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Schild A, Baur H, Hertwig ST, Fritz U, Ursenbacher S. Genetic identification, morphology and distribution of Natrixhelvetica subspecies in southern and western Switzerland (Reptilia, Squamata, Serpentes). Zookeys 2024; 1205:223-238. [PMID: 38966573 PMCID: PMC11222720 DOI: 10.3897/zookeys.1205.123911] [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: 03/25/2024] [Accepted: 05/21/2024] [Indexed: 07/06/2024] Open
Abstract
Most of Switzerland is inhabited by the nominotypical subspecies of the barred grass snake (Natrixhelveticahelvetica), which is characterized by mitochondrial DNA lineage E. Only in the northeast of the country, the common grass snake (N.natrix) occurs and hybridizes with N.h.helvetica in a narrow contact zone. However, we discovered that in southern and western Switzerland barred grass snakes representing another mtDNA lineage (lineage C) are widely distributed. Lineage C is typical for Alpine populations of the southern subspecies N.h.sicula. Our microsatellite analyses of the Swiss samples revealed differences between the two subspecies and also a substructure with two clusters in each subspecies. Furthermore, we discovered a contact and hybrid zone of N.h.helvetica and N.h.sicula along the northern shore of Lake Geneva and also confirm that interbreeding with alien common grass snakes (N.n.moreotica, mtDNA lineage 7) occurs there. This finding is of concern for nature conservation and measures should be taken to prevent further genetic pollution. Using morphometrics, we found no differences between the two subspecies of N.helvetica, while N.natrix was slightly distinct from N.helvetica.
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Affiliation(s)
- Andreas Schild
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, SwitzerlandUniversity of BernBernSwitzerland
| | - Hannes Baur
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, SwitzerlandUniversity of BernBernSwitzerland
- Naturhistorisches Museum Bern, Bernastrasse 15, 3005 Bern, SwitzerlandNatural History Museum BernBernSwitzerland
| | - Stefan T. Hertwig
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, SwitzerlandUniversity of BernBernSwitzerland
- Naturhistorisches Museum Bern, Bernastrasse 15, 3005 Bern, SwitzerlandNatural History Museum BernBernSwitzerland
| | - Uwe Fritz
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, A. B. Meyer Building, 01109 Dresden, GermanyMuseum of Zoology (Museum für Tierkunde)DresdenGermany
| | - Sylvain Ursenbacher
- Department of Environmental Sciences, Section of Conservation Biology, University of Basel, Bernoullistrasse 32, 4056 Basel, SwitzerlandUniversity of BaselBaselSwitzerland
- info fauna – karch, University of Neuchâtel, Avenue de Bellevaux 51, 2000 Neuchâtel, SwitzerlandUniversity of NeuchâtelNeuchâtelSwitzerland
- Balaton Limnological Research Institute, 8237 Tihany, Klebelsberg Kuno u. 3, HungaryBalaton Limnological Research InstituteTihanyHungary
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Spaseni P, Sahlean TC, Gherghel I, Zamfirescu ȘR, Petreanu I, Melenciuc R, Alistar CF, Gavril VD, Strugariu A. Natrix natrix after dark: citizen science sheds light on the common grass snake's nightlife. PeerJ 2024; 12:e17168. [PMID: 38680898 PMCID: PMC11056106 DOI: 10.7717/peerj.17168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/06/2024] [Indexed: 05/01/2024] Open
Abstract
Activity patterns in animals are often species-specific, and can be generally categorized as diurnal, crepuscular, or nocturnal. Understanding these patterns provides insight into ecological adaptations and behaviors. The common grass snake (Natrix natrix), one of the most common and widespread European snake species, is traditionally considered diurnal, with scarce evidence of its crepuscular and nocturnal activity. We aimed to document the distribution, environmental conditions, and potential phenotype associations of nighttime activity in N. natrix. We used citizen science data from iNaturalist (1992-2022), Observation.org (2012-2022), together with personal field observations (2010-2023) to collect 127 crepuscular and nocturnal activity records. Most observations occurred between May and August, coinciding with the peak activity period of grass snakes across their distribution range. Statistical analyses revealed no significant difference in mean daily temperatures between crepuscular and nocturnal observations. However, striped individuals displayed nocturnal activity at higher temperatures, consistent with their distribution in warmer regions, but failed to register any difference when tested on a geographic subsample, that accounted for sympatry of the phenotypes. Surprisingly, we found no significant impact of moon presence or moonlight on nighttime activity or age class, contrary to expectations based on other snake species' responses. While our study reveals that nocturnal activity in the common grass snake is geographically widespread, further research is warranted to understand its drivers and ecological implications. This study highlights the value of citizen science platforms for biological and ecological research, offering unparalleled spatial and temporal coverage by their users. In conclusion, our work extends the knowledge of nocturnal behavior in N. natrix and underlines the critical role of citizen science in discovering behavioral aspects of common and widespread species.
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Affiliation(s)
- Petronel Spaseni
- Department of Exact and Natural Sciences, Institute of Interdisciplinary Research, Alexandru Ioan Cuza University of Iași, Iași, Iași, Romania
- Faculty of Biology, Alexandru Ioan Cuza University of Iași, Iași, Iași, Romania
| | - Tiberiu C. Sahlean
- Department of Exact and Natural Sciences, Institute of Interdisciplinary Research, Alexandru Ioan Cuza University of Iași, Iași, Iași, Romania
- Institute of Biology Bucharest, Romanian Academy, Bucharest, Bucharest, Romania
| | - Iulian Gherghel
- Department of Exact and Natural Sciences, Institute of Interdisciplinary Research, Alexandru Ioan Cuza University of Iași, Iași, Iași, Romania
- Faculty of Natural and Agricultural Sciences, Ovidius University of Constanţa, Constanța, Constanța, Romania
| | | | - Ionuț C. Petreanu
- Faculty of Biology, Alexandru Ioan Cuza University of Iași, Iași, Iași, Romania
| | - Raluca Melenciuc
- Faculty of Natural and Agricultural Sciences, Ovidius University of Constanţa, Constanța, Constanța, Romania
| | - Cristina F. Alistar
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest, Bucharest, Romania
| | - Viorel D. Gavril
- Institute of Biology Bucharest, Romanian Academy, Bucharest, Bucharest, Romania
| | - Alexandru Strugariu
- Department of Exact and Natural Sciences, Institute of Interdisciplinary Research, Alexandru Ioan Cuza University of Iași, Iași, Iași, Romania
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3
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Miralles A, Puillandre N, Vences M. DNA Barcoding in Species Delimitation: From Genetic Distances to Integrative Taxonomy. Methods Mol Biol 2024; 2744:77-104. [PMID: 38683312 DOI: 10.1007/978-1-0716-3581-0_4] [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] [Indexed: 05/01/2024]
Abstract
Over the past two decades, DNA barcoding has become the most popular exploration approach in molecular taxonomy, whether for identification, discovery, delimitation, or description of species. The present contribution focuses on the utility of DNA barcoding for taxonomic research activities related to species delimitation, emphasizing the following aspects:(1) To what extent DNA barcoding can be a valuable ally for fundamental taxonomic research, (2) its methodological and theoretical limitations, (3) the conceptual background and practical use of pairwise distances between DNA barcode sequences in taxonomy, and (4) the different ways in which DNA barcoding can be combined with complementary means of investigation within a broader integrative framework. In this chapter, we recall and discuss the key conceptual advances that have led to the so-called renaissance of taxonomy, elaborate a detailed glossary for the terms specific to this discipline (see Glossary in Chap. 35 ), and propose a newly designed step-by-step species delimitation protocol starting from DNA barcode data that includes steps from the preliminary elaboration of an optimal sampling strategy to the final decision-making process which potentially leads to nomenclatural changes.
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Affiliation(s)
- Aurélien Miralles
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Miguel Vences
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany.
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4
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Dufresnes C, Poyarkov N, Jablonski D. Acknowledging more biodiversity without more species. Proc Natl Acad Sci U S A 2023; 120:e2302424120. [PMID: 37748058 PMCID: PMC10556632 DOI: 10.1073/pnas.2302424120] [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] [Indexed: 09/27/2023] Open
Abstract
Delimiting and naming biodiversity is a vital step toward wildlife conservation and research. However, species delimitation must be consistent across biota so that the limited resources available for nature protection can be spent effectively and objectively. To date, newly discovered lineages typically are either left undescribed and thus remain unprotected or are being erroneously proposed as new species despite mixed evidence for completed speciation, in turn contributing to the emerging problem of taxonomic inflation. Inspired by recent conceptual and methodological progress, we propose a standardized workflow for species delimitation that combines phylogenetic and hybrid zone analyses of genomic datasets ("genomic taxonomy"), in which phylogeographic lineages that do not freely admix are ranked as species, while those that have remained fully genetically compatible are ranked as subspecies. In both cases, we encourage their formal taxonomic naming, diagnosis, and description to promote social awareness toward biodiversity. The use of loci throughout the genome overcomes the unreliability of widely used barcoding genes when phylogeographic patterns are complex, while the evaluation of divergence and reproductive isolation unifies the long-opposed concepts of lineage species and biological species. We suggest that a shift in conservation assessments from a single level (species) toward a two-level hierarchy (species and subspecies) will lead to a more balanced perception of biodiversity in which both intraspecific and interspecific diversity are valued and more adequately protected.
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Affiliation(s)
- Christophe Dufresnes
- Laboratory of Amphibian Systematics and Evolutionary Research, College of Biology and Environment, Nanjing Forestry University, Nanjing210037, People’s Republic of China
| | - Nikolay Poyarkov
- Joint Russian-Vietnamese Tropical Research and Technological Center, Hanoi122000, Vietnam
- Department of Vertebrate Zoology, Lomonosov Moscow State University, Moscow119234, Russia
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Bratislava84215, Slovakia
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Di Nicola MR, Pozzi AV, Mezzadri S, Faraone FP, Russo G, Dorne JLMC, Minuti G. The Endangered Sardinian Grass Snake: Distribution Update, Bioclimatic Niche Modelling, Dorsal Pattern Characterisation, and Literature Review. Life (Basel) 2023; 13:1867. [PMID: 37763271 PMCID: PMC10533143 DOI: 10.3390/life13091867] [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: 07/31/2023] [Revised: 08/17/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The Sardinian grass snake, Natrix helvetica cetti, is an endangered endemic snake subspecies with a restricted and highly fragmented geographic distribution. Information on its ecology and detailed geographic distribution are scarce and may negatively impact on its conservation status. Therefore, a literature review on its taxonomy, morphology, ecology, and conservation is presented here. Moreover, field records from the authors, citizen science and the existing literature provide an updated geographic distribution highlighting its presence within 13 new and 7 historic 10 × 10 km cells. Bioclimatic niche modelling was then applied to explore patterns of habitat suitability and phenotypic variation within N. h. cetti. The geographic distribution of the species was found to be positively correlated with altitude and precipitation values, whereas temperature showed a negative correlation. Taken together, these outcomes may explain the snake's presence, particularly in eastern Sardinia. In addition, analysis of distribution overlap with the competing viperine snake (N. maura) and the urodeles as possible overlooked trophic resources (Speleomantes spp. and Euproctus platycephalus) showed overlaps of 66% and 79%, respectively. Finally, geographical or bioclimatic correlations did not explain phenotypic variation patterns observed in this highly polymorphic taxon. Perspectives on future research to investigate N. h. cetti's decline and support effective conservation measures are discussed.
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Affiliation(s)
- Matteo Riccardo Di Nicola
- Faculty of Veterinary Medicine, Department of Pathobiology, Pharmacology and Zoological Medicine, Wildlife Health Ghent, Ghent University, 9820 Merelbeke, Belgium
- Unit of Dermatology and Cosmetology, IRCCS San Raffaele Hospital, Via Olgettina 60, 20132 Milan, Italy
- Asociación Herpetológica Española, Apartado de Correos 191, 28911 Leganés, Spain
| | - Andrea Vittorio Pozzi
- Molecular Ecology and Evolution Group, School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK;
| | - Sergio Mezzadri
- Independent Researcher, Via Palmerio, 29121 Piacenza, Italy;
| | - Francesco Paolo Faraone
- Dipartimento Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, University of Palermo, Via Archirafi 18, 90123 Palermo, Italy;
| | - Giorgio Russo
- VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel, 1090 Brussels, Belgium;
| | - Jean Lou M. C. Dorne
- Methodology and Scientific Support Unit, European Food Safety Authority (EFSA), Via Carlo Magno 1A, 43126 Parma, Italy;
| | - Gianmarco Minuti
- Ecology & Biodiversity Research Unit, Department of Biology, Vrije Universiteit Brussels, 1090 Brussels, Belgium;
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6
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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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7
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Chiocchio A, Zampiglia M, Biaggini M, Biello R, Di Tizio L, Leonetti FL, Olivieri O, Sperone E, Trabalza-Marinucci M, Corti C, Canestrelli D. Unveiling a hotspot of genetic diversity in southern Italy for the endangered Hermann’s tortoise Testudo hermanni. BMC Ecol Evol 2022; 22:131. [DOI: 10.1186/s12862-022-02075-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022] Open
Abstract
Abstract
Background
Hotspots of intraspecific genetic diversity represent invaluable resources for species to cope with environmental changes, and their identification is increasingly recognized as a major goal of conservation ecology research. However, even for iconic and endangered species, conservation strategies are often planned without thorough information on the geographic patterns of genetic variation. Here, we investigated the spatial patterns of genetic variation of the endangered Hermann’s tortoise Testudo hermanni in the Italian Peninsula by genotyping 174 individuals at 7 microsatellite loci, with the aim to contribute to planning effective conservation strategies.
Results
Ordination-based and Bayesian clustering analyses consistently identified three main genetic clusters, one spread in the central and northern part of the peninsula, and two restricted to southern Italy and Sicily, respectively. The highest levels of genetic diversity were found in populations of the southern cluster and, in particular, at the northern edges of its distribution (He > 0.6, Ar > 2.8 ), that correspond to areas of putative secondary contact and admixture between distinct lineages. Our results clearly identify a hotspot of genetic diversity for the Hermann’s tortoise in southern Italy.
Conclusion
We inferred the evolutionary history and the spatial patterns of genetic variation of the Hermann’s tortoise in the Italian Peninsula. We identified three main genetic clusters along the peninsula and a hotspot of intraspecific diversity in southern Italy. Our results underline the urgent need for conservation actions to warrant the long-term persistence of viable tortoise populations in this area. Furthrmore, these data add further evidence to the role of southern Italy as a biodiversity hotspot for temperate fauna, claiming for higher consideration of this area in large scale conservation programs.
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8
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Jablonski D, Trapp B, Tzoras E, Mebert K. Erythrism in the Eastern Grass Snake, Natrix natrix (Linnaeus, 1758). HERPETOZOA 2022. [DOI: 10.3897/herpetozoa.35.e90928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We describe the unusual case of erythrism in the Eastern Grass Snake, Natrix natrix. This colour morph is very rare and has not been reported in the literature before. Despite having observed thousands of N. natrix in the field, we personally detected this morph in only three individuals originating from Slovakia, Romania, and mainland Greece, while photos of a fourth individual from a Greek island were provided to us. In addition, a recent study with a large data set from citizen scientists was unable to produce a single reddish Eastern Grass Snake. Such colouration is likewise uncommon in the western members of Grass Snakes (N. helvetica, N. astreptophora), with two examples provided herein. Because the potential biological importance of erythristic colouration is unclear, we encourage other field herpetologists and naturalists to publish their observations of reddish Grass Snakes in the printed literature.
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9
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Vecchioni L, Marrone F, Costa S, Muscarella C, Carra E, Arizza V, Arculeo M, Faraone FP. The European Pine Marten Martes martes (Linnaeus, 1758) Is Autochthonous in Sicily and Constitutes a Well-Characterised Major Phylogroup within the Species (Carnivora, Mustelidae). Animals (Basel) 2022; 12:ani12192546. [PMID: 36230287 PMCID: PMC9558521 DOI: 10.3390/ani12192546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/22/2022] [Accepted: 09/22/2022] [Indexed: 11/29/2022] Open
Abstract
Simple Summary The faunal assemblages currently occurring on islands are often a mélange of native and non-native species, and the actual status of some of them is doubtful at present. Since different laws are enforced for native and non-native species, sound knowledge about their status is pivotal for both their management and our understanding of the natural history of the studied areas. In the frame of this work, the Sicilian population of the European pine marten is genetically characterized for the first time, based on mitochondrial DNA sequences. Our results prove that the European pine marten is native on the island, where it arrived during the Pleistocene, and is represented there by a well-differentiated and endemic evolutionary lineage. Abstract No molecular data are currently available for the Sicilian populations of the European pine marten Martes martes, thus preventing any sound inference about its native or non-native status on the island, as well as the local phylogeography of the species. In order to investigate these issues, we sequenced two mtDNA markers in road-killed specimens collected in Sicily. Both markers consistently demonstrated the existence of a well-characterised Sicilian clade of the species, which is endemic to the island and constitutes the sister group of a clade including the Mediterranean and Central–North European major phylogroups of the European pine marten. Such evidence supports the autochthony of Martes martes in Sicily and points to a natural Pleistocene colonisation of the island followed by isolation. The occurrence of a, to date undetected, major phylogroup of the species in Sicily calls for the dedicated monitoring of the Sicilian populations of the species in order to preserve this evolutionarily significant unit.
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Affiliation(s)
- Luca Vecchioni
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 18, 90123 Palermo, Italy
| | - Federico Marrone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 18, 90123 Palermo, Italy
- Correspondence:
| | - Simone Costa
- Cooperativa Silene, Via D’Ondes Reggio 8a, 90127 Palermo, Italy
| | | | - Elena Carra
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 18, 90123 Palermo, Italy
| | - Vincenzo Arizza
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 18, 90123 Palermo, Italy
| | - Marco Arculeo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 18, 90123 Palermo, Italy
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Phylogeography of Sarmarutilus rubilio (Cypriniformes: Leuciscidae): Complex Genetic Structure, Clues to a New Cryptic Species and Further Insights into Roaches Phylogeny. Genes (Basel) 2022; 13:genes13061071. [PMID: 35741833 PMCID: PMC9222716 DOI: 10.3390/genes13061071] [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] [Received: 05/04/2022] [Revised: 05/27/2022] [Accepted: 06/13/2022] [Indexed: 02/06/2023] Open
Abstract
Italy hosts a large number of endemic freshwater fish species due to complex geological events which promoted genetic differentiation and allopatric speciation. Among them, the South European roach Sarmarutilus rubilio inhabits various freshwater environments in three different ichthyogeographic districts. We investigated the genetic diversity of S. rubilio using two different mitochondrial markers (COI and CR), aiming to define its relationship with other similar taxa from the Balkan area and, from a phylogeographic perspective, test the effects of past hydrogeological dynamics of Italian river basins on its genetic structure and demographic history. Our analysis highlighted a marked genetic divergence between S. rubilio and all other roach species and, among Italian samples, revealed the existence of three deeply divergent geographic haplogroups, named A, B and C. Haplogroup C likely corresponds to a new putative cryptic species and is located at the northern border of the South European roach range; haplogroup B is restricted to Southern Italy; and haplogroup A is widespread across the entire range and in some sites it is in co-occurrence with C or B. Their origin is probably related to the tectonic uplifting of the Apuan Alps in the north and of the Colli Albani Volcano in the south during the Pleistocene, which promoted isolation and vicariance followed by secondary contacts.
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11
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Schmitt T, Fritz U, Delfino M, Ulrich W, Habel JC. Biogeography of Italy revisited: genetic lineages confirm major phylogeographic patterns and a pre-Pleistocene origin of its biota. Front Zool 2021; 18:34. [PMID: 34187502 PMCID: PMC8240252 DOI: 10.1186/s12983-021-00418-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 06/06/2021] [Indexed: 11/10/2022] Open
Abstract
Warm-adapted species survived the cold stages of the past glacial-interglacial cycles in southern European peninsulas and recolonized major parts of Central and Northern Europe in the wake of postglacial warming. However, many of the genetic lineages which differentiated within these refugia predate even the Pleistocene. One of these refugia is the Italian Peninsula with its surrounding islands. In this meta-analysis, we compiled phylogeographic patterns of multiple species across this region. We transformed existing geographic information on 78 animal and plant species (with a total of 471 genetic lineages) within 17 predefined areas into presence/absence matrices. We elaborated three matrices: (i) only old lineages exclusively distinguished by deep splits, (ii) only young lineages distinguished by shallow (i.e. recent) splits, and (iii) presence/absence of the respective species. To infer biogeographic relationships between the predefined areas, we performed bootstrapped neighbour joining cluster analyses on these three matrices. In addition, we reviewed the geological history of Italy to identify causes of the observed biogeographic patterns. We found Sardinia and Corsica to be biogeographically closely linked with each other, and that they diverge strongly from all other regions. Sicily also diverges strongly from all other regions, while the intra-island differentiation was comparatively low. On the Italian mainland, Calabria exhibited the most pronounced biogeographic differentiation, often with several lineages present, resulting from old vicariance events within the region. Furthermore, southern Apulia and the Po Plain with adjoining areas of northern peninsular Italy displayed considerable distinctiveness. Admixture prevailed in the areas between these three regions. The ancient isolation of Sicily, as well as Sardinia plus Corsica, resulted in endemic lineages with only moderate recent exchange with adjacent mainland regions. Pronounced diversification occurs within the Italian Peninsula. The complex tectonic activities, such as shifting (micro)plates, submergence of major parts of peninsular Italy with the genesis of numerous Pliocene islands, in combination with the climatic cycles during the Pleistocene have most likely generated the current biogeographic pattern of species. Immigrations from the Balkan Peninsula into northern Italy partly accounted for the distinctiveness of this region.
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Affiliation(s)
- Thomas Schmitt
- Senckenberg Deutsches Entomologisches Institut, 15374, Müncheberg, Germany. .,Department of Zoology, Institute of Biology, Faculty of Natural Sciences I, Martin Luther University Halle-Wittenberg, 06099, Halle (Saale), Germany. .,Entomology and Biogeography, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, 14476, Potsdam, Germany.
| | - Uwe Fritz
- Museum of Zoology (Museum für Tierkunde), Senckenberg Natural History Collections Dresden, 01109, Dresden, Germany
| | - Massimo Delfino
- Dipartimento di Scienze della Terra, Università di Torino, Via Valperga Caluso 35, 10125, Torino, Italy.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTAICP, Carrer de les Columnes s/n, Campus de la UAB, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Werner Ulrich
- Department of Ecology and Biogeography, Nicolaus Copernicus University, 87-100, Toruń, Poland
| | - Jan Christian Habel
- Evolutionary Zoology, Department of Biosciences, University of Salzburg, 5020, Salzburg, Austria
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12
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Asztalos M, Glaw F, Franzen M, Kindler C, Fritz U. Transalpine dispersal: Italian barred grass snakes in southernmost Bavaria—This far but no further! J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marika Asztalos
- Museum of Zoology (Museum für Tierkunde) Senckenberg Dresden Dresden Germany
| | - Frank Glaw
- Zoologische Staatssammlung München (ZSM‐SNSB) Munich Germany
| | - Michael Franzen
- Zoologische Staatssammlung München (ZSM‐SNSB) Munich Germany
| | - Carolin Kindler
- Museum of Zoology (Museum für Tierkunde) Senckenberg Dresden Dresden Germany
| | - Uwe Fritz
- Museum of Zoology (Museum für Tierkunde) Senckenberg Dresden Dresden Germany
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13
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Chiocchio A, Arntzen JW, Martínez-Solano I, de Vries W, Bisconti R, Pezzarossa A, Maiorano L, Canestrelli D. Reconstructing hotspots of genetic diversity from glacial refugia and subsequent dispersal in Italian common toads (Bufo bufo). Sci Rep 2021; 11:260. [PMID: 33420098 PMCID: PMC7794404 DOI: 10.1038/s41598-020-79046-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/01/2020] [Indexed: 02/01/2023] Open
Abstract
Genetic diversity feeds the evolutionary process and allows populations to adapt to environmental changes. However, we still lack a thorough understanding of why hotspots of genetic diversity are so 'hot'. Here, we analysed the relative contribution of bioclimatic stability and genetic admixture between divergent lineages in shaping spatial patterns of genetic diversity in the common toad Bufo bufo along the Italian peninsula. We combined population genetic, phylogeographic and species distribution modelling (SDM) approaches to map ancestral areas, glacial refugia, and secondary contact zones. We consistently identified three phylogeographic lineages, distributed in northern, central and southern Italy. These lineages expanded from their ancestral areas and established secondary contact zones, before the last interglacial. SDM identified widespread glacial refugia in peninsular Italy, sometimes located under the present-day sea-level. Generalized linear models indicated genetic admixture as the only significant predictor of the levels of population genetic diversity. Our results show that glacial refugia contributed to preserving both levels and patterns of genetic diversity across glacial-interglacial cycles, but not to their formation, and highlight a general principle emerging in Mediterranean species: higher levels of genetic diversity mark populations with substantial contributions from multiple genetic lineages, irrespective of the location of glacial refugia.
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Affiliation(s)
- Andrea Chiocchio
- Department of Ecological and Biological Science, Tuscia University, Largo dell'Università s.n.c., 01100, Viterbo, Italy.
| | - Jan W Arntzen
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The Netherlands
| | - Iñigo Martínez-Solano
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, c/ José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Wouter de Vries
- Asociation Ambor, Ctra. Constantina - Pedroso 1, 41450, Constantina, Spain
| | - Roberta Bisconti
- Department of Ecological and Biological Science, Tuscia University, Largo dell'Università s.n.c., 01100, Viterbo, Italy
| | - Alice Pezzarossa
- Department of Ecological and Biological Science, Tuscia University, Largo dell'Università s.n.c., 01100, Viterbo, Italy
| | - Luigi Maiorano
- Department of Biology and Biotechnology "Charles Darwin", Università di Roma La Sapienza, Viale dell'Università 32, 00185, Rome, Italy
| | - Daniele Canestrelli
- Department of Ecological and Biological Science, Tuscia University, Largo dell'Università s.n.c., 01100, Viterbo, Italy
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14
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Asztalos M, Schultze N, Ihlow F, Geniez P, Berroneau M, Delmas C, Guiller G, Legentilhomme J, Kindler C, Fritz U. How often do they do it? An in-depth analysis of the hybrid zone of two grass snake species (Natrix astreptophora and Natrix helvetica). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
We examined the contact zone of two parapatric species of grass snake (Natrix astreptophora and Natrix helvetica) in southern France. To this end, we used comprehensive sampling, analysed mtDNA sequences and microsatellite loci, and built Species Distribution Models for current and past climatic conditions. The contact zone had established by the mid-Holocene during range expansions from glacial refuges in the Iberian Peninsula (N. astreptophora) and southern or western France (N. helvetica). The contact zone represents a narrow bimodal hybrid zone, with steep genetic transition from one taxon to the other and rare hybridization, supporting species status for N. astreptophora and N. helvetica. Our results suggest that the steepness of the clines is a more robust tool for species delimitation than cline width. In addition, we discovered in western France, beyond the hybrid zone, a remote population of N. helvetica with genetic signatures of hybridization with N. astreptophora, most likely the result of human-mediated long-distance dispersal. For N. helvetica, we identified a southern and a northern population cluster, connected by broad-scale gene flow in a unimodal hybrid zone running across France. This pattern either reflects genetic divergence caused by allopatry in two microrefuges and subsequent secondary contact or introgression of foreign alleles into the southern cluster.
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Affiliation(s)
- Marika Asztalos
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, Dresden, Germany
| | - Nadine Schultze
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, Dresden, Germany
| | - Flora Ihlow
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, Dresden, Germany
| | - Philippe Geniez
- UMR 5175 CEFE, Biogéographie et Ecologie des Vertébrés, EPHE, PSL Université Recherche, Montpellier, Cedex 5, France
| | | | - Claudine Delmas
- NEO/ANA-CEN Ariège, 18 Impasse Denis Papin, Lavelanet, France
| | | | | | - Carolin Kindler
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, Dresden, Germany
| | - Uwe Fritz
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, Dresden, Germany
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15
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Wielstra B, Salvi D, Canestrelli D. Genetic Divergence Across Glacial Refugia Despite Interglacial Gene Flow in a Crested Newt. Evol Biol 2020. [DOI: 10.1007/s11692-020-09519-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractMtDNA-based phylogeography has illuminated the impact of the Pleistocene Ice Age on species distribution dynamics and the build-up of genetic divergence. The well-known shortcomings of mtDNA in biogeographical inference can be compensated by integrating multilocus data and species distribution modelling into phylogeography. We re-visit the phylogeography of the Italian crested newt (Triturus carnifex), a species distributed in two of Europe’s main glacial refugia, the Balkan and Italian Peninsulas. While a new 51 nuclear DNA marker dataset supports the existence of three lineages previously suggested by mtDNA (Balkan, northern Italy and southern Italy), the nuclear DNA dataset also provides improved resolution where these lineages have obtained secondary contact. We observe geographically restricted admixture at the contact between the Balkan and northern Italy gene pools and identify a potential mtDNA ghost lineage here. At the contact between the northern and southern Italy gene pools we find admixture over a broader area, as well as asymmetric mtDNA introgression. Our species distribution model is in agreement with a distribution restricted to distinct refugia during Pleistocene glacial cycles and postglacial expansion with secondary contact. Our study supports: (1) the relevance of the north-western Balkan Peninsula as a discrete glacial refugium; (2) the importance of north-eastern Italy and the northern Apennine as suture zones; and (3) the applicability of a refugia-within-refugia scenario within the Italian Peninsula.
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