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The Early Stages of Speciation in Amazonian Forest Frogs: Phenotypic Conservatism Despite Strong Genetic Structure

Abstract

Phylogeographic perspectives incorporating multiple classes of characters, especially those relating to sexual signals, are promising for the elucidation of recent evolutionary mechanisms driving speciation. Here, forest frogs were used as a model system to access distinct stages in the process of evolutionary differentiation. We studied 280 individuals assigned to three species: Allobates paleovarzensis, A. nidicola and A. masniger. Samples were collected at 20 localities arranged in two study systems, along the middle Amazon and the lower Madeira Rivers, in Central Amazonia. Mantel tests, analyses of molecular variance, and the spatial distribution of haplogroups indicated that the distribution of genetic variability, as inferred from a mitochondrial DNA marker, was determined by a combination of isolation-by-distance effects and the transposition of large Amazonian rivers. These two factors had contrasting relative influences in each of the study systems, which also differed regarding the estimated time of the major cladogenetic events. Pronounced population genetic structure was observed. However, multivariate discriminant function analyses revealed that the phenotypic (morphological and acoustic) divergence was loosely related with genetic differentiation and did not successfully predict assignment of individuals to genetic groups. The observed distribution of genetic variability showed the important role of genetic drift in the diversification of the mitochondrial marker studied. The phenotypic conservatism among populations was surprising in view of the high genetic structuring observed, and indicates a prevailing role of stabilizing selective forces in the process of sexual signal and morphological differentiation.

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References

  • Adams, D. C., Berns, C. M., Kozak, K. H., & Wiens, J. (2009). Are rates of species diversification correlated with rates of morphological evolution? Proceedings of the Royal Society B, 276, 2729–2738.

    PubMed  Article  Google Scholar 

  • Amézquita, A., Lima, A. P., Jehle, R., Castellanos, L., Ramos, O., Crawford, A. J., et al. (2009). Calls, colours, shapes, and genes: A multi–trait approach to the study of geographic variation in the Amazonian frog Allobates femoralis. Biological Journal of the Linnean Society, 98, 826–838.

    Article  Google Scholar 

  • Anderson, M. J., & Legendre, P. (1999). An empirical comparison of permutation methods for tests of partial regression coefficients in a linear model. Journal of Statistical Computation and Simulation, 62, 271–303.

    Article  Google Scholar 

  • Angulo, A., & Reichle, S. (2008). Acoustic signals, species diagnosis, and species concepts: The case of a new cryptic species of Leptodactylus (Amphibia, Anura, Leptodactylidae) from the Chapare region, Bolivia. Zoological Journal of the Linnean Society, 152, 58–77.

    Google Scholar 

  • Antonelli, A., Quijada-Mascareñas, A., Crawford, A. J., Bates, J. M., Velazco, P. M., & Wüster, W. (2010). Molecular studies and phylogeography of Amazonian tetrapods and their relation to geological and climatic models. In C. Hoorn & F. P. Wesselingh (Eds.), Amazonia, landscape and species evolution (pp. 386–403). Oxford: Blackwell Publishing.

    Google Scholar 

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

    Google Scholar 

  • Avise, J. C. (2004). Molecular markers, natural history and evolution (2nd ed.). Sunderland: Sinauer Associates Inc.

    Google Scholar 

  • Ayres, J. M., & Clutton-Brock, T. H. (1992). River boundaries and species range size in Amazonian primates. The American Naturalist, 140, 531–537.

    PubMed  CAS  Article  Google Scholar 

  • Blomberg, S. P., Garland, T., Jr, & Ives, A. R. (2003). Testing for phylogenetic signal in comparative data: Behavioral traits are more labile. Evolution, 57, 717–745.

    PubMed  Google Scholar 

  • Bonnet, E., & Van de Peer, Y. (2002). ZT: A software tool for simple and partial Mantel tests. Journal of Statistical Software, 7, 1–12.

    Google Scholar 

  • Boul, K. E., Funk, W. C., Darst, C. R., Cannatella, D. C., & Ryan, M. J. (2007). Sexual selection drives speciation in an Amazonian frog. Proceedings of the Royal Society B, 274, 399–406.

    PubMed  Article  Google Scholar 

  • Caldwell, J. P., & Lima, A. P. (2003). A new Amazonian species of Colostethus (Anura: Dendrobatidae) with a nidicolous tadpole. Herpetologica, 59, 219–234.

    Article  Google Scholar 

  • Camargo, A., de Sá, R., & Heyer, W. R. (2006). Phylogenetic analyses of mtDNA sequences reveal three cryptic lineages in the widespread neotropical frog Leptodactylus fuscus (Schneider, 1799) (Anura, Leptodactylidae). Biological Journal of the Linnean Society, 87, 325–341.

    Article  Google Scholar 

  • Campbell, P., Pasch, B., Pino, J. L., Crino, O. L., Phillips, M., & Phelps, S. M. (2010). Geographic variation in the songs of neotropical singing mice: Testing the relative importance of drift and local adaptation. Evolution, 64, 1955–1972.

    PubMed  Google Scholar 

  • Capparella, A. P. (1988). Genetic variation in Neotropical birds: Implications for the speciation process. In H. Ouellet (Ed.), Acta XIX Congressus Internationalis Ornithologici (pp. 1658–1664). Ottawa: University of Ottawa Press.

    Google Scholar 

  • Charif, R. A., Clark, C. W., & Fristrup, K. M. (2004). Raven 1.2 User’s manual. Ithaca: Cornell Laboratory of Ornithology.

    Google Scholar 

  • Charif, R. A., Waack, A. M., & Strickman, L. M. (2008). Raven Pro 1.3 User’s manual. Ithaca: Cornell Laboratory of Ornithology.

    Google Scholar 

  • Cherry, L. M., Case, S. M., & Wilson, A. C. (1978). Frog perspective on the morphological difference between humans and chimpanzees. Science, 200, 209–211.

    Article  Google Scholar 

  • Clement, M., Posada, D., & Crandall, K. A. (2000). TCS: A computer program to estimate gene genealogies. Molecular Ecology, 9, 1657–1659.

    PubMed  CAS  Article  Google Scholar 

  • Cohn-Haft, M. (2000). A case study in amazonian biogeography: Vocal and DNA sequence variation in Hemitriccus flycatchers. PhD thesis. Luisiana State University.

  • Colwell, R. K. (2000). A barrier runs through it… or maybe just a river. Proceedings of the National Academy of Sciences, 97, 13470–13472.

    CAS  Article  Google Scholar 

  • Corander, J., Marttinen, P., Sirén, J., & Tang, J. (2008). Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinformatics, 9, 539.

    PubMed  Article  CAS  Google Scholar 

  • Costa, J. B. S., Bemerguy, R. L., Hasui, Y., & Borges, M. S. (2001). Tectonics and paleogeography along the Amazon River. Journal of South American Earth Sciences, 14, 335–347.

    Article  Google Scholar 

  • Coyne, J. A., & Orr, H. A. (2004). Speciation. Sunderland: Sinauer Associates Inc.

    Google Scholar 

  • Crawford, A. J. (2003). Huge populations and old species of Costa Rican and Panamanian dirt frogs inferred from mitochondrial and nuclear gene sequences. Molecular Ecology, 12, 2525–2540.

    PubMed  CAS  Article  Google Scholar 

  • Crawford, A. J., Lips, K. R., & Bermingham, E. (2010). Epidemic disease decimates amphibian abundance, species diversity, and evolutionary history in the highlands of central Panama. Proceedings of the National Academy of Sciences, 107, 13777–13782.

    CAS  Article  Google Scholar 

  • Creer, S., Thorpe, R. S., Malhotra, A., Chou, W. H., & Stenson, A. G. (2004). The utility of AFLPs for supporting mitochondrial DNA phylogeographical analyses in the Taiwanese bamboo viper, Trimeresurus stejnegeri. Journal of Evolutionary Biology, 17, 100–107.

    PubMed  CAS  Article  Google Scholar 

  • Crisci, J. V., Katinas, L., & Posadas, P. (2003). Historical biogeography: An introduction. Cambridge: Harvard University Press.

    Google Scholar 

  • Dall, S. R. X. (1997). Behaviour and speciation. Trends in Ecology & Evolution, 12, 209–210.

    CAS  Article  Google Scholar 

  • Dayrat, B. (2005). Towards integrative taxonomy. Biological Journal of the Linnean Society, 85, 407–415.

    Article  Google Scholar 

  • de Queiroz, K. (2007). Species concepts and species delineation. Systematic Biology, 56, 879–886.

    PubMed  Article  Google Scholar 

  • Diniz-Filho, J. A. F., Telles, M. P. C., Bonatto, S. L., Eizirik, E., Freitas, T. R. O., de Marco, P., et al. (2008). Mapping the evolutionary twilight zone: Molecular markers, populations and geography. Journal of Biogeography, 35, 753–763.

    Article  Google Scholar 

  • Drummond, A. J., & Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.

    PubMed  Article  CAS  Google Scholar 

  • Elmer, K. R., Dávila, J. A., & Lougheed, S. C. (2007). Cryptic diversity and deep divergence in an upper Amazonian leaflitter frog, Eleutherodactylus ockendeni. BMC Evolutionary Biology, 7, 247.

    PubMed  Article  Google Scholar 

  • Erdtmann, L., & Amézquita, A. (2009). Differential evolution of advertisement call traits in Dart–Poison Frogs (Anura: Dendrobatidae). Ethology, 115, 801–811.

    Article  Google Scholar 

  • Excoffier, L., & Lischer, H. E. L. (2010). Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Research, 10, 564–567.

    Article  Google Scholar 

  • Excoffier, L., Smouse, P., & Quattro, J. (1992). Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics, 131, 479–491.

    PubMed  CAS  Google Scholar 

  • Fernandes, A. M., Wink, M., & Aleixo, A. (2012). Phylogeography of the chestnut tailed antbird (Myrmeciza hemimelaena) clarifies the role of rivers in Amazonian biogeography. Journal of Biogeography, 39, 1524–1535.

    Article  Google Scholar 

  • Figueiredo, J., Hoorn, C., van der Ven, P., & Soares, E. (2009). Late Miocene onset of the Amazon River and the Amazon deep-sea fan: Evidence from the Foz do Amazonas Basin. Geology, 37, 619–622.

    Article  Google Scholar 

  • Fouquet, A., Gilles, A., Vences, M., Marty, C., Blanc, M., & Gemmell, N. J. (2007). Underestimation of species richness in Neotropical frogs revealed by mtDNA analyses. PLoS ONE, 10, e1109.

    Article  CAS  Google Scholar 

  • Fouquet, A., Noonan, B. P., Rodrigues, M. T., Pech, N., Gilles, A., & Gemmell, N. J. (2012a). Multiple quaternary Refugia in the Eastern Guiana shield revealed by comparative phylogeography of 12 frog species. Systematic Biology, 61, 461–489.

    PubMed  Article  Google Scholar 

  • Fouquet, A., Recoder, R., Teixeira, M., Jr, Cassimiro, J., Amaro, R. C., Camacho, A., et al. (2012b). Molecular phylogeny and morphometric analyses reveal deep divergence between Amazonia and Atlantic Forest species of Dendrophryniscus. Molecular Phylogenetics and Evolution, 62, 826–838.

    PubMed  Article  Google Scholar 

  • Fu, Y. X. (1997). Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915–925.

    PubMed  CAS  Google Scholar 

  • Funk, W. C., Caldwell, J. P., Peden, C. E., Padial, J. M., de la Riva, I., & Cannatella, D. C. (2007). Tests of biogeographic hypotheses for diversification in the Amazonian forest frog, Physalaemus petersi. Molecular Phylogenetics and Evolution, 44, 825–837.

    PubMed  CAS  Article  Google Scholar 

  • Funk, W. C., Caminer, M., & Ron, S. R. (2012). High levels of cryptic species diversity uncovered in Amazonian frogs. Proceedings of the Royal Society B, 279, 1806–1814.

    PubMed  Article  Google Scholar 

  • Funk, D. J., & Omland, K. E. (2003). Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology Evolution and Systematics, 34, 397–423.

    Article  Google Scholar 

  • Gascon, C., Lougheed, S. C., & Bogart, J. P. (1996). Genetic and morphological variation in Vanzolinius discodactylus: a direct test of the riverine barrier hypothesis. Biotropica, 28, 376–387.

    Article  Google Scholar 

  • Gascon, C., Lougheed, S. C., & Bogart, J. P. (1998). Patterns of genetic population differentiation in four species of Amazonian frogs: A test of the Riverine Barrier Hypothesis. Biotropica, 30, 104–119.

    Article  Google Scholar 

  • Gascon, C., Malcolm, J. R., Patton, J. L., Silva, M. N. F., Bogart, J. P., Lougheed, S. C., et al. (2000). Riverine barriers and the geographic distribution of Amazonian species. Proceedings of the National Academy of Sciences, 97, 13672–13677.

    CAS  Article  Google Scholar 

  • Gerhardt, H. C., & Huber, F. (2002). Acoustic communication in insects and anurans: Common problems and diverse solutions. Chicago: University of Chicago Press.

    Google Scholar 

  • Goicochea, N., De La Riva, I., & Padial, J. M. (2009). Recovering phylogenetic signal from frog mating calls. Zoologica Scripta, 39, 141–154.

    Article  Google Scholar 

  • Grant, T., Frost, D. R., Caldwell, J. P., Gagliardo, R., Haddad, C. F. B., Kok, P. J. R., et al. (2006). Phylogenetic systematics of dart–poison frogs and their relatives (Anura: Athesphatanura: Dendrobatidae). Bulletin of the American Museum of Natural History, 299, 1–262.

    Article  Google Scholar 

  • Groeneveld, L. F., Weisrock, D. W., Rasoloarison, R. M., Yoder, A. D., & Kappeler, P. M. (2009). Species delimitation in lemurs: Multiple genetic loci reveal low levels of species diversity in the genus Cheirogaleus. BMC Evolutionary Biology, 9, 30.

    PubMed  Article  CAS  Google Scholar 

  • Guerra, M. A., & Ron, S. R. (2008). Mate choice and courtship signal differentiation promotes speciation in an Amazonian frog. Behavioral Ecology, 19, 1128–1135.

    Article  Google Scholar 

  • Guillot, G., Renaud, S., Ledevin, R., Michaux, J., & Claude, J. (2012). A unifying model for the analysis of phenotypic, genetic and geographic data. Systematic Biology,. doi:10.1093/sysbio/sys038.

    PubMed  Google Scholar 

  • Haffer, J. (1969). Speciation in Amazonian Forest Birds. Science, 165, 131–137.

    PubMed  CAS  Article  Google Scholar 

  • Hafner, J. C., & Upham, N. S. (2011). Phylogeography of the dark kangaroo mouse, Microdipodops megacephalus: cryptic lineages and dispersal routes in North America’s Great Basin. Journal of Biogeography, 38, 1077–1097.

    PubMed  Article  Google Scholar 

  • Hall, T. A. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95–98.

    CAS  Google Scholar 

  • Harpending, R. C. (1994). Signature of ancient population growth in a low–resolution mitochondrial DNA mismatch distribution. Human Biology, 66, 591–600.

    PubMed  CAS  Google Scholar 

  • Hayes, F. E., & Sewlal, J. N. (2004). The Amazon River as a dispersal barrier to passerine birds: Effects of river width, habitat and taxonomy. Journal of Biogeography, 31, 1809–1818.

    Article  Google Scholar 

  • Hoorn, C. (1994). An environmental reconstruction of the palaeo-Amazon River system (Middle-Late Miocene, NW Amazonia). Palaeogeography, Palaeoclimatology, Palaeoecology, 112, 187–238.

    Article  Google Scholar 

  • Hoorn, C., Wesselingh, F. P., ter Steege, H., Bermudez, M. A., Mora, A., Sevink, J., et al. (2010). Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity. Science, 330, 927–931.

    PubMed  CAS  Article  Google Scholar 

  • Hubert, N., Meyer, C. P., Bruggemann, H. J., Guérin, F., Komeno, R. J. L., Espiau, B., et al. (2012). Cryptic diversity in Indo–Pacific coral–reef fishes revealed by DNA–barcoding provides new support to the centre–of–overlap hypothesis. PLoS ONE, 7, e28987.

    PubMed  CAS  Article  Google Scholar 

  • Hutchison, D. W., & Templeton, A. R. (1999). Correlation of pairwise genetic and geographic distance measures: Inferring the relative influences of gene flow and drift on the distribution of genetic variability. Evolution, 53, 1898–1914.

    Article  Google Scholar 

  • Irion, G., & Kalliola, R. (2010). Long–term landscape development processes in Amazonia. In C. Hoorn & F. P. Wesselingh (Eds.), Amazonia, landscape and species evolution (pp. 185–197). Oxford: Blackwell Publishing.

    Google Scholar 

  • Kaefer, I. L., & Lima, A. P. (2012). Sexual signals of the Amazonian frog Allobates paleovarzensis: Geographic variation and stereotypy of acoustic traits. Behaviour, 149, 15–33.

    Article  Google Scholar 

  • Kaefer, I. L., Montanarin, A., Costa, R. S., & Lima, A. P. (in press). Temporal patterns of reproductive activity and site attachment of the Brilliant–thighed Frog Allobates femoralis from Central Amazonia. Journal of Herpetology.

  • Kaefer, I. L., Tsuji-Nishikido, B. M., & Lima, A. P. (2012). Beyond the river: underlying determinants of population acoustic signal variability in Amazonian direct–developing Allobates (Anura: Dendrobatoidea). Acta Ethologica, 15, 187–194.

    Article  Google Scholar 

  • Kimura, M. (1980). A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111–120.

    PubMed  CAS  Article  Google Scholar 

  • Lemmon, E. M. (2009). Diversification of conspecific signals in sympatry: Geographic overlap drives multidimensional reproductive character displacement in frogs. Evolution, 63, 1155–1170.

    PubMed  Article  Google Scholar 

  • Librado, P., & Rozas, J. (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451–1452.

    PubMed  CAS  Article  Google Scholar 

  • Lima, A. P., Caldwell, J. P., Biavati, G., & Montanarin, A. (2010). A new species of Allobates (Anura: Aromobatidae) from paleovárzea forest in Amazonas, Brazil. Zootaxa, 2337, 1–17.

    Google Scholar 

  • Lougheed, S. C., Austin, J. D., Bogart, J. P., Boag, P. T., & Chek, A. A. (2006). Multi–character perspectives on the evolution of intraspecific differentiation in a neotropical hylid frog. BMC Evolutionary Biology, 6, 23.

    PubMed  Article  CAS  Google Scholar 

  • Lougheed, S. C., Gascon, C., Jones, D. A., Bogart, J. P., & Boag, P. T. (1999). Ridges and rivers: a test of competing hypothesis of Amazonian diversification using a dart–poison frog (Epipedobates femoralis). Proceedings of the Royal Society B, 266, 1829–1835.

    PubMed  CAS  Article  Google Scholar 

  • Lynch, M., & Crease, T. J. (1990). The analysis of population survey data on DNA sequence variation. Molecular Biology and Evolution, 7, 377–394.

    PubMed  CAS  Google Scholar 

  • Mantel, N. (1967). The detection of disease clustering and a generalized regression approach. Cancer Research, 27, 209–220.

    PubMed  CAS  Google Scholar 

  • McKay, B. D., & Zink, R. M. (2009). The causes of mitochondrial DNA gene tree paraphyly in birds. Molecuar Phylogenetics and Evolution, 54, 647–650.

    Article  Google Scholar 

  • Morales, V. R. (2002). Sistematica y biogeografía del grupo trilineatus (Amphibia, Anura, Dendrobatidae, Colostethus), con descripción de once nuevas especies. Publicación de la Asociación Amigos Doñana, 13, 1–59.

    Google Scholar 

  • Moritz, C., Patton, J. L., Schneider, C. J., & Smith, T. B. (2000). Diversification of rainforest faunas: An integrated molecular approach. Annual Review of Ecology and Systematics, 31, 533–563.

    Article  Google Scholar 

  • Noonan, B. P., & Gaucher, P. (2006). Refugial isolation and secondary contact in the dyeing poison frog Dendrobates tinctorius. Molecular Ecology, 15, 4425–4435.

    PubMed  CAS  Article  Google Scholar 

  • Nosil, P., Harmon, L. J., & Seehausen, O. (2009). Ecological explanations for (incomplete) speciation. Trends in Ecology & Evolution, 24, 145–156.

    Article  Google Scholar 

  • Palumbi, S. R. (1996). Nucleic acids II: the polymerase chain reaction. In D. M. Hillis, C. Moritz, & B. K. Mable (Eds.), Molecular systematics (pp. 205–247). Sunderland: Sinauer Associates Inc.

    Google Scholar 

  • Panhuis, T. M., Butlin, R., Zuk, M., & Tregenza, T. (2001). Sexual selection and speciation. Trends in Ecology & Evolution, 16, 364–371.

    Article  Google Scholar 

  • Patton, J. L., Silva, M. N. F., & Malcolm, J. R. (1994). Gene genealogy and differentiation among arboreal spiny rats (Rodentia: Echymidae) of the Amazon Basin: a test of the riverine barrier hypothesis. Evolution, 48, 1314–1323.

    Article  Google Scholar 

  • Pröhl, H. (2005). Territorial behavior in dendrobatid frogs. Journal of Herpetology, 39, 354–365.

    Article  Google Scholar 

  • Pröhl, H., Hagemann, S., Karsch, J., & Höbel, G. (2007). Geographic variation in male sexual signals in Strawberry Poison Frogs (Dendrobates pumilio). Ethology, 113, 825–837.

    Article  Google Scholar 

  • Pröhl, H., Koshy, R. A., Mueller, U. G., Rand, A. S., & Ryan, M. J. (2006). Geographic variation of genetic and behavioral traits in northern and southern túngara frogs. Evolution, 60, 1669–1679.

    PubMed  Google Scholar 

  • Rambaut, A., & Drummond, A. J. (2007). Tracer v. 1.5. [http://beast.bio.ed.ac.uk/Tracer]. Accessed 04 May 2012.

  • Ramos–Onsins, S. E., & Rozas, J. (2002). Statistical properties of new neutrality tests against population growth. Molecular Biology and Evolution, 19, 2092–2100.

    PubMed  Article  Google Scholar 

  • Ribas, C. C., Aleixo, A., Nogueira, A. C. R., Miyaki, C. Y., & Cracraft, J. (2011). A palaeobiogeographic model for biotic diversification within Amazonia over the past three million years. Proceedings of the Royal Society B, 279, 681–689.

    PubMed  Article  Google Scholar 

  • Rosen, D. E. (1978). Vicariant patterns and historical explanation in biogeography. Systematic Zoology, 27, 159–188.

    Article  Google Scholar 

  • Rossetti, D. F., de Toledo, P. M., & Góes, A. M. (2005). New geological framework for Western Amazonia (Brazil) and implications for biogeography and evolution. Quaternary Research, 63, 78–89.

    Article  Google Scholar 

  • Ryan, M. J., Rand, A. S., & Weigt, L. A. (1996). Allozyme and advertisement call variation in the túngara frog, Physalaemus pustulosus. Evolution, 50, 2435–2453.

    CAS  Article  Google Scholar 

  • Santini, F., Miglietta, M. P., & Faucci, A. (2012). Where are we now? An introduction to a special issue on speciation. Evolutionary Biology, 39, 141–147.

    Article  Google Scholar 

  • Santos, J. C., Coloma, L. A., Summers, K., Caldwell, J. P., Ree, R., & Cannatella, D. C. (2009). Amazonian amphibian diversity is primarily derived from Late Miocene Andean lineages. PLoS Biology, 7, e1000056.

    Article  CAS  Google Scholar 

  • Santos, S., Hrbek, T., Farias, I. P., Schneider, H., & Sampaio, I. (2006). Population genetic structuring of the king weakfish, Macrodon ancylodon (Sciaenidae), in Atlantic coastal waters of South America: Deep genetic divergence without morphological change. Molecular Ecology, 15, 4361–4373.

    PubMed  CAS  Article  Google Scholar 

  • Schneider, S., & Excoffier, L. (1999). Estimation of demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: Application to human mitochondrial DNA. Genetics, 152, 1079–1089.

    PubMed  CAS  Google Scholar 

  • Sequeira, F., Sodré, D., Ferrand, N., Bernardi, J., Sampaio, I., Schneider, H., et al. (2011). Hybridization and massive mtDNA unidirectional introgression between the closely related Neotropical toads Rhinella marina and R. schneideri inferred from mtDNA and nuclear markers. BMC Evolutionary Biology, 11, 264.

    PubMed  CAS  Article  Google Scholar 

  • Silva, M. N. F., & Patton, J. L. (1998). Molecular phylogeography and the evolution and conservation of mammals. Molecular Ecology, 7, 475–486.

    PubMed  Article  Google Scholar 

  • Simões, P. I. (2010). Diversificação do complexo Allobates femoralis (Anura, Dendrobatidae) em florestas da Amazônia brasileira: desvendando padrões atuais e históricos. PhD thesis. Manaus: Instituto Nacional de Pesquisas da Amazônia.

  • Simões, P. I., Lima, A. P., Magnusson, W. E., Hödl, W., & Amézquita, A. (2008). Acoustic and morphological differentiation in the frog Allobates femoralis: Relationships with the Upper Madeira River and other potential geological barriers. Biotropica, 40, 607–614.

    Article  Google Scholar 

  • Sioli, H. (1984). The Amazon: Limnology and landscape ecology of a mighty tropical river and its basin. Dordrecht: Dr W. Junk Publisher.

    Google Scholar 

  • Smouse, P. E., Long, J. C., & Sokal, R. R. (1986). Multiple regression and correlation extensions of the Mantel test of matrix correspondence. Systematic Zoology, 35, 727–732.

    Article  Google Scholar 

  • Solomon, S. E., Bacci, M., Martins, J., Vinha, G. G., & Mueller, U. G. (2008). Paleodistributions and comparative molecular phylogeography of leafcutter ants (Atta spp.) provide new insight into the origins of Amazonian diversity. PLoS ONE, 3, e2738.

    PubMed  Article  CAS  Google Scholar 

  • Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585–595.

    PubMed  CAS  Google Scholar 

  • Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731–2739.

    PubMed  CAS  Article  Google Scholar 

  • Telles, M. P. C., Silva, R. S. M., Chaves, L. J., Coelho, A. S. G., & Diniz–Filho, J. A. F. (2001). Divergência entre subpopulações de cagaiteira (Eugenia dysenterica) em resposta a padrões edáficos e distribuição espacial. Pesquisa Agropecuária Brasileira, 36, 1387–1394.

    Article  Google Scholar 

  • Templeton, A. R., Crandall, K. A., & Sing, C. F. (1992). A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics, 132, 619–633.

    PubMed  CAS  Google Scholar 

  • Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994). Improved sensitivity of profile searches through the use of sequence weights and gap excision. Computer Applications in the Biosciences, 10, 19–29.

    PubMed  CAS  Google Scholar 

  • Tsuji-Nishikido, B. M., Kaefer, I. L., Freitas, F. C., Menin, M., & Lima, A. P. (2012). Significant but not diagnostic: Differentiation through morphology and calls in the Amazonian frogs Allobates nidicola and A. masniger. Herpetological Journal, 22, 105–114.

    Google Scholar 

  • Turmelle, A. S., Kunz, T. H., & Sorenson, M. D. (2011). A tale of two genomes: contrasting patterns of phylogeographic structure in a widely distributed bat. Molecular Ecology, 20, 357–375.

    PubMed  Article  Google Scholar 

  • Vences, M., Kosuch, J., Lötters, S., Widmer, A., Jungfer, K., Köhler, J., et al. (2000). Phylogeny and classification of Poison Frogs (Amphibia: Dendrobatidae), based on mitochondrial 16S and 12S ribosomal RNA gene sequences. Molecular Phylogenetics and Evolution, 15, 34–40.

    PubMed  CAS  Article  Google Scholar 

  • Vences, M., Thomas, M., Meijden, A., Chiari, Y., & Vieites, D. R. (2005). Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. Frontiers in Zoology, 2, 5.

    PubMed  Article  CAS  Google Scholar 

  • Vences, M., & Wake, D. B. (2007). Speciation, species boundaries and phylogeography of amphibians. In H. H. Heatwole & M. Tyler (Eds.), Amphibian biology. Volume 6: Systematics (pp. 2613–2669). Chipping Norton: Surrey Beatty & Sons.

    Google Scholar 

  • Verdade, V. K., & Rodrigues, M. T. (2007). Taxonomic review of Allobates (Anura, Aromobatidae) from the Atlantic Forest, Brazil. Journal of Herpetology, 41, 566–580.

    Article  Google Scholar 

  • Vieites, D. R., Wollenberg, K. C., Adreone, F., Köhler, J., Glaw, F., & Vences, M. (2009). Vast underestimation of Madagascar’s biodiversity evidenced by an integrative amphibian inventory. Proceedings of the National Academy of Sciences, 106, 8267–8272.

    CAS  Article  Google Scholar 

  • Wallace, A. R. (1852). On the monkeys of the Amazon. Proceedings of the Zoological Society of London, 20, 107–110.

    Google Scholar 

  • West-Eberhard, M. J. (1989). Phenotypic plasticity and the origins of diversity. Annual Review of Ecology and Systematics, 20, 249–278.

    Article  Google Scholar 

  • Wiens, J. J. (2007). Species delimitation: New approaches for discovering diversity. Systematic Biology, 56, 875–878.

    PubMed  Article  Google Scholar 

  • Wiens, J. J. (2008). Systematics and herpetology in the age of genomics. BioScience, 58, 297–307.

    Article  Google Scholar 

  • Wiley, E. O. (1978). The evolutionary species concept reconsidered. Systematic Zoology, 27, 17–26.

    Article  Google Scholar 

  • Wright, S. (1951). The genetical structure of populations. Annals of Human Genetics, 15, 323–354.

    Google Scholar 

  • Wycherley, J., Doran, S., & Beebee, T. J. C. (2002). Male advertisement call characters as phylogeographical indicators in European water frogs. Biological Journal of the Linnean Society, 77, 355–365.

    Article  Google Scholar 

  • Zeisset, I., & Beebee, T. J. C. (2008). Amphibian phylogeography: a model for understanding historical aspects of species distributions. Heredity, 101, 109–119.

    PubMed  CAS  Article  Google Scholar 

  • Zhang, D. X., & Hewitt, G. M. (2003). Nuclear DNA analyses in genetic studies of populations: Practice, problems and prospects. Molecular Ecology, 12, 563–584.

    PubMed  CAS  Article  Google Scholar 

  • Zink, R. M., & Barrowclough, G. F. (2008). Mitochondrial DNA under siege in avian phylogeography. Molecular Ecology, 17, 2107–2121.

    PubMed  CAS  Article  Google Scholar 

  • Zink, R. M., Blackwell-Rago, R. C., & Ronquist, F. (2000). The shifting roles of vicariance in biogeography. Proceedings of the Royal Society B, 267, 497–503.

    PubMed  CAS  Article  Google Scholar 

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Acknowledgments

We thank Anelise Montanarin, Francisco C. de Freitas, Irene da S. Melo, Maria A. Carvalho, Moisés da S. Melo and Raimundo N. Amorim for fieldwork assistance; Daniela Leroy e Waleska Gravena for help in laboratory procedures; Adolfo Amézquita, Adrian Garda, Andrew J. Crawford, Camila Ribas, Heike Pröhl, Janet W. Reid, Jeffrey Podos, Luciana K. Erdtmann, Marcelo Gordo, Marcelo Menin, Marina Anciães, Pedro Ivo Simões, Tomas Hrbek, Vanessa Verdade and Walter Hödl for valuable suggestions during this study. We extend thanks to two anonymous reviewers whose observations led to further improvements in the text. We also thank the Brazilian Conselho de Desenvolvimento Científico e Tecnológico for financial support (CNPq-CT Amazônia 553997/2006-8 and 575572/2008-6).

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

This study complies with the current Brazilian laws and was allowed by RAN-ICMBio/IBAMA (licences 13777-2, 18516-1, 20065-2, and 21950-1).

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Correspondence to Igor L. Kaefer.

Electronic supplementary material

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11692_2012_9205_MOESM1_ESM.pdf

Online Resource 1 Advertisement call measurements of individuals of Allobates paleovarzensis in each study locality in Brazilian Amazonia. Values are presented as mean (above) and standard deviation (below). Call traits are: Note rate (NR, in notes/s); Note duration (ND, in s); Internote interval, as the silent interval between two consecutive notes of a call (InI, in s); Call rate (CR, in calls/s); Call duration (CD, in s); Intercall interval, as the silent interval between two consecutive calls (IcI, in s); Maximum (peak) frequency, as the frequency of higher intensity calculated for the entire note by a power spectrum function of Raven Pro 1.3 (MF, in Hz); Lowest frequency (LF, in Hz); Highest frequency (HF, in Hz); Note modulation, as the difference between the highest and the lowest frequencies of the call (NM, in Hz). Sampling locality codes, sample sizes and respective geographic coordinates are given on Table 1. (PDF 23 kb)

11692_2012_9205_MOESM2_ESM.pdf

Online Resource 2 Advertisement call measurements of individuals of Allobates nidicola and A. masniger in each study locality in Brazilian Amazonia. Values are presented as mean (above) and standard deviation (below). Call traits are: Note duration (ND, in s); Interval between notes (IN, in s); Lowest frequency (LF, in Hz); Highest frequency (HF, in Hz); Note modulation, calculated as the difference between the maximum and minimum frequencies (NM, in Hz); and Peak frequency (PF, in Hz). Sampling locality codes, sample sizes and respective geographic coordinates are given on Table 1. (PDF 18 kb)

11692_2012_9205_MOESM3_ESM.pdf

Online Resource 3 Morphometric measurements (in mm) of individuals of Allobates paleovarzensis in each study locality in Brazilian Amazonia. Values are presented as mean (above) and standard deviation (below). Morphometric traits are: Snout-vent length (SVL); Head length from angle of jaws to tip of snout (HL); Head width at level of angle of jaws (HW); Snout length from anterior corner of eye to tip of snout (SL); Eye to nostril distance from anterior corner of eye to centre of nostril (EN); Inter-nostril distance (IN); Eye length from anterior to posterior corner (EL); Inter-orbital distance (IO); Diameter of tympanum (TYM); Forearm length from proximal edge of palmar tubercle to outer edge of flexed elbow (FAL); Upper arm length from trunk insertion to outer edge of flexed elbow (UAL); Hand length from proximal edge of palmar tubercle to tip of fingers I, II, III and IV (HAND1, HAND2, HAND3 and HAND4); Width of disc on finger III (WFD); Tibia length from outer edge of flexed knee to heel (TL); Foot length from proximal edge of outer metatarsal tubercle to tip of toe IV (FL); Femur length (LL); Diameter of palmar tubercle (DPT); Width of tenar tubercle (WTT); Width of disc on toe IV (WTD); Width of finger III (WPF). Sampling locality codes, sample sizes and respective geographic coordinates are given on Table 1. (PDF 37 kb)

11692_2012_9205_MOESM4_ESM.pdf

Online Resource 4 Morphometric measurements (in mm) of individuals of Allobates nidicola and A. masniger in each study locality in Brazilian Amazonia. Values are presented as mean (above) and standard deviation (below). Morphometric traits are described in Online Resource 3. Sampling locality codes, sample sizes and respective geographic coordinates are given on Table 1. (PDF 37 kb)

11692_2012_9205_MOESM5_ESM.pdf

Online Resource 5 Distribution of 16S rDNA haplotypes of Allobates among 20 sampled localities in Brazilian Amazonia. Collection numbers of vouchers (INPA-H) and GenBank accession numbers are provided. Sampled localities are numbered according to Table 1. (PDF 24 kb)

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Online Resource 6 Mismatch distributions obtained from pairwise nucleotide site differences among 16S rDNA sequences composing the clusters of the (A) paleovarzensis and the (B) nidicolamasniger systems. Clusters were determined via Bayesian Analysis of Population Differentiation. Pairwise differences were not calculated for Cluster 4 of Allobates paleovarzensis due to the small number of samples that compose it. (PDF 334 kb)

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Online Resource 7 Classification matrix based on the discriminant function analysis, using phenotypic data from males of Allobates paleovazensis pertaining to four genetic clusters. Clusters are coded from C1 to C4, according to Table 4. Body-shape traits were used to discriminate individuals based on morphology. Acoustic measurements were adjusted for temperature and for both temperature and body size through linear regressions. The number and percentage of individuals correctly assigned to each genetic cluster are indicated. (PDF 18 kb)

11692_2012_9205_MOESM8_ESM.pdf

Online Resource 8 Classification matrix based on the discriminant function analysis, using phenotypic data from males of Allobates nidicola and A. masniger pertaining to seven genetic clusters. Clusters are coded from C1 to C7, according to Table 4. Body-shape traits were used to discriminate individuals based on morphology. Acoustic measurements were adjusted for temperature and for both temperature and body size through linear regressions. The number and percentage of individuals correctly assigned to each genetic cluster are indicated. (PDF 24 kb)

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Kaefer, I.L., Tsuji-Nishikido, B.M., Mota, E.P. et al. The Early Stages of Speciation in Amazonian Forest Frogs: Phenotypic Conservatism Despite Strong Genetic Structure. Evol Biol 40, 228–245 (2013). https://doi.org/10.1007/s11692-012-9205-4

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Keywords

  • Genetic drift
  • Integrative phylogeography
  • Isolation by distance
  • Mitochondrial DNA
  • River barrier
  • Sexual signals