An extended mtDNA phylogeography for the alpine newt illuminates the provenance of introduced populations

Many herpetofauna species have been introduced outside of their native range. MtDNA barcoding is regularly used to determine the provenance of such populations. The alpine newt has been introduced across the Netherlands, the United Kingdom and Ireland. However, geographical mtDNA structure across the natural range of the alpine newt is still incompletely understood and certain regions are severely undersampled. We collect mtDNA sequence data of over seven hundred individuals, from both the native and the introduced range. The main new insights from our extended mtDNA phylogeography are that 1) haplotypes from Spain do not form a reciprocally monophyletic clade, but are nested inside the mtDNA clade that covers western and eastern Europe; and 2) haplotypes from the northwest Balkans form a monophyletic clade together with those from the Southern Carpathians and Apuseni Mountains. We also home in on the regions where the distinct mtDNA clades meet in nature. We show that four out of the seven distinct mtDNA clades that comprise the alpine newt are implicated in the introductions in the Netherlands, United Kingdom and Ireland. In several introduced localities, two distinct mtDNA clades co-occur. As these mtDNA clades presumably represent cryptic species, we urge that the extent of genetic admixture between them is assessed from genome-wide nuclear DNA markers. We mobilized a large number of citizen scientists in this project to support the collection of DNA samples by skin swabbing and underscore the effectiveness of this sampling technique for mtDNA barcoding.

[1]  Tomasz Suchan,et al.  Genomic phylogeography illuminates deep cyto-nuclear discordances in midwife toads (Alytes). , 2023, Molecular phylogenetics and evolution.

[2]  C. Dufresnes,et al.  Buccal swabs for amphibian genomics , 2023, Amphibia-Reptilia.

[3]  M. Gilbert,et al.  The limits of mtDNA analysis for determining the provenance of invasive species: a midwife toad example , 2022, Amphibia-Reptilia.

[4]  B. Wielstra,et al.  The conservation paradox of an introduced population of a threatened species: spadefoot toads in the coastal dunes of the Netherlands , 2022, Amphibia-Reptilia.

[5]  B. Wielstra,et al.  An isolated crested newt population in Dutch coastal dunes: distribution relict or introduction? , 2022, Amphibia-Reptilia.

[6]  M. Gilbert,et al.  The introduction of three cryptic tree frog species in the Dutch coastal dunes challenges conservation paradigms , 2022, Amphibia-Reptilia.

[7]  C. Dufresnes,et al.  A genomics revolution in amphibian taxonomy , 2022, Science.

[8]  S. J. R. Allain.  Distribution of the alpine newt Ichthyosaura alpestris in Great Britain updated using social media , 2021, Herpetological Bulletin.

[9]  O. Marquis,et al.  A revised phylogeny of Alpine newts unravels the evolutionary distinctiveness of the Bosnian alpine newt – Ichthyosaura alpestris reiseri (Werner, 1902) , 2021, Amphibia-Reptilia.

[10]  J. Vörös,et al.  Mitochondrial DNA diversity of the alpine newt (Ichthyosaura alpestris) in the Carpathian Basin: evidence for multiple cryptic lineages associated with Pleistocene refugia , 2021, Acta Zoologica Academiae Scientiarum Hungaricae.

[11]  C. Bradshaw,et al.  High and rising economic costs of biological invasions worldwide , 2021, Nature.

[12]  M. Hofreiter,et al.  Phylotranscriptomic evidence for pervasive ancient hybridization among Old World salamanders. , 2020, Molecular phylogenetics and evolution.

[13]  R. Rakwal,et al.  DNA barcoding: a way forward to obtain deep insights about the realistic diversity of living organisms , 2020, The Nucleus.

[14]  Andrew M. Liebhold,et al.  Scientists' warning on invasive alien species , 2020, Biological reviews of the Cambridge Philosophical Society.

[15]  M. Vences,et al.  Species list of the European herpetofauna – 2020 update by the Taxonomic Committee of the Societas Europaea Herpetologica , 2020, Amphibia-Reptilia.

[16]  N. Perrin,et al.  The effect of phylogeographic history on species boundaries: a comparative framework in Hyla tree frogs , 2020, Scientific Reports.

[17]  G. Hide,et al.  Skin swabs with FTA® cards as a dry storage source for amphibian DNA , 2019, Conservation Genetics Resources.

[18]  Miriam A. Zemanova.  Poor implementation of non-invasive sampling in wildlife genetics studies , 2019, Rethinking Ecology.

[19]  M. Suchard,et al.  Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 , 2018, Systematic biology.

[20]  B. Wielstra,et al.  Molecular data reveal the hybrid nature of an introduced population of banded newts (Ommatotriton) in Spain , 2018, Conservation Genetics.

[21]  E. Ringler.  Testing skin swabbing for DNA sampling in dendrobatid frogs , 2018, Amphibia-reptilia : publication of the Societas Europaea Herpetologica.

[22]  Juan C. Sánchez-DelBarrio,et al.  DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. , 2017, Molecular biology and evolution.

[23]  M. Pabijan,et al.  Isolation and gene flow in a speciation continuum in newts. , 2017, Molecular phylogenetics and evolution.

[24]  M. Pabijan,et al.  Isolation and Gene Flow in a Speciation Continuum in Newts , 2017, bioRxiv.

[25]  S. Litvinchuk,et al.  The Near East as a cradle of biodiversity: A phylogeography of banded newts (genus Ommatotriton) reveals extensive inter- and intraspecific genetic differentiation. , 2017, Molecular phylogenetics and evolution.

[26]  G. Nascetti,et al.  Quaternary history, population genetic structure and diversity of the cold-adapted Alpine newt Ichthyosaura alpestris in peninsular Italy , 2017, Scientific Reports.

[27]  N. Perrin,et al.  Cryptic invasion of Italian pool frogs (Pelophylax bergeri) across Western Europe unraveled by multilocus phylogeography , 2017, Biological Invasions.

[28]  Thomas K. F. Wong,et al.  ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates , 2017, Nature Methods.

[29]  J. Bosch,et al.  Tracking the introduction history of Ichthyosaura alpestris in a protected area of Central Spain , 2017, Conservation Genetics.

[30]  J. Bosch,et al.  Tracking the introduction history of Ichthyosaura alpestris in a protected area of Central Spain , 2017, Conservation Genetics.

[31]  R. Butlin,et al.  Efficient screening for ‘genetic pollution’ in an anthropogenic crested newt hybrid zone , 2016, Conservation Genetics Resources.

[32]  B. Wielstra,et al.  Description of a new species of crested newt, previously subsumed in Triturus ivanbureschi (Amphibia: Caudata: Salamandridae). , 2016, Zootaxa.

[33]  Arndt von Haeseler,et al.  W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis , 2016, Nucleic Acids Res..

[34]  Dan G. Bock,et al.  Hybridization and extinction , 2016, Evolutionary applications.

[35]  Tim M. Blackburn,et al.  Alien species as a driver of recent extinctions , 2016, Biology Letters.

[36]  Jody W. Enck,et al.  Can citizen science enhance public understanding of science? , 2016, Public understanding of science.

[37]  David Bryant,et al.  popart: full‐feature software for haplotype network construction , 2015 .

[38]  B. Wielstra,et al.  Genetic pollution of a threatened native crested newt species through hybridization with an invasive congener in the Netherlands , 2015 .

[39]  M. Stastny,et al.  Invasive Species: What Everyone Needs to Know. By Daniel Simberloff. Oxford and New York: Oxford University Press. $74.00 (hardcover); $16.95 (paper). xv + 329 p.; ill.; index. ISBN: 978-0-19-992201-7 (hc); 978-0-19-992203-1 (pb). 2013. , 2015 .

[40]  E. Recuero,et al.  Evolutionary history of Ichthyosaura alpestris (Caudata, Salamandridae) inferred from the combined analysis of nuclear and mitochondrial markers. , 2014, Molecular phylogenetics and evolution.

[41]  Kevin McDonough.  Amphibian Species of the World: An Online Reference (Version 6) , 2014 .

[42]  H. B. Shaffer,et al.  Effects of tail-clipping on survivorship and growth of larval salamanders , 2013 .

[43]  A. Goesmann,et al.  Radically different phylogeographies and patterns of genetic variation in two European brown frogs, genus Rana. , 2013, Molecular phylogenetics and evolution.

[44]  K. Theissinger,et al.  Pros and cons of external swabbing of amphibians for genetic analyses , 2013, European Journal of Wildlife Research.

[45]  A. Skidmore,et al.  Tracing glacial refugia of Triturus newts based on mitochondrial DNA phylogeography and species distribution modeling , 2013, Frontiers in Zoology.

[46]  A. Skidmore,et al.  Tracing glacial refugia of Triturus newts based on mitochondrial DNA phylogeography and species distribution modeling , 2013, Frontiers in Zoology.

[47]  A. Skidmore,et al.  Corresponding Mitochondrial DNA and Niche Divergence for Crested Newt Candidate Species , 2012, PloS one.

[48]  N. Baeshen,et al.  Biological Identifications Through DNA Barcodes , 2012 .

[49]  A. Brelsford,et al.  The biogeography of mitochondrial and nuclear discordance in animals , 2012, Molecular ecology.

[50]  F. Pompanon,et al.  Skin swabbing as a new efficient DNA sampling technique in amphibians, and 14 new microsatellite markers in the alpine newt (Ichthyosaura alpestris) , 2012, Molecular ecology resources.

[51]  Maxim Teslenko,et al.  MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space , 2012, Systematic biology.

[52]  A. Fijarczyk,et al.  Nuclear and mitochondrial phylogeography of the European fire‐bellied toads Bombina bombina and Bombina variegata supports their independent histories , 2011, Molecular ecology.

[53]  G. Luikart,et al.  Genomics and the future of conservation genetics , 2010, Nature Reviews Genetics.

[54]  R. Whittaker,et al.  Beyond scarcity: citizen science programmes as useful tools for conservation biogeography , 2010 .

[55]  D. Wake,et al.  Phylogeny and biogeography of the family Salamandridae (Amphibia: Caudata) inferred from complete mitochondrial genomes. , 2008, Molecular phylogenetics and evolution.

[56]  Palle Villesen,et al.  FaBox: an online toolbox for fasta sequences , 2007 .

[57]  A. Legakis,et al.  Phylogeny and biogeography of the alpine newt Mesotriton alpestris (Salamandridae, Caudata), inferred from mtDNA sequences. , 2007, Molecular phylogenetics and evolution.

[58]  L. Fumagalli,et al.  Buccal swabs allow efficient and reliable microsatellite genotyping in amphibians , 2007, Conservation Genetics.

[59]  M. Pabijan,et al.  Genetic structure in northeastern populations of the Alpine newt (Triturus alpestris): evidence for post‐Pleistocene differentiation , 2006, Molecular ecology.

[60]  M. García‐París,et al.  Phylogeography of two European newt species — discordance between mtDNA and morphology , 2005, Molecular ecology.

[61]  K. Lips,et al.  Alternative views of amphibian toe-clipping , 2005, Nature.

[62]  Jens R. Poschadel,et al.  A versatile field method for tissue sampling on small reptiles and amphibians, applied to pond turtles, newts, frogs and toads , 2004, Conservation Genetics.

[63]  Michael A. McCarthy,et al.  Clarifying the effect of toe clipping on frogs with Bayesian statistics , 2004 .

[64]  J. Searle.  Phylogeography — The History and Formation of Species , 2000, Heredity.

[65]  J. Arntzen,et al.  MARKING AND TISSUE SAMPLING EFFECTS ON BODY CONDITION AND SURVIVAL IN THE NEWT TRITURUS CRISTATUS , 1999 .

[66]  G. Huxel.  Rapid displacement of native species by invasive species: effects of hybridization , 1999 .

[67]  D. Simberloff,et al.  Extinction by hybridization and introgression , 1996 .

[68]  J. Sites,et al.  Mitochondrial DNA Sequence Divergence and Phylogenetic Relationships among Eight Chromosome Races of the Sceloporus Grammicus Complex (Phrynosomatidae) in Central Mexico , 1994 .

[69]  D. Schmeller,et al.  Batrachochytrium salamandrivorans kills alpine newts (Ichthyosaura alpestris) in southernmost Germany , 2020 .

[70]  Fahrbach,et al.  Cracking cryptic species : external characters to distinguish two recently recognized banded newt species (Ommatotriton ophryticus and O. nesterovi) , 2019 .

[71]  mtDNA , 2019, Encyclopedic Dictionary of Archaeology.

[72]  Y. Si,et al.  The distributions of the six species constituting the smooth newt species complex (Lissotriton vulgaris sensu lato and L. montandoni) – an addition to the New Atlas of Amphibians and Reptiles of Europe , 2018 .

[73]  M. Denoël,et al.  Provenance of Ichthyosaura alpestris (Caudata: Salamandridae) introductions to France and New Zealand assessed by mitochondrial DNA analysis , 2016 .

[74]  A. Ivanović,et al.  The batrachological collections of the Institute for biological research 'Sinisa Stankovic', University of Belgrade , 2015 .

[75]  A. Martínez-Silvestre,et al.  Población introducida de tritón alpino (Mesotriton alpestris) en el Prepirineo catalán , 2015 .

[76]  João F. Gonçalves,et al.  Updated distribution and biogeography of amphibians and reptiles of Europe , 2014 .

[77]  M. Pabijan,et al.  An isolated locality of the alpine newt (Mesotriton alpestris Laurenti, 1768) in central Poland , 2009 .

[78]  C. Miaud,et al.  Buccal swabs as a non-destructive tissue sampling method for DNA analysis in amphibians , 2003 .