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Lin L, Chen H, Gaillard D, Shi H, Luo S. Phylogeography of the endangered "eyed" turtles (genus Sacalia) and the discovery of a lineage derived from natural interspecific hybridization. Ecol Evol 2022; 12:e9545. [PMID: 36568866 PMCID: PMC9772493 DOI: 10.1002/ece3.9545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 10/29/2022] [Accepted: 11/04/2022] [Indexed: 12/24/2022] Open
Abstract
The herpetofauna of the Indomalayan bioregion of Asia suffers from severe habitat loss, unsustainable harvesting, and lack of research and conservation. Here, we investigated the range-wide phylogeography of the endangered "eyed" turtles (genus Sacalia, including the Beale's Eyed Turtle S. bealei and the Four-eyed Turtle S. quadriocellata) and discovered a natural interspecific hybrid turtle population in China. Based on phylogeny of the mitochondrial Cytochrome b gene of 101 samples in this study and public data, three major clades and six subclades were identified: S. bealei (SBE) in eastern-southern China, east S. quadriocellata in South China (northern east [SQUen] and southern east [SQUes] subclades), and west S. quadriocellata mainly in Vietnam (northern west [SQUwn], central west [SQUwc], and southern west [SQUws] subclades). We sequenced 16 nuclear DNA loci of 87 samples from SBE, SQUen, SQUes, and SQUwn subclades. Population genetic clustering analysis suggested a structure similar to the mitochondrial phylogeny, where most samples were classified into four genetic clusters corresponding to the four mtDNA subclades. However, a proportion of samples carrying SQUen mtDNA haplotypes formed an additional distinct cluster SHY. Those samples are found in the contact zone of the two species bearing mosaic and intermediate morphological characteristics. We detected an admixed ancestry in SHY from SBE and SQUen that conformed to an intrapopulation breeding scenario for at least hundreds of generations after the initial hybrid event, leading to a conclusion that SHY is a distinct and near-panmictic population derived from natural interspecific hybridization. In addition, SQUes (Hainan Island endemic) is of special concern due to significant isolation and low genetic diversity. We suggest that seven evolutionarily significant units should be recognized to facilitate appropriate conservation actions. These findings also highlight the urgent need for further herpetological research and conservation in this region.
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Affiliation(s)
- Liu Lin
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life SciencesHainan Normal UniversityHaikouChina
| | - Huai‐Qing Chen
- The State Key Laboratory of Protein and Plant Gene Research, Peking‐Tsinghua Center for Life Sciences, School of Life SciencesPeking UniversityBeijingChina,Center for Nature and Society, School of Life SciencesPeking UniversityBeijingChina
| | - Daniel Gaillard
- The State Key Laboratory of Protein and Plant Gene Research, Peking‐Tsinghua Center for Life Sciences, School of Life SciencesPeking UniversityBeijingChina,School of Science, Technology, and MathematicsDalton State CollegeDaltonGeorgiaUSA
| | - Hai‐Tao Shi
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life SciencesHainan Normal UniversityHaikouChina
| | - Shu‐Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research, Peking‐Tsinghua Center for Life Sciences, School of Life SciencesPeking UniversityBeijingChina
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Ayaz D, Bayrakci Y, Çiçek K, Ihlow F, Tok CV, Fritz U. On the Brink of Extinction: Results of a 20-Year Quest for Eiselt's Pond Turtle (Emys orbicularis eiselti) in Southeastern Turkey. CHELONIAN CONSERVATION AND BIOLOGY 2021. [DOI: 10.2744/ccb-1505.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Dinçer Ayaz
- Zoology Section, Department of Biology, Faculty of Science, Ege University, Izmir,Turkey [; ; ]
| | - Yusuf Bayrakci
- Zoology Section, Department of Biology, Faculty of Science, Ege University, Izmir,Turkey [; ; ]
| | - Kerim Çiçek
- Zoology Section, Department of Biology, Faculty of Science, Ege University, Izmir,Turkey [; ; ]
| | - Flora Ihlow
- Museum of Zoology, Senckenberg Dresden, A.B. Meyer Building, 01109 Dresden, Germany [; ]
| | - Cemal Varol Tok
- Department of Biology, Çanakkale Onsekiz Mart University, Faculty of Arts and Sciences, Çanakkale, Turkey []
| | - Uwe Fritz
- Museum of Zoology, Senckenberg Dresden, A.B. Meyer Building, 01109 Dresden, Germany [; ]
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Ilhan S, Vamberger M, Ayaz D, Fritz U. Population structure and gene flow of the syntopic turtles Emys and Mauremys from coastal and inland regions of Anatolia (Turkey): results from mitochondrial and microsatellite data. Mol Biol Rep 2021; 48:4163-4169. [PMID: 34086161 DOI: 10.1007/s11033-021-06429-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 05/21/2021] [Indexed: 11/30/2022]
Abstract
Revealing the genetic basis of the existence of different species living together in different geographic regions provides clarification of this phylogeographic differentiation. In this study, we investigated the population genetics and evaluated the level of genetic variation of inland and coastal populations of Mauremys and Emys in Turkey. Tissue samples of 196 terrapins were studied which were collected from syntopic coastal (Gölbent-Söke/Aydın; M. rivulata and E. orbicularis) and inland populations (Bahçesaray/Aksaray; M. caspica and E. orbicularis). DNA was isolated using the InnuPREP DNA Mini Kit. Mitochondrial DNA sequences and allelic variation at 13 microsatellite loci for Mauremys and 12 microsatellite loci for Emys were examined. Three haplotypes were found for Emys orbicularis (Im, Ip and Iw) collected from the coastal region and two haplotypes for Emys orbicularis (Ig and Im) collected from inland. Two haplotypes were identified for M. caspica (Cmt8 and Cmt9) and three haplotypes were identified for M. rivulata (Rmt3, Rmt24 and Rmt26). Using microsatellites and the software STRUCTURE the most probable value for K was revealed as two 2 for both species. The FST value between M. rivulata and M. caspica was 0.39, and between the coastal and inland populations of E. orbicularis 0.09. It can be concluded that Emys populations tend to evolve by somehow preserving the allelic richness they have and Mauremys populations continue to differentiate so that new species emerge in the evolutionary process to reach the ideal allelic structure.
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Affiliation(s)
- Suleyman Ilhan
- Department of Biology, Faculty of Science and Letters, Manisa Celal Bayar University, Muradiye, 45140, Manisa, Turkey.
| | - Melita Vamberger
- Museum of Zoology, Senckenberg Dresden, A. B. Meyer Building, 01109, Dresden, Germany
| | - Dinçer Ayaz
- Department of Biology, Faculty of Science, Ege University, 35100, Bornova, Izmir, Turkey
| | - Uwe Fritz
- Museum of Zoology, Senckenberg Dresden, A. B. Meyer Building, 01109, Dresden, Germany
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Asztalos M, Schultze N, Ihlow F, Geniez P, Berroneau M, Delmas C, Guiller G, Legentilhomme J, Kindler C, Fritz U. How often do they do it? An in-depth analysis of the hybrid zone of two grass snake species (Natrix astreptophora and Natrix helvetica). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
We examined the contact zone of two parapatric species of grass snake (Natrix astreptophora and Natrix helvetica) in southern France. To this end, we used comprehensive sampling, analysed mtDNA sequences and microsatellite loci, and built Species Distribution Models for current and past climatic conditions. The contact zone had established by the mid-Holocene during range expansions from glacial refuges in the Iberian Peninsula (N. astreptophora) and southern or western France (N. helvetica). The contact zone represents a narrow bimodal hybrid zone, with steep genetic transition from one taxon to the other and rare hybridization, supporting species status for N. astreptophora and N. helvetica. Our results suggest that the steepness of the clines is a more robust tool for species delimitation than cline width. In addition, we discovered in western France, beyond the hybrid zone, a remote population of N. helvetica with genetic signatures of hybridization with N. astreptophora, most likely the result of human-mediated long-distance dispersal. For N. helvetica, we identified a southern and a northern population cluster, connected by broad-scale gene flow in a unimodal hybrid zone running across France. This pattern either reflects genetic divergence caused by allopatry in two microrefuges and subsequent secondary contact or introgression of foreign alleles into the southern cluster.
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Affiliation(s)
- Marika Asztalos
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, Dresden, Germany
| | - Nadine Schultze
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, Dresden, Germany
| | - Flora Ihlow
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, Dresden, Germany
| | - Philippe Geniez
- UMR 5175 CEFE, Biogéographie et Ecologie des Vertébrés, EPHE, PSL Université Recherche, Montpellier, Cedex 5, France
| | | | - Claudine Delmas
- NEO/ANA-CEN Ariège, 18 Impasse Denis Papin, Lavelanet, France
| | | | | | - Carolin Kindler
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, Dresden, Germany
| | - Uwe Fritz
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, Dresden, Germany
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Malekoutian M, Sharifi M, Vaissi S. Mitochondrial DNA sequence analysis reveals multiple Pleistocene glacial refugia for the Yellow-spotted mountain newt, Neurergus derjugini (Caudata: Salamandridae) in the mid-Zagros range in Iran and Iraq. Ecol Evol 2020; 10:2661-2676. [PMID: 32537127 PMCID: PMC7285473 DOI: 10.1002/ece3.6098] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 01/20/2020] [Indexed: 01/14/2023] Open
Abstract
Phylogeography is often used to investigate the effects of glacial cycles on current genetic structure of various plant and animal species. This approach can also identify the number and location of glacial refugia as well as the recolonization routes from those refugia to the current locations. To identify the location of glacial refugia of the Yellow‐spotted mountain newt, Neurergus derjugini, we employed phylogeography patterns and genetic variability of this species by analyzing partial ND4 sequences (867 bp) of 67 specimens from 15 sampling localities from the whole species range in Iran and Iraq. Phylogenetic trees concordant with haplotype networks showed a clear genetic structure among populations as three groups corresponding to the populations in the north, center, and south. Evolutionary ages of clades north and south ranging from 0.15 to 0.17 Myr, while the oldest clade is the central clade, corresponding to 0.32 Myr. Bayesian skyline plots of population size change through time show a relatively slight increase until about 25 kyr (around the last glacial maximum) and a decline of population size about 2.5 kyr. The presence of geographically structured clades in north, center, and south sections of the species range signifies the disjunct populations that have emerged in three different refugium. This study illustrates the importance of the effect of previous glacial cycles in shaping the genetic structure of mountain species in the Zagros range. These areas are important in terms of long‐term species persistence and therefore valuable areas for conservation of biodiversity.
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Affiliation(s)
| | - Mozafar Sharifi
- Department of Biology Baghabrisham Razi University Kermanshah Iran
| | - Somaye Vaissi
- Department of Biology Baghabrisham Razi University Kermanshah Iran
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Päckert M, Ait Belkacem A, Wolfgramm H, Gast O, Canal D, Giacalone G, Lo Valvo M, Vamberger M, Wink M, Martens J, Stuckas H. Genetic admixture despite ecological segregation in a North African sparrow hybrid zone (Aves, Passeriformes, Passer domesticus × Passer hispaniolensis). Ecol Evol 2019; 9:12710-12726. [PMID: 31788209 PMCID: PMC6875665 DOI: 10.1002/ece3.5744] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 08/30/2019] [Accepted: 09/02/2019] [Indexed: 11/29/2022] Open
Abstract
Under different environmental conditions, hybridization between the same species might result in different patterns of genetic admixture. Particularly, species pairs with large distribution ranges and long evolutionary history may have experienced several independent hybridization events over time in different zones of overlap. In birds, the diverse hybrid populations of the house sparrow (Passer domesticus) and the Spanish sparrow (Passer hispaniolensis) provide a striking example. Throughout their range of sympatry, these two species do not regularly interbreed; however, a stabilized hybrid form (Passer italiae) exists on the Italian Peninsula and on several Mediterranean islands. The spatial distribution pattern on the Eurasian continent strongly contrasts the situation in North Africa, where house sparrows and Spanish sparrows occur in close vicinity of phenotypically intermediate populations across a broad mosaic hybrid zone. In this study, we investigate patterns of divergence and admixture among the two parental species, stabilized and nonstabilized hybrid populations in Italy and Algeria based on a mitochondrial marker, a sex chromosomal marker, and 12 microsatellite loci. In Algeria, despite strong spatial and temporal separation of urban early-breeding house sparrows and hybrids and rural late-breeding Spanish sparrows, we found strong genetic admixture of mitochondrial and nuclear markers across all study populations and phenotypes. That pattern of admixture in the North African hybrid zone is strikingly different from i) the Iberian area of sympatry where we observed only weak asymmetrical introgression of Spanish sparrow nuclear alleles into local house sparrow populations and ii) the very homogenous Italian sparrow population where the mitogenome of one parent (P. domesticus) and the Z-chromosomal marker of the other parent (P. hispaniolensis) are fixed. The North African sparrow hybrids provide a further example of enhanced hybridization along with recent urbanization and anthropogenic land-use changes in a mosaic landscape.
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Affiliation(s)
- Martin Päckert
- Senckenberg Naturhistorische Sammlungen Dresden, Senckenberg|Leibniz Institution for Biodiversity and Earth System ResearchDresdenGermany
| | - Abdelkrim Ait Belkacem
- Laboratoire d'Exploration et de Valorisation des Écosystèmes SteppiquesFaculté des Sciences de la nature et de la vieUniversité de DjelfaDjelfaAlgeria
| | - Hannes Wolfgramm
- Senckenberg Naturhistorische Sammlungen Dresden, Senckenberg|Leibniz Institution for Biodiversity and Earth System ResearchDresdenGermany
| | - Oliver Gast
- Institute of Vertebrate Biology Brno & Masaryk University BrnoBrnoCzech Republic
| | - David Canal
- Department of Evolutionary EcologyEstación Biológica de Doñana—CSICSevilleSpain
- Centro para el Estudio y Conservación de las Aves Rapaces en Argentina (CECARA‐UNLPam) & Instituto de las Ciencias de la Tierra y Ambientales de La Pampa (INCITAP)Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Santa RosaArgentina
| | | | - Mario Lo Valvo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e FarmaceuticheUniversità degli Studi di PalermoPalermoItaly
| | - Melita Vamberger
- Senckenberg Naturhistorische Sammlungen Dresden, Senckenberg|Leibniz Institution for Biodiversity and Earth System ResearchDresdenGermany
| | - Michael Wink
- Department of BiologyInstitute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityHeidelbergGermany
| | - Jochen Martens
- Institute of Organismic and Molecular EvolutionJohannes Gutenberg UniversityMainzGermany
| | - Heiko Stuckas
- Senckenberg Naturhistorische Sammlungen Dresden, Senckenberg|Leibniz Institution for Biodiversity and Earth System ResearchDresdenGermany
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Araya-Donoso R, Torres-Pérez F, Véliz D, Lamborot M. Hybridization and polyploidy in the weeping lizard Liolaemus chiliensis (Squamata: Liolaemidae). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
In reptiles, polyploidy is an unusual phenomenon that can originate from interspecific hybridization. In Chile, the lizard Liolaemus chiliensis provides a unique model with which to study the origin of polyploidy because it occurs in populations of diploid individuals and a few populations that also contain triploid and diploid–triploid mosaic lizards. To test whether L. chiliensis polyploids were hybrids between lineages within the species, we analysed the karyotype, the mitochondrial gene Cytb, seven microsatellite loci, and the linear and geometric morphometry of individuals throughout the species distribution. We found polyploidy at different localities throughout the distribution. Hybrids were detected with the microsatellite loci and morphological data. A clear relationship between hybridization and polyploidy could not be established because triploid and mosaic lizards were hybrids and purebreds. However, our results support the occurrence of both phenomena, and further research is needed to clarify how hybridization could be involved in the origin of polyploidy.
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Affiliation(s)
- Raúl Araya-Donoso
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Núcleo Milenio de Ecología y Manejo Sustentable de Islas Oceánicas (ESMOI), Departamento de Biología Marina, Universidad Católica del Norte, Coquimbo, Chile
| | - Fernando Torres-Pérez
- Instituto de Biología, Pontificia Universidad Católica de Valparaiso, Valparaiso, Chile
| | - David Véliz
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Núcleo Milenio de Ecología y Manejo Sustentable de Islas Oceánicas (ESMOI), Departamento de Biología Marina, Universidad Católica del Norte, Coquimbo, Chile
| | - Madeleine Lamborot
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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Dufresnes C, Mazepa G, Jablonski D, Sadek RA, Litvinchuk SN. A river runs through it: tree frog genomics supports the Dead Sea Rift as a rare phylogeographical break. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz076] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Phylogeographical breaks can be viewed as regional hotspots of diversity where the genetic integrity of incipient species is put to the test. We focus on an understudied species transition from the Middle East, namely the Dead Sea Rift in the Levant region, which presumably divided the tree frogs Hyla savignyi and H. felixarabica. Combining multilocus genetic analyses (mitochondrial DNA and RAD-sequencing) with ecological niche modelling, we test whether the rift effectively acts as a biogeographical barrier preventing this pair from admixing and merging. The answer is yes: despite weak signs of introgression, all parapatric populations were assigned to either species without cyto-nuclear discordance. Yet, the projected distributions under present and glacial conditions largely overlapped in the area, meaning their current parapatric ranges do not represent an ecological transition. Instead, we hypothesize that H. savignyi and H. felixarabica are maintained apart by limited opportunities for dispersal across the barren Jordan Valley, combined with advanced reproductive isolation. Therefore, the Dead Sea Rift may represent a rare phylogeographical break, and we encourage international efforts to assess its contribution to the rich biodiversity of the Middle East.
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Affiliation(s)
- Christophe Dufresnes
- Laboratory for Conservation Biology, University of Lausanne, Lausanne, Switzerland
| | - Glib Mazepa
- Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Ecology and Genetics, Evolutionary Biology, Norbyvägen, Uppsala, Sweden
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Ilkovičova, Mlynská dolina, Bratislava, Slovakia
| | - Riyad A Sadek
- Biology Department, American University of Beirut, Beirut, Lebanon
| | - Spartak N Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, St. Petersburg, Russia
- Department of Zoology and Physiology, Dagestan State University, Makhachkala, Dagestan, Russia
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Afroosheh M, Rödder D, Mikulicek P, Akmali V, Vaissi S, Fleck J, Schneider W, Sharifi M. Mitochondrial DNA variation and Quaternary range dynamics in the endangered Yellow Spotted Mountain Newt, Neurergus derjugini
(Caudata, Salamandridae). J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12275] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
| | - Dennis Rödder
- Herpetology Section; Zoologisches Forschungsmuseum Alexander Koenig (ZFMK); Bonn Germany
| | - Peter Mikulicek
- Department of Zoology; Faculty of Natural Sciences; Comenius University in Bratislava; Bratislava Slovakia Republic
| | - Vahid Akmali
- Department of Biology; Bagabrisham; Razi University; Kermanshah Iran
| | - Somaye Vaissi
- Department of Biology; Bagabrisham; Razi University; Kermanshah Iran
| | | | | | - Mozafar Sharifi
- Department of Biology; Bagabrisham; Razi University; Kermanshah Iran
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