315
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Historical connections between Atlantic Forest and Amazonia drove genetic and ecological diversity in Lithobates palmipes (Anura, Ranidae)

ORCID Icon, , , ORCID Icon, ORCID Icon & ORCID Icon

References

  • Alan Pounds, J., Bustamante, M. R., Coloma, L. A., Consuegra, J. A., Fogden, M. P. L., Foster, P. N., Marca, E. L., Masters, K. L., Merino-Viteri, A., Puschendorf, R., Ron, S. R., Sánchez-Azofeifa, G. A., Still, C. J., & Young, B. E. (2006). Widespread amphibian extinctions from epidemic disease driven by global warming. Nature, 439, 161–167. https://doi.org/10.1038/nature04246
  • Allouche, O., Tsoar, A., & Kadmon, R. (2006). Assessing the accuracy of species distribution models: Prevalence, kappa and the true skill statistic (TSS). Journal of Applied Ecology, 43, 1223–1232. https://doi.org/10.1111/j.1365-2664.2006.01214.x
  • Antonelli, A., Zizka, A., Carvalho, F. A., Scharn, R., Bacon, C. D., Silvestro, D., & Condamine, F. L. (2018). Amazonia is the primary source of Neotropical biodiversity. Proceedings of the National Academy of Sciences of the United States of America, 115, 6034–6039. https://doi.org/10.1073/pnas.1713819115
  • Arteaga, A., Pyron, R. A., Peñafiel, N., Romero-Barreto, P., Culebras, J., Bustamante, L., Yánez-Muñoz, M. H., & Guayasamin, J. M. (2016). Comparative phylogeography reveals cryptic diversity and repeated patterns of cladogenesis for amphibians and reptiles in northwestern Ecuador. PLoS One, 11, e0151746–40. https://doi.org/10.1371/journal.pone.0151746
  • Baker, P. A., Fritz, S. C., Battisti, D. S., Dick, C. W., Vargas, O. M., Asner, G. P., Martin, R. E., Wheatley, A., & Prates, I. (2020). Beyond refugia: New insights on quaternary climate variation and the evolution of biotic diversity in tropical South America. In V. Rull, & A. C. Carnaval (Eds.), Neotropical diversification: Patterns and processes (pp. 683–712). Springer.
  • Ballard, J. W. O., & Whitlock, M. C. (2004). The incomplete natural history of mitochondria. Molecular Ecology, 13, 729–744. https://doi.org/10.1046/j.1365-294X.2003.02063.x
  • Batalha-Filho, H., Fjeldså, J., Fabre, P. H., & Miyaki, C. Y. (2013). Connections between the Atlantic and the Amazonian forest avifaunas represent distinct historical events. Journal of Ornithology, 154, 41–50. https://doi.org/10.1007/s10336-012-0866-7
  • Beddek, M., Zenboudji-Beddek, S., Geniez, P., Fathalla, R., Sourouille, P., Arnal, V., Dellaoui, B., Koudache, F., Telailia, S., Peyre, O., & Crochet, P. A. (2018). Comparative phylogeography of amphibians and reptiles in Algeria suggests common causes for the east-west phylogeographic breaks in the Maghreb. PLoS One, 13, e0201218–e0201226. https://doi.org/10.1371/journal.pone.0201218
  • Berv, J. S., & Prum, R. O. (2014). A comprehensive multilocus phylogeny of the Neotropical cotingas (Cotingidae, Aves) with a comparative evolutionary analysis of breeding system and plumage dimorphism and a revised phylogenetic classification. Molecular Phylogenetics and Evolution, 81, 120–136. https://doi.org/10.1016/j.ympev.2014.09.001
  • Bielejec, F., Baele, G., Vrancken, B., Suchard, M. A., Rambaut, A., & Lemey, P. (2016). SpreaD3: Interactive visualization of spatiotemporal history and trait evolutionary processes. Molecular Biology and Evolution, 33, 2167–2169. https://doi.org/10.1093/molbev/msw082
  • Blaustein, A. R., Walls, S. C., Bancroft, B. A., Lawler, J. J., Searle, C. L., & Gervasi, S. S. (2010). Direct and indirect effects of climate change on amphibian populations. Diversity, 2, 281–313. https://doi.org/10.3390/d2020281
  • Booth, T. H., Nix, H. A., Busby, J. R., & Hutchinson, M. F. (2014). BIOCLIM: The first species distribution modelling package, its early applications and relevance to most current MAXENT studies. Diversity and Distributions, 20, 1–9. https://doi.org/10.1111/ddi.12144
  • Bovo, R., Navas, C., Tejedo, M., Valença, S., & Gouveia, S. (2018). Ecophysiology of amphibians: Information for best mechanistic models. Diversity, 10, 118. https://doi.org/10.3390/d10040118
  • Boyce, M. S., Vernier, P. R., Nielsen, S. E., & Schmiegelow, F. K. A. (2002). Evaluating resource selection functions. Ecological Modelling, 157, 281–300. https://doi.org/10.1016/S0304-3800(02)00200-4
  • Broennimann, O., Fitzpatrick, M. C., Pearman,P. B., Petitpierre1, B., Pellissier1, L., Yoccoz, N. G., Thuiller, W., Fortin, M., Randin, C., Zimmermann, N. E., Graham, C. H., & Guisan, A. (2012). Measuring ecological niche overlap from occurrence and spatial environmental data. Global Ecology and Biogeography, 21, 481–497. https://doi.org/10.1111/j.1466-8238.2011.00698.x
  • Bruford, M. W., Hanotte, O., Brookfield, J. F. Y., & Burke, T. (1992). Single-locus and multilocus DNA fingerprinting. In A. R. Hoelzel (Ed.), Molecular genetics analyses of populations: A practical approach (pp. 225–269). IRL Press at Oxford University Press.
  • Camurugi, F., Gehara, M., Fonseca, E. M., Zamudio, K. R., Haddad, C. F. B., Colli, G. R., Thomé, M. T. C., Prado, C. P. A., Napoli, M. F., & Garda, A. A. (2021). Isolation by environment and recurrent gene flow shaped the evolutionary history of a continentally distributed Neotropical treefrog. Journal of Biogeography, 48, 760–713. https://doi.org/10.1111/jbi.14035
  • Carnaval, A. C., Hickerson, M. J., Haddad, C. F. B., Rodrigues, M. T., & Moritz, C. (2009). Stability predicts genetic diversity in the Brazilian Atlantic Forest hotspot. Science (New York, N.Y.), 323, 785–789. https://doi.org/10.1126/science.1166955
  • Carnaval, A. C., Waltari, E., Rodrigues, M. T., Rosauer, D., VanDerWal, J., Damasceno, R., Prates, I., Strangas, M., Spanos, Z., Rivera, D., Pie, M. R., Firkowski, C. R., Bornschein, M. R., Ribeiro, L. F., & Moritz, C. (2014). Prediction of phylogeographic endemism in an environmentally complex biome. Proceedings of the Royal Society B: Biological Sciences, 281, 20141461–20141468. https://doi.org/10.1098/rspb.2014.1461
  • Chen, X., Chen, Z., Jian, J., Qiao, L., Lu, Y., Zhou, K., Zheng, G., Zhai, X., & Liu, J. (2013). Molecular phylogeny and diversification of the genus Odorrana (Amphibia, Anura, Ranidae) inferred from two mitochondrial genes. Molecular Phylogenetics and Evolution, 69, 1196–1202. https://doi.org/10.1016/j.ympev.2013.07.023
  • Cheng, H., Sinha, A., Cruz, F. W., Wang, X., Edwards, R. L., D'Horta, F. M., Ribas, C. C., Vuille, M., Stott, L. D., & Auler, A. S. (2013). Climate change patterns in Amazonia and biodiversity. Nature Communications, 4, 1411. https://doi.org/10.1038/ncomms2415
  • Collevatti, R. G., Terribile, L. C., Oliveira, G. d., Lima-Ribeiro, M. S., Nabout, J. C., Rangel, T. F., & Diniz-Filho, J. A. F. (2013). Drawbacks to palaeodistribution modelling: The case of South American seasonally dry forests. Journal of Biogeography, 40, 345–358. https://doi.org/10.1111/jbi.12005
  • Constable, H., Guralnick, R., Wieczorek, J., Spencer, C., Peterson, A. T., Bart, H., Bates, J., Cotter, G., Hanken, J., Moritz, C., Simmons, N., & Trueb, L., VertNet Steering Committee. (2010). VertNet: A new model for biodiversity data sharing. PLoS Biology, 8, e1000309. https://doi.org/10.1371/journal.pbio.1000309
  • Corander, J., & Marttinen, P. (2006). Bayesian identification of admixture events using multilocus molecular markers . Molecular Ecology, 15, 2833–2843. https://doi.org/10.1111/j.1365-294X.2006.02994.x
  • Corander, J., Sirén, J., & Arjas, E. (2008). Bayesian spatial modeling of genetic population structure. Computational Statistics, 23, 111–129. https://doi.org/10.1007/s00180-007-0072-x
  • Costa, L. (2003). The historical bridge between the Amazon and the Atlantic Forest of Brazil: A study of molecular phylogeography with small mammals. Journal of Biogeography, 30, 71–86. https://doi.org/10.1046/j.1365-2699.2003.00792.x
  • D’Horta, F. M., Cuervo, A. M., Ribas, C. C., Brumfield, R. T., & Miyaki, C. Y. (2013). Phylogeny and comparative phylogeography of Sclerurus (Aves: Furnariidae) reveal constant and cryptic diversification in an old radiation of rain forest understorey specialists. Journal of Biogeography, 40, 37–49. https://doi.org/10.1111/j.1365-2699.2012.02760.x
  • Dal Vechio, F., Prates, I., Grazziotin, F. G., Zaher, H., & Rodrigues, M. T. (2018). Phylogeography and historical demography of the arboreal pit viper Bothrops bilineatus (Serpentes, Crotalinae) reveal multiple connections between Amazonian and Atlantic rain forests. Journal of Biogeography, 45, 2415–2426. https://doi.org/10.1111/jbi.13421
  • Di Cola, V., Broennimann, O., Petitpierre, B., Breiner, F. T., D’Amen, M., Randin, C., Engler, R., Pottier, J., Pio, D., Dubuis, A., Pellissier, L., Mateo, R. G., Hordijk, W., Salamin N., & Guisan, A. (2016). ecospat: An R package to support spatial analyses and modeling of species niches and distributions. Ecography, 40, 774–787. 10.1111/ecog.02671
  • Drummond, A. J., Suchard, M. A., Xie, D., & Rambaut, A. (2012). Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution, 29, 1969–1973. https://doi.org/10.1093/molbev/mss075
  • Edgar, R. C. (2004). MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 113. https://doi.org/10.1186/1471-2105-5-113
  • 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 resources, 10, 564–567. https://doi.org/10.1111/j.1755-0998.2010.02847.x
  • Fonseca, E. M., Duckett, D. J., & Carstens, B. C. (2021). P2C2M.GMYC: An R package for assessing the utility of the Generalized Mixed Yule Coalescent model. Methods in Ecology and Evolution, 12, 487–493. https://doi.org/10.1111/2041-210X.13541
  • 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, 2, e1109. https://doi.org/10.1371/journal.pone.0001109
  • Fouquet, A., Loebmann, D., Castroviejo-Fisher, S., Padial, J. M., Orrico, V. G. D., Lyra, M. L., Roberto, I. J., Kok, P. J. R., Haddad, C. F. B., & Rodrigues, M. T. (2012b). From Amazonia to the Atlantic forest: Molecular phylogeny of Phyzelaphryninae frogs reveals unexpected diversity and a striking biogeographic pattern emphasizing conservation challenges. Molecular phylogenetics and evolution, 65, 547–561. https://doi.org/10.1016/j.ympev.2012.07.012
  • Fouquet, A., Recoder, R., Teixeira, M., Cassimiro, J., Amaro, R. C., Camacho, A., Damasceno, R., Carnaval, A. C., Moritz, C., & Rodrigues, M. T. (2012a). Molecular phylogeny and morphometric analyses reveal deep divergence between Amazonia and Atlantic Forest species of Dendrophryniscus. Molecular Phylogenetics and Evolution, 62, 826–838. https://doi.org/10.1016/j.ympev.2011.11.023
  • Frost, D. R. (2020). Amphibian Species of the World: An Online Reference. Version 6.1 20/X/2020. Electronic Database accessible at https://amphibiansoftheworld.amnh.org/index.php. American Museum of Natural History, New York, USA. https://doi.org/10.5531/db.vz.0001
  • Fujita, M. K., Leaché, A. D., Burbrink, F. T., McGuire, J. A., & Moritz, C. (2012). Coalescent-based species delimitation in an integrative taxonomy. Trends in Ecology & Evolution, 27, 480–488. https://doi.org/10.1016/j.tree.2012.04.012
  • Gehara, M., Crawford, A. J., Orrico, V. G. D., Rodríguez, A., Lötters, S., Fouquet, A., Barrientos, L. S., Brusquetti, F., De la Riva, I., Ernst, R., Urrutia, G. G., Glaw, F., Guayasamin, J. M., Holting, M., Jansen, M., Kok, P. J. R., Kwet, A., Lingnau, R., Lyra, M., … Köhler, J. (2014). High levels of diversity uncovered in a widespread nominal taxon: Continental phylogeography of the Neotropical tree frog Dendropsophus minutus. PLoS ONE, 9, e103958. https://doi.org/10.1371/journal.pone.0103958
  • Geurgas, S. R., & Rodrigues, M. T. (2010). The hidden diversity of Coleodactylus amazonicus (Sphaerodactylinae, Gekkota) revealed by molecular data. Molecular phylogenetics and evolution, 54, 583–593. https://doi.org/10.1016/j.ympev.2009.10.004
  • Hall, J. P., & Harvey, D. J. (2002). The phylogeography of Amazonia revisited: New evidence from Riodinid butterflies. Evolution; International Journal of Organic Evolution, 56, 1489–1497. doi: 10.1554/0014-3820(2002)056[1489:TPOARN]2.0.CO;2 https://doi.org/10.1554/0014-3820(2002)056[1489:TPOARN2.0.CO;2]
  • 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. International Journal of Climatology, 25, 1965–1978. https://doi.org/10.1002/joc.1276
  • Hillis, D. M., & Wilcox, T. (2005). Phylogeny of the New World true frogs (Rana). Molecular Phylogenetics and Evolution, 34, 299–314. https://doi.org/10.1016/j.ympev.2004.10.007
  • Hillis, D. M., & de Sá, R. (1988). Phylogeny and taxonomy of the Rana palmipes group (Salientia: Ranidae). Herpetological Monographs, 2, 1–26. https://doi.org/10.2307/1467024
  • Hirzel, A. H., Le Lay, G., Helfer, V., Randin, C., & Guisan, A. (2006). Evaluating the ability of habitat suitability models to predict species presences. Ecological Modelling, 199, 142–152. https://doi.org/10.1016/j.ecolmodel.2006.05.017
  • Hubert, N., Duponchelle, F., Nuñez, J., Rivera, R., Bonhomme, F., & Renno, J. F. (2007). Isolation by distance and Pleistocene expansion of the lowland populations of the white piranha Serrasalmus rhombeus. Molecular Ecology, 16, 2488–2503. https://doi.org/10.1111/j.1365-294X.2007.03338.x
  • Jiménez-Valverde, A. (2012). Insights into the area under the receiver operating characteristic curve (AUC) as a discrimination measure in species distribution modelling. Global Ecology and Biogeography, 21, 498–507. https://doi.org/10.1111/j.1466-8238.2011.00683.x
  • Jongsma, G. F. M., Barej, M. F., Barratt, C. D., Burger, M., Conradie, W., Ernst, R., Greenbaum, E., Hirschfeld, M., Leaché, A. D., Penner, J., Portik, D. M., Zassi-Boulou, A.-G., Rödel, M.-O., & Blackburn, D. C. (2018). Diversity and biogeography of frogs in the genus Amnirana (Anura: Ranidae) across sub-Saharan Africa. Molecular Phylogenetics and Evolution, 120, 274–285. https://doi.org/10.1016/j.ympev.2017.12.006
  • Kumar, S., Stecher, G., & Tamura, k. (2016). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33, 1870–1874. https://doi.org/10.1093/molbev/msw054
  • Lanfear, R., Frandsen, P. B., Wright, A. M., Senfeld, T., & Calcott, B. (2017). PartitionFinder 2: New methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular Biology and Evolution, 34, 772–773. https://doi.org/10.1093/molbev/msw260
  • Laraque, A., Ronchail, J., Cochonneau, G., Pombosa, R., & Guyot, J. L. (2007). Heterogeneous distribution of rainfall and discharge regimes in the Ecuadorian Amazon basin. Journal of Hydrometeorology, 8, 1364–1381. https://doi.org/10.1175/2007JHM784.1
  • Lawson, L. P. (2013). Diversification in a biodiversity hot spot: Landscape correlates of phylogeographic patterns in the African spotted reed frog. Molecular Ecology, 22, 1947–1960. https://doi.org/10.1111/mec.12229
  • Ledo, R. M. D., & Colli, G. R. (2017). The historical connections between the Amazon and the Atlantic Forest revisited. Journal of Biogeography, 44, 2551–2563. https://doi.org/10.1111/jbi.13049
  • Leigh, J. W., & Bryant, D. (2015). PopART: Full-feature software for haplotype network construction. Methods in Ecology and Evolution, 6, 1110–1116. https://doi.org/10.1111/2041-210X.12410
  • Lemey, P., Rambaut, A., Welch, J. J., & Suchard, M. A. (2010). Phylogeography takes a relaxed random walk in continuous space and time. Molecular Biology and Evolution, 27, 1877–1885. https://doi.org/10.1093/molbev/msq067
  • Lisiecki, L. E., & Raymo, M. E. (2005). A pliocene-pleistocene stack of 57 globally distributed benthic D18O records. Paleoceanography, 20, 17. https://doi.org/10.1029/2004PA001071
  • Lobo, J. M., Jiménez-Valverde, A., & Real, R. (2008). AUC: A misleading measure of the performance of predictive distribution models. Global Ecology and Biogeography, 17, 145–151. https://doi.org/10.1111/j.1466-8238.2007.00358.x
  • Longo, M., Knox, R. G., Levine, N. M., Alves, L. F., Bonal, D., Camargo, P. B., Fitzjarrald, D. R., Hayek, M. N., Restrepo-Coupe, N., Saleska, S. R., da Silva, R., Stark, S. C., Tapajós, R. P., Wiedemann, K. T., Zhang, K., Wofsy, S. C., & Moorcroft, P. R. (2018). Ecosystem heterogeneity and diversity mitigate Amazon forest resilience to frequent extreme droughts. The New Phytologist, 219, 914–931. https://doi.org/10.1111/nph.15185
  • Macey, J. R., Schulte, J. A., Larson, A., Fang, Z., Wang, Y., Tuniyev, B. S., & Papenfuss, T. J. (1998). Phylogenetic relationships of toads in the Bufo bufo species group from the eastern escarpment of the Tibetan Plateau: A case of vicariance and dispersal. Molecular Phylogenetics and Evolution, 9, 80–87. https://doi.org/10.1006/mpev.1997.0440
  • Miller, D. A. W., Grant, E. H. C., Muths, E., Amburgey, S. M., Adams, M. J., Joseph, M. B., Waddle, J. H., Johnson, P. T. J., Ryan, M. E., Schmidt, B. R., Calhoun, D. L., Davis, C. L., Fisher, R. N., Green, D. M., Hossack, B. R., Rittenhouse, T. A. G., Walls, S. C., Bailey, L. L., Cruickshank, S. S., … Sigafus, B. H. (2018). Quantifying climate sensitivity and climate-driven change in North American amphibian communities. Nature Communications, 9, 1–15. https://doi.org/10.1038/s41467-018-06157-6
  • Miller, M. P. (2005). Alleles in space (AIS): Computer software for the joint analysis of interindividual spatial and genetic information. The Journal of Heredity, 96, 722–724. https://doi.org/10.1093/jhered/esi119
  • Minin, V. N., Bloomquist, E. W., & Suchard, M. A. (2008). Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Molecular Biology and Evolution, 25, 1459–1471. https://doi.org/10.1093/molbev/msn090
  • Moraes, L. J. C. L., Pavan, D., Barros, M. C., & Ribas, C. C. (2016). The combined influence of riverine barriers and flooding gradients on biogeographical patterns for amphibians and squamates in south-eastern Amazonia. Journal of Biogeography, 43, 2113–2124. https://doi.org/10.1111/jbi.12756
  • Moraes, L. J. C. L., Ribas, C. C., Pavan, D., & Werneck, F. P. (2020). Biotic and landscape evolution in an Amazonian contact zone: Insights from the herpetofauna of the Tapajós River basin. In V. Rull, & A. C. Carnaval (Eds.), Neotropical diversification: Patterns and processes (pp. 683–712). Springer.
  • Mota, E. P., Kaefer, I. L., Nunes, M. S., Lima, A. P., & Farias, I. P. (2020). Hidden diversity within the broadly distributed Amazonian giant monkey frog (Phyllomedusa bicolor: Phyllomedusidae). Amphibia-Reptilia, 41, 349–359. https://doi.org/10.1163/15685381-bja10003
  • Muscarella, R., Galante, P. J., Soley-Guardia, M., Boria, R. A., Kass, J. M., Uriarte, M., & Anderson, R. P. (2014). ENMeval: An R package for conducting spatially independent evaluations and estimating optimal model complexity for Maxent ecological niche models. Methods in Ecology and Evolution, 5, 1198–1205. https://doi.org/10.1111/2041-210X.12261
  • Oliveira, R. M., Maciel, N. M., & Vaz-Silva, W. (2010). New state record of Lithobates palmipes (Spix, 1824) (Anura: Ranidae) in Brazil. Herpetology Notes, 3, 277–278.
  • Olson, D. M., Dinerstein, E., Wikramanayake, E. D., Burgess, N. D., Powell, G. V. N., Underwood, E. C., D’amico, J. A., Itoua, I., Strand, H. E., Morrison, J. C., Loucks, C. J., Allnutt, T. F., Ricketts, T. H., Kura, Y., Lamoreux, J. F., Wettengel, W. W., Hedao, P., & Kassem, K. R. (2001). Terrestrial ecoregions of the World: A new map of life on Earth. BioSience, 51, 933–938. https://doi.org/10.1641/0006-3568(2001)051[0933:TEOTWA]2.0.CO;2
  • Otto-Bliesner, B. L., Marshall, S. J., Overpeck, J. T., Miller, G. H., & Hu, A., & CAPE Last Interglacial Project members. (2006). Simulating arctic climate warmth and icefield retreat in the Last Interglaciation. Science (New York, N.Y.), 311, 1751–1753. https://doi.org/10.1126/science.1120808
  • Pearse, D. E., Arndt, A. D., Valenzuela, N., Miller, B. A., Cantarelli, V., & Sites, J. W. (2006). Estimating population structure under nonequilibrium conditions in a conservation context: Continent-wide population genetics of the giant Amazon river turtle, Podocnemis expansa (Chelonia; Podocnemididae). Molecular Ecology, 15, 985–1006. https://doi.org/10.1111/j.1365-294X.2006.02869.x
  • Phillips, S. J., Anderson, R. P., & Schapire, R. E. (2006). Maximum entropy modeling of species geographic distributions. Ecological Modelling, 190, 231–259. https://doi.org/10.1016/j.ecolmodel.2005.03.026
  • Pirani, R. M., Werneck, F. P., Thomaz, A. T., Kenney, M. L., Sturaro, M. J., Ávila‐Pires, T. C. S., Peloso, P. L. V., Rodrigues, M. T., & Knowles, L. L. (2019). Testing main Amazonian rivers as barriers across time and space within widespread taxa. Journal of Biogeography, 46, 2444–2456. https://doi.org/10.1111/jbi.13676
  • Por, F. D. (1992). Sooterama: The Atlantic Rain Forest of Brazil. SPB Academic Publishing.
  • Prates, I., Rivera, D., Rodrigues, M. T., & Carnaval, A. C. (2016a). A mid-Pleistocene rainforest corridor enabled synchronous invasions of the Atlantic Forest by Amazonian anole lizards. Molecular Ecology, 25, 5174–5186. https://doi.org/10.1111/mec.13821
  • Prates, I., Xue, A. T., Brown, J. L., Alvarado-Serrano, D. F., Rodrigues, M. T., Hickerson, M. J., & Carnaval, A. C. (2016b). Inferring responses to climate dynamics from historical demography in neotropical forest lizards. Proceedings of the National Academy of Sciences of the United States of America, 113, 7978–7985. https://doi.org/10.1073/pnas.1601063113
  • Puillandre, N., Lambert A., Brouillet, S., & Achaz, G. (2012). ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Molecular Ecology, 21, 1864–1877. https://doi.org/10.1111/j.1365-294X.2011.05239.x
  • Pyron, R. A., Costa, G. C., Patten, M. A., & Burbrink, F. T. (2015). Phylogenetic niche conservatism and the evolutionary basis of ecological speciation. Biological Reviews of the Cambridge Philosophical Society, 90, 1248–1262. https://doi.org/10.1111/brv.12154
  • Ramalho, W. P., Viana, F., Benevides, R., Silva, E. P., & Alves-Silva, R. (2011). First record of Lithobates palmipes (Spix, 1824) (Anura, Ranidae) for the state of Piauí, Northeastern Brazil. Herpetology Notes, 4, 249–251.
  • Rambaut, A., Suchard, M. A., Xie, D., Drummond, A. J. (2014). Tracer v1.6. http://tree.bio.ed.ac.uk/software/tracer/.
  • Reid, N. M., & Carstens, B. C. (2012). Phylogenetic estimation error can decrease the accuracy of species delimitation: A Bayesian implementation of the general mixed Yule-coalescent model. BMC Evolutionary Biology, 12, 196. https://doi.org/10.1186/1471-2148-12-196
  • Rocha, T. C., Sequeira, F., Aleixo, A., Rêgo, P. S., Sampaio, I., Schneider, H., & Vallinoto, M. (2015). Molecular phylogeny and diversification of a widespread Neotropical rainforest bird group: The Buff-throated Woodcreeper complex, Xiphorhynchus guttatus/susurrans (Aves: Dendrocolaptidae). Molecular phylogenetics and evolution, 85, 131–140. https://doi.org/10.1016/j.ympev.2015.02.004
  • Rödder, D., & Engler, J. O. (2011). Quantitative metrics of overlaps in Grinnellian niches: Advances and possible drawbacks. Global Ecology and Biogeography, 20, 915–927. https://doi.org/10.1111/j.1466-8238.2011.00659.x
  • 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 Data Sets. Molecular Biology and Evolution, 34, 3299–3302. https://doi.org/10.1093/molbev/msx248
  • Rull, V., & Carnaval, A. C. (2020). Neotropical diversification: Patterns and processes. Springer. https://doi.org/10.1007/978-3-030-31167-4
  • Santa-Cruz, R., Delgado, J. A., Salas, C. Y., & Von May, R. (2016). New distributional records of the Amazon River Frog Lithobates palmipes (Spix, 1824) in Peru. Amphibian & Reptile Conservation, 10, 17–20.
  • Santos, D. L., & Vaz-Silva, L. (2012). Amphibia, Anura, Ranidae, Lithobates palmipes (Spix, 1824): New record and geographic distribution map in South America. Check List, 8, 1331–1332. https://doi.org/10.15560/8.6.1331
  • Shaw, K. L. (2002). Conflict between nuclear and mitochondrial DNA phylogenies of a recent species radiation: What mtDNA reveals and conceals about modes of speciation in Hawaiian crickets. Proceedings of the National Academy of Sciences of the United States of America, 99, 16122–16127. Doi: 10.1073pnas.242585899
  • Sillero, N., Arenas-Castro, S., Enriquez-Urzelai, U., Vale, C. G., Sousa-Guedes, D., Martínez-Freiría, F., Real, R., & Barbosa, A. (2021). Want to model a species niche? A step-by-step guideline on correlative ecological niche modelling. Ecological Modelling, 456, 109671. https://doi.org/10.1016/j.ecolmodel.2021.109671
  • Sobral-Souza, T., Lima-Ribeiro, M. S., & Solferini, V. N. (2015). Biogeography of Neotropical Rainforests: Past connections between Amazon and Atlantic Forest detected by ecological niche modeling. Evolutionary Ecology, 29, 643–655. https://doi.org/10.1007/s10682-015-9780-9
  • Swofford, D. L. (2002). PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates.
  • Thomé, M. T. C., Sequeira, F., Brusquetti, F., Carstens, B., Haddad, C. F. B., Rodrigues, M. T., & Alexandrino, J. (2016). Recurrent connections between Amazon and Atlantic forests shaped diversity in Caatinga four-eyed frogs. Journal of Biogeography, 43, 1045–1056. https://doi.org/10.1111/jbi.12685
  • Wang, X., Auler, A. S., Edwards, L. L., Cheng, H., Cristalli, P. S., Smart, P. L., Richards, D. A., & Shen, C. C. (2004). Wet periods in Northeastern Brazil over the past 210 kyr linked to distant climate anomalies. Nature, 432, 740–743. https://doi.org/10.1038/nature03067
  • Werneck, F. P. (2011). The diversification of eastern South American open vegetation biomes: Historical biogeography and perspectives. Quaternary Science Reviews, 30, 1630–1648. https://doi.org/10.1016/j.quascirev.2011.03.009
  • Zamborlini Saiter, F., Brown, J. L., Thomas, W. W., Oliveira‐Filho, A. T., & Carnaval, A. C. (2016). Environmental correlates of floristic regions and plant turnover in the Atlantic Forest hotspot. Journal of Biogeography, 43, 2322–2331. https://doi.org/10.1111/jbi.12774
  • Zamudio, K. R., & Greene, H. W. (1997). Phylogeography of the bushmaster (Lachesis muta: Viperidae): Implications for neotropical biogeography, systematics, and conservation. Biological Journal of the Linnean Society, 62, 421–442. https://doi.org/10.1111/j.1095-8312.1997.tb01634.x
  • Zamudio, K. R., Bell, R. C., & Mason, N. A. (2016). Phenotypes in phylogeography: Species' traits, environmental variation, and vertebrate diversification. Proceedings of the National Academy of Sciences of the United States of America, 113, 8041–8048. https://doi.org/10.1073/pnas.1602237113
  • Zeh, J. A., Zeh, D. W., & Bonilla, M. M. (2003). Phylogeography of the harlequin beetle-riding pseudoscorpion and the rise of the Isthmus of Panamá. Molecular Ecology, 12, 2759–2769. https://doi.org/10.1046/j.1365-294X.2003.01914.x
  • Zhang, D. R., Hui, H., Yu, G. H., Song, X. Q., Liu, S., Yuan, S. Q., Xiao, H., & Rao, D. Q. (2020). Shared response to changes in drainage basin: Phylogeography of the Yunnan small narrow-mouthed frog, Glyphoglossus yunnanensis (Anura: Microhylidae). Ecology and Evolution, 10, 1567–1580. https://doi.org/10.1002/ece3.6011
  • Zhang, J., Kapli, P., Pavlidis, P., Stamatakis, A. (2013). A general species delimitation method with applications to phylogenetic placements. Bioinformatics, 29, 2869–2876. https://doi.org/10.1093/bioinformatics/btt499

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.