in

The effect of phylogeographic history on species boundaries: a comparative framework in Hyla tree frogs

  • 1.

    Avise, J. Phylogeography: The history and formation of species. Cambridge, (Harvard University Press) (2000).

  • 2.

    Coyne, J. A. & Orr, H. A. Speciation. (Sinauer Associates) (2004).

  • 3.

    Mayr, E. Systematics and the origin of species, from the viewpoint of a zoologist. (Harvard University Press), (1942).

  • 4.

    Roux, C. et al. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biol. 14, e20000234 (2016).

  • 5.

    Singhal, S. & Moritz, C. Reproductive isolation between phylogeographic lineages scales with divergence. Proc. R. Soc. Lond. 280, 20132246 (2013).

    • Article
    • Google Scholar
  • 6.

    Arntzen, J. W., Wielstra, B. & Wallis, G. P. The modality of nine Triturus newt hybrid zones assessed with nuclear, mitochondrial and morphological data. Biol. J. Linn. Soc. 113, 604–622 (2014).

    • Article
    • Google Scholar
  • 7.

    Dufresnes, C. et al. Phylogeography of a cryptic speciation continuum in Eurasian spadefoot toads (Pelobates). Mol. Ecol. 28, 3257–3270 (2019).

  • 8.

    Padial, J., Miralles, A., De la Riva, I. & Vences, M. The integrative future of taxonomy. Front. Zool. 7, 16 (2010).

  • 9.

    Barton, N. H. & Hewitt, G. M. Analysis of hybrid zones. Annu. Rev. Ecol. Evol. Syst. 16, 113–148 (1985).

    • Article
    • Google Scholar
  • 10.

    Dufkova, P., Macholan, M. & Pialek, J. Inference of selection and stochastic effects in the house mouse hybrid zone. Evolution 65, 993–1010 (2011).

    • Article
    • Google Scholar
  • 11.

    Beysard, N. & Heckel, G. Structure and dynamics of hybrid zones at different stages of speciation in the common vole (Microtus arvalis). Mol. Ecol. 23, 673–687 (2014).

  • 12.

    Wielstra, B. et al. A genomic footprint of hybrid zone movement in crested newts. Evol. Lett. 1, 93–101 (2017).

  • 13.

    Hewitt, G. Quaternary phylogeography: the roots of hybrid zones. Genetica 139, 617–638 (2011).

    • Article
    • Google Scholar
  • 14.

    Butlin, R. Speciation by reinforcement. Trends Ecol. Evol. 2, 8–13 (1987).

  • 15.

    Servedio, M. R. & Noor, M. A. F. The role of reinforcement in speciation: theory and data. Annu. Rev. Ecol. Evol. Syst. 34, 339–364 (2003).

    • Article
    • Google Scholar
  • 16.

    Saestre, G.-P., Kral, K., Bures, S. & Ims, R.-A. Dynamics of a clinal hybrid zone and a comparison with island hybrid zones of flycatchers (Ficedula hypoleuca and F. albicollis). J. Zool. 247, 53–64 (1999).

    • Article
    • Google Scholar
  • 17.

    Saestre, G.-P. et al. A sexually selected character displacement in flycatchers reinforces premating isolation. Nature 387, 589–592 (1997).

  • 18.

    Zeng, Y. F., Lia, W. J., Petit, R. J. & Zang, D. Y. Geographic variation in the structure of oak hybrid zones provides insights into the dynamics of speciation. Mol. Ecol. 20, 4995–5011 (2011).

  • 19.

    Croucher, P. J., Jones, R. R., Searle, J. B. & Oxford, G. S. Contrasting patterns of hybridization in large house spiders (Tegenaria atrica group, Agelenidae). Evolution 61, 1622–1640 (2007).

  • 20.

    Dufresnes, C. et al. Genomic evidence for cryptic speciation in tree frogs from the Apennine Peninsula, with description of Hyla perrini sp. nov. Front. Ecol. Evol. 6, 144 (2018).

    • Article
    • Google Scholar
  • 21.

    Stöck, M. et al. Cryptic diversity among Western Paleartic tree frogs: Postglacial range expansion, range limits, and secondary contacts of three European tree frog lineages (Hyla arborea group). Mol. Phylogenet. Evol. 65, 1–9 (2012).

  • 22.

    Drillon, O., Dufresnes, G., Perrin, N., Crochet, P.-A. & Dufresnes, C. Reaching the edge of the speciation continuum: hybridization between three sympatric species of tree frogs (Hyla). Biol. J. Linn. Soc. 126, 743–750 (2019).

    • Article
    • Google Scholar
  • 23.

    Gvoždík, V. et al. Speciation history and widespread introgression in the European short-call tree frogs (Hyla arborea sensu lato, H. intermedia and H. sarda). Mol. Phylogenet. Evol. 83, 143–155 (2015).

    • Article
    • Google Scholar
  • 24.

    Dufresnes, C., Brelsford, A., Béziers, P. & Perrin, N. Stronger transferability but lower variability in transcriptomic- than in anonymous microsatellites: evidence from Hylid frogs. Mol. Ecol. Resour. 14, 716–725 (2014).

  • 25.

    Dufresnes, C. et al. Sex-chromosome homomorphy in Palearctic tree frogs results from both turnovers and X-Y recombination. Mol. Biol. Evol. 32, 2328–2337 (2015).

  • 26.

    Dufresnes, C. et al. Conservation phylogeography: does historical diversity contribute to regional vulnerability in European tree frogs (Hyla arborea)? Mol. Ecol. 22, 5669–5684 (2013).

    • Article
    • Google Scholar
  • 27.

    Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945–959 (2000).

  • 28.

    Earl, D. A. & vonHoldt, B. M. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Resour. 4, 359–361 (2012).

    • Article
    • Google Scholar
  • 29.

    Jakobsson, M. & Rosenberg, N. A. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23, 1801–1806 (2007).

  • 30.

    Rosenberg, N. A. Distruct: a program for the graphical display of population structure. Mol. Ecol. Resour. 4, 137–138 (2004).

    • Article
    • Google Scholar
  • 31.

    Jombart, T. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24, 1403–1405 (2008).

  • 32.

    Goudet, J. Hierfstat, a package for R to compute and test hierarchical F-statistics. Mol. Ecol. Notes 5, 184–186 (2005).

    • Article
    • Google Scholar
  • 33.

    Dufresnes, C. et al. Timeframe of speciation inferred from secondary contact zones in the European tree frog radiation (Hyla arborea group). BMC Evol. Biol. 15, 155 (2015).

  • 34.

    Derryberry, E. P., Derryberry, G. E., Maley, J. M. & Brumfield, R. T. HZAR: hybrid zone analysis using an R software package. Mol. Ecol. Resour. 14, 652–663 (2014).

  • 35.

    Stöck, M. et al. Mitochondrial and nuclear phylogeny of circum-Mediterranean tree frogs from the Hyla arborea group. Mol. Phylogenet. Evol. 49, 1019–1024 (2008).

  • 36.

    Recuero, E., Iraola, A., Rubio, X., Mahordom, A. & García-París, M. Mitochondrial differentiation and biogeography of Hyla meridionalis (Anura: Hylidae): an unsual phylogeographical pattern. J. Biogeogr. 34, 1207–1219 (2007).

    • Article
    • Google Scholar
  • 37.

    Dufresnes, C. et al. Diversification and speciation in tree frogs from the Maghreb (Hyla meridionalis sensu lato), with description of a new African endemic. Mol. Phylogenet. Evol. 134, 291–299 (2019).

  • 38.

    Gvoždík, V., Moravec, J., Klütsch, C. & Kotlík, P. Phylogeography of the Middle Eastern tree frogs (Hyla, Hylidae, Amphibia) as inferred from nuclear and mitochondrial DNA variation, with a description of a new species. Mol. Phylogenet. Evol. 55, 1146–1166 (2010).

    • Article
    • Google Scholar
  • 39.

    Gül, S., Kutrup, B. & Özdemir, N. Patterns of distribution of tree frogs in Turkey based on molecular data. Amphibia-Reptilia 33, 95–103 (2012).

    • Article
    • Google Scholar
  • 40.

    Bisconti, R., Canestrelli, D., Colangelo, P. & Nascetti, G. Multiple lines of evidence for demographic and range expansion of a temperate species (Hyla sarda) during the last glaciation. Mol. Ecol. 20, 5313–5327 (2011).

  • 41.

    Bisconti, R., Canestrelli, D. & Nascetti, G. Genetic diversity and evolutionary history of the Tyrrhenian treefrog Hyla sarda (Anura: Hylidae): adding pieces to the puzzle of Corsica–Sardinia biota. Biol. J. Linn. Soc. 103, 159–167 (2011).

    • Article
    • Google Scholar
  • 42.

    Canestrelli, D., Cimmaruta, R. & Nascetti, G. Phylogeography and historical demography of the Italian treefrog, Hyla intermedia, reveals multiple refugia, population expansions and secondary contacts within peninsular Italy. Mol. Ecol. 16, 4808–4821 (2007).

  • 43.

    Canestrelli, D., Verardi, A. & Nascetti, G. Genetic differentiation and history of populations of the Italian treefrog Hyla intermedia: lack of concordance between mitochondrial and nuclear makers. Genetica 130, 241–255 (2007).

  • 44.

    Dufresnes, C. et al. Sex-chromosome differentiation parallels postglacial range expansion in European tree frogs (Hyla arborea). Evolution 68, 3445–3456 (2014).

  • 45.

    Barth, A. et al. Mitochondrial uniformity in populations of the treefrog Hyla molleri across the Iberian Peninsula. Amphibia-Reptilia 32, 557–564 (2011).

    • Article
    • Google Scholar
  • 46.

    Sánchez-Montes, G., Recuero, E., Marcia Barbosa, A. & Martinez-Solano, I. Complementing the Pleistocene biogeography of European amphibians: Testimony from a southern Atlantic species. J. Biogeogr. 46, 568–583 (2019).

    • Article
    • Google Scholar
  • 47.

    Dufresnes, C. et al. Evolutionary melting pots: a biodiversity hotspot shaped by ring diversifications around the Black Sea in the Eastern tree frog (Hyla orientalis). Mol. Ecol. 25, 4285–4300 (2016).

  • 48.

    Dufresnes, C., Mazepa, G., Jablonski, D., Sadek, R. A. & Litvinchuk, S. N. A river runs through it: tree frogs genomics supports the Dead Sea Rift as a rare phylogeographic break. Biol. J. Linn. Soc. 128, 130–137 (2019).

    • Article
    • Google Scholar
  • 49.

    Verardi, A., Canestrelli, D. & Nascetti, G. Nuclear and mitochondrial patterns of introgression between the parapatric European tree frogs Hyla arborea and H. intermedia. Ann. Zool. Fenn. 46, 247–258 (2009).

    • Article
    • Google Scholar
  • 50.

    Dufresnes, C., Dubey, S., Ghali, K., Canestrelli, D. & Perrin, N. Introgressive hybridization of threatened European tree frogs (Hyla arborea) by introduced H. intermedia in Western Switzerland. Conserv. Genet. 16, 1507–1513 (2015).

    • Article
    • Google Scholar
  • 51.

    Dufresnes, C. et al. Empirical evidence for large X-effects in animals with undifferentiated sex chromosomes. Sci. Rep. 6, 21029 (2016).

  • 52.

    Smith, S. A., Stephens, P. R. & Wiens, J. J. Replicate patterns of species richness, historical biogeography and phylogeny in Holarctic treefrogs. Evolution 59, 2433–2450 (2005).

  • 53.

    Li, J.-T. et al. Amphibians crossing the Bering Land Bridge: evidence from Holarctic treefrogs (Hyla, Hylidae, Anura). Mol. Phylogenet. Evol. 87, 80–90 (2015).

    • Article
    • Google Scholar
  • 54.

    Kotsakis, T. Osservazioni sui vertebrati quaternary della sardegna. Boll. Soc. geol. ital. 99, 151–165 (1980).

    • Google Scholar
  • 55.

    Phillips, S., Anderson, R. & Schapire, R. Maximum entropy modeling of species geographic distributions. Ecol. Model. 190, 231–259 (2006).

    • Article
    • Google Scholar
  • 56.

    Osorio-Olvera, L., Barve, V., Barve, N., Soberón, J., & Falconi, M. ntbox: From getting biodiversity data to evaluating species distribution models in a friendly GUI environment, https://github.com/luismurao/ntbox (2018).

  • 57.

    Watanabe, S. et al. MIROC-ESM 2010: model description and basic results of CMIP5-20c3 m experiments. Geosci. Model Dev. 4, 845–872 (2011).

  • 58.

    Warren, D. L., Glor, R. E. & Turelli, M. ENMTOOLS: a toolbox for comparative studies of environmental niche models. Ecography 33, 607–611 (2010).

    • Article
    • Google Scholar
  • 59.

    Cobos, M. E., Peterson, A. T., Barve, N. & Osorio-Olvera, L. kuenm: an R package for detailed development of ecological niche models using Maxent. PeerJ 7, e6281 (2019).

  • 60.

    Becker, D., Verheul, J., Zickel, M., & Willmes C. LGM paleoenvironment of Europe – Map. CRC 806 Database. https://doi.org/10.5880/SFB806.15 (2015).

  • 61.

    Zickel, M. Paleocoastline 130m below mean sea level. CRC 806 Database, https://crc806db.uni-koeln.de/layer/show/324/ (2016).

  • 62.

    Berroneau, M. Atlas des amphibians et reptiles d’Aquitaine. (Cistude Nature), (2014).

  • 63.

    Dufresnes, C. et al. Inferring the degree of incipient speciation in secondary contact zones of closely related lineages of Palearctic green toads (Bufo viridis subgroup). Heredity 113, 9–20 (2014).

  • 64.

    Feng, Y.-J. et al. Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous-Paleogene boundary. PNAS 114, E5864–E5870 (2017).

  • 65.

    Dubey, S., Lavanchy, G., Thiébaud, J. & Dufresnes, C. Herps without border: a new newt case and a review of transalpine alien introductions in Western Europe. Amphibia-Reptilia 40, 13–27 (2019).

    • Article
    • Google Scholar
  • 66.

    Vos, C. C., Ter Braak, C. J. F. & Nieuwenhuizen, W. Incidence function modelling and conservation of the tree frog Hyla arborea in the Netherlands. Ecol. Bull. 48, 165–180 (2000).

    • Google Scholar
  • 67.

    Trochet, A. et al. A database of life-history traits of European amphibians. Biodivers. Data J. 2, e4123 (2014).

    • Article
    • Google Scholar
  • 68.

    Peter, B. M. & Slatkin, M. Detecting range expansions from genetic data. Evolution 67, 3274–3289 (2013).

  • 69.

    Currat, M., Ruedi, M., Petit, R. J. & Excoffier, L. The hidden side of invasions: massive introgression by local genes. Evolution 62, 1908–1920 (2008).

    • Google Scholar
  • 70.

    Hoskin, C. J., Higgie, M., McDonald, K. R. & Moritz, C. Reinforcement drives rapid allopatric speciation. Nature 437, 1353–1356 (2005).

  • 71.

    Dufresnes, C. et al. Integrating hybrid zone analyses in species delimitation: lessons from two anuran radiations of the Western Mediterranean. Heredity 124, 423–438 (2020).

  • 72.

    Barton, N., & Gale, K. S. Genetic analysis of hybrid zones in Hybrid zones and the evolutionary process (ed. R., Harrison) 13–45 (Oxford University Press), (1993).

  • 73.

    Özdemir, N. et al. Variation in body size and age structure among three Turkish populations of the treefrog Hyla arborea. Amphibia-Reptilia 33, 25–35 (2012).

    • Article
    • Google Scholar
  • 74.

    Petit, R. J. Biological invasion at the gene level. Divers. Distrib. 10, 159–165 (2004).

    • Article
    • Google Scholar
  • 75.

    Gaskin, J. T. The role of hybridization in facilitating tree invasion. AoB Plants 9, plw079 (2017).

    • Google Scholar
  • 76.

    Hasselman, D. et al. Human disturbance causes the formation of a hybrid swarm between two naturally sympatric fish species. Mol. Ecol. 23, 1137–1152 (2014).

  • 77.

    Dufresnes, C. Amphibians of Europe, North Africa and the Middle East. (Bloomsbury), (2019)


  • Source: Ecology - nature.com

    Global conservation of species’ niches

    Online characterization of bacterial processes in drinking water systems