rocha
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), InBIO Laboratório AssociadoUniversidade do PortoVairãoPortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIOVairãoPortugal
| | - Viola Di Canio
- Dipartimento di Scienze e Politiche AmbientaliUniversità degli Studi di MilanoMilanoItaly
| | - Miguel Angel Carretero
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), InBIO Laboratório AssociadoUniversidade do PortoVairãoPortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIOVairãoPortugal
- Departamento de Biologia, Faculdade de CiênciasUniversidade do PortoPortoPortugal
| | | | - Daniele Salvi
- Dipartimento di Medicina Clinica, Sanità Pubblica, Scienze della Vita e dell'AmbienteUniversità degli Studi dell'AquilaL'Aquila‐CoppitoItaly
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5
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Everitt T, Wallberg A, Christmas MJ, Olsson A, Hoffmann W, Neumann P, Webster MT. The Genomic Basis of Adaptation to High Elevations in Africanized Honey Bees. Genome Biol Evol 2023; 15:evad157. [PMID: 37625795 PMCID: PMC10484329 DOI: 10.1093/gbe/evad157] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
A range of different genetic architectures underpin local adaptation in nature. Honey bees (Apis mellifera) in the Eastern African Mountains harbor high frequencies of two chromosomal inversions that likely govern adaptation to this high-elevation habitat. In the Americas, honey bees are hybrids of European and African ancestries and adaptation to latitudinal variation in climate correlates with the proportion of these ancestries across the genome. It is unknown which, if either, of these forms of genetic variation governs adaptation in honey bees living at high elevations in the Americas. Here, we performed whole-genome sequencing of 29 honey bees from both high- and low-elevation populations in Colombia. Analysis of genetic ancestry indicated that both populations were predominantly of African ancestry, but the East African inversions were not detected. However, individuals in the higher elevation population had significantly higher proportions of European ancestry, likely reflecting local adaptation. Several genomic regions exhibited particularly high differentiation between highland and lowland bees, containing candidate loci for local adaptation. Genes that were highly differentiated between highland and lowland populations were enriched for functions related to reproduction and sperm competition. Furthermore, variation in levels of European ancestry across the genome was correlated between populations of honey bees in the highland population and populations at higher latitudes in South America. The results are consistent with the hypothesis that adaptation to both latitude and elevation in these hybrid honey bees are mediated by variation in ancestry at many loci across the genome.
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Affiliation(s)
- Turid Everitt
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Andreas Wallberg
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Matthew J Christmas
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna Olsson
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Wolfgang Hoffmann
- Grupo de Biocalorimetría, Universidad de Pamplona, Pamplona, Colombia
| | - Peter Neumann
- Institute of Bee Health, Vetsuisse Faculty, University of Bern and Agroscope, Bern, Switzerland
| | - Matthew T Webster
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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6
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Salvi D. Climbing on the La Canna Volcanic Sea Stack to Obtain First-Hand Data on the Tiniest Population of the Critically Endangered Aeolian Wall Lizard Podarcis raffonei. Animals (Basel) 2023; 13:2289. [PMID: 37508066 PMCID: PMC10376861 DOI: 10.3390/ani13142289] [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: 06/23/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Among the extant populations of the critically endangered Aeolian wall lizard, the most vulnerable is the one surviving on La Canna, a columnar volcanic stack off the Filicudi Island. Here, I report the results of the first climbing expedition by a biologist on La Canna, that contributed direct observations and updated information on the size, morphology, and genetic variability of this population. Lizard density at the sampling site (a small terrace at 50 m of elevation) was 1.7 m-2, twice of a previous estimate. Standard methods for estimating population size are unsuitable for La Canna. An educated guess of about a hundred individuals can be drawn, considering the extent of habitat available on the stack and the number of observed lizards. Lizards on La Canna were not fearless, despite what was reported by alpinists, possibly because of aggressive intraspecific interactions or high environmental temperatures during sampling. Biometric data significantly extend the body size of La Canna's lizards and indicate that it is not smaller than other P. raffonei populations. A complete lack of genetic diversity was found at the mitochondrial nd4 gene, in line with previous allozyme data and with estimates on other microinsular Podarcis populations. The small size of the La Canna population implies severe genetic drift and an extremely high level of inbreeding, as supported by low heterozygosity found across the genome. Detrimental effects of inbreeding depression are evident as cephalic malformations observed in all captured lizards of La Canna and might represent the more immediate threat to the persistence of this population.
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Affiliation(s)
- Daniele Salvi
- Department of Health, Life and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
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Gable SM, Mendez JM, Bushroe NA, Wilson A, Byars MI, Tollis M. The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order. Genes (Basel) 2023; 14:1387. [PMID: 37510292 PMCID: PMC10379679 DOI: 10.3390/genes14071387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
Squamates include more than 11,000 extant species of lizards, snakes, and amphisbaenians, and display a dazzling diversity of phenotypes across their over 200-million-year evolutionary history on Earth. Here, we introduce and define squamates (Order Squamata) and review the history and promise of genomic investigations into the patterns and processes governing squamate evolution, given recent technological advances in DNA sequencing, genome assembly, and evolutionary analysis. We survey the most recently available whole genome assemblies for squamates, including the taxonomic distribution of available squamate genomes, and assess their quality metrics and usefulness for research. We then focus on disagreements in squamate phylogenetic inference, how methods of high-throughput phylogenomics affect these inferences, and demonstrate the promise of whole genomes to settle or sustain persistent phylogenetic arguments for squamates. We review the role transposable elements play in vertebrate evolution, methods of transposable element annotation and analysis, and further demonstrate that through the understanding of the diversity, abundance, and activity of transposable elements in squamate genomes, squamates can be an ideal model for the evolution of genome size and structure in vertebrates. We discuss how squamate genomes can contribute to other areas of biological research such as venom systems, studies of phenotypic evolution, and sex determination. Because they represent more than 30% of the living species of amniote, squamates deserve a genome consortium on par with recent efforts for other amniotes (i.e., mammals and birds) that aim to sequence most of the extant families in a clade.
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Affiliation(s)
- Simone M Gable
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Jasmine M Mendez
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Nicholas A Bushroe
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Adam Wilson
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Michael I Byars
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Marc Tollis
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
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8
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Schöneberg Y, Winter S, Arribas O, Riccardo Di Nicola M, Master M, Benjamin Owens J, Rovatsos M, Wüster W, Janke A, Fritz U. Genomics reveals broad hybridization in deeply divergent Palearctic grass and water snakes (Natrix spp.). Mol Phylogenet Evol 2023; 184:107787. [PMID: 37080398 DOI: 10.1016/j.ympev.2023.107787] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/03/2023] [Accepted: 04/13/2023] [Indexed: 04/22/2023]
Abstract
Understanding speciation is one of the cornerstones of biological diversity research. Currently, speciation is often understood as a continuous process of divergence that continues until genetic or other incompatibilities minimize or prevent interbreeding. The Palearctic snake genus Natrix is an ideal group to study speciation, as it comprises taxa representing distinct stages of the speciation process, ranging from widely interbreeding parapatric taxa through parapatric species with very limited gene flow in narrow hybrid zones to widely sympatric species. To understand the evolution of reproductive isolation through time, we have sequenced the genomes of all five species within this genus and two additional subspecies. We used both long-read and short-read methods to sequence and de-novo-assemble two high-quality genomes (Natrix h. helvetica, Natrix n. natrix) to their 1.7 Gb length with a contig N50 of 4.6 Mbp and 1.5 Mbp, respectively, and used these as references to assemble the remaining short-read-based genomes. Our phylogenomic analyses yielded a well-supported dated phylogeny and evidence for a surprisingly complex history of interspecific gene flow, including between widely sympatric species. Furthermore, evidence for gene flow was also found for currently allopatric species pairs. Genetic exchange among these well-defined, distinct, and several million-year-old reptile species emphasizes that speciation and maintenance of species distinctness can occur despite continued genetic exchange.
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Affiliation(s)
- Yannis Schöneberg
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 9, 60325 Frankfurt am Main, Germany
| | - Sven Winter
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstraße 1, 1160 Vienna, Austria
| | - Oscar Arribas
- IES Castilla, Junta de Castilla, Castilla y León, 42003 Soria, Spain
| | | | - Maya Master
- Molecular Ecology and Evolution at Bangor (MEEB), School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor LL57 2UW, Wales, UK
| | - John Benjamin Owens
- Molecular Ecology and Evolution at Bangor (MEEB), School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor LL57 2UW, Wales, UK
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Praha 2, Czech Republic
| | - Wolfgang Wüster
- Molecular Ecology and Evolution at Bangor (MEEB), School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor LL57 2UW, Wales, UK
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 9, 60325 Frankfurt am Main, Germany; LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Uwe Fritz
- Senckenberg Dresden, Museum of Zoology, A. B. Meyer Building, 01109 Dresden, Germany.
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Ambu J, Martínez-Solano Í, Suchan T, Hernandez A, Wielstra B, Crochet PA, Dufresnes C. Genomic phylogeography illuminates deep cyto-nuclear discordances in midwife toads (Alytes). Mol Phylogenet Evol 2023; 183:107783. [PMID: 37044190 DOI: 10.1016/j.ympev.2023.107783] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 03/28/2023] [Accepted: 04/06/2023] [Indexed: 04/14/2023]
Abstract
The advent of genomic methods allows us to revisit the evolutionary history of organismal groups for which robust phylogenies are still lacking, particularly in species complexes that frequently hybridize. In this study, we conduct RAD-sequencing (RAD-seq) analyses of midwife toads (genus Alytes), an iconic group of western Mediterranean amphibians famous for their parental care behavior, but equally infamous for the difficulties to reconstruct their evolutionary history. Through admixture and phylogenetic analyses of thousands of loci, we provide the most comprehensive phylogeographic framework for the A. obstetricans complex to date, as well as the first fully resolved phylogeny for the entire genus. As part of this effort, we carefully explore the influence of different sampling schemes and data filtering thresholds on tree reconstruction, showing that several, slightly different, yet robust topologies may be retrieved with small datasets obtained by stringent SNP calling parameters, especially when admixed individuals are included. In contrast, analyses of incomplete but larger datasets converged on the same phylogeny, irrespective of the reconstruction method used or the proportion of missing data. The Alytes tree features three Miocene-diverged clades corresponding to the proposed subgenera Ammoryctis (A. cisternasii), Baleaphryne (A. maurus, A. dickhilleni and A. muletensis), and Alytes (A. obstetricans complex). The latter consists of six evolutionary lineages, grouped into three clades of Pliocene origin, and currently delimited as two species: (1) A. almogavarii almogavarii and A. a. inigoi; (2) A. obstetricans obstetricans and A. o. pertinax; (3) A. o. boscai and an undescribed taxon (A. o. cf. boscai). These results contradict the mitochondrial tree, due to past mitochondrial captures in A. a. almogavarii (central Pyrenees) and A. o. boscai (central Iberia) by A. obstetricans ancestors during the Pleistocene. Patterns of admixture between subspecies appear far more extensive than previously assumed from microsatellites, causing nomenclatural uncertainties, and even underlying the reticulate evolution of one taxon (A. o. pertinax). All Ammoryctis and Baleaphryne species form shallow clades, so their taxonomy should remain stable. Amid the prevalence of cyto-nuclear discordance among terrestrial vertebrates and the usual lack of resolution of conventional nuclear markers, our study advocates for phylogeography based on next-generation sequencing, but also encourages properly exploring parameter space and sampling schemes when building and analyzing genomic datasets.
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Affiliation(s)
- Johanna Ambu
- LASER, College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Íñigo Martínez-Solano
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Tomasz Suchan
- W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
| | - Axel Hernandez
- LASER, College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Ben Wielstra
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
| | | | - Christophe Dufresnes
- LASER, College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China
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10
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Sacchi R, Mangiacotti M, Scali S, Storniolo F, Zuffi MAL. Species-Specific Spatial Patterns of Variation in Sexual Dimorphism by Two Lizards Settled in the Same Geographic Context. Animals (Basel) 2023; 13:ani13040736. [PMID: 36830523 PMCID: PMC9952635 DOI: 10.3390/ani13040736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
The evolution of sexual dimorphism (SD) results from intricate interactions between sexual and natural selections. Sexually selected traits are expected to depend on individual condition, while natural selected traits should not be. Islands offer an ideal context to test how these drivers interact with one another, as the size is a reliable proxy for resource availability. Here, we analysed SD in body size (snout-vent length) and head shape (assessed by geometric morphometric) in two species of lizards (Podarcis muralis and P. siculus) inhabiting the Tuscan archipelago (Central Italy). We found a strong SD variation among islands in both species. Furthermore, in P. muralis emerged some significant correlations between SD and island size, supporting the occurrence of possible effects of individual condition on SD. By contrast, SD in P. siculus followed opposite trajectories than in P. muralis, suggesting that in this species, natural selection could play a major role as a driver of SD. Our findings show that natural and sexual selection can interact in complex ways, and the responses are species-specific. Therefore, spatial patterns of variation in SD may strongly differ among species, even when they settle in the same geographic contest.
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Affiliation(s)
- Roberto Sacchi
- Department of Earth and Environmental Sciences, University of Pavia, I-27100 Pavia, Italy
- Correspondence:
| | - Marco Mangiacotti
- Department of Earth and Environmental Sciences, University of Pavia, I-27100 Pavia, Italy
| | - Stefano Scali
- Museo di Storia Naturale, Comune di Milano, I-20121 Milano, Italy
| | - Federico Storniolo
- Department of Earth and Environmental Sciences, University of Pavia, I-27100 Pavia, Italy
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11
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Genetic diversity, phylogenetic position, and co-phylogenetic relationships of Karyolysus, a common blood parasite of lizards in the western Mediterranean. Int J Parasitol 2023; 53:185-196. [PMID: 36736608 DOI: 10.1016/j.ijpara.2022.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 02/05/2023]
Abstract
The genus Karyolysus was originally proposed to accommodate blood parasites of lacertid lizards in Western Europe. However, recent phylogenetic analyses suggested an inconclusive taxonomic position of these parasites of the order Adeleorina based on the available genetic information. Inconsistencies between molecular phylogeny, morphology, and/or life cycles can reflect lack of enough genetic information of the target group. We therefore surveyed 28 localities and collected blood samples from 828 lizards of 23 species including lacertids, skinks, and geckoes in the western Mediterranean, North Africa, and Macaronesia, where species of Karyolysus and other adeleorine parasites have been described. We combined molecular and microscopic methods to analyze the samples, including those from the host type species and the type locality of Karyolysus bicapsulatus. The phylogenetic relationship of these parasites was analyzed based on the 18S rRNA gene and the co-phylogenetic relationship with their vertebrate hosts was reconstructed. We molecularly detected adeleorine parasites in 37.9% of the blood samples and found 22 new parasite haplotypes. A phylogenetic reconstruction with 132 sequences indicated that 20 of the newly detected haplotypes clustered in a well-supported clade with another 18 sequences that included Karyolysus galloti and Karyolysus lacazei. Morphological evidence also supported that K. bicapsulatus clustered in this monophyletic clade. These results supported the taxonomic validity of the genus. In addition, we found some parasite haplotypes that infected different lizard host genera with ancient diverging histories, which suggested that Karyolysus is less host-specific than other blood parasites of lizards in the region. A co-phylogenetic analysis supported this interpretation because no significant co-speciation signal was shown between Karyolysus and lizard hosts.
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Lin XQ, Hou YM, Yang WZ, Shi SC, Zheng PY, Shih CK, Jiang JP, Xie F, Jiang JP, Xie F. A wide hybrid zone mediated by precipitation contributed to confused geographical structure of Scutiger boulengeri. Zool Res 2023; 44:3-19. [PMID: 36171715 PMCID: PMC9841186 DOI: 10.24272/j.issn.2095-8137.2022.108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Confused geographical structure of a population and mitonuclear discordance are shaped by a combination of rapid changes in population demographics and shifts in ecology. In this study, we generated a time-calibrated phylogeny of Scutiger boulengeri, an endemic Xizang alpine toad occurring in mountain streams on the Qinghai-Xizang (Tibet) Plateau (QTP). Based on three mitochondrial DNA (mtDNA) genes, eight clades were assigned to three deeply divergent lineages. Analysis of nuclear DNA (nuDNA) genes revealed three distinct clusters without geographic structure, indicating significantly high rates of gene flow. Coalescent theory framework analysis (approximate Bayesian computation model DIYABC and Migrate-N) suggested that divergence of the main intraspecific clusters was the result of hybridization after secondary contact in the Holocene around 0.59 million years ago (Ma). The ratio of mtDNA F ST (fixation index) to nuDNA F ST was 2.3, thus failing to show male-biased dispersal. Geographic cline analysis showed that a wide hybrid zone was initially established in southwestern China, without significant reproductive isolation but with strong introgression in S. boulengeri, suggesting high hybrid fitness. Furthermore, mtDNA genes exhibited isolation by distance (IBD) while nuDNA genes exhibited significant isolation by environment (IBE). Results suggested that mitonuclear discordance may have initially been caused by geographic isolation, followed by precipitation-mediated hybridization, producing a wide hybrid zone and geographic structure confusion of nuDNA genes in S. boulengeri. This study indicated that complicated historical processes may have led to specific genetic patterns, with a specific climate factor facilitating gene flow in the system.
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Affiliation(s)
- Xiu-Qin Lin
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yin-Meng Hou
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei-Zhao Yang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sheng-Chao Shi
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pu-Yang Zheng
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chung-Kun Shih
- College of Life Sciences, Capital Normal University, Beijing 100048, China,Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington DC 20013–7012, USA
| | - Jian-Ping Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China,University of Chinese Academy of Sciences, Beijing 100049, China,Mangkang Biodiversity and Ecological Station, Xizang Ecological Safety Monitor Network, Changdu, Xizang 854500, China
| | - Feng Xie
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China,University of Chinese Academy of Sciences, Beijing 100049, China,Mangkang Biodiversity and Ecological Station, Xizang Ecological Safety Monitor Network, Changdu, Xizang 854500, China,E-mail:
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GÖCEK Ç, TOK V. Identifying the Past, Present, and Future Distribution Patterns of the Balkan Wall Lizard (Sauria: Lacertidae: Podarcis tauricus) by Ecological Niche Modelling. COMMAGENE JOURNAL OF BIOLOGY 2022. [DOI: 10.31594/commagene.1133846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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Oskyrko O, Sos T, Vacheva E, Vlad SE, Cogălniceanu D, Uller T, Feiner N, Carretero MA. Unravelling the origin of the common wall lizards ( Podarcismuralis) in south-eastern Europe using mitochondrial evidence. Biodivers Data J 2022; 10:e90337. [PMID: 36761656 PMCID: PMC9836615 DOI: 10.3897/bdj.10.e90337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/20/2022] [Indexed: 11/12/2022] Open
Abstract
The origin of the common wall lizards (Podarcismuralis) populations in south-eastern Europe (namely in Bulgaria and Romania), representing the north-eastern range border of this species, was addressed using mitochondrial DNA. We compared cytochrome b sequences from Bulgaria and Romania with those from the contiguous range in Central Europe that are available from previous studies. We recorded five main haplogroups in Bulgaria and Romania, belonging to the Central Balkan clade. However, haplogroup III was recorded in more localities than previously found. Additionally, signs of haplotype admixture were identified in several populations along the Danube River. The presence of the Southern Alps haplotype in one population from Otopeni, Bucharest (Romania) and its close phylogenetic relationships to north Italy populations suggests human-mediated introductions of this wall lizard clade in Romania. Our results confirm that P.muralis can have non-native lineages and admixture through active human-mediated transport.
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Affiliation(s)
- Oleksandra Oskyrko
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, PortugalCIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus de Vairão, 4485-661VairãoPortugal,Department of Zoology, Faculty of Science, Charles University, Vinićná 7, 12844, Prague, Czech RepublicDepartment of Zoology, Faculty of Science, Charles University, Vinićná 7, 12844PragueCzech Republic
| | - Tibor Sos
- Evolutionary Ecology Group, Hungarian Department of Biology and Ecology, Babeș-Bolyai University, Clinicilor Street 5–7, 400006, Cluj Napoca, RomaniaEvolutionary Ecology Group, Hungarian Department of Biology and Ecology, Babeș-Bolyai University, Clinicilor Street 5–7, 400006Cluj NapocaRomania,“Milvus Group” Bird and Nature Protection Association, 540445, Tîrgu Mureș, Romania“Milvus Group” Bird and Nature Protection Association, 540445Tîrgu MureșRomania
| | - Emiliya Vacheva
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd, 1000, Sofia, BulgariaInstitute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd, 1000SofiaBulgaria
| | - Sabina E. Vlad
- Faculty of Natural and Agricultural Sciences, Ovidius University Constanţa, Aleea Universități 1, Campus - Corp B, 900470, Constanƫa, RomaniaFaculty of Natural and Agricultural Sciences, Ovidius University Constanţa, Aleea Universități 1, Campus - Corp B, 900470ConstanƫaRomania,CEDMOG Center, Ovidius University Constanța, Tomis Avenue 145, Constanƫa, RomaniaCEDMOG Center, Ovidius University Constanța, Tomis Avenue 145ConstanƫaRomania,Asociația Chelonia România, 062082, Bucharest, RomaniaAsociația Chelonia România, 062082BucharestRomania
| | - Dan Cogălniceanu
- Faculty of Natural and Agricultural Sciences, Ovidius University Constanţa, Aleea Universități 1, Campus - Corp B, 900470, Constanƫa, RomaniaFaculty of Natural and Agricultural Sciences, Ovidius University Constanţa, Aleea Universități 1, Campus - Corp B, 900470ConstanƫaRomania,Asociația Chelonia România, 062082, Bucharest, RomaniaAsociația Chelonia România, 062082BucharestRomania
| | - Tobias Uller
- Department of Biology, Lund University, Sölvegatan 37, 223 62, Lund, SwedenDepartment of Biology, Lund University, Sölvegatan 37, 223 62LundSweden
| | - Nathalie Feiner
- Department of Biology, Lund University, Sölvegatan 37, 223 62, Lund, SwedenDepartment of Biology, Lund University, Sölvegatan 37, 223 62LundSweden
| | - Miguel A. Carretero
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, PortugalCIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus de Vairão, 4485-661VairãoPortugal,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, R. Campo Alegre, s/n, 4169 - 007, Porto, PortugalDepartamento de Biologia, Faculdade de Ciências da Universidade do Porto, R. Campo Alegre, s/n, 4169 - 007PortoPortugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661VairãoPortugal
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15
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Dispersed emergence and protracted domestication of polyploid wheat uncovered by mosaic ancestral haploblock inference. Nat Commun 2022; 13:3891. [PMID: 35794156 PMCID: PMC9259585 DOI: 10.1038/s41467-022-31581-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 06/23/2022] [Indexed: 12/15/2022] Open
Abstract
Major crops are all survivors of domestication bottlenecks. Studies have focused on the genetic loci related to the domestication syndrome, while the contribution of ancient haplotypes remains largely unknown. Here, an ancestral genomic haploblock dissection method is developed and applied to a resequencing dataset of 386 tetraploid/hexaploid wheat accessions, generating a pan-ancestry haploblock map. Together with cytoplastic evidences, we reveal that domesticated polyploid wheat emerged from the admixture of six founder wild emmer lineages, which contributed the foundation of ancestral mosaics. The key domestication-related loci, originated over a wide geographical range, were gradually pyramided through a protracted process. Diverse stable-inheritance ancestral haplotype groups of the chromosome central zone are identified, revealing the expanding routes of wheat and the trends of modern wheat breeding. Finally, an evolution model of polyploid wheat is proposed, highlighting the key role of wild-to-crop and interploidy introgression, that increased genomic diversity following bottlenecks introduced by domestication and polyploidization. The contribution of ancient haplotypes to domestication is largely unknown. Here, the authors develop an ancestral genomic haploblock dissection method to generate a mosaic pan-ancestry genomic map and reveal that the domesticated polyploidy wheat emerged from the admixture of six founder wild emmer linages.
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Bodensteiner BL, Gangloff EJ, Kouyoumdjian L, Muñoz MM, Aubret F. Thermal-metabolic phenotypes of the lizard Podarcis muralis differ across elevation, but converge in high-elevation hypoxia. J Exp Biol 2021; 224:273727. [PMID: 34761802 DOI: 10.1242/jeb.243660] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/08/2021] [Indexed: 11/20/2022]
Abstract
In response to a warming climate, many montane species are shifting upslope to track the emergence of preferred temperatures. Characterizing patterns of variation in metabolic, physiological and thermal traits along an elevational gradient, and the plastic potential of these traits, is necessary to understand current and future responses to abiotic constraints at high elevations, including limited oxygen availability. We performed a transplant experiment with the upslope-colonizing common wall lizard (Podarcis muralis) in which we measured nine aspects of thermal physiology and aerobic capacity in lizards from replicate low- (400 m above sea level, ASL) and high-elevation (1700 m ASL) populations. We first measured traits at their elevation of origin and then transplanted half of each group to extreme high elevation (2900 m ASL; above the current elevational range limit of this species), where oxygen availability is reduced by ∼25% relative to sea level. After 3 weeks of acclimation, we again measured these traits in both the transplanted and control groups. The multivariate thermal-metabolic phenotypes of lizards originating from different elevations differed clearly when measured at the elevation of origin. For example, high-elevation lizards are more heat tolerant than their low-elevation counterparts (counter-gradient variation). Yet, these phenotypes converged after exposure to reduced oxygen availability at extreme high elevation, suggesting limited plastic responses under this novel constraint. Our results suggest that high-elevation populations are well suited to their oxygen environments, but that plasticity in the thermal-metabolic phenotype does not pre-adapt these populations to colonize more hypoxic environments at higher elevations.
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Affiliation(s)
- Brooke L Bodensteiner
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06511, USA
| | - Eric J Gangloff
- Station d'Ecologie Théorique et Expérimentale du CNRS - UMR 5321, 09200 Moulis, France.,Department of Biological Sciences, Ohio Wesleyan University, Delaware, 43015 OH, USA
| | - Laura Kouyoumdjian
- Station d'Ecologie Théorique et Expérimentale du CNRS - UMR 5321, 09200 Moulis, France
| | - Martha M Muñoz
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06511, USA
| | - Fabien Aubret
- Station d'Ecologie Théorique et Expérimentale du CNRS - UMR 5321, 09200 Moulis, France.,School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
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17
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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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18
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Kiourtsoglou A, Kaliontzopoulou A, Poursanidis D, Jablonski D, Lymberakis P, Poulakakis N. Evidence of cryptic diversity in
Podarcis peloponnesiacus
and re‐evaluation of its current taxonomy; insights from genetic, morphological, and ecological data. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Athina Kiourtsoglou
- Department of Biology School of Sciences and Engineering University of Crete Heraklion Greece
- Natural History Museum of Crete School of Sciences and Engineering University of Crete Heraklion Greece
| | - Antigoni Kaliontzopoulou
- CIBIO‐InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal
| | - Dimitris Poursanidis
- Institute of Applied and Computational Mathematics Foundation for Research and Technology ‐ Hellas Heraklion Greece
| | - Daniel Jablonski
- Department of Zoology Comenius University in Bratislava Bratislava Slovakia
| | - Petros Lymberakis
- Natural History Museum of Crete School of Sciences and Engineering University of Crete Heraklion Greece
| | - Nikos Poulakakis
- Department of Biology School of Sciences and Engineering University of Crete Heraklion Greece
- Natural History Museum of Crete School of Sciences and Engineering University of Crete Heraklion Greece
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19
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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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Ficetola GF, Silva-Rocha I, Carretero MA, Vignoli L, Sacchi R, Melotto A, Scali S, Salvi D. Status of the largest extant population of the critically endangered Aeolian lizard Podarcis raffonei (Capo Grosso, Vulcano island). PLoS One 2021; 16:e0253631. [PMID: 34161384 PMCID: PMC8221524 DOI: 10.1371/journal.pone.0253631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/10/2021] [Indexed: 11/29/2022] Open
Abstract
The Aeolian wall lizard Podarcis raffonei is an island endemic that survives only on three tiny islets, and on the Capo Grosso peninsula of the Vulcano island, thus is among the European vertebrates with the smallest range and one of the most threatened by extinction. This species is declining due to competition and hybridization with the non-native lizard Podarcis siculus, but a regular monitoring program is lacking. Here we assessed the size and status of the Capo Grosso population of P. raffonei on Vulcano. In September 2015 we captured 30 individuals showing the typical brown phenotype of P. raffonei, while one single male showed a green phenotype, apparently intermediate between P. raffonei and the non-native Podarcis siculus. In May 2017, only 47% of 131 individuals showed the typical brown phenotype (P. raffonei-like) and 53% showed the green phenotype (P. siculus-like). Based on N-mixture models and removal sampling the estimated size of the Capo Grosso population was of 800–1300 individuals in 2017, being similar to 2015; available data suggest that the total range of the species could be as small as 2 ha. The frequency of individuals with the typical P. raffonei phenotype dramatically dropped between two samplings with a parallel increase of individuals displaying the green phenotype. Observation on outdoor captive-bred individuals demonstrates plasticity for colouration in P. raffonei individuals from Capo Grosso, with several individuals showing the typical brown pattern in September 2017 and a green pattern in March 2021. Non-exclusive hypotheses, including hybridization with P. siculus and plasticity in colour pattern of P. raffonei, are discussed to explain the phenotypic shifts of the P. raffonei population of Capo Grosso. While genomic evidence is required to reach conclusions and investigate eventual hybridization, it is urgent to undertake a programme for the monitoring and management of this lizard.
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Affiliation(s)
- Gentile Francesco Ficetola
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milano, Italy
- CNRS, Laboratoire d’Ecologie Alpine (LECA), Univ. Grenoble Alpes, Grenoble, France
| | - Iolanda Silva-Rocha
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBio Laboratório Associado, Vairão, Portugal
| | - Miguel A. Carretero
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBio Laboratório Associado, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | | | - Roberto Sacchi
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
| | - Andrea Melotto
- Centre of Excellence for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, Western Cape, South Africa
| | | | - Daniele Salvi
- Department of Health, Life and Environmental Sciences, University of L’Aquila, Via Vetoio, L’Aquila, Italy
- * E-mail:
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