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Physical and ecological isolation contribute to maintain genetic differentiation between fire salamander subspecies

  • Abellán P, Svenning JC (2014) Refugia within refugia–patterns in endemism and genetic divergence are linked to Late Quaternary climate stability in the Iberian Peninsula. Biol J Linn Soc 113:13–28

    Article  Google Scholar 

  • Alarcón-Ríos L, Nicieza AG, Kaliontzopoulou A, Buckley D, Velo-Antón G (2020) Evolutionary history and not heterochronic modifications associated with viviparity drive head shape differentiation in a reproductive polymorphic species, Salamandra salamandra. Evol Biol 47:43–55

    Article  Google Scholar 

  • Alcobendas M, Castanet J (2000) Bone growth plasticity among populations of Salamandra salamandra: interactions between internal and external factors. Herpetologica 56:14–26

    Google Scholar 

  • Alcobendas M, Buckley D, Tejedo M (2004) Variability in survival, growth and metamorphosis in the larval fire salamander (Salamandra salamandra): effects of larval birth size, sibship and environment. Herpetologica 60:232–245

    Article  Google Scholar 

  • Antunes B, Lourenço A, Caeiro-Dias G, Dinis M, Gonçalves H, Martínez-Solano I et al. (2018) Combining phylogeography and landscape genetics to infer the evolutionary history of a short-range Mediterranean relict, Salamandra salamandra longirostris. Conserv Genet 19:1411–1424

    CAS  Article  Google Scholar 

  • Arntzen JW, van Belkom J (2020) ‘Mainland-island’ population structure of a terrestrial salamander in a forest-bocage landscape with little evidence for in situ ecological speciation. Sci Rep 10:1–15

    Article  CAS  Google Scholar 

  • Balkenhol N, Cushman SA, Waits LP, Storfer A (2016) Current status, future opportunities, and remaining challenges in landscape genetics. In: Balkenhol N, Cushman SA, Storfer AT, Waits LP (eds) Landscape genetics: concepts, methods, applications, John Wiley and Sons Ltd, Chichester, pp 247–255.

  • Barton NH, Gale KS (1993) Genetic analysis of hybrid zones. Hybrid zones and the evolutionary process. In: Harrison RG (ed) Hybrid zones and the evolutionary process. Oxford University Press, Oxford, p 13–45

    Google Scholar 

  • Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Stat Methodol 57:289–300

    Google Scholar 

  • Beukema W, Nicieza AG, Lourenço A, Velo‐Antón G (2016) Colour polymorphism in Salamandra salamandra (Amphibia: Urodela), revealed by a lack of genetic and environmental differentiation between distinct phenotypes. J Zool Syst Evol 54:127–136

    Article  Google Scholar 

  • Bisconti R, Porretta D, Arduino P, Nascetti G, Canestrelli D (2018) Hybridization and extensive mitochondrial introgression among fire salamanders in peninsular Italy. Sci Rep 8:13187

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  • Bosch J, López-Bueis I (1994) Comparative study of the dorsal pattern in Salamandra salamandra bejarae (Wolterstorff, 1934) and S. s. almanzoris (Müller & Hellmich, 1935). Herpetol J 4:46–48

    Google Scholar 

  • Burgon JD, Vieites DR, Jacobs A, Weidt SK, Gunter HM, Steinfartz S et al. (2020) Functional colour genes and signals of selection in colour polymorphic salamanders. Mol Ecol 29:1284–1299

    CAS  PubMed  Article  Google Scholar 

  • Burgon JD, Vences M, Steinfartz S, Bogaerts S, Bonato L, Donaire-Barroso D, Martínez-Solano I, Velo-Antón G, Vieites DR, Mable BK, Elmer KR (2021) Phylogenomic inference of species and subspecies diversity in the Pal earctic salamander genus Salamandra. Molecular Phylogenetics and Evolution 157:107063

  • Chybicki IJ, Burczyk J (2009) Simultaneous estimation of null alleles and inbreeding coefficients. J Hered 100:106–113

    CAS  PubMed  Article  Google Scholar 

  • Clarke RT, Rothery P, Raybould AF (2002) Confidence limits for regression relationships between distance matrices: estimating gene flow with distance. JABES 7:361

    Google Scholar 

  • Cushman SA (2006) Effects of habitat loss and fragmentation on amphibians: a review and prospectus. Biol Conserv 128:231–240

    Article  Google Scholar 

  • Czypionka T, Goedbloed DJ, Steinfartz S, Nolte AW (2018) Plasticity and evolutionary divergence in gene expression associated with alternative habitat use in larvae of the European Fire Salamander. Mol Ecol 27:2698–2713

    PubMed  Article  Google Scholar 

  • Dinis M, Joger U, Slimani T, Martínez-Freiría F, Merabet K, Donaire D et al. (2018) Allopatric diversification and evolutionary melting pot in a North African Palearctic relict: the biogeographic history of Salamandra algira. Mol Phylogenet Evol 130:81–91

    PubMed  Article  Google Scholar 

  • Domínguez-Villar D, Carrasco RM, Pedraza J, Cheng H, Edwards R, Willenbring JK (2013) Early maximum extent of paleoglaciers from Mediterranean mountains during the last glaciation. Sci Rep. 3:2034

    PubMed  PubMed Central  Article  Google Scholar 

  • Dufresnes C, Pribille M, Alard B, Dubey S, Perrin N, Gonçalves H et al. (2020) Integrating hybrid zone analyses in species delimitation: lessons from two anuran radiations of the Western Mediterranean. Heredity 124:423–438

    CAS  PubMed  Article  Google Scholar 

  • Earl DA, VonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361

    Article  Google Scholar 

  • Emel SL, Olson DH, Knowles LL, Storfer A (2019) Comparative landscape genetics of two endemic torrent salamander species, Rhyacotriton kezeri and R. variegatus: implications for forest management and species conservation. Conserv Genet 20:801–815

    CAS  Article  Google Scholar 

  • Epps CW, Keyghobadi N (2015) Landscape genetics in a changing world: disentangling historical and contemporary influences and inferring change. Mol Ecol 24:6021–6040

    PubMed  Article  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Ficetola GF, Colleoni E, Renaud J, Scali S, Padoa‐Schioppa E, Thuiller W (2016) Morphological variation in salamanders and their potential response to climate change. Glob Chang Biol 22:2013–2024

    PubMed  PubMed Central  Article  Google Scholar 

  • Fletcher R, Fortin M (2018) Spatial ecology and conservation modeling. Springer International Publishing, Cham

    Google Scholar 

  • Fourcade Y, Engler JO, Rödder D, Secondi J (2014) Mapping species distributions with MAXENT using a geographically biased sample of presence data: a performance assessment of methods for correcting sampling bias. PLoS ONE 9:e97122

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  • Francis RM (2016) pophelper: An r package and web app to analyse and visualize population structure. Mol Ecol Resour 17:27–32

    PubMed  Article  CAS  Google Scholar 

  • García-París M, Alcobendas M, Alberch P (1998) Influence of the Guadalquivir river basin on mitochondrial DNA evolution of Salamandra salamandra (Caudata: Salamandridae) from southern Spain. Copeia 1998:173–176

    Article  Google Scholar 

  • García-París M, Alcobendas M, Buckley D, Wake DB (2003) Dispersal of viviparity across contact zones in iberian populations of fire salamanders (Salamandra) inferred from discordance of genetic and morphological traits. Evolution 57:129–143

  • Gomez A, Lunt DH (2007) Refugia within refugia: patterns of phylogeographic concordance in the Iberian Peninsula. In: Weiss S, Ferrand N (eds). Phylogeography of Southern European Refugia. Springer: Dordrecht. pp 155–188

  • Gray LN, Barley AJ, Poe S, Thomson RC, Nieto‐Montes de Oca A, Wang IJ (2019) Phylogeography of a widespread lizard complex reflects patterns of both geographic and ecological isolation. Mol Ecol 28:644–657

    PubMed  Article  Google Scholar 

  • Gutiérrez-Rodríguez J, Barbosa AM, Martínez-Solano I (2017a) Present and past climatic effects on the current distribution and genetic diversity of the Iberian spadefoot toad (Pelobates cultripes): an integrative approach. J Biogeogr 44:245–258

    Article  Google Scholar 

  • Gutiérrez-Rodríguez J, Barbosa AM, Martínez-Solano I (2017b) Integrative inference of population history in the Ibero-Maghrebian endemic Pleurodeles waltl (Salamandridae). Mol Phylogenet Evol 112:122–137

    PubMed  Article  Google Scholar 

  • Hendrix R, Schmidt BR, Schaub M, Krause ET, Steinfartz S (2017) Differentiation of movement behaviour in an adaptively diverging salamander population. Mol Ecol 26:6400–6413

    PubMed  Article  Google Scholar 

  • Hendrix R, Susanne Hauswaldt J, Veith M, Steinfartz S (2010) Strong correlation between cross-amplification success and genetic distance across all members of “True Salamanders” (Amphibia: Salamandridae) revealed by Salamandra salamandra-specific microsatellite loci. Mol Ecol Resour 10:1038–1047

    CAS  PubMed  Article  Google Scholar 

  • Hendry AP (2017) Eco-evolutionary dynamics. Princeton University Press, Princeton

    Google Scholar 

  • Hewitt G (2000) The genetic legacy of the Quaternary ice ages. Nature 405:907–913

    CAS  Article  Google Scholar 

  • Hijmans RJ, Van Etten J (2016) raster: Geographic Data Analysis and Modeling. R package version 2.5-8. Available from: http://CRAN.R-project.org/package=raster

  • Jombart T, Devillard S, Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet 11:1–94

    Article  Google Scholar 

  • Kalinowski ST (2005) HP-RARE 10: a computer program for performing rarefaction on measures of allelic richness. Mol Ecol Notes 5:187–189

    CAS  Article  Google Scholar 

  • Keenan K, Mcginnity P, Cross TF, Crozier WW, Prodöhl PA (2013) DiveRsity: an R package for the estimation and exploration of population genetics parameters and their associated errors. Methods Ecol Evol 4:782–788

    Article  Google Scholar 

  • Linnaeus C (1758) Systema Naturae per Regna Tria Naturae, Secundum Classes, Ordines, Genera, Species, cum Characteribus, Differentiis, Synonymis, Locis. 10th Edition. Volume 1. Stockholm, Sweden: L. Salvii

  • Lourenço A, Gonçalves J, Carvalho F, Wang IJ, Velo-Antón G (2019) Comparative landscape genetics reveals the evolution of viviparity reduces genetic connectivity in fire salamanders. Mol Ecol 28:4573–4591

    PubMed  Article  CAS  Google Scholar 

  • Maia-Carvalho B, Vale CG, Sequeira F, Ferrand N, Martínez-Solano I, Gonçalves H (2018) The roles of allopatric fragmentation and niche divergence in intraspecific lineage diversification in the common midwife toad (Alytes obstetricans). J Biogeogr 45:2146–2158

    Article  Google Scholar 

  • Martínez-Freiría F, Freitas I, Zuffi MAL, Golay P, Ursenbacher S, Velo-Antón G (2020) Climatic refugia boosted allopatric diversification in Western Mediterranean vipers. J Biogeogr 47:1698–1713

    Article  Google Scholar 

  • Martínez-Solano I (2006) Atlas de distribución y estado de conservación de los anfibios de la Comunidad de Madrid. Graellsia 62:253–291

    Article  Google Scholar 

  • Martínez-Solano I, Alcobendas M, Buckley D, García-París M (2005) Molecular characterisation of the endangered Salamandra salamandra almanzoris (Caudata, Salamandridae). Ann Zool Fenn 42:57–68

    Google Scholar 

  • McRae BH (2006) Isolation by resistance. Evolution 60:1551–1561

    PubMed  PubMed Central  Article  Google Scholar 

  • McRae BH, Dickson BG, Keitt TH, Shah VB (2008) Concepts and synthesis emphasizing new ideas to stimulate research in ecology using circuit theory to model connectivity in ecology, evolution, and conservation. Ecology 89:2712–2724

    PubMed  Article  Google Scholar 

  • Méndez L, Perdices A, Machordom A (2019) Genetic structure and diversity of the Iberian populations of the freshwater blenny Salaria fluviatilis (Asso, 1801) and its conservation implications. Conserv Genet 20:1223–1236

    Article  Google Scholar 

  • Miraldo A, Hewitt GM, Paulo OS, Emerson BC (2011) Phylogeography and demographic history of Lacerta lepida in the Iberian Peninsula: multiple refugia, range expansions and secondary contact zones. BMC Evol Biol 11:170

    PubMed  PubMed Central  Article  Google Scholar 

  • Mulder KP, Rodriguez NC, Grant EHC, Brand A, Fleischer RC (2019) North ‐ facing slopes and elevation shape asymmetric genetic structure in the range ‐ restricted salamander Plethodon shenandoah. Ecol Evol 9:5094–5105

    PubMed  PubMed Central  Article  Google Scholar 

  • Noguerales V, Cordero PJ, Ortego J (2017) Testing the role of ancient and contemporary landscapes on structuring genetic variation in a specialist grasshopper. Ecol Evol 7:3110–3122

    PubMed  PubMed Central  Article  Google Scholar 

  • Nosil P (2012) Ecological speciation. Oxford University Press, New York

    Google Scholar 

  • Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295

    Article  Google Scholar 

  • Pereira RJ, Martínez-Solano I, Buckley D (2016) Hybridization during altitudinal range shifts: nuclear introgression leads to extensive cyto-nuclear discordance in the fire salamander. Mol Ecol 25:1551–1565

    CAS  PubMed  Article  Google Scholar 

  • Peterman WE (2018) ResistanceGA: an R package for the optimization of resistance surfaces using genetic algorithms. Methods Ecol Evol 9:1638–1647

    Article  Google Scholar 

  • Phillips SB, Aneja VP, Kang D, Arya SP (2006) Modelling and analysis of the atmospheric nitrogen deposition in North Carolina. IJGEI 6:231–252

    Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  • Prunier JG, Colyn M, Legendre X, Nimon KF, Flamand MC (2015) Multicollinearity in spatial genetics: Separating the wheat from the chaff using commonality analyses. Mol Ecol 24:263–283

    CAS  Article  Google Scholar 

  • R Core Team (2018) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria, https://wwwR-project.org/

    Google Scholar 

  • Rousset F (2008) GENEPOP’007: a complete re-implementation of the GENEPOP software for Windows and Linux. Mol Ecol Resour 8:103–106

    PubMed  PubMed Central  Article  Google Scholar 

  • Sánchez‐Montes G, Wang J, Ariño AH, Martínez‐Solano I (2018) Mountains as barriers to gene flow in amphibians: quantifying the differential effect of a major mountain ridge on the genetic structure of four sympatric species with different life history traits. J Biogeogr 45:318–331

    Article  Google Scholar 

  • Sánchez-Montes G, Recuero E, Barbosa AM, Martínez-Solano I (2019) Complementing the Pleistocene biogeography of European amphibians: testimony from a southern Atlantic species. J Biogeogr 46:568–583

    Article  Google Scholar 

  • Sexton JP, Hangartner SB, Hoffmann AA (2014) Genetic isolation by environment or distance: which pattern of gene flow is most common? Evolution 68:1–15

    CAS  Article  Google Scholar 

  • Silva P, López-Bao JV, Llaneza L, Álvares F, Lopes S, Blanco JC et al. (2018) Cryptic population structure reveals low dispersal in Iberian wolves. Sci Rep 8:14108

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  • Steinfartz S, Küsters D, Tautz D (2004) Isolation and characterization of polymorphic tetranucleotide microsatellite loci in the fire salamander Salamandra salamandra (Amphibia: Caudata). Mol Ecol Notes 4:626–628

    CAS  Article  Google Scholar 

  • Velo-Antón G, García-París M, Galán P, Cordero Rivera A (2007) The evolution of viviparity in Holocene islands: ecological adaptation versus phylogenetic descent along the transition from aquatic to terrestrial environments. J Zool Syst Evol 45:345–352

    Article  Google Scholar 

  • Velo‐Antón G, Parra JL, Parra‐Olea G, Zamudio KR (2013) Tracking climate change in a dispersal‐limited species: reduced spatial and genetic connectivity in a montane salamander. Mol Ecol 22:3261–3278

    PubMed  Article  Google Scholar 

  • Velo-Antón G, Buckley D (2015) Salamandra común—Salamandra salamandra. In: Salvador A, Martínez-Solano I (eds), Enciclopedia Virtual de los Vertebrados Españoles, Museo Nacional de Ciencias Naturales, CSIC www.vertebradosibericos.org

  • Wang IJ (2013) Examining the full effects of landscape heterogeneity on spatial genetic variation: a multiple matrix regression approach for quantifying geographic and ecological isolation. Evolution 67:3403–3411

    PubMed  Article  Google Scholar 

  • Wang IJ, Bradburd GS (2014) Isolation by environment. Mol Ecol 23:5649–5662

    PubMed  PubMed Central  Article  Google Scholar 

  • Wang IJ, Glor RE, Losos JB (2013) Quantifying the roles of ecology and geography in spatial genetic divergence. Ecol Lett 16:175–182

    PubMed  Article  Google Scholar 

  • Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370

    CAS  Google Scholar 

  • Winiarski KJ, Peterman WE, Whiteley AR, McGarigal K (2020) Multiscale resistant kernel surfaces derived from inferred gene flow: an application with vernal pool breeding salamanders. Mol Ecol Resour 20:97–113

    CAS  PubMed  Article  Google Scholar 

  • Wogan GOU, Yuan ML, Mahler DL, Wang IJ (2020) Genome-wide epigenetic isolation by environment in a widespread Anolis lizard. Mol Ecol 29:40–55

    CAS  PubMed  Article  Google Scholar 

  • Wright S (1943) Isolation by distance. Genetics 28:114–138

    CAS  PubMed  PubMed Central  Google Scholar 


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