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Kotsakiozi P, Antoniou A, Psonis N, Sagonas Κ, Karameta E, Ilgaz Ç, Kumlutaş Y, Avcı A, Jablonski D, Darriba D, Stamatakis A, Lymberakis P, Poulakakis N. Cryptic diversity and phylogeographic patterns of Mediodactylus species in the Eastern Mediterranean region. Mol Phylogenet Evol 2024; 197:108091. [PMID: 38719080 DOI: 10.1016/j.ympev.2024.108091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 04/18/2024] [Accepted: 05/04/2024] [Indexed: 05/20/2024]
Abstract
Cryptic diversity poses a great obstacle in our attempts to assess the current biodiversity crisis and may hamper conservation efforts. The gekkonid genus Mediodactylus, a well-known case of hidden species and genetic diversity, has been taxonomically reclassified several times during the last decade. Focusing on the Mediterranean populations, a recent study within the M. kotschyi species complex using classic mtDNA/nuDNA markers suggested the existence of five distinct species, some being endemic and some possibly threatened, yet their relationships have not been fully resolved. Here, we generated genome-wide SNPs (using ddRADseq) and applied molecular species delimitation approaches and population genomic analyses to further disentangle these relationships. Τhe most extensive nuclear dataset, so far, encompassing 2,360 loci and ∼ 699,000 bp from across the genome of Mediodactylus gecko, enabled us to resolve previously obscure phylogenetic relationships among the five, recently elevated, Mediodactylus species and to support the hypothesis that the taxon includes several new, undescribed species. Population genomic analyses within each of the proposed species showed strong genetic structure and high levels of genetic differentiation among populations.
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Affiliation(s)
- Panayiota Kotsakiozi
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece.
| | - Aglaia Antoniou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Heraklion 71003, P.O. Box 2214, Crete, Greece
| | - Nikolaos Psonis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
| | - Κostas Sagonas
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
| | - Emmanouela Karameta
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
| | - Çetin Ilgaz
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca/İzmir 35160, Türkiye
| | - Yusuf Kumlutaş
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca/İzmir 35160, Türkiye
| | - Aziz Avcı
- Department of Biology, Faculty of Science, Aydın Adnan Menderes University, Aydın 09010, Türkiye
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Diego Darriba
- Computer Architecture Group, Centro de investigación CITIC, University of A Coruña, A Coruña, Spain
| | - Alexandros Stamatakis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Greece; Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany; Department of Informatics, Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe 76128, Germany
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
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2
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Pogorevc N, Dotsev A, Upadhyay M, Sandoval-Castellanos E, Hannemann E, Simčič M, Antoniou A, Papachristou D, Koutsouli P, Rahmatalla S, Brockmann G, Sölkner J, Burger P, Lymberakis P, Poulakakis N, Bizelis I, Zinovieva N, Horvat S, Medugorac I. Whole-genome SNP genotyping unveils ancestral and recent introgression in wild and domestic goats. Mol Ecol 2024; 33:e17190. [PMID: 37909668 DOI: 10.1111/mec.17190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/04/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023]
Abstract
After the domestication of goats around 10,000 years before the present (BP), humans transported goats far beyond the range of their wild ancestor, the bezoar goat. This brought domestic goats into contact with many wild goat species such as ibex and markhor, enabling introgression between domestic and wild goats. To investigate this, while shedding light on the taxonomic status of wild and domestic goats, we analysed genome-wide SNP data of 613 specimens from 14 taxonomic units, including Capra hircus, C. pyrenaica, C. ibex (from Switzerland, Austria, Germany and Slovenia), C. aegagrus aegagrus, C. a. cretica, C. h. dorcas, C. caucasica caucasica, C. c. severtzovi, C. c. cylindricornis, C. falconeri, C. sibirica sibirica, C. s. alaiana and C. nubiana, as well as Oreamnos americanus (mountain goat) as an outgroup. To trace gene flow between domestic and wild goats, we integrated genotype data of local goat breeds from the Alps as well as from countries such as Spain, Greece, Türkiye, Egypt, Sudan, Iran, Russia (Caucasus and Altai) and Pakistan. Our phylogenetic analyses displayed a clear separation between bezoar-type and ibex-type clades with wild goats from the Greek islands of Crete and Youra clustered within domestic goats, confirming their feral origin. Our analyses also revealed gene flow between the lineages of Caucasian tur and domestic goats that most likely occurred before or during early domestication. Within the clade of domestic goats, analyses inferred gene flow between African and Iberian goats. The detected events of introgression were consistent with previous reports and offered interesting insights into the historical relationships among domestic and wild goats.
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Affiliation(s)
- Neža Pogorevc
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University of Munich, Martinsried/Planegg, Germany
| | - Arsen Dotsev
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, Russia
| | - Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University of Munich, Martinsried/Planegg, Germany
| | - Edson Sandoval-Castellanos
- Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University of Munich, Martinsried/Planegg, Germany
| | - Elisabeth Hannemann
- Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University of Munich, Martinsried/Planegg, Germany
| | - Mojca Simčič
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Aglaia Antoniou
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Crete, Greece
| | - Dimitris Papachristou
- Laboratory of Animal Breeding and Husbandry, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Athens, Greece
| | - Panagiota Koutsouli
- Laboratory of Animal Breeding and Husbandry, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Athens, Greece
| | - Siham Rahmatalla
- Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Animal Breeding and Molecular Genetics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gudrun Brockmann
- Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Animal Breeding and Molecular Genetics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Johann Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Pamela Burger
- Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, Vetmeduni Vienna, Vienna, Austria
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Irakleio, Greece
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Irakleio, Greece
- Biology Department, School of Sciences and Engineering, University of Crete, Irakleio, Greece
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio, Greece
| | - Iosif Bizelis
- Laboratory of Animal Breeding and Husbandry, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Athens, Greece
| | - Natalia Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, Russia
| | - Simon Horvat
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University of Munich, Martinsried/Planegg, Germany
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Meadows JRS, Kidd JM, Wang GD, Parker HG, Schall PZ, Bianchi M, Christmas MJ, Bougiouri K, Buckley RM, Hitte C, Nguyen AK, Wang C, Jagannathan V, Niskanen JE, Frantz LAF, Arumilli M, Hundi S, Lindblad-Toh K, Ginja C, Agustina KK, André C, Boyko AR, Davis BW, Drögemüller M, Feng XY, Gkagkavouzis K, Iliopoulos G, Harris AC, Hytönen MK, Kalthof DC, Liu YH, Lymberakis P, Poulakakis N, Pires AE, Racimo F, Ramos-Almodovar F, Savolainen P, Venetsani S, Tammen I, Triantafyllidis A, vonHoldt B, Wayne RK, Larson G, Nicholas FW, Lohi H, Leeb T, Zhang YP, Ostrander EA. Author Correction: Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture. Genome Biol 2023; 24:255. [PMID: 37936157 PMCID: PMC10631033 DOI: 10.1186/s13059-023-03101-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Affiliation(s)
- Jennifer R S Meadows
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden.
| | - Jefrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA.
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Heidi G Parker
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Peter Z Schall
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA
| | - Matteo Bianchi
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Matthew J Christmas
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Katia Bougiouri
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Reuben M Buckley
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Christophe Hitte
- University of Rennes, CNRS, Institute Genetics and Development Rennes - UMR6290, 35000, Rennes, France
| | - Anthony K Nguyen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA
| | - Chao Wang
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Julia E Niskanen
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Laurent A F Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E14NS, UK and Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, D-80539, Munich, Germany
| | - Meharji Arumilli
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Sruthi Hundi
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Catarina Ginja
- BIOPOLIS-CIBIO-InBIO-Centro de Investigação Em Biodiversidade E Recursos Genéticos - ArchGen Group, Universidade Do Porto, 4485-661, Vairão, Portugal
| | | | - Catherine André
- University of Rennes, CNRS, Institute Genetics and Development Rennes - UMR6290, 35000, Rennes, France
| | - Adam R Boyko
- Department of Biomedical Sciences, Cornell University, 930 Campus Road, Ithaca, NY, 14853, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Michaela Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Xin-Yao Feng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Konstantinos Gkagkavouzis
- Department of Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Macedonia 54124, Greece and Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH, Balkan Center, Thessaloniki, Greece
| | - Giorgos Iliopoulos
- NGO "Callisto", Wildlife and Nature Conservation Society, 54621, Thessaloniki, Greece
| | - Alexander C Harris
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Marjo K Hytönen
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Daniela C Kalthof
- NGO "Callisto", Wildlife and Nature Conservation Society, 54621, Thessaloniki, Greece
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Petros Lymberakis
- Natural History Museum of Crete & Department of Biology, University of Crete, 71202, Irakleio, Greece
- Biology Department, School of Sciences and Engineering, University of Crete, Heraklion, Greece
- Palaeogenomics and Evolutionary Genetics Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Nikolaos Poulakakis
- Natural History Museum of Crete & Department of Biology, University of Crete, 71202, Irakleio, Greece
- Biology Department, School of Sciences and Engineering, University of Crete, Heraklion, Greece
- Palaeogenomics and Evolutionary Genetics Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Ana Elisabete Pires
- BIOPOLIS-CIBIO-InBIO-Centro de Investigação Em Biodiversidade E Recursos Genéticos - ArchGen Group, Universidade Do Porto, 4485-661, Vairão, Portugal
| | - Fernando Racimo
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | | | - Peter Savolainen
- Department of Gene Technology, Science for Life Laboratory, KTH - Royal Institute of Technology, 17121, Solna, Sweden
| | - Semina Venetsani
- Department of Genetics, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece
| | - Imke Tammen
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, 2570, Australia
| | - Alexandros Triantafyllidis
- Department of Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Macedonia 54124, Greece and Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH, Balkan Center, Thessaloniki, Greece
| | - Bridgett vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-7246, USA
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, OX1 3TG, UK
| | - Frank W Nicholas
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, 2570, Australia
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA.
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4
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Meadows JRS, Kidd JM, Wang GD, Parker HG, Schall PZ, Bianchi M, Christmas MJ, Bougiouri K, Buckley RM, Hitte C, Nguyen AK, Wang C, Jagannathan V, Niskanen JE, Frantz LAF, Arumilli M, Hundi S, Lindblad-Toh K, Ginja C, Agustina KK, André C, Boyko AR, Davis BW, Drögemüller M, Feng XY, Gkagkavouzis K, Iliopoulos G, Harris AC, Hytönen MK, Kalthoff DC, Liu YH, Lymberakis P, Poulakakis N, Pires AE, Racimo F, Ramos-Almodovar F, Savolainen P, Venetsani S, Tammen I, Triantafyllidis A, vonHoldt B, Wayne RK, Larson G, Nicholas FW, Lohi H, Leeb T, Zhang YP, Ostrander EA. Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture. Genome Biol 2023; 24:187. [PMID: 37582787 PMCID: PMC10426128 DOI: 10.1186/s13059-023-03023-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 07/25/2023] [Indexed: 08/17/2023] Open
Abstract
BACKGROUND The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function. RESULTS We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection. CONCLUSIONS We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.
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Affiliation(s)
- Jennifer R S Meadows
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden.
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA.
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Heidi G Parker
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Peter Z Schall
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA
| | - Matteo Bianchi
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Matthew J Christmas
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Katia Bougiouri
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Reuben M Buckley
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Christophe Hitte
- University of Rennes, CNRS, Institute Genetics and Development Rennes - UMR6290, 35000, Rennes, France
| | - Anthony K Nguyen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA
| | - Chao Wang
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Julia E Niskanen
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Laurent A F Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E14NS, UK and Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, D-80539, Munich, Germany
| | - Meharji Arumilli
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Sruthi Hundi
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Catarina Ginja
- BIOPOLIS-CIBIO-InBIO-Centro de Investigação Em Biodiversidade E Recursos Genéticos - ArchGen Group, Universidade Do Porto, 4485-661, Vairão, Portugal
| | | | - Catherine André
- University of Rennes, CNRS, Institute Genetics and Development Rennes - UMR6290, 35000, Rennes, France
| | - Adam R Boyko
- Department of Biomedical Sciences, Cornell University, 930 Campus Road, Ithaca, NY, 14853, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Michaela Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Xin-Yao Feng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Konstantinos Gkagkavouzis
- Department of Genetics, School of Biology, ), Aristotle University of Thessaloniki, Thessaloniki, Macedonia 54124, Greece and Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH, Balkan Center, Thessaloniki, Greece
| | - Giorgos Iliopoulos
- NGO "Callisto", Wildlife and Nature Conservation Society, 54621, Thessaloniki, Greece
| | - Alexander C Harris
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Marjo K Hytönen
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Daniela C Kalthoff
- NGO "Callisto", Wildlife and Nature Conservation Society, 54621, Thessaloniki, Greece
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Petros Lymberakis
- Natural History Museum of Crete & Department of Biology, University of Crete, 71202, Irakleio, Greece
- Biology Department, School of Sciences and Engineering, University of Crete, Heraklion, Greece
- Palaeogenomics and Evolutionary Genetics Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Nikolaos Poulakakis
- Natural History Museum of Crete & Department of Biology, University of Crete, 71202, Irakleio, Greece
- Biology Department, School of Sciences and Engineering, University of Crete, Heraklion, Greece
- Palaeogenomics and Evolutionary Genetics Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Ana Elisabete Pires
- BIOPOLIS-CIBIO-InBIO-Centro de Investigação Em Biodiversidade E Recursos Genéticos - ArchGen Group, Universidade Do Porto, 4485-661, Vairão, Portugal
| | - Fernando Racimo
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | | | - Peter Savolainen
- Department of Gene Technology, Science for Life Laboratory, KTH - Royal Institute of Technology, 17121, Solna, Sweden
| | - Semina Venetsani
- Department of Genetics, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece
| | - Imke Tammen
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, 2570, Australia
| | - Alexandros Triantafyllidis
- Department of Genetics, School of Biology, ), Aristotle University of Thessaloniki, Thessaloniki, Macedonia 54124, Greece and Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH, Balkan Center, Thessaloniki, Greece
| | - Bridgett vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-7246, USA
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, OX1 3TG, UK
| | - Frank W Nicholas
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, 2570, Australia
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA.
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5
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Strachinis I, Marschang RE, Lymberakis P, Karagianni KM, Azmanis P. Infectious disease threats to amphibians in Greece: new localities positive for Batrachochytrium dendrobatidis. Dis Aquat Organ 2022; 152:127-138. [PMID: 36519684 DOI: 10.3354/dao03712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
In the early 2000s, numerous cases of European amphibian population declines and mass die-offs started to emerge. Investigating those events led to the discovery that wild European amphibians were confronted with grave disease threats caused by introduced pathogens, namely the amphibian and the salamander chytrid fungi Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal) and ranaviruses. In Greece, Bd was previously documented among wild amphibian populations in 2 different locations and 3 different species. However, no disease-related mass declines or mortality events have been reported. In this work, we build upon previous findings with new, subsequently obtained data, resulting in a 225-sample dataset of 14 species from 17 different locations throughout Greece, in order to examine the occurrence status of all 3 pathogens responsible for emerging infectious diseases in European amphibians. No positive samples for Bsal or ranavirus were recorded in any location. We confirmed the presence of Bd in 4 more localities and in 4 more species, including 1 urodelan (Macedonian crested newt Triturus macedonicus) and 1 introduced anuran (American bullfrog Lithobates catesbeianus). All insular localities were negative for Bd, except for Crete, where Bd was identified in 2 different locations. Again, no mass declines or die-offs were recorded in any Bd-positive area or elsewhere. However, given the persistence of Bd across Greece over the past ~20 yr, monitoring efforts should continue, and ideally be further expanded.
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Affiliation(s)
- Ilias Strachinis
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Natural Sciences, Aristotle University of Thessaloniki, 54636, Greece
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6
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Li Y, Bletsa M, Zisi Z, Boonen I, Gryseels S, Kafetzopoulou L, Webster JP, Catalano S, Pybus OG, Van de Perre F, Li H, Li Y, Li Y, Abramov A, Lymberakis P, Lemey P, Lequime S. Endogenous Viral Elements in Shrew Genomes Provide Insights into Pestivirus Ancient History. Mol Biol Evol 2022; 39:6692409. [PMID: 36063436 PMCID: PMC9550988 DOI: 10.1093/molbev/msac190] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
As viral genomic imprints in host genomes, endogenous viral elements (EVEs) shed light on the deep evolutionary history of viruses, ancestral host ranges, and ancient viral-host interactions. In addition, they may provide crucial information for calibrating viral evolutionary timescales. In this study, we conducted a comprehensive in silico screening of a large data set of available mammalian genomes for EVEs deriving from members of the viral family Flaviviridae, an important group of viruses including well-known human pathogens, such as Zika, dengue, or hepatitis C viruses. We identified two novel pestivirus-like EVEs in the reference genome of the Indochinese shrew (Crocidura indochinensis). Homologs of these novel EVEs were subsequently detected in vivo by molecular detection and sequencing in 27 shrew species, including 26 species representing a wide distribution within the Crocidurinae subfamily and one in the Soricinae subfamily on different continents. Based on this wide distribution, we estimate that the integration event occurred before the last common ancestor of the subfamily, about 10.8 million years ago, attesting to an ancient origin of pestiviruses and Flaviviridae in general. Moreover, we provide the first description of Flaviviridae-derived EVEs in mammals even though the family encompasses numerous mammal-infecting members. This also suggests that shrews were past and perhaps also current natural reservoirs of pestiviruses. Taken together, our results expand the current known Pestivirus host range and provide novel insight into the ancient evolutionary history of pestiviruses and the Flaviviridae family in general.
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Affiliation(s)
- Yiqiao Li
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Magda Bletsa
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Zafeiro Zisi
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Ine Boonen
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Sophie Gryseels
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium,Belgium Evolutionary Ecology Group, University of Antwerp, 2610 Wilrijk, Belgium
| | - Liana Kafetzopoulou
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium,Virology Department, Belgium Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Joanne P Webster
- Department of Pathobiology and Population Science, Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - Stefano Catalano
- Department of Pathobiology and Population Science, Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - Oliver G Pybus
- Department of Pathobiology and Population Science, Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | | | - Haotian Li
- Marine College, Shandong University (Weihai), 264209 Weihai, China
| | - Yaoyao Li
- Marine College, Shandong University (Weihai), 264209 Weihai, China
| | - Yuchun Li
- Marine College, Shandong University (Weihai), 264209 Weihai, China
| | - Alexei Abramov
- Laboratory of Theriology, Zoological Institute of the Russian Academy of Sciences, 190121 Saint Petersburg, Russia
| | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
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7
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Şahin MK, Candan K, Karakasi D, Lymberakis P, Poulakakis N, Kumlutaş Y, Yildirim E, Ilgaz Ç. Ecological niche differentiation in the Anatolian rock lizards (Genus: Anatololacerta) (Reptilia: Lacertidae) of the Anatolian Peninsula and Aegean Islands. Acta Herpetol 2022. [DOI: 10.36253/a_h-13089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The genus Anatololacerta is distributed in the eastern Mediterranean region including Asia Minor and some east Aegean islands. Recent phylogenetic studies suggested that this genus displayed cryptic diversity and was divided into five species: A. anatolica, A. pelasgiana, A. ibrahimi, A. finikensis and A. danfordi. The ecological niche differentiations of these species have not been studied so far. Our aims for this study were to predict the potential suitable habitats for the species nested in genus Anatololacerta, and to examine the niche overlaps and differentiations via identity and background tests. The occurrence data were obtained from literature and our own field surveys. Occurrence records were rarefied and assessed in a 30 arc-second resolution layer, compatible with several bioclimatic and topographic variables. Species distribution analyses were performed using maximum entropy approach and pairwise niche comparisons were evaluated by identity and background tests. Our results demonstrated that the species delimitation among this genus was not only affected by geographic isolation but also that precipitation and temperature influenced the habitat suitability for these species. Predicted suitability usually well matched the actual species distributions. Moreover, the niche overlap (identity test) analyses verified that allopatric Anatololacerta species show clear ecological differentiations. However, a niche overlap between parapatric species A. pelasgiana and A. finikensis, was confirmed by identity and background tests. It has been suggested that these parapatric species could be more affected by microclimatological parameters than the others. The results of our study are in agreement with the latest phylogenetic study within this genus.
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8
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Stratakis M, Koutmanis I, Ilgaz Ç, Jablonski D, Kukushkin OV, Crnobrnja‐Isailovic J, Carretero MA, Liuzzi C, Kumlutaş Y, Lymberakis P, Poulakakis N. Evolutionary divergence of the smooth snake (Serpentes, Colubridae): The role of the Balkans and Anatolia. ZOOL SCR 2022. [DOI: 10.1111/zsc.12533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Manos Stratakis
- Department of Biology School of Sciences and Engineering University of Crete Irakleio Greece
- Natural History Museum of Crete School of Sciences and Engineering University of Crete Irakleio Greece
| | - Iraklis Koutmanis
- Department of Biology School of Sciences and Engineering University of Crete Irakleio Greece
- Natural History Museum of Crete School of Sciences and Engineering University of Crete Irakleio Greece
| | - Çetin Ilgaz
- Department of Biology Faculty of Science Dokuz Eylül University Buca‐İzmir Turkey
- Research and Application Center for Fauna and Flora Dokuz Eylul University Buca‐İzmir Turkey
| | - Daniel Jablonski
- Department of Zoology Comenius University in Bratislava Bratislava Slovakia
| | - Oleg V. Kukushkin
- Department of Biodiversity Studies and Ecological Monitoring T.I. Vyazemski Karadag Research Station – Nature Reserve of Russian Academy of Sciences Theodosia Crimea
- Department of Herpetology Institute of Zoology of Russian Academy of Sciences Saint Petersburg Russia
| | - Jelka Crnobrnja‐Isailovic
- Department of Biology and Ecology Faculty of Sciences and Mathematics University of Niš Niš Serbia
- Department of Evolutionary Biology Institute for Biological Research “Siniša Stanković” ‐ National Institute of Republic of Serbia University of Belgrade Beograd Serbia
| | - Miguel A. Carretero
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Universidade do Porto Vila do Conde Portugal
- Departamento de Biologia Faculdade de Ciências da Universidade do Porto Porto Portugal
- BIOPOLIS Program in Genomics Biodiversity and Land Planning CIBIO Vairão Portugal
| | | | - Yusuf Kumlutaş
- Department of Biology Faculty of Science Dokuz Eylül University Buca‐İzmir Turkey
- Research and Application Center for Fauna and Flora Dokuz Eylul University Buca‐İzmir Turkey
| | - Petros Lymberakis
- Natural History Museum of Crete School of Sciences and Engineering University of Crete Irakleio Greece
| | - Nikos Poulakakis
- Department of Biology School of Sciences and Engineering University of Crete Irakleio Greece
- Natural History Museum of Crete School of Sciences and Engineering University of Crete Irakleio Greece
- Institute of Molecular Biology and Biotechnology (IMBB) Foundation for Research and Technology ‐ Hellas (FORTH) Irakleio Greece
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9
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Karameta E, Lymberakis P, Grillitsch H, Ilgaz Ç, Avci A, Kumlutaş Y, Candan K, Wagner P, Sfenthourakis S, Pafilis P, Poulakakis N. The story of a rock-star: multilocus phylogeny and species delimitation in the starred or roughtail rock agama, Laudakia stellio (Reptilia: Agamidae). Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlab107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Situated at the junction of three continents, Europe, Asia and Africa, the Eastern Mediterranean is an ideal region to study the effects of palaeogeography, ecology and long human presence on animal evolution. Laudakia stellio (Squamata: Agamidae) is found across this region and offers an excellent opportunity for such studies. The high morphological variation across their range suggests that these lizards might represent a species complex. This is the first study exploring their evolutionary history, using molecular markers and individuals from all described subspecies. We employed the latest phylogenetic and species-delimitation methods to identify all distinct evolutionary lineages, their genetic variation and divergence times. The phenotypical diversity of L. stellio matches its genetic differentiation: almost all subspecies correspond to well-supported retrieved subclades and additional distinct lineages representing intermediate morphs have been retrieved. ‘Laudakia stellio’ represents three distinct evolutionary entities that diverged during the Plio-Pleistocene transition, which we propose as distinct species. One includes Greek and Turkish populations, as well as cryptic Anatolian lineages. The second comprises all other Near East populations and the third is endemic to Cyprus. Our results indicate a role of humans in shaping present distribution patterns, and highlight the importance of the Aegean, Anatolia and the Levant as glacial refugia and diversity hotspots.
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Affiliation(s)
- Emmanouela Karameta
- Section of Zoology and Marine Biology, Department of Biology, University of Athens, Panepistimioupolis, 15771 Athens, Greece
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, 71409 Irakleio, Greece
- Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, 70013 Irakleio, Greece
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, 71409 Irakleio, Greece
| | - Heinz Grillitsch
- Herpetological Collection, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Çetin Ilgaz
- Department of Biology, Faculty of Science, Dokuz Eylül University, 35160 Buca- İzmir, Turkey
- Fauna and Flora Research Centre, Dokuz Eylül University, 35610 Buca- İzmir, Turkey
| | - Aziz Avci
- Department of Biology, Faculty of Science and Arts, Aydın Adnan Menderes University, Aydın, Turkey
| | - Yusuf Kumlutaş
- Department of Biology, Faculty of Science, Dokuz Eylül University, 35160 Buca- İzmir, Turkey
- Fauna and Flora Research Centre, Dokuz Eylül University, 35610 Buca- İzmir, Turkey
| | - Kamil Candan
- Department of Biology, Faculty of Science, Dokuz Eylül University, 35160 Buca- İzmir, Turkey
| | | | - Spyros Sfenthourakis
- Department of Biological Sciences, University of Cyprus, University Campus, 2109 Aglantzia, Nicosia, Cyprus
| | - Panayiotis Pafilis
- Section of Zoology and Marine Biology, Department of Biology, University of Athens, Panepistimioupolis, 15771 Athens, Greece
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, 71409 Irakleio, Greece
- Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, 70013 Irakleio, Greece
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10
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Machado AP, Topaloudis A, Cumer T, Lavanchy E, Bontzorlos V, Ceccherelli R, Charter M, Kassinis N, Lymberakis P, Manzia F, Ducrest AL, Dupasquier M, Guex N, Roulin A, Goudet J. Genomic consequences of colonisation, migration and genetic drift in barn owl insular populations of the eastern Mediterranean. Mol Ecol 2021; 31:1375-1388. [PMID: 34894026 PMCID: PMC9305133 DOI: 10.1111/mec.16324] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/01/2021] [Accepted: 11/17/2021] [Indexed: 01/25/2023]
Abstract
The study of insular populations was key in the development of evolutionary theory. The successful colonisation of an island depends on the geographic context, and specific characteristics of the organism and the island, but also on stochastic processes. As a result, apparently identical islands may harbour populations with contrasting histories. Here, we use whole genome sequences of 65 barn owls to investigate the patterns of inbreeding and genetic diversity of insular populations in the eastern Mediterranean Sea. We focus on Crete and Cyprus, islands with similar size, climate and distance to mainland, that provide natural replicates for a comparative analysis of the impacts of microevolutionary processes on isolated populations. We show that barn owl populations from each island have a separate origin, Crete being genetically more similar to other Greek islands and mainland Greece, and Cyprus more similar to the Levant. Further, our data show that their respective demographic histories following colonisation were also distinct. On the one hand, Crete harbours a small population and maintains very low levels of gene flow with neighbouring populations. This has resulted in low genetic diversity, strong genetic drift, increased relatedness in the population and remote inbreeding. Cyprus, on the other hand, appears to maintain enough gene flow with the mainland to avoid such an outcome. Our study provides a comparative population genomic analysis of the effects of neutral processes on a classical island‐mainland model system. It provides empirical evidence for the role of stochastic processes in determining the fate of diverging isolated populations.
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Affiliation(s)
- Ana Paula Machado
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Tristan Cumer
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Eléonore Lavanchy
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Vasileios Bontzorlos
- Green Fund, Kifisia, Athens, Greece.,"TYTO" - Organization for the Management and Conservation of Biodiversity in Agricultural Ecosystems, Larisa, Greece
| | | | - Motti Charter
- Shamir Research Institute, University of Haifa, Katzrin, Israel.,Department of Geography and Environmental Sciences, University of Haifa, Haifa, Israel
| | | | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Herakleio, Greece
| | | | - Anne-Lyse Ducrest
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Nicolas Guex
- Bioinformatics Competence Centre, University of Lausanne, Lausanne, Switzerland
| | - Alexandre Roulin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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11
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Yousefabadi F, Rastegar Pouyani E, Keikhosravi A, Rastegar Pouyani N, Avcı A, Üzüm N, Olgun K, Kumlutaş Y, Lymberakis P, Ilgaz Ç, Hosseinian Yousefkhani SS. An integrative approach uncovered variation within
Trapelus ruderatus
(Olivier, 1804) (Squamata: Agamidae) in Western Asia. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fariba Yousefabadi
- Department of Biology Faculty osf Science Hakim Sabzevari University Sabzevar Iran
| | | | - Alireza Keikhosravi
- Department of Biology Faculty osf Science Hakim Sabzevari University Sabzevar Iran
| | | | - Aziz Avcı
- Faculty of Science and Arts Department of Biology Aydın Adnan Menderes University Aydın Turkey
| | - Nazan Üzüm
- Faculty of Science and Arts Department of Biology Aydın Adnan Menderes University Aydın Turkey
| | - Kurtuluş Olgun
- Faculty of Science and Arts Department of Biology Aydın Adnan Menderes University Aydın Turkey
| | - Yusuf Kumlutaş
- Department of Biology Faculty of Science Dokuz Eylül University Buca‐İzmir Turkey
- Research and Application Center for Fauna Flora Dokuz Eylul University Buca‐İzmir Turkey
| | | | - Çetin Ilgaz
- Department of Biology Faculty of Science Dokuz Eylül University Buca‐İzmir Turkey
- Research and Application Center for Fauna Flora Dokuz Eylul University Buca‐İzmir Turkey
| | - Seyyed Saeed Hosseinian Yousefkhani
- Department of Animal Science School of Biology Damghan University Damghan Iran
- Institute of Biological Science School of Biology Damghan University Damghan Iran
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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Jablonski D, Sillero N, Oskyrko O, Bellati A, Čeirāns A, Cheylan M, Cogălniceanu D, Crnobrnja-Isailović J, Crochet PA, Crottini A, Doronin I, Džukić G, Geniez P, Ilgaz Ç, Iosif R, Jandzik D, Jelić D, Litvinchuk S, Ljubisavljević K, Lymberakis P, Mikulíček P, Mizsei E, Moravec J, Najbar B, Pabijan M, Pupins M, Sourrouille P, Strachinis I, Szabolcs M, Thanou E, Tzoras E, Vergilov V, Vörös J, Gvoždík V. The distribution and biogeography of slow worms (Anguis, Squamata) across the Western Palearctic, with an emphasis on secondary contact zones. AMPHIBIA-REPTILIA 2021. [DOI: 10.1163/15685381-bja10069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
The slow-worm lizards (Anguis) comprise five species occurring throughout most of the Western Palearctic. Although these species are relatively uniform morphologically – with the exception of A. cephallonica, which exhibits a quite unique morphology – they are genetically deeply divergent. Here, we provide detailed distribution maps for each species and discuss their biogeography and conservation based on updated genetic data and a robust distribution database. We pay particular attention to the so called ‘grey zone’, which typically represents secondary contact zones and in some cases confirmed or presumed hybrid zones. Four of the five species live in parapatry, while only two species, A. cephallonica and A. graeca from the southern Balkans occur in partial sympatry. Further research should focus on the eco-evolutionary interactions between species in contact, including their hybridization rates, to reveal deeper details of the slow-worm evolutionary and natural history.
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Affiliation(s)
- Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 842 15 Bratislava, Slovakia
| | - Neftalí Sillero
- CICGE Centro de Investigação em Ciências Geo-Espaciais, Faculdade de Ciências da Universidade do Porto (FCUP), Alameda do Monte da Virgem, 4430-146, Vila Nova de Gaia, Portugal
| | - Oleksandra Oskyrko
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague, Czech Republic
| | - Adriana Bellati
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’università snc, 01100 Viterbo, Italy
| | - Andris Čeirāns
- Daugavpils University, Department of Ecology, Daugavpils, Latvia
| | - Marc Cheylan
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Biogeography and Ecology of Vertebrates, Montpellier, France
| | - Dan Cogălniceanu
- University Ovidius Constanţa, Faculty of Natural Sciences and Agricultural Sciences, Al. Universităţii 1, 900470 Constanţa, Romania
| | - Jelka Crnobrnja-Isailović
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18000 Niš, Serbia
- Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković” – National Institute of Republic of Serbia, University of Belgrade, Despota Stefana 142, 11060 Belgrade, Serbia
| | | | - Angelica Crottini
- CIBIO, Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, No 7, 4485-661 Vairão, Portugal
| | - Igor Doronin
- Zoological Institute of the Russian Academy of Sciences, Universitetskaya Emb. 1, 199034 Saint Petersburg, Russia
| | - Georg Džukić
- Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković” – National Institute of Republic of Serbia, University of Belgrade, Despota Stefana 142, 11060 Belgrade, Serbia
| | - Philippe Geniez
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Biogeography and Ecology of Vertebrates, Montpellier, France
| | - Çetin Ilgaz
- Dokuz Eylül University, Faculty of Science, Department of Biology, Buca-İzmir, Turkey
- Dokuz Eylül University, Fauna and Flora Research Centre, 35610, Buca-İzmir, Turkey
| | - Ruben Iosif
- University Ovidius Constanţa, Faculty of Natural Sciences and Agricultural Sciences, Al. Universităţii 1, 900470 Constanţa, Romania
| | - David Jandzik
- Department of Zoology, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 842 15 Bratislava, Slovakia
| | - Dušan Jelić
- Croatian Institute for Biodiversity, BIOTA Ltd, Zagreb, Croatia
| | - Spartak Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, 194064 Saint Petersburg, Russia
| | - Katarina Ljubisavljević
- Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković” – National Institute of Republic of Serbia, University of Belgrade, Despota Stefana 142, 11060 Belgrade, Serbia
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Ave. 71409 Irakleio, Greece
| | - Peter Mikulíček
- Department of Zoology, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 842 15 Bratislava, Slovakia
| | - Edvárd Mizsei
- Department of Ecology, University of Debrecen, Debrecen, Hungary
| | - Jiří Moravec
- National Museum, Department of Zoology, Prague, Czech Republic
| | - Bartłomiej Najbar
- University of Zielona Góra, Faculty of Biological Sciences, Department of Zoology, Prof. Z. Szafrana 1, 65-616, Zielona Góra, Poland
| | - Maciej Pabijan
- Institute of Zoology and Biomedical Research, Jagiellonian University, ul. Gronostajowa 9, 30-387, Kraków, Poland
| | - Mihails Pupins
- Daugavpils University, Department of Ecology, Daugavpils, Latvia
| | | | - Ilias Strachinis
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Natural Sciences, Aristotle University of Thessaloniki, Greece
| | - Márton Szabolcs
- Department of Tisza River Research, Institute of Aquatic Ecology, Centre for Ecological Research, Bem tér 18/C, 4026, Debrecen, Hungary
| | - Evanthia Thanou
- Section of Animal Biology, Department of Biology, School of Natural Sciences, University of Patras, Rion University Campus, GR-26500 Patras, Greece
| | | | - Vladislav Vergilov
- National Museum of Natural History at the Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000 Sofia, Bulgaria
| | - Judit Vörös
- Department of Zoology, Hungarian Natural History Museum, Baross u. 13., 1088, Budapest, Hungary
| | - Václav Gvoždík
- National Museum, Department of Zoology, Prague, Czech Republic
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
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15
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Itescu Y, Foufopoulos J, Schwarz R, Lymberakis P, Slavenko A, Gavriilidi IA, Meiri S, Pafilis P. The Island of Extremes: Giants and Dwarfs on a Small Remote Island. RUSS J HERPETOL 2021. [DOI: 10.30906/1026-2296-2021-28-4-225-230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Body size evolution on islands is widely studied and hotly debated. Gigantism and dwarfism are thought to evolve under strong natural selection, especially on small remote islands. We report a curious co-occurrence of both dwarf and giant lizards on the same small, remote island (Plakida): the largest Podarcis erhardii (Lacertidae) and smallest Mediodactylus kotschyi sensu lato; Gekkonidae — the two commonest insular reptiles in the Aegean Sea. The geckos of Plakida have a peculiar tail-waving behavior, documented here for the first time in this genus. We suspect that P. erhardii evolved large size to consume geckos and the geckos evolved a unique tail-waving behavior as a defensive mechanism.
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16
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Diakou A, Migli D, Dimzas D, Morelli S, Di Cesare A, Youlatos D, Lymberakis P, Traversa D. Endoparasites of European Wildcats ( Felis silvestris) in Greece. Pathogens 2021; 10:pathogens10050594. [PMID: 34068209 PMCID: PMC8153176 DOI: 10.3390/pathogens10050594] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/07/2021] [Accepted: 05/12/2021] [Indexed: 11/25/2022]
Abstract
The European wildcat (Felis silvestris) is the only wild felid living in Greece. Wildcat populations are declining due to anthropogenic and phenological unfavourable conditions, and parasites may have an additional negative impact. In the present study, the occurrence of endoparasites in wildcats in Greece and the potential threats posed to wildcats, domestic animals, and humans in the study areas has been investigated. In a six-year period, 23 road-killed wildcats and 62 wildcat faecal samples were collected from different areas of the country. Necropsy for the detection of endoparasites and standard parasitological examinations of faecal samples were performed. Parasites were morphologically identified and, in selected cases, molecularly analysed. All necropsied wildcats (100%) were infected by three to 10 different parasite taxa, with the most prevalent being Taenia taeniaeformis (73.9%), Toxocara cati (60.9%), Angiostrongylus chabaudi (56.5%), Ancylostoma tubaeforme (39.1%), Cylicospirura spp. (34.8%), Troglostrongylus brevior (34.8%), and Capillaria aerophila (33.8%). Of the 62 faecal samples examined, 53 (85.5%) were positive for one or more parasite elements (larvae, eggs, or oocysts). The most frequent were T. cati (45.2%), A. chabaudi (29%), C. aerophila (24.2%), and Ancylostomatidae (17.7%). This is the first survey on endoparasites affecting wildcats in Greece. Some of the parasites here found are frequent in domestic and wild felids, while others, i.e., Oslerus rostratus and Cylicospirura petrowi, were described for the first time in the European wildcat. Most of them have a significant pathogenic potential, causing severe to hazardous diseases to infected felids and some, under specific circumstances, can also threaten human health.
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Affiliation(s)
- Anastasia Diakou
- School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
- Correspondence:
| | - Despina Migli
- School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (D.M.); (D.Y.)
| | - Dimitris Dimzas
- School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Simone Morelli
- Faculty of Veterinary Medicine, University Teaching Veterinary Hospital, University of Teramo, 64100 Teramo, Italy; (S.M.); (A.D.C.); (D.T.)
| | - Angela Di Cesare
- Faculty of Veterinary Medicine, University Teaching Veterinary Hospital, University of Teramo, 64100 Teramo, Italy; (S.M.); (A.D.C.); (D.T.)
| | - Dionisios Youlatos
- School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (D.M.); (D.Y.)
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossou Avenue, 71409 Irakleio, Greece;
| | - Donato Traversa
- Faculty of Veterinary Medicine, University Teaching Veterinary Hospital, University of Teramo, 64100 Teramo, Italy; (S.M.); (A.D.C.); (D.T.)
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17
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Mazzoleni S, Němec P, Albrecht T, Lymberakis P, Kratochvíl L, Rovatsos M. Long-term stability of sex chromosome gene content allows accurate qPCR-based molecular sexing across birds. Mol Ecol Resour 2021; 21:2013-2021. [PMID: 33720488 DOI: 10.1111/1755-0998.13381] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/13/2021] [Accepted: 03/08/2021] [Indexed: 12/14/2022]
Abstract
Embryos, juveniles, and even adults of many bird species lack pronounced external sexually dimorphic characteristics. Accurate identification of sex is crucial for research (e.g., developmental, population, and evolutionary studies), management of wildlife species, and captive breeding programmes for both conservation and poultry. An accurate molecular sexing method applicable across the entire bird radiation is theoretically possible thanks to the long-term stability of their ZZ/ZW sex chromosomes, but current methods are not applicable in a wide range of bird lineages. Here, we developed a novel molecular sexing method based on the comparison of gene copy number variation by quantitative real-time PCR (qPCR) in conserved Z-specific genes (CHRNA6, DDX4, LPAR1, TMEM161B, VPS13A), i.e. genes linked to Z but absent from W chromosomes. We tested the method across three paleognath and 70 neognath species covering the avian phylogeny. In addition, we designed primers for four Z-specific genes (DOCK8, FUT10, PIGG and PSD3) for qPCR-based molecular sexing in three paleognath species. We have demonstrated that the genes DOCK8, FUT10, PIGG and PSD3 can identify sex in paleognath birds and the genes CHRNA6, DDX4, TMEM161B, and VPS13A can reveal sex in neognath birds. The gene LPAR1 can be used to accurately identify sex in both paleognath and neognath species. Along with outlining a novel method of practical importance for molecular sexing in birds, our study also documents in detail the conservation of sex chromosomes across the avian phylogeny.
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Affiliation(s)
- Sofia Mazzoleni
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Pavel Němec
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tomáš Albrecht
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Irakleio, Greece
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
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18
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Jablonski D, Gkontas I, Poursanidis D, Lymberakis P, Poulakakis N. Stability in the Balkans: phylogeography of the endemic Greek stream frog, Rana graeca. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
We still have little knowledge concerning the phylogeography of amphibians and reptiles from the Balkan Peninsula compared with the other two Mediterranean peninsulas. This raises concerns for endemic taxa from these peninsulas, because it might interfere with further conservation efforts. Here we focus on the endemic Greek stream frog (Rana graeca) and reconstruct its biogeography and evolutionary history. Using four genetic markers (Cytb, 16S, COI and BDNF) in > 350 sequences covering the whole distribution range, we conducted phylogenetic, demographic and ecological niche analyses, which revealed the phylogeography of this species. Surprisingly, this examination of R. graeca reveals a very shallow level of intraspecific genetic variability through the Balkans, with two main, statistically supported lineages having a partly sympatric distribution. The most variable marker was Cytb, which showed 19 haplotypes in 123 analysed sequences in the whole species distribution area. Here presented genetic data, together with the environmental niche projection and demographic analyses suggest that R. graeca was probably affected only marginally by climatic oscillations, with the Hellenides as the most suitable area for the occurrence of the species in different geological periods. This is consistent with the observed genetic diversity, which is mostly related to these mountains. Although the species shows a certain level of phenotypic variability and ecological preferences, this might be related to species plasticity affected by the micro-climatic conditions in small areas, which merits further research. Comparing phylogeography of other amphibian and reptile species in the Balkans, we showed that the observed pattern represents a new view on the phylogeography of the Balkan herpetofauna.
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Affiliation(s)
- Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
| | - Ioannis Gkontas
- Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Irakleio, Greece
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio, Greece
| | - Dimitris Poursanidis
- Foundation for Research and Technology Hellas, Institute of Applied and Computational Mathematics, The Remote Sensing Lab, Vassilika Vouton, Irakleio, Greece
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio, Greece
| | - Nikos Poulakakis
- Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Irakleio, Greece
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio, Greece
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19
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Psonis N, Antoniou A, Karameta E, Darriba D, Stamatakis A, Lymberakis P, Poulakakis N. The wall lizards of the Balkan peninsula: Tackling questions at the interface of phylogenomics and population genomics. Mol Phylogenet Evol 2021; 159:107121. [PMID: 33609707 DOI: 10.1016/j.ympev.2021.107121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 01/12/2021] [Accepted: 02/09/2021] [Indexed: 11/24/2022]
Abstract
Wall lizards of the genus Podarcis (Sauria, Lacertidae) are the predominant reptile group in southern Europe, including 24 recognized species. Mitochondrial DNA data have shown that, with the exception of P. muralis, the Podarcis species distributed in the Balkan peninsula form a species group that is further sub-divided into two subgroups: the one of "P. tauricus" consisting of P. tauricus, P. milensis, P. gaigeae, and P. melisellensis, and the other of "P. erhardii" comprising P. erhardii, P. levendis, P. cretensis, and P. peloponnesiacus. In an attempt to explore the Balkan Podarcis phylogenomic relationships, assess the levels of genetic structure and to re-evaluate the number of extant species, we employed phylogenomic and admixture approaches on ddRADseq (double digested Restriction site Associated DNA sequencing) genomic data. With this efficient Next Generation Sequencing approach, we were able to obtain a large number of genomic loci randomly distributed throughout the genome and use them to resolve the previously obscure phylogenetic relationships among the different Podarcis species distributed in the Balkans. The obtained phylogenomic relationships support the monophyly of both aforementioned subgroups and revealed several divergent lineages within each subgroup, stressing the need for taxonomic re-evaluation of Podarcis' species in Balkans. The phylogenomic trees and the species delimitation analyses confirmed all recently recognized species (P. levendis, P. cretensis, and P. ionicus) and showed the presence of at least two more species, one in P. erhardii and the other in P. peloponnesiacus.
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Affiliation(s)
- Nikolaos Psonis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Irakleio 70013, Greece.
| | - Aglaia Antoniou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Gournes Pediados, Irakleio, P.O. Box 2214, 71003 Crete, Greece
| | - Emmanouela Karameta
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Irakleio 70013, Greece
| | - Diego Darriba
- Universidade da Coruña, CITIC, Computer Architecture Group, Campus de Elviña, 15071 A Coruña, Spain
| | - Alexandros Stamatakis
- The Exelixis Lab, Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany; Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Postfach 6980, 76128 Karlsruhe, Germany
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio 71409, Greece
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Irakleio 70013, Greece
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20
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Karakasi D, Ilgaz Ç, Kumlutaş Y, Candan K, Güçlü Ö, Kankılıç T, Beşer N, Sindaco R, Lymberakis P, Poulakakis N. More evidence of cryptic diversity in Anatololacerta species complex Arnold, Arribas and Carranza, 2007 (Squamata: Lacertidae) and re-evaluation of its current taxonomy. AMPHIBIA-REPTILIA 2021. [DOI: 10.1163/15685381-bja10045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Genetic diversity is not always congruent with phenotypic heterogeneity, resulting in cryptic species complexes which cause a great struggle for scientists trying to define ‘species’ and describe relationships among taxa. Anatololacerta is a lizard genus distributed in southern and western Anatolia and some neighboring Aegean islands. Three morphospecies were recognized in Anatololacerta but a recent molecular study revealed the presence of cryptic diversity within the genus which led to the raise of a subspecies to species level. Currently the genus includes the species A. anatolica, A. danfordi, A. budaki and A. pelasgiana. Using a comprehensive sampling concerning both the number of specimens (218 specimens) and the genetic markers (3 nuclear and 3 mitochondrial), we performed phylogenetic analyses including tree reconstruction, species delimitation and divergence times estimation. The results revealed the occurrence of one more cryptic lineage which should be regarded as a separate species for which the name A. ibrahimi stat. nov. has priority. The existence of five well differentiated species with parapatric distributions in Anatololacerta is strongly supported. There is also evidence of recent and rapid radiation of the genus which probably causes phylogenetic relationships between these species to remain largely unresolved. At last, we proceeded to some nomenclatorial changes: The current name A. budaki was synonymized with A. pelasgiana because specimens of the type-locality of A. budaki are assigned genetically to A. pelasgiana. The genetic lineage including specimens currently assigned to A. budaki was named A. finikensis stat. nov., raising the subspecies A. b. finikensis to species level.
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Affiliation(s)
- Danae Karakasi
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Av, 71409 Irakleio, Greece
| | - Çetin Ilgaz
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca, İzmir, Turkey
- Research and Application Center for Fauna Flora, Dokuz Eylül University, Buca, İzmir, Turkey
| | - Yusuf Kumlutaş
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca, İzmir, Turkey
- Research and Application Center for Fauna Flora, Dokuz Eylül University, Buca, İzmir, Turkey
| | - Kamil Candan
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca, İzmir, Turkey
| | - Özgür Güçlü
- Department of Plant and Animal Production, Sultanhisar Vocational School, Aydın Adnan Menderes University, Sultanhisar, Aydın, Turkey
| | - Tolga Kankılıç
- Department of Biology, Faculty of Science and Arts, Aksaray University, Aksaray, Turkey
| | - Nurettin Beşer
- Department of Biology, Graduate School of Natural and Applied Sciences, Aydın Adnan Menderes University, Aydın, Turkey
| | - Roberto Sindaco
- Museo Civico di Storia Naturale, 10022 Carmagnola (Torino), Italy
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Av, 71409 Irakleio, Greece
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Av, 71409 Irakleio, Greece
- Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, 70013, Irakleio, Greece
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21
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Li Z, Martel A, Bogaerts S, Göçmen B, Pafilis P, Lymberakis P, Woeltjes T, Veith M, Pasmans F. Landscape Connectivity Limits the Predicted Impact of Fungal Pathogen Invasion. J Fungi (Basel) 2020; 6:E205. [PMID: 33022972 PMCID: PMC7712934 DOI: 10.3390/jof6040205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 12/11/2022] Open
Abstract
Infectious diseases are major drivers of biodiversity loss. The risk of fungal diseases to the survival of threatened animals in nature is determined by a complex interplay between host, pathogen and environment. We here predict the risk of invasion of populations of threatened Mediterranean salamanders of the genus Lyciasalamandra by the pathogenic chytrid fungus Batrachochytrium salamandrivorans by combining field sampling and lab trials. In 494 samples across all seven species of Lyciasalamandra, B. salamandrivorans was found to be absent. Single exposure to a low (1000) number of fungal zoospores resulted in fast buildup of lethal infections in three L. helverseni. Thermal preference of the salamanders was well within the thermal envelope of the pathogen and body temperatures never exceeded the fungus' thermal critical maximum, limiting the salamanders' defense opportunities. The relatively low thermal host preference largely invalidates macroclimatic based habitat suitability predictions and, combined with current pathogen absence and high host densities, suggests a high probability of local salamander population declines upon invasion by B. salamandrivorans. However, the unfavorable landscape that shaped intraspecific host genetic diversity, lack of known alternative hosts and rapid host mortality after infection present barriers to further, natural pathogen dispersal between populations and thus species extinction. The risk of anthropogenic spread stresses the importance of biosecurity in amphibian habitats.
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Affiliation(s)
- Zhimin Li
- Wildlife Health Ghent, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B9820 Merelbeke, Belgium; (Z.L.); (A.M.)
| | - An Martel
- Wildlife Health Ghent, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B9820 Merelbeke, Belgium; (Z.L.); (A.M.)
| | | | - Bayram Göçmen
- Faculty of Science, Department of Biology, Zoology Section, Ege University, TR-35100 İzmir, Turkey
| | - Panayiotis Pafilis
- Department of Zoology and Marine Biology, School of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, Ilissia, 15784 Athens, Greece;
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Ave., 1409 Irakleio, Greece;
| | | | - Michael Veith
- Department of Biogeography, Trier University, Universitätsring 15, D-54296 Trier, Germany;
| | - Frank Pasmans
- Wildlife Health Ghent, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B9820 Merelbeke, Belgium; (Z.L.); (A.M.)
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22
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Spilani L, Bougiouri K, Antoniou A, Psonis N, Poursanidis D, Lymberakis P, Poulakakis N. Corrigendum to "Multigene phylogeny, phylogeography and population structure of Podarcis cretensis species group in south Balkans" [Mol. Phylogenet. Evol. 138 (2019) 193-204]. Mol Phylogenet Evol 2020; 152:106919. [PMID: 32781420 DOI: 10.1016/j.ympev.2020.106919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Loukia Spilani
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio GR71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Irakleio GR70013, Greece
| | - Katia Bougiouri
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio GR71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Irakleio GR70013, Greece
| | - Aglaia Antoniou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Gournes Pediados, Irakleio, P.O. Box 2214, GR71003, Greece
| | - Nikolaos Psonis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio GR71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Irakleio GR70013, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, N. Plastira 100, Vassilika Vouton, Irakleio GR70013, Greece
| | - Dimitris Poursanidis
- Institute of Applied and Computational Mathematics, Foundation for Research and Technology - Hellas, N. Plastira 100, Vassilika Vouton, Irakleio GR70013, Greece
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio GR71409, Greece
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio GR71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Irakleio GR70013, Greece.
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23
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Speybroeck J, Beukema W, Dufresnes C, Fritz U, Jablonski D, Lymberakis P, Martínez-Solano I, Razzetti E, Vamberger M, Vences M, Vörös J, Crochet PA. Species list of the European herpetofauna – 2020 update by the Taxonomic Committee of the Societas Europaea Herpetologica. AMPHIBIA-REPTILIA 2020. [DOI: 10.1163/15685381-bja10010] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
The last species list of the European herpetofauna was published by Speybroeck, Beukema and Crochet (2010). In the meantime, ongoing research led to numerous taxonomic changes, including the discovery of new species-level lineages as well as reclassifications at genus level, requiring significant changes to this list. As of 2019, a new Taxonomic Committee was established as an official entity within the European Herpetological Society, Societas Europaea Herpetologica (SEH). Twelve members from nine European countries reviewed, discussed and voted on recent taxonomic research on a case-by-case basis. Accepted changes led to critical compilation of a new species list, which is hereby presented and discussed. According to our list, 301 species (95 amphibians, 15 chelonians, including six species of sea turtles, and 191 squamates) occur within our expanded geographical definition of Europe. The list includes 14 non-native species (three amphibians, one chelonian, and ten squamates).
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Affiliation(s)
- Jeroen Speybroeck
- 1Research Institute for Nature and Forest, Havenlaan 88 bus 73, 1000 Brussel, Belgium
| | - Wouter Beukema
- 2Wildlife Health Ghent, Department of Pathology, Bacteriology and Avian Diseases, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Christophe Dufresnes
- 3LASER, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Uwe Fritz
- 4Museum of Zoology, Senckenberg Dresden, A.B. Meyer Building, Königsbrücker Landstraße 159, 01109 Dresden, Germany
| | - Daniel Jablonski
- 5Department of Zoology, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 842 15 Bratislava, Slovakia
| | - Petros Lymberakis
- 6Natural History Museum of Crete, University of Crete, Knossou Ave. 71409, Crete, Irakleio, Greece
| | - Iñigo Martínez-Solano
- 7Museo Nacional de Ciencias Naturales (MNCN-CSIC), c/ José Gutiérrez Abascal, 2, 28006 Madrid, Spain
| | - Edoardo Razzetti
- 8Kosmos – Museo di Storia Naturale, Università di Pavia, Piazza Botta 9, 27100 Pavia, Italy
| | - Melita Vamberger
- 4Museum of Zoology, Senckenberg Dresden, A.B. Meyer Building, Königsbrücker Landstraße 159, 01109 Dresden, Germany
| | - Miguel Vences
- 9Division of Evolutionary Biology, Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Judit Vörös
- 10Department of Zoology, Hungarian Natural History Museum, 1088 Budapest, Baross u. 13, Hungary
| | - Pierre-André Crochet
- 11CEFE, Université Montpellier, CNRS, EPHE, IRD, Université Paul Valéry Montpellier 3, Montpellier, France
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24
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Renaud S, Hardouin EA, Chevret P, Papayiannis K, Lymberakis P, Matur F, Garcia-Rodriguez O, Andreou D, Çetintaş O, Sözen M, Hadjisterkotis E, Mitsainas GP. Morphometrics and genetics highlight the complex history of Eastern Mediterranean spiny mice. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa063] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Spiny mice of the Acomys cahirinus group display a complex geographical structure in the Eastern Mediterranean area, as shown by previous genetic and chromosomal studies. To better elucidate the evolutionary relationships between insular populations from Crete and Cyprus and continental populations from North Africa and Cilicia in Turkey, genetic and morphometric variations were investigated, based on mitochondrial D-loop sequences, and the size and shape of the first upper molar. The Cypriot and the Cilician populations show idiosyncratic divergence in molar size and shape, while Cretan populations present a geographical structure with at least three differentiated subpopulations, as shown by congruent distributions of haplogroups, Robertsonian fusions and morphometric variation. A complex history of multiple introductions is probably responsible for this structure, and insular isolation coupled with habitat shift should have further promoted a pronounced and rapid morphological evolution in molar size and shape on Crete and Cyprus.
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Affiliation(s)
- Sabrina Renaud
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, CNRS, Université Claude Bernard Lyon 1, Université de Lyon, Campus de la Doua, Villeurbanne, France
| | - Emilie A Hardouin
- Department of Life and Environmental Sciences, Faculty of Science and Technology, Bournemouth University, Poole, Dorset, UK
| | - Pascale Chevret
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, CNRS, Université Claude Bernard Lyon 1, Université de Lyon, Campus de la Doua, Villeurbanne, France
| | - Katerina Papayiannis
- Archéozoologie – Archéobotanique, Société, Pratiques et Environnements (ASPE), UMR 7209 CNRS, Muséum National d’Histoire Naturelle, 55 rue Buffon, Paris, France
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Heraklion, Crete, Greece
| | - Ferhat Matur
- Faculty of Science, Department of Biology, Dokuz Eylül University, Buca, Izmir, Turkey
| | - Oxala Garcia-Rodriguez
- Department of Life and Environmental Sciences, Faculty of Science and Technology, Bournemouth University, Poole, Dorset, UK
| | - Demetra Andreou
- Department of Life and Environmental Sciences, Faculty of Science and Technology, Bournemouth University, Poole, Dorset, UK
| | - Ortaç Çetintaş
- Department of Biology, Zonguldak Bulent Ecevit University, Zonguldak, Turkey
| | - Mustafa Sözen
- Department of Biology, Zonguldak Bulent Ecevit University, Zonguldak, Turkey
| | | | - George P Mitsainas
- Section of Animal Biology, Department of Biology, University of Patras, Patras, Greece
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25
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Thanou E, Paragamian K, Lymberakis P. Social but lonely: Species delimitation of social voles and the evolutionary history of the only
Microtus
species living in Africa. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Evanthia Thanou
- Department of Biology, Section of Animal Biology University of Patra Patra Greece
- Department of Biology University of Washington Seattle Washington USA
- The Molecular Ecology Backshop Loutraki Greece
| | | | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete Irakleio Greece
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26
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Galanaki A, Kominos T, Zogaris S, Gasteratos I, Lymberakis P. Presence of the Eurasian otter Lutra lutra on the islands of Greece: a review. Folia Zoologica 2019. [DOI: 10.25225/fozo.073.2019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Antonia Galanaki
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece; e-mail:
| | - Theodoros Kominos
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece; e-mail:
| | - Stamatis Zogaris
- Hellenic Centre for Marine Research – HCMR, Institute of Marine Biological Sciences and Inland Waters, 46.7 km Athens-Sounio Avenue, 19013 Anavyssos, Attica, Greece
| | | | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Knossou Avenue, 71409 Herakleio, Crete, Greece
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27
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Affiliation(s)
- Panagiotis Kornilios
- Department of Biology University of Washington Seattle WA USA
- Institute of Evolutionary Biology (CSIC – Universitat Pompeu Fabra) Barcelona Spain
- The Molecular Ecology Backshop Loutraki Greece
| | - Evanthia Thanou
- Department of Biology University of Washington Seattle WA USA
- The Molecular Ecology Backshop Loutraki Greece
| | - Petros Lymberakis
- Natural History Museum of Crete University of Crete Irakleio, Crete Greece
| | - Çetin Ilgaz
- Department of Biology, Faculty of Science Dokuz Eylül University Buca‐İzmir Turkey
- Research and Application Center for Fauna Flora Dokuz Eylul University Buca‐İzmir Turkey
| | - Yusuf Kumlutaş
- Department of Biology, Faculty of Science Dokuz Eylül University Buca‐İzmir Turkey
- Research and Application Center for Fauna Flora Dokuz Eylul University Buca‐İzmir Turkey
| | - Adam Leaché
- Department of Biology University of Washington Seattle WA USA
- Burke Museum of Natural History and Culture University of Washington Seattle WA USA
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28
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Affiliation(s)
- Nikolaos Kiamos
- Natural History Museum of Crete, University of Crete, Heraklion Crete, Greece
- Department of Biology, University of Crete, Heraklion Crete, Greece
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Heraklion Crete, Greece
| | - Georgios Rallis
- Natural History Museum of Crete, University of Crete, Heraklion Crete, Greece
- Department of Biology, University of Crete, Heraklion Crete, Greece
| | - Nikos Poulakakis
- Natural History Museum of Crete, University of Crete, Heraklion Crete, Greece
- Department of Biology, University of Crete, Heraklion Crete, Greece
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29
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Rozenblut-Kościsty B, Ogielska M, Hahn J, Kleemann D, Kossakowski R, Tamschick S, Schöning V, Krüger A, Lutz I, Lymberakis P, Kloas W, Stöck M. Impacts of the synthetic androgen Trenbolone on gonad differentiation and development - comparisons between three deeply diverged anuran families. Sci Rep 2019; 9:9623. [PMID: 31270347 PMCID: PMC6610071 DOI: 10.1038/s41598-019-45985-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 06/20/2019] [Indexed: 11/25/2022] Open
Abstract
Using a recently developed approach for testing endocrine disruptive chemicals (EDCs) in amphibians, comprising synchronized tadpole exposure plus genetic and histological sexing of metamorphs in a flow-through-system, we tested the effects of 17β-Trenbolone (Tb), a widely used growth promoter in cattle farming, in three deeply diverged anuran families: the amphibian model species Xenopus laevis (Pipidae) and the non-models Bufo(tes) viridis (Bufonidae) and Hyla arborea (Hylidae). Trenbolone was applied in three environmentally and/or physiologically relevant concentrations (0.027 µg/L (10-10 M), 0.27 µg/L (10-9 M), 2.7 µg/L (10-8 M)). In none of the species, Tb caused sex reversals or masculinization of gonads but had negative species-specific impacts on gonad morphology and differentiation after the completion of metamorphosis, independently of genetic sex. In H. arborea and B. viridis, mounting Tb-concentration correlated positively with anatomical abnormalities at 27 µg/L (10-9 M) and 2.7 µg/L (10-8 M), occurring in X. laevis only at the highest Tb concentration. Despite anatomical aberrations, histologically all gonadal tissues differentiated seemingly normally when examined at the histological level but at various rates. Tb-concentration caused various species-specific mortalities (low in Xenopus, uncertain in Bufo). Our data suggest that deep phylogenetic divergence modifies EDC-vulnerability, as previously demonstrated for Bisphenol A (BPA) and Ethinylestradiol (EE2).
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Affiliation(s)
- Beata Rozenblut-Kościsty
- Department of Evolutionary Biology and Conservation of Vertebrates, Wroclaw University, Sienkiewicza 21, 50-335, Wroclaw, Poland
| | - Maria Ogielska
- Department of Evolutionary Biology and Conservation of Vertebrates, Wroclaw University, Sienkiewicza 21, 50-335, Wroclaw, Poland
| | - Juliane Hahn
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 & 310, D-12587, Berlin, Germany
| | - Denise Kleemann
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 & 310, D-12587, Berlin, Germany
| | - Ronja Kossakowski
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 & 310, D-12587, Berlin, Germany
| | - Stephanie Tamschick
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 & 310, D-12587, Berlin, Germany
| | - Viola Schöning
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 & 310, D-12587, Berlin, Germany
| | - Angela Krüger
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 & 310, D-12587, Berlin, Germany
| | - Ilka Lutz
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 & 310, D-12587, Berlin, Germany
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Knossou Ave., 71409, Heraklion, Crete, Greece
| | - Werner Kloas
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 & 310, D-12587, Berlin, Germany
- Department of Endocrinology, Institute of Biology, Faculty of Life Sciences, Humboldt University, Unter den Linden 6, 10099, Berlin, Germany
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 & 310, D-12587, Berlin, Germany.
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30
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Dufresnes C, Strachinis I, Suriadna N, Mykytynets G, Cogălniceanu D, Székely P, Vukov T, Arntzen JW, Wielstra B, Lymberakis P, Geffen E, Gafny S, Kumlutaş Y, Ilgaz Ç, Candan K, Mizsei E, Szabolcs M, Kolenda K, Smirnov N, Géniez P, Lukanov S, Crochet PA, Dubey S, Perrin N, Litvinchuk SN, Denoël M. Phylogeography of a cryptic speciation continuum in Eurasian spadefoot toads (Pelobates). Mol Ecol 2019; 28:3257-3270. [PMID: 31254307 DOI: 10.1111/mec.15133] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/30/2019] [Accepted: 05/17/2019] [Indexed: 12/15/2022]
Abstract
Cryptic phylogeographic diversifications provide unique models to examine the role of phylogenetic divergence on the evolution of reproductive isolation, without extrinsic factors such as ecological and behavioural differentiation. Yet, to date very few comparative studies have been attempted within such radiations. Here, we characterize a new speciation continuum in a group of widespread Eurasian amphibians, the Pelobates spadefoot toads, by conducting multilocus (restriction site associated DNA sequencing and mitochondrial DNA) phylogenetic, phylogeographic and hybrid zone analyses. Within the P. syriacus complex, we discovered species-level cryptic divergences (>5 million years ago [My]) between populations distributed in the Near-East (hereafter P. syriacus sensu stricto [s.s.]) and southeastern Europe (hereafter P. balcanicus), each featuring deep intraspecific lineages. Altogether, we could scale hybridizability to divergence time along six different stages, spanning from sympatry without gene flow (P. fuscus and P. balcanicus, >10 My), parapatry with highly restricted hybridization (P. balcanicus and P. syriacus s.s., >5 My), narrow hybrid zones (~15 km) consistent with partial reproductive isolation (P. fuscus and P. vespertinus, ~3 My), to extensive admixture between Pleistocene and refugial lineages (≤2 My). This full spectrum empirically supports a gradual build up of reproductive barriers through time, reversible up until a threshold that we estimate at ~3 My. Hence, cryptic phylogeographic lineages may fade away or become reproductively isolated species simply depending on the time they persist in allopatry, and without definite ecomorphological divergence.
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Affiliation(s)
- Christophe Dufresnes
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Hintermann & Weber SA, Montreux, Switzerland.,Laboratory for Conservation Biology, University of Lausanne, Lausanne, Switzerland
| | - Ilias Strachinis
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nataliia Suriadna
- Melitopol Insitute of Ecology and Social Technologies of University "Ukraine", Melitopol, Zaporizhia, Ukraine
| | | | - Dan Cogălniceanu
- Faculty of Natural Sciences and Agricultural Sciences, University Ovidius Constanţa, Constanţa, Romania
| | - Paul Székely
- Departamento de Ciencias Biológicas, EcoSs Lab, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Tanja Vukov
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Jan W Arntzen
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Ben Wielstra
- Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Irakleio, Crete, Greece
| | - Eli Geffen
- School of Zoology, Tel Aviv University, Tel Aviv, Israel
| | - Sarig Gafny
- School of Marine Sciences, Ruppin Academic Center, Michmoret, Israel
| | - Yusuf Kumlutaş
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca, İzmir, Turkey.,Research and Application Center for Fauna and Flora, Dokuz Eylül University, Buca, İzmir, Turkey
| | - Çetin Ilgaz
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca, İzmir, Turkey.,Research and Application Center for Fauna and Flora, Dokuz Eylül University, Buca, İzmir, Turkey
| | - Kamil Candan
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca, İzmir, Turkey.,Research and Application Center for Fauna and Flora, Dokuz Eylül University, Buca, İzmir, Turkey
| | - Edvárd Mizsei
- Department of Tisza River Research, Danube Research Institute, Centre for Ecological Research, Hungarian Academy of Sciences, Debrecen, Hungary
| | - Márton Szabolcs
- Department of Tisza River Research, Danube Research Institute, Centre for Ecological Research, Hungarian Academy of Sciences, Debrecen, Hungary
| | - Krzysztof Kolenda
- Department of Evolutionary Biology and Conservation of Vertebrates, Institute of Environmental Biology, University of Wrocław, Wrocław, Poland
| | - Nazar Smirnov
- Department of Nature, Chernivtsi Regional Museum, Chernivtsi, Ukraine
| | - Philippe Géniez
- CEFE, EPHE-PSL, CNRS, University of Montpellier, University Paul Valéry Montpellier 3, IRD, Montpellier, France
| | - Simeon Lukanov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Pierre-André Crochet
- CEFE, CNRS, University of Montpellier, University Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France
| | - Sylvain Dubey
- Hintermann & Weber SA, Montreux, Switzerland.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Agrosustain SA, Nyon, Switzerland
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Spartak N Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia.,Department of Zoology and Physiology, Dagestan State University, Makhachkala, Russia
| | - Mathieu Denoël
- Laboratory of Fish and Amphibian Ethology, Behavioural Biology Group, Freshwater and OCeanic science Unit of reSearch (FOCUS), University of Liège, Liège, Belgium
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31
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Pafilis P, Kapsalas G, Lymberakis P, Protopappas D, Sotiropoulos K. Diet composition of the Karpathos marsh frog (Pelophylax cerigensis): what does the most endangered frog in Europe eat? Anim Biodiv Conserv 2019. [DOI: 10.32800/abc.2018.42.0001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Thanou E, Kornilios P, Lymberakis P, Leaché AD. Genomic and mitochondrial evidence of ancient isolations and extreme introgression in the four-lined snake. Curr Zool 2019; 66:99-111. [PMID: 32467710 PMCID: PMC7245017 DOI: 10.1093/cz/zoz018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/11/2019] [Indexed: 12/04/2022] Open
Abstract
Comparing mitochondrial and genomic phylogenies is an essential tool for investigating speciation processes, because each genome carries different inheritance properties and evolutionary characteristics. Furthermore, mitonuclear discordance may arise from ecological adaptation, historic isolation, population size changes, and sex-biased dispersal. Closely related taxa are expected to experience gene flow; however, this may not be true for insular populations or populations isolated in refugia. The four-lined snake Elaphe quatuorlineata has a fragmented distribution, separating populations of the Italian and Balkan Peninsulas, whereas several insular Aegean populations of significantly smaller body size (Cyclades island group and Skyros Island, Greece) are currently considered distinct subspecies. We constructed the species-tree phylogeny of this species utilizing genome-wide single nucleotide polymorphisms and a gene-tree based on complete cytochrome b sequences, aiming to detect convergence and discrepancies between biparentally and maternally inherited genomes. Population structuring, phylogenetic patterns and migration events among geographically defined lineages supported our hypothesis of isolation in multiple sub-refugia. Where biogeographical barriers did not restrict subsequent dispersal, extensive genetic exchange occurred between mainland Balkan populations. This process has led to the mitochondrial sweep of an ancestral mitolineage that survived only in peripheral (East Greece) and insular populations (North Cyclades and Skyros). The Central Cyclades represent an ancient lineage for both molecular markers that emerged almost 3.3 Mya. Considering their distinct morphology, insular E. quatuorlineata populations should be the future focus of an extensive sampling, especially since the mitonuclear discordance observed in this species could be related to ecological adaptations, such as the island-dwarfism phenomenon.
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Affiliation(s)
- Evanthia Thanou
- Department of Biology, University of Washington, Seattle, WA, USA.,The Molecular Ecology Backshop, Loutraki, Greece
| | - Panagiotis Kornilios
- Department of Biology, University of Washington, Seattle, WA, USA.,The Molecular Ecology Backshop, Loutraki, Greece.,Institute of Evolutionary Biology (CSIC - Universitat Pompeu Fabra), Barcelona, Spain
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Irakleio, Greece
| | - Adam D Leaché
- Department of Biology, University of Washington, Seattle, WA, USA
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33
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Sagonas K, Runemark A, Antoniou A, Lymberakis P, Pafilis P, Valakos ED, Poulakakis N, Hansson B. Selection, drift, and introgression shape MHC polymorphism in lizards. Heredity (Edinb) 2019; 122:468-484. [PMID: 30258107 PMCID: PMC6460769 DOI: 10.1038/s41437-018-0146-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 07/27/2018] [Accepted: 08/09/2018] [Indexed: 01/12/2023] Open
Abstract
The major histocompatibility complex (MHC) has long served as a model for the evolution of adaptive genetic diversity in wild populations. Pathogen-mediated selection is thought to be a main driver of MHC diversity, but it remains elusive to what degree selection shapes MHC diversity in complex biogeographical scenarios where other evolutionary processes (e.g. genetic drift and introgression) may also be acting. Here we focus on two closely related green lizard species, Lacerta trilineata and L. viridis, to address the evolutionary forces acting on MHC diversity in populations with different biogeographic structure. We characterized MHC class I exon 2 and exon 3, and neutral diversity (microsatellites), to study the relative importance of selection, drift, and introgression in shaping MHC diversity. As expected, positive selection was a significant force shaping the high diversity of MHC genes in both species. Moreover, introgression significantly increased MHC diversity in mainland populations, with a primary direction of gene flow from L. viridis to L. trilineata. Finally, we found significantly fewer MHC alleles in island populations, but maintained MHC sequence and functional diversity, suggesting that positive selection counteracted the effect of drift. Overall, our data support that different evolutionary processes govern MHC diversity in different biogeographical scenarios: positive selection occurs broadly while introgression acts in sympatry and drift when the population sizes decrease.
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Affiliation(s)
- K Sagonas
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK.
- Department of Human and Animal Physiology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimioupoli Zografou, 15784, Athens, Greece.
| | - A Runemark
- Department of Biology, Lund University, Ecology Building, SE-223 62, Lund, Sweden
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - A Antoniou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Gournes Pediados, 71003, Heraklion, Crete, Greece
| | - P Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, 71409, Heraklion, Crete, Greece
| | - P Pafilis
- Department of Zoology and Marine Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimioupoli Zografou, 15784, Athens, Greece
| | - E D Valakos
- Department of Human and Animal Physiology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimioupoli Zografou, 15784, Athens, Greece
| | - N Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, 71409, Heraklion, Crete, Greece
- Department of Biology, School of Sciences and Engineering, University of Crete, Vasilika Vouton, 71003, Heraklion, Crete, Greece
| | - B Hansson
- Department of Biology, Lund University, Ecology Building, SE-223 62, Lund, Sweden
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Pafilis P, Kapsalas G, Lymberakis P, Protopappas D, Sotiropoulos K. Diet composition of the Karpathos marsh frog (Pelophylax cerigensis): what does the most endangered frog in Europe eat? Anim Biodiv Conserv 2018. [DOI: 10.32800/abc.2019.42.0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Kotsakiozi P, Jablonski D, Ilgaz Ç, Kumlutaş Y, Avcı A, Meiri S, Itescu Y, Kukushkin O, Gvoždík V, Scillitani G, Roussos SA, Jandzik D, Kasapidis P, Lymberakis P, Poulakakis N. Multilocus phylogeny and coalescent species delimitation in Kotschy's gecko, Mediodactylus kotschyi: Hidden diversity and cryptic species. Mol Phylogenet Evol 2018; 125:177-187. [DOI: 10.1016/j.ympev.2018.03.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 03/12/2018] [Accepted: 03/15/2018] [Indexed: 01/07/2023]
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Psonis N, Antoniou A, Karameta E, Leaché AD, Kotsakiozi P, Darriba D, Kozlov A, Stamatakis A, Poursanidis D, Kukushkin O, Jablonski D, Crnobrnja–Isailović J, Gherghel I, Lymberakis P, Poulakakis N. Resolving complex phylogeographic patterns in the Balkan Peninsula using closely related wall-lizard species as a model system. Mol Phylogenet Evol 2018; 125:100-115. [DOI: 10.1016/j.ympev.2018.03.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 03/08/2018] [Accepted: 03/14/2018] [Indexed: 10/17/2022]
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Dufresnes C, Lymberakis P, Kornilios P, Savary R, Perrin N, Stöck M. Phylogeography of Aegean green toads (Bufo viridis subgroup): continental hybrid swarm vs. insular diversification with discovery of a new island endemic. BMC Evol Biol 2018; 18:67. [PMID: 29720079 PMCID: PMC5930823 DOI: 10.1186/s12862-018-1179-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 04/16/2018] [Indexed: 11/18/2022] Open
Abstract
Background Debated aspects in speciation research concern the amount of gene flow between incipient species under secondary contact and the modes by which post-zygotic isolation accumulates. Secondary contact zones of allopatric lineages, involving varying levels of divergence, provide natural settings for comparative studies, for which the Aegean (Eastern Mediterranean) geography offers unique scenarios. In Palearctic green toads (Bufo viridis subgroup or Bufotes), Plio-Pleistocene (~ 2.6 Mya) diverged species show a sharp transition without contemporary gene flow, while younger lineages, diverged in the Lower-Pleistocene (~ 1.9 Mya), admix over tens of kilometers. Here, we conducted a fine-scale multilocus phylogeographic analysis of continental and insular green toads from the Aegean, where a third pair of taxa, involving Mid-Pleistocene diverged (~ 1.5 Mya) mitochondrial lineages, earlier tentatively named viridis and variabilis, (co-)occurs. Results We discovered a new lineage, endemic to Naxos (Central Cyclades), while coastal islands and Crete feature weak genetic differentiation from the continent. In continental Greece, both lineages, viridis and variabilis, form a hybrid swarm, involving massive mitochondrial and nuclear admixture over hundreds of kilometers, without obvious selection against hybrids. Conclusions The genetic signatures of insular Aegean toads appear governed by bathymetry and Quaternary sea level changes, resulting in long-term isolation (Central Cyclades: Naxos) and recent land-bridges (coastal islands). Conversely, Crete has been isolated since the end of the Messinian salinity crisis (5.3 My) and Cretan populations thus likely result from human-mediated colonization, at least since Antiquity, from Peloponnese and Anatolia. Comparisons of green toad hybrid zones support the idea that post-zygotic hybrid incompatibilities accumulate gradually over the genome. In this radiation, only one million years of divergence separate a scenario of complete reproductive isolation, from a secondary contact resulting in near panmixia. Electronic supplementary material The online version of this article (10.1186/s12862-018-1179-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christophe Dufresnes
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland.,Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield, S10 2TN, UK
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Knosos Av, P.O. Box 2208, 71409, Irakleio, Crete, Greece
| | - Panagiotis Kornilios
- Section of Animal Biology, Department of Biology, School of Natural Sciences, University of Patras, GR-26500, Patras, Greece.,Department of Biology, University of Washington, Box 351800, Seattle, WA, 98195-1800, USA
| | - Romain Savary
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
| | - Nicolas Perrin
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, D-12587, Berlin, Germany.
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Kornilios P, Kumlutaş Y, Lymberakis P, Ilgaz Ç. Cryptic diversity and molecular systematics of the Aegean Ophiomorus
skinks (Reptilia: Squamata), with the description of a new species. J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12205] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
| | - Yusuf Kumlutaş
- Department of Biology; Faculty of Science; Dokuz Eylül University; Buca-Izmir Turkey
| | - Petros Lymberakis
- Natural History Museum of Crete; University of Crete; Irakleio, Crete Greece
| | - Çetin Ilgaz
- Department of Biology; Faculty of Science; Dokuz Eylül University; Buca-Izmir Turkey
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Ahmadzadeh F, Lymberakis P, Pirouz RS, Kapli P. The evolutionary history of two lizards (Squamata: Lacertidae) is linked to the geological development of Iran. ZOOL ANZ 2017. [DOI: 10.1016/j.jcz.2017.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Šmíd J, Moravec J, Gvoždík V, Štundl J, Frynta D, Lymberakis P, Kapli P, Wilms T, Schmitz A, Shobrak M, Yousefkhani SH, Rastegar-Pouyani E, Castilla AM, Els J, Mayer W. Cutting the Gordian Knot: Phylogenetic and ecological diversification of theMesalina brevirostrisspecies complex (Squamata, Lacertidae). ZOOL SCR 2017. [DOI: 10.1111/zsc.12254] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jiří Šmíd
- Department of Zoology; National Museum; Prague Czech Republic
- South African National Biodiversity Institute; Claremont Cape Town South Africa
| | - Jiří Moravec
- Department of Zoology; National Museum; Prague Czech Republic
| | - Václav Gvoždík
- Department of Zoology; National Museum; Prague Czech Republic
| | - Jan Štundl
- Department of Zoology; National Museum; Prague Czech Republic
- Department of Zoology; Faculty of Science; Charles University; Prague Czech Republic
| | - Daniel Frynta
- Department of Zoology; Faculty of Science; Charles University; Prague Czech Republic
| | - Petros Lymberakis
- Natural History Museum of Crete - University of Crete; Herakleio Greece
| | - Paschalia Kapli
- The Exelixis Lab; Scientific Computing Group; Heidelberg Institute for Theoretical Studies; Heidelberg Germany
| | | | - Andreas Schmitz
- Department of Herpetology and Ichthyology; Natural History Museum of Geneva; Geneva Switzerland
| | - Mohammed Shobrak
- Biology Department; Faculty of Science; Taif University; Taif Saudi Arabia
| | | | | | - Aurora M. Castilla
- Qatar Environment and Energy Research Institute; Hamad Bin Khalifa University (Qatar Foundation); Doha Qatar
| | - Johannes Els
- Breeding Centre for Endangered Arabian Wildlife, Environment and Protected Areas Authority; Sharjah United Arab Emirates
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Černa Bolfíková B, Eliášová K, Loudová M, Kryštufek B, Lymberakis P, Sándor AD, Hulva P. Glacial allopatry vs. postglacial parapatry and peripatry: the case of hedgehogs. PeerJ 2017; 5:e3163. [PMID: 28462018 PMCID: PMC5407276 DOI: 10.7717/peerj.3163] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/08/2017] [Indexed: 11/20/2022] Open
Abstract
Although hedgehogs are well-known examples of postglacial recolonisation, the specific processes that shape their population structures have not been examined by detailed sampling and fast-evolving genetic markers in combination with model based clustering methods. This study aims to analyse the impacts of isolation within glacial refugia and of postglacial expansion on the population structure of the Northern White-breasted hedgehog (Erinaceus roumanicus). It also discusses the role of the processes at edges of species distribution in its evolutionary history. The maternally inherited mitochondrial control region and the bi-parentally inherited nuclear microsatellites were used to examine samples within the Central Europe, Balkan Peninsula and adjacent islands. Bayesian coalescent inference and neutrality tests proposed a recent increase in the population size. The most pronounced pattern of population structure involved differentiation of the insular populations in the Mediterranean Sea and the population within the contact zone with E. europaeus in Central Europe. An interspecies hybrid was detected for the first time in Central Europe. A low genetic diversity was observed in Crete, while the highest genetic distances among individuals were found in Romania. The recent population in the post-refugial area related to the Balkan Peninsula shows a complex pattern with pronounced subpopulations located mainly in the Pannonian Basin and at the Adriatic and Pontic coasts. Detailed analyses indicate that parapatry and peripatry may not be the only factors that limit range expansion, but also strong microevolutionary forces that may change the genetic structure of the species. Here we present evidence showing that population differentiation may occur not only during the glacial restriction of the range into the refugia, but also during the interglacial range expansion. Population differentiation at the Balkan Peninsula and adjacent regions could be ascribed to diversification in steppe/forest biomes and complicated geomorphology, including pronounced geographic barriers as Carpathians.
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Affiliation(s)
- Barbora Černa Bolfíková
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Kristýna Eliášová
- Faculty of Science, Charles University in Prague, Prague, Czech Republic.,Department of Zoology, National Museum, Prague, Czech Republic
| | - Miroslava Loudová
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | | | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Heraklion, Greece
| | - Attila D Sándor
- Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Cluj-Napoca, Romania
| | - Pavel Hulva
- Faculty of Science, Charles University in Prague, Prague, Czech Republic.,Faculty of Science, University of Ostrava, Ostrava, Czech Republic
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Abstract
Amniote vertebrates possess various mechanisms of sex determination, but their variability is not equally distributed. The large evolutionary stability of sex chromosomes in viviparous mammals and birds was believed to be connected with their endothermy. However, some ectotherm lineages seem to be comparably conserved in sex determination, but previously there was a lack of molecular evidence to confirm this. Here, we document a stability of sex chromosomes in advanced snakes based on the testing of Z-specificity of genes using quantitative PCR (qPCR) across 37 snake species (our qPCR technique is suitable for molecular sexing in potentially all advanced snakes). We discovered that at least part of sex chromosomes is homologous across all families of caenophidian snakes (Acrochordidae, Xenodermatidae, Pareatidae, Viperidae, Homalopsidae, Colubridae, Elapidae and Lamprophiidae). The emergence of differentiated sex chromosomes can be dated back to about 60 Ma and preceded the extensive diversification of advanced snakes, the group with more than 3000 species. The Z-specific genes of caenophidian snakes are (pseudo)autosomal in the members of the snake families Pythonidae, Xenopeltidae, Boidae, Erycidae and Sanziniidae, as well as in outgroups with differentiated sex chromosomes such as monitor lizards, iguanas and chameleons. Along with iguanas, advanced snakes are therefore another example of ectothermic amniotes with a long-term stability of sex chromosomes comparable with endotherms.
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Affiliation(s)
- Michail Rovatsos
- Faculty of Science, Department of Ecology, Charles University in Prague, Viničná 7, 12844 Praha 2, Czech Republic
| | - Jasna Vukić
- Faculty of Science, Department of Ecology, Charles University in Prague, Viničná 7, 12844 Praha 2, Czech Republic
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Knossou Avenue, 71409 Irakleio, Crete, Greece
| | - Lukáš Kratochvíl
- Faculty of Science, Department of Ecology, Charles University in Prague, Viničná 7, 12844 Praha 2, Czech Republic
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Psonis N, Antoniou A, Kukushkin O, Jablonski D, Petrov B, Crnobrnja-Isailović J, Sotiropoulos K, Gherghel I, Lymberakis P, Poulakakis N. Hidden diversity in the Podarcis tauricus (Sauria, Lacertidae) species subgroup in the light of multilocus phylogeny and species delimitation. Mol Phylogenet Evol 2017; 106:6-17. [DOI: 10.1016/j.ympev.2016.09.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 08/19/2016] [Accepted: 09/12/2016] [Indexed: 10/21/2022]
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Vamberger M, Stuckas H, Vargas-Ramírez M, Kehlmaier C, Ayaz D, Aloufi AA, Lymberakis P, Široký P, Fritz U. Unexpected hybridization patterns in Near Eastern terrapins (Mauremys caspica,M. rivulata) indicate ancient gene flow across the Fertile Crescent. ZOOL SCR 2016. [DOI: 10.1111/zsc.12227] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Melita Vamberger
- Museum of Zoology; Senckenberg Dresden; A. B. Meyer Building 01109 Dresden Germany
| | - Heiko Stuckas
- Museum of Zoology; Senckenberg Dresden; A. B. Meyer Building 01109 Dresden Germany
| | - Mario Vargas-Ramírez
- Museum of Zoology; Senckenberg Dresden; A. B. Meyer Building 01109 Dresden Germany
| | - Christian Kehlmaier
- Museum of Zoology; Senckenberg Dresden; A. B. Meyer Building 01109 Dresden Germany
| | - Dinçer Ayaz
- Faculty of Science; Biology Department; Zoology Section; Ege University; 35100 Bornova Izmir Turkey
| | | | - Petros Lymberakis
- Natural History Museum of Crete; University of Crete; Knossou Ave. 71409 Irakleio Crete Greece
| | - Pavel Široký
- Department of Biology and Wildlife Diseases; Faculty of Veterinary Hygiene and Ecology; University of Veterinary and Pharmaceutical Sciences; Palackého 1/3 612 42 Brno Czech Republic
| | - Uwe Fritz
- Museum of Zoology; Senckenberg Dresden; A. B. Meyer Building 01109 Dresden Germany
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Pafilis P, Lymberakis P, Sagonas K, Valakos E. The particularities of a remote islet shape the thermoregulatory profile of an endemic Mediterranean lizard. J Therm Biol 2016; 61:55-60. [DOI: 10.1016/j.jtherbio.2016.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/23/2016] [Accepted: 08/23/2016] [Indexed: 11/25/2022]
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Tamschick S, Rozenblut-Kościsty B, Ogielska M, Lehmann A, Lymberakis P, Hoffmann F, Lutz I, Schneider RJ, Kloas W, Stöck M. Impaired gonadal and somatic development corroborate vulnerability differences to the synthetic estrogen ethinylestradiol among deeply diverged anuran lineages. Aquat Toxicol 2016; 177:503-514. [PMID: 27434076 DOI: 10.1016/j.aquatox.2016.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 06/29/2016] [Accepted: 07/04/2016] [Indexed: 06/06/2023]
Abstract
Amphibians are undergoing a global decline. One poorly investigated reason could be the pollution of aquatic habitats by endocrine disrupting compounds (EDCs). We tested the susceptibility to the synthetically stabilized estrogen 17α-ethinylestradiol (EE2) in three deeply diverged anuran species, differing in sex determination systems, types of gonadogenesis and larval ecologies. To understand whether data from the amphibian model Xenopus laevis (Pipidae) are analogous and applicable to only distantly related non-model amphibians, tadpoles of X. laevis, Hyla arborea (Hylidae) and Bufo viridis (Bufonidae) were simultaneously exposed to 50, 500 and 5000ng/L EE2 from hatching until completion of metamorphosis, using a flow-through-system under identical experimental conditions. Comparing molecularly established genetic with histologically assessed phenotypic sex in all species, we have recently shown that EE2 provoked numerous genetic-male-to-phenotypic-female sex reversals and mixed sex individuals, confirming overall its expected feminizing effect. In the present study, we focus on the influence of EE2 on gonadal and somatic development. Anatomy and histology revealed several species-specific effects. In both non-model species, H. arborea and B. viridis, high numbers of anatomically impaired gonads were observed. In H. arborea, exposed to 5000ng/L EE2, numerous underdeveloped gonads were detected. Whereas EE2 did not alter snout-to-vent length and body weight of X. laevis metamorphs, H. arborea showed a treatment-dependent decrease, while B. viridis exhibited an increase in body weight and snout-to-vent length. Apart from a concentration-dependent occurrence of yellowish skin color in several H. arborea, no organ-specific effects were detected. Since EE2 ubiquitously occurs in many aquatic ecosystems and affects sexual and somatic development, among EDCs, it may indeed contribute to amphibian decline. The inter-species variation in developmental EE2-effects corroborates species-specific vulnerability differences towards EDCs between deeply diverged amphibian groups.
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Affiliation(s)
- Stephanie Tamschick
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 & 310, D-12587 Berlin, Germany.
| | - Beata Rozenblut-Kościsty
- Department of Evolutionary Biology and Conservation of Vertebrates, Wroclaw University, Sienkiewicza 21, 50-335 Wroclaw, Poland.
| | - Maria Ogielska
- Department of Evolutionary Biology and Conservation of Vertebrates, Wroclaw University, Sienkiewicza 21, 50-335 Wroclaw, Poland.
| | - Andreas Lehmann
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Str. 11, D-12489 Berlin, Germany.
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Knossou Ave., 71409 Heraklion, Crete, Greece.
| | - Frauke Hoffmann
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 & 310, D-12587 Berlin, Germany.
| | - Ilka Lutz
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 & 310, D-12587 Berlin, Germany.
| | - Rudolf J Schneider
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Str. 11, D-12489 Berlin, Germany.
| | - Werner Kloas
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 & 310, D-12587 Berlin, Germany.
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 & 310, D-12587 Berlin, Germany.
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Skourtanioti E, Kapli P, Ilgaz Ç, Kumlutaş Y, Avcı A, Ahmadzadeh F, Crnobrnja-Isailović J, Gherghel I, Lymberakis P, Poulakakis N. A reinvestigation of phylogeny and divergence times of the Ablepharus kitaibelii species complex (Sauria, Scincidae) based on mtDNA and nuDNA genes. Mol Phylogenet Evol 2016; 103:199-214. [PMID: 27404043 DOI: 10.1016/j.ympev.2016.07.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 02/25/2016] [Accepted: 07/07/2016] [Indexed: 10/21/2022]
Abstract
Morphological and DNA data support that the East Mediterranean snake-eyed skink Ablepharus kitaibelii represents a species complex that includes four species A. kitaibelii, A. budaki, A. chernovi, and A. rueppellii, highlighting the need of its taxonomic reevaluation. Here, we used Bayesian and Maximum Likelihood methods to estimate the phylogenetic relationships of all members of the complex based on two mitochondrial (cyt b, 16S rRNA) and two nuclear markers (MC1R, and NKTR) and using Chalcides, Eumeces, and Eutropis as outgroups. The biogeographic history of the complex was also investigated through the application of several phylogeographic (BEAST) and biogeographic (BBM) analyses. Paleogeographic and paleoclimatic data were used to support the inferred phylogeographic patterns. The A. kitaibelli species complex exhibits high genetic diversity, revealing cases of hidden diversity and cases of non-monophyletic species such as A. kitaibelii and A. budaki. Our results indicate that A. pannonicus branches off first and a group that comprises specimens of A. kitaibelli and A. budaki from Kastelorizo Island group (southeast Greece) and southwest Turkey, respectively is differentiated from the rest A. kitaibelli and A. budaki populations and may represent a new species. The estimated divergence times place the origin of the complex in the Middle Miocene (∼16Mya) and the divergence of most currently recognized species in the Late Miocene. The inferred ancestral distribution suggests that the complex originated in Anatolia, supposing that several vicariance and dispersal events that are related with the formation of the Mid-Aegean Trench, the Anatolian Diagonal and the orogenesis of the mountain chains in southern and eastern Anatolia have led to current distribution pattern of A. kitaibelii species complex in the Balkans and Middle East.
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Affiliation(s)
- Eirini Skourtanioti
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, GR-71409 Herakleio, Crete, Greece; Biology Department, School of Sciences and Engineering, University of Crete, Vassilika Vouton, GR-70013 Herakleio, Crete, Greece
| | - Paschalia Kapli
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, GR-71409 Herakleio, Crete, Greece; Biology Department, School of Sciences and Engineering, University of Crete, Vassilika Vouton, GR-70013 Herakleio, Crete, Greece
| | - Çetin Ilgaz
- Department of Biology, Faculty of Science, Dokuz Eylül University, TR-35160, Buca-İzmir, Turkey
| | - Yusuf Kumlutaş
- Department of Biology, Faculty of Science, Dokuz Eylül University, TR-35160, Buca-İzmir, Turkey
| | - Aziz Avcı
- Adnan Menderes University, Faculty of Science and Arts, Department of Biology, 09010 Aydın, Turkey
| | - Faraham Ahmadzadeh
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran
| | - Jelka Crnobrnja-Isailović
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, Niš 18000, Serbia; Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", Despota Stefana 142, Beograd 11000, Serbia
| | - Iulian Gherghel
- Department of Biology, Case Western Reserve University, 2080 Adelbert Road, Cleveland 44106, Ohio, USA
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, GR-71409 Herakleio, Crete, Greece
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, GR-71409 Herakleio, Crete, Greece; Biology Department, School of Sciences and Engineering, University of Crete, Vassilika Vouton, GR-70013 Herakleio, Crete, Greece.
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Kohl KD, Samuni-Blank M, Lymberakis P, Kurnath P, Izhaki I, Arad Z, Karasov WH, Dearing MD. Effects of Fruit Toxins on Intestinal and Microbial β-Glucosidase Activities of Seed-Predating and Seed-Dispersing Rodents (Acomys spp.). Physiol Biochem Zool 2016; 89:198-205. [DOI: 10.1086/685546] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Tamschick S, Rozenblut-Kościsty B, Ogielska M, Lehmann A, Lymberakis P, Hoffmann F, Lutz I, Kloas W, Stöck M. Sex reversal assessments reveal different vulnerability to endocrine disruption between deeply diverged anuran lineages. Sci Rep 2016; 6:23825. [PMID: 27029458 PMCID: PMC4814869 DOI: 10.1038/srep23825] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/15/2016] [Indexed: 01/17/2023] Open
Abstract
Multiple anthropogenic stressors cause worldwide amphibian declines. Among several poorly investigated causes is global pollution of aquatic ecosystems with endocrine disrupting compounds (EDCs). These substances interfere with the endocrine system and can affect the sexual development of vertebrates including amphibians. We test the susceptibility to an environmentally relevant contraceptive, the artificial estrogen 17α-ethinylestradiol (EE2), simultaneously in three deeply divergent systematic anuran families, a model-species, Xenopus laevis (Pipidae), and two non-models, Hyla arborea (Hylidae) and Bufo viridis (Bufonidae). Our new approach combines synchronized tadpole exposure to three EE2-concentrations (50, 500, 5,000 ng/L) in a flow-through-system and pioneers genetic and histological sexing of metamorphs in non-model anurans for EDC-studies. This novel methodology reveals striking quantitative differences in genetic-male-to-phenotypic-female sex reversal in non-model vs. model species. Our findings qualify molecular sexing in EDC-analyses as requirement to identify sex reversals and state-of-the-art approaches as mandatory to detect species-specific vulnerabilities to EDCs in amphibians.
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Affiliation(s)
- Stephanie Tamschick
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 & 310, D-12587 Berlin, Germany
| | - Beata Rozenblut-Kościsty
- Department of Evolutionary Biology and Conservation of Vertebrates, Wroclaw University, Sienkiewicza 21, 50-335 Wroclaw, Poland
| | - Maria Ogielska
- Department of Evolutionary Biology and Conservation of Vertebrates, Wroclaw University, Sienkiewicza 21, 50-335 Wroclaw, Poland
| | - Andreas Lehmann
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Str. 11, D-12489 Berlin, Germany
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Knossou Ave., 71409 Heraklion, Crete, Greece
| | - Frauke Hoffmann
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 & 310, D-12587 Berlin, Germany
| | - Ilka Lutz
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 & 310, D-12587 Berlin, Germany
| | - Werner Kloas
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 & 310, D-12587 Berlin, Germany
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 & 310, D-12587 Berlin, Germany
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50
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Strzała T, Grochowalska R, Najbar B, Mikulíček P, Jandzik D, Lymberakis P, Jablonski D. Complete mitochondrial genome of the endemic legless lizard Anguis cephallonica Werner, 1894 and its comparison with mitogenome of Anguis fragilis Linnaeus, 1758. Mitochondrial DNA B Resour 2016; 1:83-85. [PMID: 33473417 PMCID: PMC7800002 DOI: 10.1080/23802359.2015.1137834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Complete mitochondrial genome of the Peloponnese endemic lizard species Anguis cephallonica is presented in this study. The complete sequence is 17 208 bp long and consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one control region. The gene order is same as in the relative species Anguis fragilis. Length of the 22 tRNA genes varies from 64 bp to 73 bp. The Anguis cephallonica mitogenome base composition is: A (30.5%), T (24.2%), C (30.5%), G (14.8%), with an A + T bias (54.7%). Six protein coding genes have incomplete stop codons. This is the first complete mitogenome described in this species as well as in any endemic Peloponnese lizard. Presented complete mitochondrial genome will form a basis for future comparative analysis within the genus Anguis.
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Affiliation(s)
- Tomasz Strzała
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Renata Grochowalska
- Nature Museum, Faculty of Biological Sciences, University of Zielona Góra, Zielona Góra, Poland
| | - Bartłomiej Najbar
- Nature Museum, Faculty of Biological Sciences, University of Zielona Góra, Zielona Góra, Poland
| | - Peter Mikulíček
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Bratislava, Slovakia
| | - David Jandzik
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Bratislava, Slovakia.,Department of Ecology and Evolutionary Biology (EBIO), University of Colorado at Boulder, Boulder, CO, USA
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Irakleio, Crete, Greece
| | - Daniel Jablonski
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Bratislava, Slovakia
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