751
Views
7
CrossRef citations to date
0
Altmetric
Articles

Adding ecology into phylogeography: ecological niche models and phylogeography in tandem reveals the demographic history of the subalpine warbler complex

ORCID Icon, , &
Pages 234-242 | Received 13 Feb 2019, Accepted 05 Aug 2019, Published online: 05 Sep 2019

References

  • Avise, J.C. 2000. Phylogeography: the history and formation of species. Harvard University Press, Cambridge.
  • Barve, N. & Barve, V. 2013. ENMGadgets: tools for pre and post processing in ENM workflows. https://github.com/vijaybarve/ENMGadgets (accessed December 2013).
  • Barve, N., Barve, V., Jiménez-Valverde, A., Lira-Noriega, A., Maher, S.P., Peterson, A.T., Soberón, J. & Villalobos, F. 2011. The crucial role of the accessible area in ecological niche modeling and species distribution modelling. Ecol. Model 11: 1810–1819. doi: 10.1016/j.ecolmodel.2011.02.011
  • Birks, H.H. & Birks, H.J.B. 2004. The rise and fall of forests. Science 305: 484–485. doi: 10.1126/science.1101357
  • Brambilla, M., Tellini Florenzano, G., Sorace, A. & Guidali, F. 2006. Geographical distribution of Subalpine Warbler Sylvia cantillans subspecies in mainland Italy. Ibis 148: 568–571. doi: 10.1111/j.1474-919X.2006.00562.x
  • Brambilla, M., Janni, O., Guidali, F. & Sorace, A. 2008a. Song perception among incipient species as a mechanism for reproductive isolation. J. Evolution. Biol. 21: 651–657. doi: 10.1111/j.1420-9101.2008.01523.x
  • Brambilla, M., Vitulano, S., Spina, F., Baccetti, N., Gargallo, G., Fabbri, E., Guidali, F. & Randi, E. 2008b. A molecular phylogeny of the Sylvia cantillans complex: cryptic species within the Mediterranean basin. Mol. Phylogenet. Evolution 48: 461–472. doi: 10.1016/j.ympev.2008.05.013
  • Brambilla, M., Vitulano, S., Ferri, A., Spina, F., Fabbri, E. & Randi, E. 2010. What are we dealing with? An explicit test reveals different levels of taxonomic diagnosibility in the Sylvia cantillans species complex. J. Ornithol 151: 309–315. doi: 10.1007/s10336-009-0457-4
  • Brito, P. 2005. The influence of Pleistocene glacial refugia on tawny owl genetic diversity and phylogeography in western Europe. Mol. Ecol. 14: 3077–3094. doi: 10.1111/j.1365-294X.2005.02663.x
  • Brown, J.L. 2014. SDMtoolbox: a python-based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses. Methods Ecol. Evol. 5: 694–700. doi: 10.1111/2041-210X.12200
  • Canestrelli, D., Cimmurata, R. & Nascetti, G. 2007. 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. doi: 10.1111/j.1365-294X.2007.03534.x
  • Canestrelli, D., Cimmaruta, R. & Nascetti, G. 2008. Population genetic structure and diversity of the Apennine endemicstream frog, Rana italica – insights on the Pleistocene evolutionary history of the Italian peninsular biota. Mol. Ecol. 17: 3856–3872. doi: 10.1111/j.1365-294X.2008.03870.x
  • Canestrelli, D., Salvi, D., Maura, M., Bologna, M.A. & Nascetti, G. 2012. One species, three pleistocene evolutionary histories: phylogeography of the Italian Crested Newt, Triturus carnifex. PLoS ONE 7: e41754. doi: 10.1371/journal.pone.0041754
  • Clark, P.U., Dyke, A.S., Shakun, J.D., Carlson, A.E., Clark, J., Wohlfarth, B., Mitrovica, J.X., Hostetler, S.W. & McCabe, A.M. 2009. The last glacial maximum. Science 325: 710–713. doi: 10.1126/science.1172873
  • Combourieu-Nebout, N., Peyron, O., Dormoy, I., Desprat, S., Beaudouin, C., Kotthoff, U. & Marret, F. 2009. Rapid climatic variability in the west Mediterranean during the last 25000 years from high resolution pollen data. Clim. Past 5: 503–521. doi: 10.5194/cp-5-503-2009
  • Cooper, S.J., Ibrahim, K.M. & Hewitt, G.M. 1995. Postglacial expansion and genome subdivision in the European grasshopper Chorthippus parallelus. Mol. Ecol. 4: 49–60. doi: 10.1111/j.1365-294X.1995.tb00191.x
  • Cramp, S. 1992. The Birds of the Western Palearctic. Vol. 6. Oxford University Press, Oxford.
  • Dai, C., Zhao, N., Wang, W., Lin, C., Gao, B., Yang, X., Zhang, Z. & Lei, F. 2011. Profound climatic effects on two east Asian Black-Throated Tits (Ave: Aegithalidae), revealed by ecological niche models and phylogeographic analysis. PLoS ONE 6 (12): e29329. doi: 10.1371/journal.pone.0029329
  • Del Hoyo, J., Elliott, A. & Christie, D. 2006. Handbook of the birds of the world, old world flycatchers to old world warblers, vol. 11. Lynx Edicions, Barcelona, Spain.
  • Dickinson, E.C. & Christidis, L. 2014. The Howard and Moore Complete Checklist of the Birds of the World. Vol. 2, 4th edn., Passerines. Aves Press, Eastbourne.
  • Drovetski, S.V. 2003. Plio-Pleistocene climatic oscillations, Holarctic biogeography and speciation in an avian subfamily. J. Biogeogr. 30: 1173–1181. doi: 10.1046/j.1365-2699.2003.00920.x
  • Drummond, A.J., Suchard, M.A., Xie, D. & Rambaut, A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29: 1969–1973. doi: 10.1093/molbev/mss075
  • Elith, J. & Leathwick, J. 2009. Species distribution models: Ecological explanation and prediction across space and time. Annu. Rev. Ecol. Evol. S 40: 677–697. doi: 10.1146/annurev.ecolsys.110308.120159
  • Fletcher, W.J. & Goñi, M.F.S. 2008. Orbital-and sub-orbital-scale climate impacts on vegetation of the western Mediterranean basin over the last 48,000 yr. Quat. Res. 70: 451–464. doi: 10.1016/j.yqres.2008.07.002
  • Gómez, A. & Lunt, D.H. 2007. Refugia within refugia: patterns of phylogeographic concordance in the Iberian Peninsula. In Weiss, S. & Ferrand, N. (eds) Phylogeography of Southern European refugia, 155–188. Dordrecht, Springer Netherlands.
  • Gür, H. 2013. The effects of the late Quaternary glacial–interglacial cycles on Anatolian ground squirrels: range expansion during the glacial periods? Biol. J. Linn. Soc. 109: 19–32. doi: 10.1111/bij.12026
  • Heled, J. & Drummond, A.J. 2012. Calibrated tree priors for relaxed phylogenetics and divergence time estimation. Syst. Biol 61: 138–149. doi: 10.1093/sysbio/syr087
  • Hewitt, G.M. 1996. Some genetic consequences of ice ages, and their role in divergence and speciation. Biol. J. Linn. Soc. 58: 247–276. doi: 10.1111/j.1095-8312.1996.tb01434.x
  • Hewitt, G.M. 1999. Post-glacial re-colonization of European biota. Biol. J. Linn. Soc. 68: 87–112. doi: 10.1111/j.1095-8312.1999.tb01160.x
  • Hijmans, R.J., Cameron, S.E., Parra, J.L., Jones, P.G. & Jarvis, A. 2005. Very high resolution interpolated climate surfaces for global land areas. Int. J. Climatol. 25: 1965–1978.
  • Hung, C.-M., Drovetski, S.V. & Zink, R.M. 2012. Multilocus coalescence analyses support a mtDNA-based phylogeographic history for a widespread Palearctic passerine bird, Sitta europaea. Evolution 66: 2850–2864. doi: 10.1111/j.1558-5646.2012.01657.x
  • Ingenloff, K., Hensz, C.H., Anamza, T., Barve, V., Campbell, L.P., Cooper, J.C., Komp, E., Jimenez, L., Olson, K.V., Osorio-Olvera, L., Owens, H.L., Peterson, A.T., Samy, A.M., Slimões, M. & Soberón, J. 2017. Predictable invasion dynamics in North American populations of the Eurasian collared dove Streptopelia decaocto. Proc. R. Soc. B. 284: 20171157. doi: 10.1098/rspb.2017.1157
  • IPCC. 2001. Climate change 2001: the scientific basis. In: Houghton J.T., Griggs D.J., Noguer M., van der Linden P.J., Dai X., Maskell K. and Johnson C.A. (eds), Third Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge University Press, New York.
  • Kamp, L., Pasinelli, G., Milanesi, P., Drovetski, S.V., Kosiński, Z., Kossenko, S., Robles, H. & Schweizer, M. 2019. Significant Asia-Europe divergence in the middle spotted woodpecker (Aves, Picidae). Zool. Scr. 48: 17–32. doi: 10.1111/zsc.12320
  • Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. 2018. MEGA x: Molecular Evolutionary Genetics Analysis across computing platforms. Mol. Biol. Evol. 35: 1547–1549. doi: 10.1093/molbev/msy096
  • McInerny, C.J., Musgrove, A.J., Stoddart, A., Harrop, A.H.J., Dudley, S.P. & the British Ornithologists’ Union Records Committee. 2018. The British list: a checklist of birds of Britain (9th Edition). Ibis 160: 190 –240. doi: 10.1111/ibi.12536
  • Nogués-Bravo, D. 2009. Predicting the past distribution of species climatic niches. Global Ecol. Biogeogr. 18: 521–531. doi: 10.1111/j.1466-8238.2009.00476.x
  • Otto-Bliesner, B.L., Marshall, S.J., Overpeck, J.T., Miller, G.H., Hu, A. & CAPE Last Interglacial Project members. 2006. Simulating arctic warmth and icefield retreat in the Last Interglaciation. Science 311: 1751–1753. doi: 10.1126/science.1120808
  • Pellegrino, I., Negri, A., Cucco, M., Mucci, N., Pavia, M., Šálek, M., Boano, G. & Randi, E. 2014. Phylogeography and Pleistocene refugia of the Little Owl Athene noctua inferred from mtDNA sequence data. Ibis 156: 639–657. doi: 10.1111/ibi.12162
  • Pereira, S.L. & Baker, A.J. 2006. A molecular timescale for galliform birds accounting for uncertainty in time estimates and heterogeneity of rates of DNA substitutions across lineages and sites. Mol. Phylogenet. Evol. 38: 499–509. doi: 10.1016/j.ympev.2005.07.007
  • Perktaş, U. & Quintero, E. 2013. A wide geographical survey of mitochondrial DNA variation in the great spotted woodpecker complex, Dendrocopos major (Aves: Picidae). Biol. J. Linn. Soc. 108: 173–188. doi: 10.1111/j.1095-8312.2012.02003.x
  • Perktaş, U. & Gür, H. 2015. Guest editors’ introduction to the special issue: integrating phylogeography and ecological niche modelling. Folia Zool. 64: 185–186. doi: 10.25225/fozo.v64.i3.a1.2015
  • Perktaş, U., Barrowclough, G.F. & Groth, J.G. 2011. Phylogeography and species limits in the green woodpecker complex (Aves: Picidae): multiple Pleistocene refugia and range expansion across Europe and the Near East. Biol. J. Linn. Soc. 104: 710–723. doi: 10.1111/j.1095-8312.2011.01750.x
  • Perktaş, U., Gür, H. & Ada, E. 2015. Historical demography of the Eurasian Green Woodpecker: integrating phylogeography and ecological niche modeling to test glacial refugia hypothesis. Folia Zool. 64: 284–295. doi: 10.25225/fozo.v64.i3.a9.2015
  • Perktas, U., Peterson, A.T. & Dyer, D. 2017. Integrating morphology, phylogeography, and ecological niche modeling to explore population differentiation in North African Common Chaffinches. J. Ornithol. 158: 1–13. doi: 10.1007/s10336-016-1361-3
  • Petit, R.J., Hampe, A. & Cheddadi, R. 2005. Climate changes and tree phylogeography in the Mediterranean. Taxon 54: 877–885. doi: 10.2307/25065568
  • Phillips, S.J., Anderson, R.P. & Schapire, R.E. 2006. Maximum entropy modeling of species geographic distributions. Ecol. Model 190: 231–259. doi: 10.1016/j.ecolmodel.2005.03.026
  • Pons, A. & Reille, M. 1988. The Holocene-and Upper Pleistocene pollen record from Padul (Granada. Spain): a new study. Palaeogeogr Palaeoclimatol Palaeoecol. 66: 243–263. doi: 10.1016/0031-0182(88)90202-7
  • Pons, J.M., Olioso, G., Cruaud, C. & Fuchs, J. 2011. Phylogeography of the Eurasian green woodpecker (Picus viridis). J. Biogeogr. 38: 311–325. doi: 10.1111/j.1365-2699.2010.02401.x
  • Provan, J. & Bennett, K.D. 2008. Phylogeographic insights into cryptic glacial refugia. Trends Ecol. Evol. 23: 564–571. doi: 10.1016/j.tree.2008.06.010
  • Radosavljevic, A. & Anderson, R.P. 2014. Making better Maxent models of species distributions: complexity, overfitting and evaluation. J. Biogeogr. 41: 629–643. doi: 10.1111/jbi.12227
  • Rousset, F. 1997. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145: 1219–1228.
  • Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J.C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S.E. & Sánchez-Gracia, A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large datasets. Mol. Biol. Evol. 34: 3299–3302. doi: 10.1093/molbev/msx248
  • Shirihai, H., Gargallo, G. & Helbig, A.J. 2001. Sylvia Warblers. Identification, Taxonomy and Phylogeny of the Genus Sylvia. A & C Black, London.
  • Slatkin, M. 1993. Isolation by distance in equilibrium and non-equilibrium populations. Evolution 47: 264–279. doi: 10.1111/j.1558-5646.1993.tb01215.x
  • Soberon, J. & Peterson, A.T. 2005. Interpretation of models of fundamental ecological niches and species’ distributional areas. Biodivers. Informatics 2: 1–10. doi: 10.17161/bi.v2i0.4
  • Stewart, J.R., Lister, A.M., Barnes, I. & Dalén, L. 2010. Refugia revisited: Individualistic responses of species in space and time. Proc. Biol. Sci. 277: 661–671. doi: 10.1098/rspb.2009.1272
  • Svensson, L. 2013. A taxonomic revision of the Subalpine Warbler Sylvia cantillans. Bull. Br. Ornithol. Club 133: 240–248.
  • Tellería, J.L., Fernández-López, J. & Fandos, G. 2016. Effect of Climate Change on Mediterranean Winter Ranges of Two Migratory Passerines. PLoS ONE 11: e0146958. doi: 10.1371/journal.pone.0146958
  • Thévenot, M., Vernon, R. & Bergier, P. 2003. The birds of Morocco. An annotated checklist. BOU Checklist 20. Tring.
  • Tucker, G.M. & Evans, M.I. 1997. Habitats for birds in Europe: a conservation strategy for the wilder environment. BirdLife International, Cambridge.
  • Ülker, E.D., Tavşanoğlu, Ç. & Perktaş, U. 2018. Ecological niche modelling of pedunculate oak (Quercus robur) supports the ‘expansion–contraction’ model of Pleistocene biogeography. Biol. J. Linn. Soc. 123: 338–347. doi: 10.1093/biolinnean/blx154
  • Warren, D.L., Glor, R.E. & Turelli, M. 2010. ENMTools: a toolbox for comparative studies of environmental niche models. Ecography 33: 607–611. doi: 10.1111/j.1600-0587.2009.06041.x
  • Weir, J.T. & Schluter, D. 2008. Calibrating the avian molecular clock. Mol. Ecol. 17: 2321–2328. doi: 10.1111/j.1365-294X.2008.03742.x
  • Zhao, N., Dai, C., Wang, W., Zhang, R., Qu, Y., Song, G., Chen, K., Yang, X., Zou, F. & Lei, F. 2012. Pleistocene climate changes shaped the divergence and demography of Asian populations of the great tit Parus major: Evidence from phylogeographic analysis and ecological niche models. J. Avian Biol. 43: 297–310. doi: 10.1111/j.1600-048X.2012.05474.x

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.