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Kazilas C, Dufresnes C, France J, Kalaentzis K, Martínez-Solano I, de Visser MC, Arntzen JW, Wielstra B. Spatial genetic structure in European marbled newts revealed with target enrichment by sequence capture. Mol Phylogenet Evol 2024; 194:108043. [PMID: 38382821 DOI: 10.1016/j.ympev.2024.108043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/21/2023] [Accepted: 02/18/2024] [Indexed: 02/23/2024]
Abstract
European marbled newts come in two species that have abutting ranges. The northern species, Triturus marmoratus, is found in France and the northern part of the Iberian Peninsula, whereas the southern species, T. pygmaeus, is found in the southwestern corner of the Iberian Peninsula. We study the intraspecific genetic differentiation of the group because morphological data show geographical variation and because the Iberian Peninsula is a recognized center of speciation and intraspecific genetic diversity for all kinds of organisms, amphibians included. We use target enrichment by sequence capture to generate c. 7 k nuclear DNA markers. We observe limited genetic exchange between the species, which confirms their distinctiveness. Both species show substantial genetic structuring that is only in part mirrored by morphological variation. Genetically differentiated groups are found in the south (T. marmoratus) and west (T. pygmaeus) of the species ranges. Our observations highlight the position of the Iberian Peninsula as a hotspot for genetic differentiation.
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Affiliation(s)
- Christos Kazilas
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands.
| | - Christophe Dufresnes
- LASER, College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China; Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - James France
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
| | - Konstantinos Kalaentzis
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
| | - Iñigo Martínez-Solano
- Museo Nacional de Ciencias Naturales, MNCN-CSIC, c/ José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Manon C de Visser
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
| | - Jan W Arntzen
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
| | - Ben Wielstra
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
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de Amaral M, Carvajalino-Fernández JM, Nicieza AG, Tejedo M. Urea and glucose modulation during freezing exposure in three temperate frogs reveals specific targets in relation to climate. J Therm Biol 2024; 121:103854. [PMID: 38657317 DOI: 10.1016/j.jtherbio.2024.103854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/21/2024] [Accepted: 04/01/2024] [Indexed: 04/26/2024]
Abstract
Amphibian diversity is most prominent in the warm and humid tropical and subtropical regions across the globe. Nonetheless, amphibians also inhabit high-altitude tropical mountains and regions at medium and high latitudes, exposing them to subzero temperatures and requiring behavioural or physiological adaptations to endure freezing events. While freeze tolerance has been predominantly reported in high-latitude zones where species endure prolonged freezing (several weeks or months), less is known about mid-latitudes amphibians exposed to occasional subzero temperatures. In this study, we employed a controlled ecological protocol, subjecting three frog species from the Iberian Peninsula (Rana parvipalmata, Epidalea calamita, and Pelobates cultripes) to a 2-h exposure to temperatures of -2 °C to investigate the accumulation of urea and glucose as physiological mechanisms associated with survival at freezing temperatures. Our results revealed a moderate response in the production of cryoprotectant metabolites under experimental freezing conditions, particularly urea, with notable findings in R. parvipalmata and E. calamita and no response in P. cultripes. However, no significant alterations in glucose concentrations were observed in any of the studied frog species. This relatively weak freezing tolerance response differs from the strong response exhibited by amphibians inhabiting high latitudes and enduring prolonged freezing conditions, suggesting potential reliance on behavioural adaptations to cope with occasional freezing episodes.
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Affiliation(s)
- Marjoriane de Amaral
- Laboratory of Metabolism and Comparative Endocrinology, Department of Physiology, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil; Department of Evolutionary Ecology, Estación Biológica de Doñana, CSIC, Sevilla, Spain
| | | | - Alfredo G Nicieza
- Biodiversity Research Institute (IMIB), University of Oviedo-Principality of Asturias-CSIC, Mieres, Spain; Department of Biology of Organisms and Systems, University of Oviedo, Oviedo, Spain
| | - Miguel Tejedo
- Department of Evolutionary Ecology, Estación Biológica de Doñana, CSIC, Sevilla, Spain.
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Dufresnes C, Monod-Broca B, Bellati A, Canestrelli D, Ambu J, Wielstra B, Dubey S, Crochet PA, Denoël M, Jablonski D. Piecing the barcoding puzzle of Palearctic water frogs (Pelophylax) sheds light on amphibian biogeography and global invasions. GLOBAL CHANGE BIOLOGY 2024; 30:e17180. [PMID: 38465701 DOI: 10.1111/gcb.17180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/04/2024] [Accepted: 01/11/2024] [Indexed: 03/12/2024]
Abstract
Palearctic water frogs (genus Pelophylax) are an outstanding model in ecology and evolution, being widespread, speciose, either threatened or threatening to other species through biological invasions, and capable of siring hybrid offspring that escape the rules of sexual reproduction. Despite half a century of genetic research and hundreds of publications, the diversity, systematics and biogeography of Pelophylax still remain highly confusing, in no small part due to a lack of correspondence between studies. To provide a comprehensive overview, we gathered >13,000 sequences of barcoding genes from >1700 native and introduced localities and built multigene mitochondrial (~17 kb) and nuclear (~10 kb) phylogenies. We mapped all currently recognized taxa and their phylogeographic lineages (>40) to get a grasp on taxonomic issues, cyto-nuclear discordances, the genetic makeup of hybridogenetic hybrids, and the origins of introduced populations. Competing hypotheses for the molecular calibration were evaluated through plausibility tests, implementing a new approach relying on predictions from the anuran speciation continuum. Based on our timetree, we propose a new biogeographic paradigm for the Palearctic since the Paleogene, notably by attributing a prominent role to the dynamics of the Paratethys, a vast paleo-sea that extended over most of Europe. Furthermore, our results show that distinct marsh frog lineages from Eastern Europe, the Balkans, the Near East, and Central Asia (P. ridibundus ssp.) are naturally capable of inducing hybridogenesis with pool frogs (P. lessonae). We identified 14 alien lineages (mostly of P. ridibundus) over ~20 areas of invasions, especially in Western Europe, with genetic signatures disproportionally pointing to the Balkans and Anatolia as the regions of origins, in line with exporting records of the frog leg industry and the stocks of pet sellers. Pelophylax thus emerges as one of the most invasive amphibians worldwide, and deserves much higher conservation concern than currently given by the authorities fighting biological invasions.
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Affiliation(s)
- Christophe Dufresnes
- Laboratory of Amphibian Systematics and Evolutionary Research (LASER), College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Benjamin Monod-Broca
- Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
| | - Adriana Bellati
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Daniele Canestrelli
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Johanna Ambu
- Laboratory of Amphibian Systematics and Evolutionary Research (LASER), College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Ben Wielstra
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Sylvain Dubey
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Mathieu Denoël
- Laboratory of Ecology and Conservation of Amphibians (LECA), FOCUS, University of Liège, Liège, Belgium
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
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Pyron RA, Kakkera A, Beamer DA, O'Connell KA. Discerning structure versus speciation in phylogeographic analysis of Seepage Salamanders (Desmognathus aeneus) using demography, environment, geography, and phenotype. Mol Ecol 2024; 33:e17219. [PMID: 38015012 DOI: 10.1111/mec.17219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/26/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023]
Abstract
Numerous mechanisms can drive speciation, including isolation by adaptation, distance, and environment. These forces can promote genetic and phenotypic differentiation of local populations, the formation of phylogeographic lineages, and ultimately, completed speciation. However, conceptually similar mechanisms may also result in stabilizing rather than diversifying selection, leading to lineage integration and the long-term persistence of population structure within genetically cohesive species. Processes that drive the formation and maintenance of geographic genetic diversity while facilitating high rates of migration and limiting phenotypic differentiation may thereby result in population genetic structure that is not accompanied by reproductive isolation. We suggest that this framework can be applied more broadly to address the classic dilemma of "structure" versus "species" when evaluating phylogeographic diversity, unifying population genetics, species delimitation, and the underlying study of speciation. We demonstrate one such instance in the Seepage Salamander (Desmognathus aeneus) from the southeastern United States. Recent studies estimated up to 6.3% mitochondrial divergence and four phylogenomic lineages with broad admixture across geographic hybrid zones, which could potentially represent distinct species supported by our species-delimitation analyses. However, while limited dispersal promotes substantial isolation by distance, microhabitat specificity appears to yield stabilizing selection on a single, uniform, ecologically mediated phenotype. As a result, climatic cycles promote recurrent contact between lineages and repeated instances of high migration through time. Subsequent hybridization is apparently not counteracted by adaptive differentiation limiting introgression, leaving a single unified species with deeply divergent phylogeographic lineages that nonetheless do not appear to represent incipient species.
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Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Anvith Kakkera
- Thomas Jefferson High School for Science and Technology, Alexandria, Virginia, USA
| | - David A Beamer
- Office of Research, Economic Development and Engagement, East Carolina University, Greenville, North Carolina, USA
| | - Kyle A O'Connell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
- Deloitte Consulting LLP, Health and Data AI, Arlington, Virginia, USA
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Safaei-Mahroo B, Ghaffari H, Niamir A. A synoptic review of the Amphibians of Iran: bibliography, taxonomy, synonymy, distribution, conservation status, and identification key to the eggs, larvae, and adults. Zootaxa 2023; 5279:1-112. [PMID: 37518755 DOI: 10.11646/zootaxa.5279.1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Indexed: 08/01/2023]
Abstract
This study provides an illustrated account, a comprehensive update of the systematics, and a bibliography of the 15 species of anurans in five families, eight genera; and of the six species of urodeles in two families, four genera in Iran. Bufonidae, with eight species, is the most diverse family; Salamandridae has five species and Ranidae has four species. This study also presents updated identification keys for the eggs, larvae, and metamorphosed amphibians of Iran. We designated specimen NMW 19855.1 as neotype of Pelophylax persicus (Schneider, 1799) comb. nov.. Along with distribution maps obtained from all the reliable localities and museum specimens known at this time, the modelled habitat of species, and for the first time, the National Red List of amphibians based on the IUCN red list categories and criteria. Based on our evaluation we propose to categorize Bufo eichwaldi, Paradactylodon persicus, Neurergus derjugini, and N. kaiseri as Vulnerable at National Red List, and to move Bufotes (Calliopersa) luristanicus, B. (C.) surdus, Firouzophrynus olivaceus, and Rana pseudodalmatina from the category of Least Concern (LC) to Near Threatened (NT). The National Red List of amphibians that we propose has significant implications for endangered species management and conservation. Forty-one percent of amphibian species in Iran are endemic to the country, and more than forty percent of the Iranian amphibians are at risk of extinction. Zagros Mountain forest and Hyrcaniain forests have more than 80% (i.e. 18 species) of the diversity of Iranian amphibians. A considerable amount of scientific literature published on Iranian amphibians in Persian language is not easily accessible to researchers outside Iran. This monograph attempts to remedy the situation and provides broader access to international herpetology. We recognize that taxonomy is always in a state of flux, and the names and synonymies used here reflect our current view.
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Affiliation(s)
| | - Hanyeh Ghaffari
- Department of Environmental Sciences; Faculty of Natural Resources; University of Kurdistan; Sanandaj; Iran.
| | - Aidin Niamir
- Senckenberg Biodiversity and Climate Research Centre; Frankfurt am Main; Germany.
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Dufresnes C, Dutoit L, Brelsford A, Goldstein-Witsenburg F, Clément L, López-Baucells A, Palmeirim J, Pavlinić I, Scaravelli D, Ševčík M, Christe P, Goudet J. Inferring genetic structure when there is little: population genetics versus genomics of the threatened bat Miniopterus schreibersii across Europe. Sci Rep 2023; 13:1523. [PMID: 36707640 PMCID: PMC9883447 DOI: 10.1038/s41598-023-27988-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 01/11/2023] [Indexed: 01/28/2023] Open
Abstract
Despite their paramount importance in molecular ecology and conservation, genetic diversity and structure remain challenging to quantify with traditional genotyping methods. Next-generation sequencing holds great promises, but this has not been properly tested in highly mobile species. In this article, we compared microsatellite and RAD-sequencing (RAD-seq) analyses to investigate population structure in the declining bent-winged bat (Miniopterus schreibersii) across Europe. Both markers retrieved general patterns of weak range-wide differentiation, little sex-biased dispersal, and strong isolation by distance that associated with significant genetic structure between the three Mediterranean Peninsulas, which could have acted as glacial refugia. Microsatellites proved uninformative in individual-based analyses, but the resolution offered by genomic SNPs illuminated on regional substructures within several countries, with colonies sharing migrators of distinct ancestry without admixture. This finding is consistent with a marked philopatry and spatial partitioning between mating and rearing grounds in the species, which was suspected from marked-recaptured data. Our study advocates that genomic data are necessary to properly unveil the genetic footprints left by biogeographic processes and social organization in long-distant flyers, which are otherwise rapidly blurred by their high levels of gene flow.
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Affiliation(s)
- Christophe Dufresnes
- Laboratory for Amphibian Systematic and Evolutionary Research, College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China.
| | - Ludovic Dutoit
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.,Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Alan Brelsford
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, USA
| | | | - Laura Clément
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Adria López-Baucells
- Bat Research Area, Granollers Museum of Natural Sciences, Carrer Palaudaries 102, 08402, Granollers, Spain
| | - Jorge Palmeirim
- Department of Animal Biology, Centre for Ecology, Evolution and Environmental Change - cE3c, University of Lisbon, 1749-016, Lisbon, Portugal
| | - Igor Pavlinić
- Department of Zoology, Croatian Natural History Museum, Demetrova 1, 10000, Zagreb, Croatia
| | - Dino Scaravelli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Martin Ševčík
- Department of Zoology, Faculty of Science, Charles University in Prague, Viničná 7, 128 44, Prague 2, Czech Republic
| | - Philippe Christe
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.
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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. DISEASES OF AQUATIC ORGANISMS 2022; 152:127-138. [PMID: 36519684 DOI: 10.3354/dao03712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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Koster S, Prins N, Dufresnes C, France J, de Visser MC, Struijk RP, Wielstra B. The conservation paradox of an introduced population of a threatened species: spadefoot toads in the coastal dunes of the Netherlands. AMPHIBIA-REPTILIA 2022. [DOI: 10.1163/15685381-bja10106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Abstract
Species that are threatened in their native range may actually prosper as introduced populations. To investigate how such introduced populations were established involves determining from where within the natural range the founder individuals originated. This can be accomplished through mtDNA barcoding. The common spadefoot toad (Pelobates fuscus) naturally occurs in the south and east of the Netherlands and has shown a rapid decline. Yet, a flourishing introduced population was recently discovered in the coastal dunes in the west of the country. We use mtDNA barcoding to determine the provenance of the introduced population. We sampled both native and introduced populations from the Netherlands and compared our sequences to haplotypes from across the entire distribution range. The mtDNA haplotypes found in the introduced population are distinct from those naturally occurring in the Netherlands and point towards an origin in the Pannonian Basin, on the boundary between Central and Southeastern Europe. Paradoxically, the thriving P. fuscus population in the Dutch coastal dunes should be considered a conservation risk to local biodiversity, even though within the native range in the Netherlands the species is severely threatened. Our study illustrates the complicated conservation questions associated with species that are both native and invasive.
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Affiliation(s)
- Stephanie Koster
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
| | - Nienke Prins
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
| | - Christophe Dufresnes
- LASER, College of Biology and The Environment, Nanjing Forestry University, Nanjing 210037, China
| | - James France
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
| | - Manon C. de Visser
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
| | - Richard P.J.H. Struijk
- Reptile, Amphibian and Fish Conservation Netherlands (RAVON), P.O. Box 1413, 6501 BK Nijmegen, The Netherlands
| | - Ben Wielstra
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
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Yermokhin MV, Tabachishin VG. False Spring in the Spawning Migrations of Spadefoot Toads (Pelobates, Anura): Distribution in European Russia and the Phenomenon Scale in 2020. BIOL BULL+ 2022. [DOI: 10.1134/s1062359022100235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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10
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Natchev N, Koynova T, Tachev K, Doichev D, Marinova P, Velkova V, Jablonski D. Temperature regulation in the Balkan spadefoot ( Pelobates balcanicus Karaman, 1928) at the beginning of nocturnal activity. PeerJ 2022; 10:e13647. [PMID: 35860047 PMCID: PMC9291013 DOI: 10.7717/peerj.13647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/07/2022] [Indexed: 01/17/2023] Open
Abstract
On land, the amphibians interact with the environment in a complex way-even small changes in the physiological conditions may significantly impact the behaviour and vice versa. In ectothermic tetrapods, the transition from inactive to active phase may be related to important changes in their thermal status. We studied the thermal ecology of adult Balkan spadefoots (Pelobates balcanicus Karaman, 1928) in northeastern Bulgaria. These toads spend the daytime buried between 10 and 15 cm in sandy substrates, and emerge after sunset. On the substrate, their thermal energy exchange is defined by the absence of heat flow from the sun. Secondary heat sources, like stored heat and infrared radiation from the soil play an important role for the thermal balance of the active spadefoot toads. At the beginning of their daily activity, we measured substrate temperature (at a depth of 11-12 cm), toad's surface body temperature, and also provided thermal profiles of the animals and the substrate surface in their microhabitats. In animals which recently emerged from the substrate, the temperature was comparatively higher and was closer to that of the subsoil on the spot. After that, body temperature decreased rapidly and continued to change slowly, in correlation with air temperature. We detected a temperature gradient on the dorsal surface of the toads. On the basis of our measurements and additional data, we discuss the eventual role of air humidity and the effects of surface and skin water evaporation on the water balance and activity of the investigated toads.
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Affiliation(s)
- Nikolay Natchev
- Shumen University, Shumen, Bulgaria,University of Vienna, Vienna, Austria
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11
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Liedtke HC, Cruz F, Gómez-Garrido J, Fuentes Palacios D, Marcet-Houben M, Gut M, Alioto T, Gabaldón T, Gomez-Mestre I. Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad. DNA Res 2022; 29:6588074. [PMID: 35583263 PMCID: PMC9164646 DOI: 10.1093/dnares/dsac013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/12/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Genomic resources for amphibians are still hugely under-represented in vertebrate genomic research, despite being a group of major interest for ecology, evolution and conservation. Amphibians constitute a highly threatened group of vertebrates, present a vast diversity in reproductive modes, are extremely diverse in morphology, occupy most ecoregions of the world, and present the widest range in genome sizes of any major group of vertebrates. We combined Illumina, Nanopore and Hi-C sequencing technologies to assemble a chromosome-level genome sequence for an anuran with a moderate genome size (assembly span 3.09 Gb); Pelobates cultripes, the western spadefoot toad. The genome has an N50 length of 330 Mb with 98.6% of the total sequence length assembled into 14 super scaffolds, and 87.7% complete BUSCO genes. We use published transcriptomic data to provide annotations, identifying 32,684 protein-coding genes. We also reconstruct the P. cultripes phylome and identify 2,527 gene expansions. We contribute the first draft of the genome of the western spadefoot toad, P. cultripes. This species represents a relatively basal lineage in the anuran tree with an interesting ecology and a high degree of developmental plasticity, and thus is an important resource for amphibian genomic research.
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Affiliation(s)
- Hans Christoph Liedtke
- Ecology, Evolution and Development Group, Department of Wetland Ecology, Estación Biológica de Doñana (CSIC) , 41092 Sevilla, Spain
| | - Fernando Cruz
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , 08028 Barcelona, Spain
| | - Jèssica Gómez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , 08028 Barcelona, Spain
| | - Diego Fuentes Palacios
- Barcelona Supercomputing Centre (BSC-CNS) , 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology (BIST) , 08028 Barcelona, Spain
| | - Marina Marcet-Houben
- Barcelona Supercomputing Centre (BSC-CNS) , 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology (BIST) , 08028 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , 08028 Barcelona, Spain
| | - Tyler Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF) , Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS) , 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology (BIST) , 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA) , Barcelona, Spain
| | - Ivan Gomez-Mestre
- Ecology, Evolution and Development Group, Department of Wetland Ecology, Estación Biológica de Doñana (CSIC) , 41092 Sevilla, Spain
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12
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Sequeira F, Arntzen JW, van Gulik D, Hajema S, Diaz RL, Wagt M, van Riemsdijk I. Genetic traces of hybrid zone movement across a fragmented habitat. J Evol Biol 2022; 35:400-412. [PMID: 35043504 DOI: 10.1111/jeb.13982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 11/27/2022]
Abstract
Theoretical and empirical studies suggest that the structure and position of hybrid zones can change over time. Evidence for moving hybrid zones has been directly inferred by repeated sampling over time, or indirectly through the detection of genetic footprints left by the receding species and the resulting asymmetric patterns of introgression across markers. We here investigate a hybrid zone formed by two subspecies of the Iberian golden-striped salamander, Chioglossa lusitanica, using a panel of 35 nuclear loci (31 SNPs and 4 allozymes) and one mitochondrial locus in a transect in central Portugal. We found concordant and coincident clines for most of the nuclear loci (n=22, 63%), defining a narrow hybrid zone of ca. 6 km wide, with the centre positioned ca. 15 km south of the Mondego river. Asymmetric introgression was observed at another 14 loci. Their clines are displaced towards the north, with positions located either close to the Mondego river (n=6), or further northwards (n=8). We interpret these profiles as genetic traces of the southward displacement of C. lusitanica lusitanica by C. l. longipes over the wider Mondego river valley. We noted the absence of significant linkage disequilibrium and we inferred low levels of effective selection per locus against hybrids, suggesting that introgression in the area of species replacement occurred under a neutral diffusion process. A species distribution model suggests that the C. lusitanica hybrid zone coincides with a narrow corridor of fragmented habitat. From the position of the displaced clines, we infer that patches of locally suitable habitat trapped some genetic variants that became disassociated from the southward moving hybrid zone. This study highlights the influence of habitat availability on hybrid zone movement.
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Affiliation(s)
- Fernando Sequeira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Jan W Arntzen
- Institute of Biology, Leiden University, Leiden, The Netherlands.,Naturalis Biodiversity Centre, P. O. Box 9517, 2300 RA, Leiden, The Netherlands
| | - Davy van Gulik
- Hogeschool Leiden, P. O. Box 382, 2300 AJ, Leiden, The Netherlands
| | - Steven Hajema
- Hogeschool Leiden, P. O. Box 382, 2300 AJ, Leiden, The Netherlands
| | - Ruben Lopez Diaz
- Hogeschool Leiden, P. O. Box 382, 2300 AJ, Leiden, The Netherlands
| | - Mattijn Wagt
- Hogeschool Leiden, P. O. Box 382, 2300 AJ, Leiden, The Netherlands
| | - Isolde van Riemsdijk
- Naturalis Biodiversity Centre, P. O. Box 9517, 2300 RA, Leiden, The Netherlands.,Hogeschool Leiden, P. O. Box 382, 2300 AJ, Leiden, The Netherlands
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13
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Muniz AC, Pimenta RJG, Cruz MV, Rodrigues JG, Buzatti RSDO, Heuertz M, Lemos‐Filho JP, Lovato MB. Hybrid zone of a tree in a Cerrado/Atlantic Forest ecotone as a hotspot of genetic diversity and conservation. Ecol Evol 2022; 12:e8540. [PMID: 35127043 PMCID: PMC8803295 DOI: 10.1002/ece3.8540] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 12/17/2021] [Indexed: 01/10/2023] Open
Abstract
The Cerrado, the largest Neotropical savanna, and the Brazilian Atlantic Forest form large ecotonal areas where savanna and forest habitats occupy adjacent patches with closely related species occurring side by side, providing opportunities for hybridization. Here, we investigated the evolutionary divergence between the savanna and forest ecotypes of the widely distributed tree Plathymenia reticulata (n = 233 individuals). Genetic structure analysis of P. reticulata was congruent with the recognition of two ecotypes, whose divergence captured the largest proportion of genetic variance in the data (F CT = 0.222 and F ST = 0.307). The ecotonal areas between the Cerrado and the Atlantic Forest constitute a hybrid zone in which a diversity of hybrid classes was observed, most of them corresponding to second-generation hybrids (F2) or backcrosses. Gene flow occurred mainly toward the forest ecotype. The genetic structure was congruent with isolation by environment, and environmental correlates of divergence were identified. The observed pattern of high genetic divergence between ecotypes may reflect an incipient speciation process in P. reticulata. The low genetic diversity of the P. reticulata forest ecotype indicate that it is threatened in areas with high habitat loss on Atlantic Forest. In addition, the high divergence from the savanna ecotype suggests it should be treated as a different unit of management. The high genetic diversity found in the ecotonal hybrid zone supports the view of ecotones as important areas for the origin and conservation of biodiversity in the Neotropics.
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Affiliation(s)
- André Carneiro Muniz
- Departamento de Genética, Ecologia e EvoluçãoUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | - Mariana Vargas Cruz
- Departamento de Genética, Ecologia e EvoluçãoUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | | | | | - José P. Lemos‐Filho
- Departamento de BotânicaUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | - Maria Bernadete Lovato
- Departamento de Genética, Ecologia e EvoluçãoUniversidade Federal de Minas GeraisBelo HorizonteBrazil
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14
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A decharming metamorphosis: The larval and adult morphology of the common spadefoot toad, Pelobates fuscus. ZOOL ANZ 2022. [DOI: 10.1016/j.jcz.2021.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Dufresnes C, Litvinchuk SN. Diversity, distribution and molecular species delimitation in frogs and toads from the Eastern Palaearctic. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Abstract
Biodiversity analyses can greatly benefit from coherent species delimitation schemes and up-to-date distribution data. In this article, we have made the daring attempt to delimit and map described and undescribed lineages of anuran amphibians in the Eastern Palaearctic (EP) region in its broad sense. Through a literature review, we have evaluated the species status considering reproductive isolation and genetic divergence, combined with an extensive occurrence dataset (nearly 85k localities). Altogether 274 native species from 46 genera and ten families were retrieved, plus eight additional species introduced from other realms. Independent hotspots of species richness were concentrated in southern Tibet (Medog County), the circum-Sichuan Basin region, Taiwan, the Korean Peninsula and the main Japanese islands. Phylogeographic breaks responsible for recent in situ speciation events were shared around the Sichuan Mountains, across Honshu and between the Ryukyu Island groups, but not across shallow water bodies like the Yellow Sea and the Taiwan Strait. Anuran compositions suggested to restrict the zoogeographical limits of the EP to East Asia. In a rapidly evolving field, our study provides a checkpoint to appreciate patterns of species diversity in the EP under a single, spatially explicit, species delimitation framework that integrates phylogeographic data in taxonomic research.
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Affiliation(s)
- Christophe Dufresnes
- LASER, College of Biology & Environment, Nanjing Forestry University, Nanjing, China
| | - Spartak N Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
- Department of Biology, Dagestan State University, Makhachkala, Russia
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16
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Tang Q, Burri R, Liu Y, Suh A, Sundev G, Heckel G, Schweizer M. Seasonal migration patterns and the maintenance of evolutionary diversity in a cryptic bird radiation. Mol Ecol 2021; 31:632-645. [PMID: 34674334 PMCID: PMC9298432 DOI: 10.1111/mec.16241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 10/07/2021] [Accepted: 10/12/2021] [Indexed: 02/03/2023]
Abstract
Morphological differentiation associated with evolutionary diversification is often explained with adaptive benefits but the processes and mechanisms maintaining cryptic diversity are still poorly understood. Using genome‐wide data, we show here that the pale sand martin Riparia diluta in Central and East Asia consists of three genetically deeply differentiated lineages which vary only gradually in morphology but broadly reflect traditional taxonomy. We detected no signs of gene flow along the eastern edge of the Qinghai‐Tibetan plateau between lowland south‐eastern Chinese R. d. fohkienensis and high‐altitude R. d. tibetana. Largely different breeding and migration timing between these low and high altitude populations as indicated by phenology data suggests that allochrony might act as prezygotic isolation mechanism in the area where their ranges abut. Mongolian populations of R. d. tibetana, however, displayed signs of limited mixed ancestries with Central Asian R. d. diluta. Their ranges meet in the area of a well‐known avian migratory divide, where western lineages take a western migration route around the Qinghai‐Tibetan plateau to winter quarters in South Asia, and eastern lineages take an eastern route to Southeast Asia. This might also be the case between western R. d. diluta and eastern R. d. tibetana as indicated by differing wintering grounds. We hypothesize that hybrids might have nonoptimal intermediate migration routes and selection against them might restrict gene flow. Although further potential isolation mechanisms might exist in the pale sand martin, our study points towards contrasting migration behaviour as an important factor in maintaining evolutionary diversity under morphological stasis.
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Affiliation(s)
- Qindong Tang
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Natural History Museum, Bern, Switzerland
| | - Reto Burri
- Schweizerische Vogelwarte, Sempach, Switzerland
| | - Yang Liu
- State Key Laboratory of Biocontrol, College of Ecology School of Life Science, Sun Yat-sen University, Guangzhou, China
| | - Alexander Suh
- School of Biological Sciences-Organisms and the Environment, University of East Anglia, Norwich, UK.,Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
| | - Gombobaatar Sundev
- National University of Mongolia and Mongolian Ornithological Society, Ulaanbaatar, Mongolia
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Manuel Schweizer
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Natural History Museum, Bern, Switzerland
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17
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Zhu G, Yang S, Savitzky AH, Cheng Y, Mori A, Ding L, Rao D, Wang Q. Cryptic diversity and phylogeography of the Rhabdophis nuchalis group (Squamata: Colubridae). Mol Phylogenet Evol 2021; 166:107325. [PMID: 34655748 DOI: 10.1016/j.ympev.2021.107325] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 11/18/2022]
Abstract
Previous studies, have found that the rapid uplift of the Tibetan plateau accelerated the diversification of species. However, there are few relevant biogeographic data for the Colubridae in this region. We conducted a comprehensive study of the Rhabdophis nuchalis Group, which presently contains four nominal species, R. nuchalis, R. pentasupralabialis, R. leonardi, and R. chiwen. Building upon previous studies with specimens we have recently examined, greater interspecific and intraspecific diversity has been revealed. Here we address three questions: (1) Do the intraspecific differences represent only geographic variation within lineages, or are there cryptic species? (2) What are the interspecific relationships among members of the R. nuchalis Group? (3) What has been the biogeographic history of this species group? To resolve these questions we used four mitochondrial gene sequences and one nuclear sequence to investigate the molecular phylogenetic and geographic relationships among populations. Our molecular analysis reveals cryptic species diversity within the R. nuchalis Group, and seven clades were identified in the analysis. Ancestral area estimation suggests that the R. nuchalis Group originated in the Hengduan Mountains approximately 6.24 Mya and expanded its range northward to the Qinling-Daba Mountains. The Sichuan Basin appears to have been a barrier to migration. Species divergence seems to have been related to the rapid uplift of the Qinghai-Tibet Plateau.
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Affiliation(s)
- Guangxiang Zhu
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Shijun Yang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Alan H Savitzky
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
| | - Yuqi Cheng
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Akira Mori
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Li Ding
- Chengdu Institute of Biology, Chinese Academy of Sciences. Chengdu 610041, China
| | - Dingqi Rao
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Qin Wang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
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18
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Cogălniceanu D, Stănescu F, Székely D, Topliceanu TS, Iosif R, Székely P. Age, size and body condition do not equally reflect population response to habitat change in the common spadefoot toad Pelobates fuscus. PeerJ 2021; 9:e11678. [PMID: 34316392 PMCID: PMC8286710 DOI: 10.7717/peerj.11678] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/04/2021] [Indexed: 11/20/2022] Open
Abstract
Urbanization impacts biodiversity both directly through physical expansion over land, and indirectly due to land use conversion and human behaviors associated with urban areas. We assessed the response of a common spadefoot toad population (Pelobates fuscus) to habitat loss and fragmentation resulting from urban development by studying changes in size, body condition and age parameters. We compared samples collected in the early 2000s (sample A) and later on during 2012-2014 (sample B). The terrestrial habitats in the study area were severely reduced and fragmented due to the expansion of the human settlement. We found no significant differences in the age parameters between the two sampling periods; the median lifespan shortened from 3.5 (sample A) to 3.0 years (sample B), while the other age parameters were similar in both samples. In contrast, snout-vent length, body mass and body condition experienced a significant decrease over time. Our results suggest that changes in body size and body condition, rather than age parameters, better reflect the response of the common spadefoot toad population to declining habitat quality. Therefore, body measurements can provide reliable estimates of the impact of habitat degradation in amphibian populations.
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Affiliation(s)
- Dan Cogălniceanu
- Faculty of Natural and Agricultural Sciences, Ovidius University Constanța, Constanța, Romania.,Asociația Chelonia Romania, Bucharest, Romania
| | - Florina Stănescu
- Faculty of Natural and Agricultural Sciences, Ovidius University Constanța, Constanța, Romania.,Black Sea Institute for Development and Security Studies, Ovidius University Constanța, Constanța, Romania.,CEDMOG-Center for Morphological and Genetic Studies of Malignant Pathology, Ovidius University Constanța, Constanța, Romania
| | - Diana Székely
- Asociația Chelonia Romania, Bucharest, Romania.,Departamento de Ciencias Biológicas y Agropecuarias, Laboratorio de Ecología Tropical y Servicios Ecosistémicos (EcoSs Lab), Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Theodor-Sebastian Topliceanu
- Faculty of Natural and Agricultural Sciences, Ovidius University Constanța, Constanța, Romania.,Black Sea Institute for Development and Security Studies, Ovidius University Constanța, Constanța, Romania.,CEDMOG-Center for Morphological and Genetic Studies of Malignant Pathology, Ovidius University Constanța, Constanța, Romania
| | - Ruben Iosif
- Faculty of Natural and Agricultural Sciences, Ovidius University Constanța, Constanța, Romania.,Asociația Chelonia Romania, Bucharest, Romania
| | - Paul Székely
- Asociația Chelonia Romania, Bucharest, Romania.,Departamento de Ciencias Biológicas y Agropecuarias, Laboratorio de Ecología Tropical y Servicios Ecosistémicos (EcoSs Lab), Universidad Técnica Particular de Loja, Loja, Ecuador
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19
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Strachinis I, Poulakakis N, Karaiskou N, Patronidis P, Patramanis I, Poursanidis D, Jablonski D, Triantafyllidis A. Phylogeography and systematics of
Algyroides
(Sauria: Lacertidae) of the Balkan Peninsula. ZOOL SCR 2021. [DOI: 10.1111/zsc.12471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Ilias Strachinis
- Department of Genetics, Development and Molecular Biology School of Biology Faculty of Natural Sciences Aristotle University of Thessaloniki Greece
| | - Nikos Poulakakis
- Department of Biology University of Crete Irakleio Greece
- Natural History Museum of CreteUniversity of Crete Irakleio Greece
| | - Nikoleta Karaiskou
- Department of Genetics, Development and Molecular Biology School of Biology Faculty of Natural Sciences Aristotle University of Thessaloniki Greece
| | - Politis Patronidis
- Department of Genetics, Development and Molecular Biology School of Biology Faculty of Natural Sciences Aristotle University of Thessaloniki Greece
| | | | - Dimitris Poursanidis
- Foundation for Research and Technology – Hellas (FORTH) Institute of Applied and Computational Mathematics Iraklion Greece
| | | | - Alexandros Triantafyllidis
- Department of Genetics, Development and Molecular Biology School of Biology Faculty of Natural Sciences Aristotle University of Thessaloniki Greece
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20
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Jablonski D, Ribeiro-Júnior MA, Meiri S, Maza E, Kukushkin OV, Chirikova M, Pirosová A, Jelić D, Mikulíček P, Jandzik D. Morphological and genetic differentiation in the anguid lizard Pseudopus apodus supports the existence of an endemic subspecies in the Levant. VERTEBRATE ZOOLOGY 2021. [DOI: 10.3897/vz.71.e60800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The Levant represents one of the most important reptile diversity hotspots and centers of endemism in the Western Palearctic. The region harbored numerous taxa in glacial refugia during the Pleistocene climatic oscillations. Due to the hostile arid conditions in the warmer periods they were not always able to spread or come into contact with populations from more distant regions. One large and conspicuous member of the Levantine herpetofauna is the legless anguid lizardPseudopus apodus. This species is distributed from the Balkans to Central Asia with a portion of its range running along the eastern Mediterranean coast. Mitochondrial and nuclear DNA sequences, microsatellite genotypes, and morphology show that populations in this region differ from the two named subspecies and presumably had a long independent evolutionary history during the Quaternary. Here we describe the Levantine population as a new subspecies and present biogeographic scenarios for its origin and diversification. The new subspecies is genetically highly diverse, and it forms a sister lineage toPseudopusfrom the remaining parts of the range according to mtDNA. It is the largest-bodied of the three subspecies, but occupies the smallest range.
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21
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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] [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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22
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Landler L, Stefke K. Long-term monitoring of common spadefoot toad activity in a European steppe using barn owl pellets. JOURNAL OF BIOLOGICAL RESEARCH-THESSALONIKI 2021; 28:4. [PMID: 33579379 PMCID: PMC7879639 DOI: 10.1186/s40709-021-00133-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 01/07/2021] [Indexed: 11/11/2022]
Abstract
Background One third of the worldwide amphibian species are threatened, therefore, efficient monitoring efforts are needed. Amphibians which adopt a hidden lifestyle, such as the common spadefoot toad, are often missed with standard surveying efforts. Spadefoot toads can be identified in regurgitated pellets of the barn owl, which provides an effective way to estimate toad activity. In our study we analyzed frequency of spadefoot toad remains from 2004 to 2016 in a steppe landscape in eastern Austria. Methods We used an automated model selection procedure together with a GLM analysis using a zero inflated error Poisson distribution, to analyze the presence of Pelobates fuscus in barn owl pellets. All analyses were done in the statistical software R, and the scripts to reproduce our results are available within this publication. Our approach may provide a template for other researchers to use for their own pellet data. Conclusions Our analysis suggested that activity of the common spadefoot toad is mainly influenced by rainfalls, while time of the year and temperature had small but significant effects. Interestingly, our data confirmed the possibility of a second breeding period in summer, triggered by heavy rainfalls. There were no indications for a population decrease in the observed years and locations. Our study shows that barn owl pellets can be used effectivley to assess pelobatid activity in an area. This might constitute a useful monitoring tool for conservation management for amphibians.
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Affiliation(s)
- Lukas Landler
- Institute of Zoology, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33/I, Vienna, 1180, Austria.
| | - Katharina Stefke
- Natural History Museum Vienna, Mammal Collection, Burgring 7, Wien, 1010, Austria
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23
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Cerca J, Rivera-Colón AG, Ferreira MS, Ravinet M, Nowak MD, Catchen JM, Struck TH. Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species. PeerJ 2021; 9:e10896. [PMID: 33614296 PMCID: PMC7879940 DOI: 10.7717/peerj.10896] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/13/2021] [Indexed: 12/14/2022] Open
Abstract
Morphologically similar species, that is cryptic species, may be similar or quasi-similar owing to the deceleration of morphological evolution and stasis. While the factors underlying the deceleration of morphological evolution or stasis in cryptic species remain unknown, decades of research in the field of paleontology on punctuated equilibrium have originated clear hypotheses. Species are expected to remain morphologically identical in scenarios of shared genetic variation, such as hybridization and incomplete lineage sorting, or in scenarios where bottlenecks reduce genetic variation and constrain the evolution of morphology. Here, focusing on three morphologically similar Stygocapitella species, we employ a whole-genome amplification method (WGA) coupled with double-digestion restriction-site associated DNA sequencing (ddRAD) to reconstruct the evolutionary history of the species complex. We explore population structure, use population-level statistics to determine the degree of connectivity between populations and species, and determine the most likely demographic scenarios which generally reject for recent hybridization. We find that the combination of WGA and ddRAD allowed us to obtain genomic-level data from microscopic eukaryotes (∼1 millimetre) opening up opportunities for those working with population genomics and phylogenomics in such taxa. The three species share genetic variance, likely from incomplete lineage sorting and ancient admixture. We speculate that the degree of shared variation might underlie morphological similarity in the Atlantic species complex.
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Affiliation(s)
- José Cerca
- Department of Environmental Science, Policy, and Management, University of California, University of California, Berkeley, Berkeley, CA, United States of America
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Angel G. Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana Champaign, IL, United States of America
| | - Mafalda S. Ferreira
- Division of Biological Sciences, University of Montana, Missoula, MT, United States of America
- Departamento de Biologia, Universidade do Porto, Porto, Porto, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Porto, Porto, Portugal
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | | | - Julian M. Catchen
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana Champaign, IL, United States of America
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24
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Svinin A, Dedukh DV, Borkin LJ, Ermakov O, Ivanov A, Litvinchuk J, Zamaletdinov R, Mikhaylova R, Trubyanov AB, Skorinov D, Rosanov Y, Litvinchuk S. Genetic structure, morphological variation, and gametogenic peculiarities in water frogs (
Pelophylax
) from northeastern European Russia. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12447] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anton Svinin
- Mari State University Yoshkar‐Ola Russia
- National Research Tomsk State University Tomsk Russia
| | | | - Leo J. Borkin
- Zoological Institute Russian Academy of Sciences Saint‐Petersburg Russia
| | | | | | | | | | | | | | - Dmitriy Skorinov
- Institute of Cytology Russian Academy of Sciences Saint‐Petersburg Russia
| | - Yurij Rosanov
- Institute of Cytology Russian Academy of Sciences Saint‐Petersburg Russia
| | - Spartak Litvinchuk
- Institute of Cytology Russian Academy of Sciences Saint‐Petersburg Russia
- Dagestan State University Makhachkala Russia
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Ruchin A, Artaev O, Sharapova E, Ermakov O, Zamaletdinov R, Korzikov V, Bashinsky I, Pavlov A, Svinin AO, Ivanov A, Tabachishin V, Klenina A, Ganshchuk S, Litvinov N, Chetanov N, Vlasov A, Vlasova O. Occurrence of the amphibians in the Volga, Don River basins and adjacent territories (Russia): research in 1996-2020. Biodivers Data J 2020; 8:e61378. [PMID: 33414673 PMCID: PMC7785717 DOI: 10.3897/bdj.8.e61378] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 12/22/2020] [Indexed: 11/12/2022] Open
Abstract
Background Knowledge about the distribution of living organisms on Earth is very important for many areas of biological science and understanding of the surrounding world. However, much of the existing distributional data are scattered throughout a multitude of sources, such as taxonomic publications, checklists and natural history collections and often, bringing them together is difficult. A very successful attempt to solve this problem is the GBIF project, which allows a huge number of researchers to publish data in one place in a single standard. Our dataset represents a significant addition to the occurrences of amphibians in the Volga, Don riverine basins and adjacent territories. The dataset contains up-to-date information on amphibian occurrences in the Volga river basin and adjacent territories, located for the most part on the Russian plain of European Russia. The dataset is based on our own studies that were conducted in the years 1996-2020. The dataset consists of 5,030 incident records, all linked to geographical coordinates. A total of 13 amphibian species belonging to nine genera and six families have been registered within the studied territory, although the distribution of amphibian species in this region of Russia has not yet been fully studied. This is especially relevant with the spread of cryptic species that can only be identified using molecular genetic research methods. The main purpose of publishing a database is to make our data available in the global biodiversity system to a wide range of users. The data can be used by researchers, as well as helping the authorities to manage their territory more efficiently. New information All occurrences are published in GBIF for the first time. Most of the data are stored in field diaries and we would like to make it available to everyone by adding it in the global biodiversity database (GBIF).
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Affiliation(s)
- Alexander Ruchin
- Joint Directorate of the Mordovia State Nature Reserve and National Park "Smolny", Saransk, Russia Joint Directorate of the Mordovia State Nature Reserve and National Park "Smolny" Saransk Russia
| | - Oleg Artaev
- Papanin Institute for Biology of Inland Waters Russian Academy of Sciences, Borok, Russia Papanin Institute for Biology of Inland Waters Russian Academy of Sciences Borok Russia
| | - Elvira Sharapova
- Municipal budgetary institution of the additional education "Station of young naturalists" in Sarov, Sarov, Russia Municipal budgetary institution of the additional education "Station of young naturalists" in Sarov Sarov Russia
| | - Oleg Ermakov
- Penza State University, Penza, Russia Penza State University Penza Russia
| | - Renat Zamaletdinov
- Kazan Federal University, Kazan, Russia Kazan Federal University Kazan Russia
| | - Vjacheslav Korzikov
- Federal Hygienic and Epidemiological Center in Kaluga Region of Rospotrebnadzor, Kaluga, Russia Federal Hygienic and Epidemiological Center in Kaluga Region of Rospotrebnadzor Kaluga Russia
| | - Ivan Bashinsky
- A.N. Severtsov Institute of Ecology and Evolution of RAS, Moscow, Russia A.N. Severtsov Institute of Ecology and Evolution of RAS Moscow Russia
| | - Alexey Pavlov
- Volzhsko-Kamsky National Nature Biosphere Rezerve, Sadoviy, Russia Volzhsko-Kamsky National Nature Biosphere Rezerve Sadoviy Russia
| | - Anton O Svinin
- Mari State University, Yoshkar-Ola, Russia Mari State University Yoshkar-Ola Russia
| | - Alexander Ivanov
- Penza State University, Penza, Russia Penza State University Penza Russia
| | - Vasily Tabachishin
- A.N. Severtsov Institute of Ecology and Evolution of RAS, Saratov, Russia A.N. Severtsov Institute of Ecology and Evolution of RAS Saratov Russia
| | - Anastasiya Klenina
- Samara Federal Research Center of Russian Academy of Sciences, Institute of Ecology of the Volga River basin of RAS, Togliatti, Russia Samara Federal Research Center of Russian Academy of Sciences, Institute of Ecology of the Volga River basin of RAS Togliatti Russia
| | - Svetlana Ganshchuk
- Perm State Humanitarian Pedagogical University, Perm, Russia Perm State Humanitarian Pedagogical University Perm Russia
| | - Nikolai Litvinov
- Perm State Humanitarian Pedagogical University, Perm, Russia Perm State Humanitarian Pedagogical University Perm Russia
| | - Nikolai Chetanov
- Perm State Humanitarian Pedagogical University, Perm, Russia Perm State Humanitarian Pedagogical University Perm Russia
| | - Andrei Vlasov
- Central Chernozem Nature Reserve, Zapovednyi, Russia Central Chernozem Nature Reserve Zapovednyi Russia
| | - Olga Vlasova
- Central Chernozem Nature Reserve, Zapovednyi, Russia Central Chernozem Nature Reserve Zapovednyi Russia
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26
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Bulakhova N, Alfimov A, Berman D. The eastern boundary of the geographic range of the Pallas’ spadefoot Pelobates vespertinus (Anura, Amphibia) is limited by overwintering temperatures. HERPETOZOA 2020. [DOI: 10.3897/herpetozoa.33.e58050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We studied the relationship between the geographic distribution of the Pallas’ spadefoot (Pelobates vespertinus) and the soil temperature regime at the eastern boundary of this species’ range (south-western West Siberia and northwest Kazakhstan). This species overwinters underground, burrowing down to 1.5 m or deeper and has poor frost tolerance – it is unable to withstand temperatures below 0 °C, therefore, the temperature at its overwintering depth has to be above zero. A cartographic approach to identifying the distribution of zero isotherms was used. Winter soil temperatures at depths of 80 cm, 120 cm, 160 cm and 240 cm were plotted, based on deep soil thermometer data and the outline of the spadefoot’s range was compared with close-to-zero isotherms in deep soil. Within the range of this species, the depth of the position of zero isotherms increases eastwards: from 80 cm in European Russia, to more than 160 cm in the south-west of Western Siberia. The eastern boundary of the species’ range lies in the forest-steppe, steppe and semi-desert zones in the Tobol-Ishim interfluve and further south, on the left bank area of the Turgai River. This boundary clearly coincides with the zero isotherm, which lies here at a depth of 160 cm, forming an impermeable barrier to the spadefoot’s distribution.
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27
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Dufresnes C, Probonas NM, Strachinis I. A reassessment of the diversity of green toads (Bufotes) in the circum-Aegean region. Integr Zool 2020; 16:420-428. [PMID: 32978888 DOI: 10.1111/1749-4877.12494] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The dynamic biogeography of glacial refugia may cause complex patterns of genetic admixture between parapatric taxa, which in turn can mislead their systematics, diversity, and distributions. We investigated this issue for green toads (Bufotes) inhabiting the circum-Aegean region, a biodiversity hotspot of the Eastern Mediterranean. A previous phylogeographic study based on mitochondrial and microsatellite loci identified the hybrid zone between the European (viridis) and Anatolian (sitibundus) lineages of B. viridis all over the Balkan Peninsula, but subsequent range-wide genomic analyses (>1000 SNPs) located this transition in Turkey, a thousand kilometers eastwards. In order to clarify the diversity and taxonomy of the circum-Aegean populations, we reconciled these conflicting findings by integrating previous data with pure sitibundus individuals. Our results confirmed that the viridis/sitibundus hybrid zone extends in Western Anatolia, but that southeastern European populations feature cytonuclear discordances and a high and structured microsatellite diversity. This remarkable situation may stem from a massive geographic displacement of the hybrid zone during the last glacial fluctuations, an underappreciated yet seemingly common feature among the herpetofauna of the region. Our study thus contributes to the rising view that mitochondrial DNA can be a poor predictor of current phylogeographic structure, hence the need for genomic data, especially for narrowly distributed taxa. Finally, the analyses unambiguously support the distinction of a micro-endemic clade of green toads unique to some Cyclades islands, for which we provide a formal taxonomic description.
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Affiliation(s)
- Christophe Dufresnes
- LASER, College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China
| | | | - Ilias Strachinis
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Natural Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
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28
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Wei S, Li Z, Momigliano P, Fu C, Wu H, Merilä J. The roles of climate, geography and natural selection as drivers of genetic and phenotypic differentiation in a widespread amphibian Hyla annectans (Anura: Hylidae). Mol Ecol 2020; 29:3667-3683. [PMID: 32762086 DOI: 10.1111/mec.15584] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/16/2020] [Accepted: 07/28/2020] [Indexed: 01/02/2023]
Abstract
The role of geological events and Pleistocene climatic fluctuations as drivers of current patterns of genetic variation in extant species has been a topic of continued interest among evolutionary biologists. Nevertheless, comprehensive studies of widely distributed species are still rare, especially from Asia. Using geographically extensive sampling of many individuals and a large number of nuclear single nucleotide polymorphisms (SNPs), we studied the phylogeography and historical demography of Hyla annectans populations in southern China. Thirty-five sampled populations were grouped into seven clearly defined genetic clusters that closely match phenotype-based subspecies classification. These lineages diverged 2.32-5.23 million years ago (Ma), a timing that closely aligns with the rapid and drastic uplifting of the Qinghai-Tibet Plateau and adjacent southwest China. Demographic analyses and species distribution models indicate that different populations of this species have responded differently to past climatic changes. In the Hengduan Mountains, most populations experienced a bottleneck, whereas the populations located outside of the Hengduan Mountains have gradually declined in size since the end of the last glaciation. In addition, the levels of phenotypic and genetic divergence were strongly correlated across major clades. These results highlight the combined effects of geological events and past climatic fluctuations, as well as natural selection, as drivers of contemporary patterns of genetic and phenotypic variation in a widely distributed anuran in Asia.
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Affiliation(s)
- Shichao Wei
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Zitong Li
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Paolo Momigliano
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Chao Fu
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Hua Wu
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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29
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The effect of phylogeographic history on species boundaries: a comparative framework in Hyla tree frogs. Sci Rep 2020; 10:5502. [PMID: 32218506 PMCID: PMC7099067 DOI: 10.1038/s41598-020-62382-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/11/2020] [Indexed: 01/13/2023] Open
Abstract
Because it is indicative of reproductive isolation, the amount of genetic introgression across secondary contact zones is increasingly considered in species delimitation. However, patterns of admixture at range margins can be skewed by the regional dynamics of hybrid zones. In this context, we posit an important role for phylogeographic history: hybrid zones located within glacial refugia (putatively formed during the Late-Pleistocene) should be better defined than those located in post-glacial or introduced ranges (putatively formed during the Holocene and the Anthropocene). We test this hypothesis in a speciation continuum of tree frogs from the Western Palearctic (Hyla), featuring ten identified contacts between species spanning Plio-Pleistocene to Miocene divergences. We review the rich phylogeographic literature of this group and examine the overlooked transition between H. arborea and H. molleri in Western France using a multilocus dataset. Our comparative analysis supports a trend that contacts zones resulting from post-glacial expansions and human translocations feature more extensive introgression than those established within refugial areas. Integrating the biogeographic history of incipient species, i.e. their age since first contact together with their genetic divergence, thus appears timely to draw sound evolutionary and taxonomic inferences from patterns of introgression across hybrid zones.
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30
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Dufresnes C, Nicieza AG, Litvinchuk SN, Rodrigues N, Jeffries DL, Vences M, Perrin N, Martínez-Solano Í. Are glacial refugia hotspots of speciation and cytonuclear discordances? Answers from the genomic phylogeography of Spanish common frogs. Mol Ecol 2020; 29:986-1000. [PMID: 32012388 DOI: 10.1111/mec.15368] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 01/23/2020] [Accepted: 01/27/2020] [Indexed: 12/16/2022]
Abstract
Subdivided Pleistocene glacial refugia, best known as "refugia within refugia", provided opportunities for diverging populations to evolve into incipient species and/or to hybridize and merge following range shifts tracking the climatic fluctuations, potentially promoting extensive cytonuclear discordances and "ghost" mtDNA lineages. Here, we tested which of these opposing evolutionary outcomes prevails in northern Iberian areas hosting multiple historical refugia of common frogs (Rana cf. temporaria), based on a genomic phylogeography approach (mtDNA barcoding and RAD-sequencing). We found evidence for both incipient speciation events and massive cytonuclear discordances. On the one hand, populations from northwestern Spain (Galicia and Asturias, assigned to the regional endemic R. parvipalmata), are deeply-diverged at mitochondrial and nuclear genomes (~4 My of independent evolution), and barely admix with northeastern populations (assigned to R. temporaria sensu stricto) across a narrow hybrid zone (~25 km) located in the Cantabrian Mountains, suggesting that they represent distinct species. On the other hand, the most divergent mtDNA clade, widespread in Cantabria and the Basque country, shares its nuclear genome with other R. temporaria s. s. lineages. Patterns of population expansions and isolation-by-distance among these populations are consistent with past mitochondrial capture and/or drift in generating and maintaining this ghost mitochondrial lineage. This remarkable case study emphasizes the complex evolutionary history that shaped the present genetic diversity of refugial populations, and stresses the need to revisit their phylogeography by genomic approaches, in order to make informed taxonomic inferences.
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Affiliation(s)
- Christophe Dufresnes
- LASER, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Alfredo G Nicieza
- Department of Organisms and Systems Biology, University of Oviedo, Oviedo, Spain.,Research Unit of Biodiversity (UMIB, CSIC-UO-PA), Mieres, Spain
| | - Spartak N Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, Russia.,Dagestan State University, Makhachkala, Russia
| | - Nicolas Rodrigues
- Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland
| | - Daniel L Jeffries
- Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Nicolas Perrin
- Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland
| | - Íñigo Martínez-Solano
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
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31
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Dufresnes C, Pribille M, Alard B, Gonçalves H, Amat F, Crochet PA, Dubey S, Perrin N, Fumagalli L, Vences M, Martínez-Solano I. Integrating hybrid zone analyses in species delimitation: lessons from two anuran radiations of the Western Mediterranean. Heredity (Edinb) 2020; 124:423-438. [PMID: 31959977 DOI: 10.1038/s41437-020-0294-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 01/08/2020] [Accepted: 01/10/2020] [Indexed: 12/19/2022] Open
Abstract
Molecular ecologists often rely on phylogenetic evidence for assessing the species-level systematics of newly discovered lineages. Alternatively, the extent of introgression at phylogeographic transitions can provide a more direct test to assign candidate taxa into subspecies or species categories. Here, we compared phylogenetic versus hybrid zone approaches of species delimitation in two groups of frogs from the Western Mediterranean region (Discoglossus and Pelodytes), by using genomic data (ddRAD). In both genera, coalescent analyses recovered almost all nominal taxa as "species". However, the least-diverged pairs D. g. galganoi/jeanneae and P. punctatus/hespericus admix over hundreds of kilometers, suggesting that they have not yet developed strong reproductive isolation and should be treated as conspecifics. In contrast, the comparatively older D. scovazzi/pictus and P. atlanticus/ibericus form narrow contact zones, consistent with species distinctiveness. Due to their complementarity, we recommend taxonomists to combine phylogenomics with hybrid zone analyses to scale the gray zone of speciation, i.e., the evolutionary window separating widely admixing lineages versus nascent reproductively isolated species. The radically different transitions documented here conform to the view that genetic incompatibilities accumulating with divergence generate a weak barrier to gene flow for long periods of time, until their effects multiply and the speciation process then advances rapidly. Given the variability of the gray zone among taxonomic groups, at least from our current abilities to measure it, we recommend to customize divergence thresholds within radiations to categorize lineages for which no direct test of speciation is possible.
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Affiliation(s)
- Christophe Dufresnes
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK. .,Laboratory for Conservation Biology, Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland. .,Hintermann & Weber, Montreux, Switzerland.
| | - Manon Pribille
- Laboratory for Conservation Biology, Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland
| | - Bérénice Alard
- CIBIO-InBIO, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
| | - Helena Gonçalves
- CIBIO-InBIO, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal.,Museu de História Natural e da Ciência, Universidade do Porto, Porto, Portugal
| | - Fèlix Amat
- Àrea d'Herpetologia, Museu de Granollers-Ciències Naturals, Francesc Macià 51, 08400, Granollers, Catalonia, Spain
| | - Pierre-André Crochet
- CEFE, CNRS, University of Montpellier, University Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France
| | - Sylvain Dubey
- Hintermann & Weber, Montreux, Switzerland.,Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland.,AgroSustain SA, Nyon, Switzerland
| | - Nicolas Perrin
- Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland
| | - Luca Fumagalli
- Laboratory for Conservation Biology, Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Iñigo Martínez-Solano
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
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32
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Dufresnes C, Mazepa G, Jablonski D, Oliveira RC, Wenseleers T, Shabanov DA, Auer M, Ernst R, Koch C, Ramírez-Chaves HE, Mulder KP, Simonov E, Tiutenko A, Kryvokhyzha D, Wennekes PL, Zinenko OI, Korshunov OV, Al-Johany AM, Peregontsev EA, Masroor R, Betto-Colliard C, Denoël M, Borkin LJ, Skorinov DV, Pasynkova RA, Mazanaeva LF, Rosanov JM, Dubey S, Litvinchuk S. Fifteen shades of green: The evolution of Bufotes toads revisited. Mol Phylogenet Evol 2019; 141:106615. [DOI: 10.1016/j.ympev.2019.106615] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/14/2019] [Accepted: 09/10/2019] [Indexed: 01/01/2023]
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33
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Jablonski D, Sadek RA. The Caucasian Toad, Bufo verrucosissimus (Pallas, 1814) in the Levant: evidence from mitochondrial DNA. HERPETOZOA 2019. [DOI: 10.3897/herpetozoa.32.e37560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We present the first molecular analysis of the Bufo bufo (Linnaeus, 1758) complex population in the Levant. This complex contains four species distributed through the Western Palearctic. Based on the analysis of the widely used mitochondrial marker 16S rRNA, populations from the Levant belong to B. verrucosissimus (Pallas, 1814) and have a close affiliation to populations from the Transcaucasian region rather than southern Turkey. Such identified relationships may imply past rapid colonisation from north to south and support the need for further research.
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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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35
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Dufresnes C, Strachinis I, Tzoras E, Litvinchuk SN, Denoël M. Call a spade a spade: taxonomy and distribution of Pelobates, with description of a new Balkan endemic. Zookeys 2019; 859:131-158. [PMID: 31327926 PMCID: PMC6616056 DOI: 10.3897/zookeys.859.33634] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 06/10/2019] [Indexed: 11/20/2022] Open
Abstract
The genomic era contributes to update the taxonomy of many debated terrestrial vertebrates. In an accompanying work, we provided a comprehensive molecular assessment of spadefoot toads (Pelobates) using genomic data. Our results call for taxonomic updates in this group. First, nuclear phylogenomics confirmed the species-level divergence between the Iberian P.cultripes and its Moroccan relative P.varaldii. Second, we inferred that P.fuscus and P.vespertinus, considered subspecies until recently, feature partial reproductive isolation and thus deserve a specific level. Third, we evidenced cryptic speciation and diversification among deeply diverged lineages collectively known as Pelobatessyriacus. Populations from the Near East correspond to the Eastern spadefoot toad P.syriacus sensu stricto, which is represented by two subspecies, one in the Levant (P.s.syriacus) and the other in the rest of the range (P.s.boettgeri). Populations from southeastern Europe correspond to the Balkan spadefoot toad, P.balcanicus. Based on genetic evidence, this species is also polytypic: the nominal P.b.balcanicus inhabits the Balkan Peninsula; a new subspecies P.b.chloeaessp. nov. appears endemic to the Peloponnese. In this paper, we provide an updated overview of the taxonomy and distribution of all extant Pelobates taxa and describe P.b.chloeaessp. nov.
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Affiliation(s)
- Christophe Dufresnes
- Laboratory for Conservation Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Hintermann & Weber SA, Avenue des Alpes 25, 1820 Montreux, Switzerland.,Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, S10 2TN Sheffield, United Kingdom
| | - Ilias Strachinis
- School of Biology, Aristotle University of Thessaloniki 54124 Thessaloniki, Greece
| | | | - Spartak N Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, St. 194064 Petersburg, Russia.,Department of Zoology and Physiology, Dagestan State University, Gadzhiyev str. 43-a, 336700 Makhachkala, Dagestan, 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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