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Late Pleistocene landscape changes and habitat specialization as promoters of population genomic divergence in Amazonian floodplain birds
dc.contributor.authorLuna, Leilton Willians
dc.contributor.authorNaka, Luciano Nicolas
dc.contributor.authorThom, Gregory
dc.contributor.authorKnowles, Laura lacey
dc.contributor.authorSawakuchi, André Oliveira
dc.contributor.authorAleixo, Alexandre
dc.contributor.authorRibas, Camila cherem
dc.date.accessioned2023-01-11T16:24:47Z
dc.date.available2024-02-11 11:24:43en
dc.date.available2023-01-11T16:24:47Z
dc.date.issued2023-01
dc.identifier.citationLuna, Leilton Willians; Naka, Luciano Nicolas; Thom, Gregory; Knowles, Laura lacey ; Sawakuchi, André Oliveira ; Aleixo, Alexandre; Ribas, Camila cherem (2023). "Late Pleistocene landscape changes and habitat specialization as promoters of population genomic divergence in Amazonian floodplain birds." Molecular Ecology (1): 214-228.
dc.identifier.issn0962-1083
dc.identifier.issn1365-294X
dc.identifier.urihttps://hdl.handle.net/2027.42/175467
dc.description.abstractAlthough vicariant processes are expected to leave similar genomic signatures among codistributed taxa, ecological traits such as habitat and stratum can influence genetic divergence within species. Here, we combined landscape history and habitat specialization to understand the historical and ecological factors responsible for current levels of genetic divergence in three species of birds specialized in seasonally flooded habitats in muddy rivers and which are widespread in the Amazon basin but have isolated populations in the Rio Branco. Populations of the white-bellied spinetail (Mazaria propinqua), lesser wagtail-tyrant (Stigmatura napensis) and bicolored conebill (Conirostrum bicolor) are currently isolated in the Rio Branco by the black-waters of the lower Rio Negro, offering a unique opportunity to test the effect of river colour as a barrier to gene flow. We used ultraconserved elements (UCEs) to test alternative hypotheses of population history in a comparative phylogeographical approach by modelling genetic structure, demographic history and testing for shared divergence time among codistributed taxa. Our analyses revealed that (i) all three populations from the Rio Branco floodplains are genetically distinct from other populations along the Amazon River floodplains; (ii) these divergences are the result of at least two distinct events, consistent with species habitat specialization; and (iii) the most likely model of population evolution includes lower population connectivity during the Late Pleistocene transition (~250,000 years ago), with gene flow being completely disrupted after the Last Glacial Maximum (~21,000 years ago). Our findings highlight how landscape evolution modulates population connectivity in habitat specialist species and how organisms can have different responses to the same historical processes of environmental change, depending on their habitat affinity.
dc.publisherWiley Periodicals, Inc.
dc.publisherSmithsonian Institution Press
dc.subject.otherecological traits
dc.subject.otherbiogeographical barrier
dc.subject.othercomparative phylogeography
dc.subject.othergeogenomics
dc.subject.otherpopulation structure
dc.subject.otherRio Branco
dc.titleLate Pleistocene landscape changes and habitat specialization as promoters of population genomic divergence in Amazonian floodplain birds
dc.typeArticle
dc.rights.robotsIndexNoFollow
dc.subject.hlbsecondlevelEcology and Evolutionary Biology
dc.subject.hlbtoplevelScience
dc.description.peerreviewedPeer Reviewed
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/175467/1/mec16741.pdf
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/175467/2/mec16741-sup-0001-TablesS1-S4-FiguresS1-S8.pdf
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/175467/3/mec16741_am.pdf
dc.identifier.doi10.1111/mec.16741
dc.identifier.sourceMolecular Ecology
dc.identifier.citedreferencePrado, A. H., Almeida, R. P., Galeazzi, C. P., Sacek, V., & Schlunegger, F. ( 2022 ). Climate change and the formation of fluvial terraces in central Amazonia inferred from landscape evolution modeling. Earth Surface Dynamics, 10, 457 – 471.
dc.identifier.citedreferenceOaks, J. R. ( 2019 ). Full Bayesian comparative phylogeography from genomic data. Systematic Biology, 68, 371 – 395.
dc.identifier.citedreferenceOaks, J. R., Siler, C. D., & Brown, R. M. ( 2019 ). The comparative biogeography of Philippine geckos challenges predictions from a paradigm of climate-driven vicariant diversification across an Island archipelago. Evolution, 73, 1151 – 1167.
dc.identifier.citedreferencePapadopoulou, A., & Knowles, L. L. ( 2016 ). Toward a paradigm shift in comparative phylogeography driven by trait-based hypotheses. Proceedings of the National Academy of Sciences of the United States of America, 116, 8018 – 8024.
dc.identifier.citedreferencePassos, M. S., Soares, E. A. A., Tatumi, S. H., Yee, M., Mittani, J. C. R., Hayakawa, E. H., & Salazar, C. A. ( 2020 ). Pleistocene-Holocene sedimentar deposits of the Solimões-Amazonas fluvial system, Western Amazonia. Journal of South American Earth Sciences, 98, 102455.
dc.identifier.citedreferencePavlidis, P., Laurent, S., & Stephan, W. ( 2010 ). msABC: A modification of Hudson’s ms to facilitate multi-locus ABC analysis. Molecular Ecology Resources, 10, 723 – 727.
dc.identifier.citedreferenceProvost, K. L., Myers, E. A., & Smith, B. T. ( 2021 ). Community phylogeographic patterns reveal how a barrier filters and structures taxa in North American warm deserts. Journal of Biogeography, 48, 1267 – 1283.
dc.identifier.citedreferencePupim, F. N., Sawakuchi, A. O., Almeida, R. P., Ribas, C. C., Kern, A. K., Hartmann, G. A., Chiessi, C. M., Tamura, L. N., Mineli, T. D., Savian, J. F., Grohmann, C. H., Bertassoli, D. J., Stern, A. G., Cruz, F. W., & Cracraft, J. ( 2019 ). Chronology of Terra Firme formation in Amazonian lowlands reveals a dynamic Quaternary landscape. Quaternary Science Reviews, 210, 154 – 163.
dc.identifier.citedreferenceRambaut, A., & Drummond, A. J. ( 2015 ). Trace v1.6. http://tree.bio.ed.ac.uk/software/tracer/
dc.identifier.citedreferenceRemsen, J. V., & Parker, T. A. ( 1983 ). Contribution of river-created habitats to bird species richness in Amazonia. Biotropica, 15, 223 – 231.
dc.identifier.citedreferenceRibas, C. C., & Aleixo, A. ( 2019 ). Diversity and evolution of Amazonian birds: Implications for conservation and biogeography. Anais da Academia Brasileira de Ciências, 91, e20190218.
dc.identifier.citedreferenceRibas, C. C., Aleixo, A., Nogueira, A. C. R., Miyaki, C. Y., & Cracraft, J. ( 2012 ). A palaebiogeographic model for biotic diversification within Amazonia over the past three million years. Proceedings of the Royal Society B, 279, 681 – 689.
dc.identifier.citedreferenceRogers, J. S. ( 1972 ). Measures of similarity and genetic distance. In M. R. Wheeler (Ed.), Studies in genetics VII (pp. 145 – 153 ). University of Texas Publication 7213.
dc.identifier.citedreferenceRosenberg, G. H. ( 1990 ). Habitat specialization and foraging behavior by birds of Amazonian river islands in northeastern Peru. The Condor, 92, 427 – 443.
dc.identifier.citedreferenceRowedder, A. R. P., Laranjeiras, T. O., Haugaasen, T., Gilmore, B., & Conh-Haft, M. ( 2021 ). Response of understory avifauna to annual flooding of Amazonian floodplain forest. Forests, 12, 1004.
dc.identifier.citedreferenceRuokolainen, K., Moulatlet, G. M., Zuquim, G., Hoorn, C., & Toumisto, H. ( 2019 ). Geologically recent rearrangements in central Amazonian river network and their importance for the rivenerine barrier hypothesis. Frontiers of Biogeography, 11, e45046.
dc.identifier.citedreferenceSawakuchi, A. O., Schultz, E. D., Pupim, F. N., Bertassoli, D. J., Jr., Souza, D. F., Cunha, D. F., Mazoca, C. E., Ferreira, M. P., Grohmann, C. H., Wahnfried, I. D., Chiessi, C. M., Cruz, F. W., Almeida, R. P., & Ribas, C. C. ( 2022 ). Rainfall and sea level drove the expansion of seasonally flooded habits and associated bird populations across Amazonia. Nature Communications, 13, 4945.
dc.identifier.citedreferenceSchulenberg, T. S., & Rosenberg, G. H. ( 2020 ). White-bellied Spinetail ( Mazaria propinqua ), version 1.0. In T. S. Schulenberg (Ed.), Birds of the world. Cornell Lab of Ornithology.
dc.identifier.citedreferenceSmith, B. T., McCormack, J. E., Cuervo, A. M., Hickerson, J., Aleixo, A., Cadena, C. D., Pérez-Emán, J., Burney, C. W., Xie, X., Harvey, M. G., Faircloth, B. C., Glenn, T. C., Derryberry, E. P., Prejean, J., Fields, S., & Brumfield, R. T. ( 2014 ). The drivers of tropical speciation. Nature, 515, 406 – 409.
dc.identifier.citedreferenceTajima, F. ( 1989 ). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585 – 595.
dc.identifier.citedreferenceThom, G., Xue, A., Sawakuchi, A. O., Ribas, C. C., Hickerson, M. J., Aleixo, A., & Miyaki, C. ( 2020 ). Quaternary climate changes as speciation drivers in the Amazon floodplains. Science Advances, 6, eaa4718.
dc.identifier.citedreferenceThomaz, A. T., & Knowles, L. L. ( 2020 ). Common barriers, but temporal dissonance: Genomic tests suggest ecological and paleo-landscape sieves structure a coastal riverine fish community. Molecular Ecology, 29, 783 – 796.
dc.identifier.citedreferenceTobias, J. A., Sheard, C., Pigot, A. L., Devenish, A. J. M., Yang, J., Sayol, F., Neate-Clegg, M. H. C., Alioravainen, N., Weeks, T. L., Barber, R. A., Walkden, P. A., MacGregor, H. E. A., Jones, S. E. I., Vincent, C., Phillips, A. G., Marples, N. M., Montaño-Centellas, F. A., Leandro-Silva, V., Claramunt, S., … Schleuning, M. ( 2022 ). AVONET: morphological, ecological and geographical data for all birds. Ecology Letters, 25 ( 3 ), 581 – 597.
dc.identifier.citedreferenceTyers, M. ( 2020 ). riverdist: River network distance computation and applications. (R package version 0.15.3). https://cran.r-project.org/package=riverdist
dc.identifier.citedreferenceWang, I. ( 2013 ). Examining the full effects of landscape heterogeneity on spatial genetic variation: A multiple matrix regression approach for quantifying geographic and ecological isolation. Evolution, 67, 3403 – 3411.
dc.identifier.citedreferenceWatterson, G. A. ( 1975 ). On the number of segregating sites in genetical models without recombination. Theoretical Population Biology, 7, 256 – 276.
dc.identifier.citedreferenceWittmann, F., Schöngart, J., & Junk, W. J. ( 2010 ). Phytogeography, species diversity, community structure and dynamics of central Amazonian floodplains forest. In W. J. Junk, M. T. F. Piedade, F. Wittmann, J. Schöngart, & P. Parolin (Eds.), Amazon floodplain forest: Ecophysiology, biodiversity and sustainable management. Ecological studies (Vol. 210, pp. 61 – 102 ). Springer Verlag.
dc.identifier.citedreferenceWright, S. ( 1950 ). Genetical structure of population. Nature, 166, 247 – 249.
dc.identifier.citedreferenceZular, A., Sawakuchi, A. O., Chiessi, C. M., d’Horta, F. M., Cruz, F. W., Demattê, J. A. M., Ribas, C. C., Hartmann, G. A., Giannini, C. F., & Soares, E. A. A. ( 2019 ). The role of abrupt climate change in the formation of an open vegetation enclave in northern Amazonia during the late Quaternary. Global and Planetary Change, 172, 140 – 149.
dc.identifier.citedreferenceAdamack, A. T., & Gruber, B. ( 2014 ). PopGenReport: Simplifying basic population genetic analyses in R. Methods in Ecology and Evolution, 5 ( 4 ), 384 – 387.
dc.identifier.citedreferenceAkabane, T. K., Sawakuchi, A. O., Chiessi, C. M., Kern, A. K., Pinaya, J. L. D., Ceccantini, G. C. T., & De Oliveira, P. E. ( 2020 ). Modern pollen signatures of Amazonian rivers and new insights for environmental reconstructions. Palaeogeography, Palaeoclimatology, Palaeoecology, 554, 109802.
dc.identifier.citedreferenceAleixo, A. ( 2006 ). Historical diversification of floodplain forest specialist species in the Amazon: A case study with two species of the avian genus Xiphorhynchus (Aves: Dendrocolaptidae). Biological Journal of the Linnean Society, 89, 383 – 395.
dc.identifier.citedreferenceAmaral, F. R., Maldonado-Coelho, M., Aleixo, A., Luna, L. W., Rêgo, P. S., Araripe, J., Souza, T. O., Silva, W. A. G., & Thom, G. ( 2018 ). Recent chapters of Neotropical history overlooked in phylogeography: Shallow divergence explains phenotype and genotype uncoupling in Antilophia manakins. Molecular Ecology, 27, 4108 – 4120.
dc.identifier.citedreferenceAndrews, S. ( 2014 ). FastQC: A quality control tool for high-throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
dc.identifier.citedreferenceBarbosa, W. E. S., Ferreira, M., Schultz, E. D., Luna, L. W., Laranjeiras, T. O., Aleixo, A., & Ribas, C. C. ( 2022 ). Habitat association constrains population history in two sympatric ovenbirds along Amazonian floodplains. Journal of Biogeography, 49, 1683 – 1695.
dc.identifier.citedreferenceBogotá-Gregory, J. D., Lima, F. C. T., Correa, S. B., Silva-Oliveira, C., Jenkins, D. G., Ribeiro, F. R., Lovejoy, N. R., Reis, R. E., & Campton, W. G. R. ( 2020 ). Biogeochemical water type influences community composition, species richness, and biomass in megadiverse Amazonian fish assemblages. Scientific Reports, 10, 15349.
dc.identifier.citedreferenceBradburd, G. S., Coop, G. M., & Ralph, P. L. ( 2018 ). Inferring continuous and discrete population genetic structure across space. Genetics, 210, 33 – 52.
dc.identifier.citedreferenceBurney, C. W., & Brumfield, R. T. ( 2009 ). Ecology predicts levels of genetic differentiation in Neotropical birds. The American Naturalist, 174, 358 – 368.
dc.identifier.citedreferenceCadena, D., Gutiérrez-Pinto, N., Dávila, N., & Chesser, R. T. ( 2011 ). No population genetic structure in a widespread aquatic songbird from the Neotropics. Molecular Phylogenetics and Evolution, 58, 540 – 545.
dc.identifier.citedreferenceCamacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. ( 2008 ). BLAST+: Architecture and applications. BMC Bioinformatics, 10, 421.
dc.identifier.citedreferenceCheng, H., Sinha, A., Cruz, F. W., Wang, W., 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.
dc.identifier.citedreferenceChoueri, E. L., Gubilli, C., Borges, S. H., Thom, G., Sawakuchi, A. O., Soares, E. A. A., & Ribas, C. C. ( 2017 ). Phylogeography and population dynamic of Antbirds (Thamnophilidae) from Amazonian fluvial islands. Journal of Biogeography, 44, 2284 – 2294.
dc.identifier.citedreferenceCintra, R., Sanaiotti, T. M., & Cohn-Haft, M. ( 2007 ). Spatial distribution and habitat of the Anavilhanas Archipelago bird community in the Brazilian Amazon. Biodiversity and Conservation, 16 ( 2 ), 313 – 336.
dc.identifier.citedreferenceCsilléry, K., François, O., & Blum, M. G. B. ( 2012 ). abc: An R package for approximate Bayesian computation (ABC). Methods in Ecology and Evolution, 3, 475 – 479.
dc.identifier.citedreferenceFaircloth, B. C., McCormarck, J. E., Crawford, N. G., Harvey, M. G., Brumfield, M. G., & Glenn, T. C. ( 2012 ). Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescale. Systematic Biology, 61, 717 – 726.
dc.identifier.citedreferenceGautheron, C., Sawakuchi, A. O., Albuquerque, M. F. S., Cabriolu, C., Parra, M., Ribas, C. C., Pupim, F. N., Schwartz, S., Kern, A. K., Gómez, S., Almeida, R. P., Horbe, A. M. C., Haurine, F., Miska, S., Julius, N., Findling, N., Riffel, S. B., & Jamme-Pina, R. ( 2022 ). Cenozoic weathering of fluvial terraces and emergence of biogeographic boundries in Central Amazonia. Global and Planetary Change, 212, 103815.
dc.identifier.citedreferenceGehara, M., Garda, A. A., Werneck, F. P., Oliveira, E. F., da Fonseca, E. M., Camurugi, F., Magalhães, F. M., Lanna, F. M., Sites, J. W., Jr., Marques, R., Silveira-Filho, R., São Pedro, V. A., Colli, G. R., Costa, G. C., & Burbrink, F. T. ( 2017 ). Estimating synchronous demographic changes across populations using hABC and its application for a herpetological community from northeastern Brazil. Molecular Ecology, 26, 4756 – 4771.
dc.identifier.citedreferenceGoulding, M., Barthem, R., & Ferreira, E. J. G. ( 2003 ). The Smithsonian atlas of the Amazon. Smithsonian Institution Press.
dc.identifier.citedreferenceGuindon, S., Dufayard, J. F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. ( 2010 ). New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Systematic Biology, 59, 307 – 321.
dc.identifier.citedreferenceGrabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., Chen, Z., Mauceli, E., Hacohen, N., Gnirke, A., Rhind, N., di Palma, F., Birren, B. W., Nusbaum, C., Lindblad-Toh, K., … Regev, A. ( 2011 ). Full-length transcriptome assembly from RNA-seq data without a reference genome. Nature Biotechnology, 29, 644 – 652.
dc.identifier.citedreferenceHaffer, J. ( 1969 ). Speciation in Amazon forest birds. Science, 165, 131 – 137.
dc.identifier.citedreferenceHäggi, C., Chiessi, C. M., Merkel, U., Mulitza, S., Prange, M., Schultz, M., & Schefuß, E. ( 2017 ). Response of the Amazon rainforest to late Pleistocene climate variability. Earth and Planetary Science Letters, 479, 50 – 59.
dc.identifier.citedreferenceHarvey, M. G., Aleixo, A., Ribas, C. C., & Brumfield, R. T. ( 2017 ). Habitat association predicts genetic diversity and population divergence in Amazonian birds. The American Naturalist, 190, 631 – 648.
dc.identifier.citedreferenceHarvey, M. G., Smith, B. T., Glenn, T. C., Faircloth, B. C., & Brumfield, R. T. ( 2016 ). Sequence capture versus restriction site associated DNA sequencing for shallow systematics. Systematic Biology, 65, 910 – 924.
dc.identifier.citedreferenceHoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q., & Vinh, L. S. ( 2018 ). UFBoot2: Improving the ultrafast bootstrap approximation. Molecular Biology and Evolution, 35, 518 – 522.
dc.identifier.citedreferenceHilty, S., & Kirwan, G. M. ( 2020 ). Bicolored Conebill ( Conirostrum bicolor ), version 1.0. In J. del Hoyo, A. Elliott, J. Sargatal, D. A. Christie, & E. de Juana (Eds.), Birds of the world. Cornell Lab of Ornithology.
dc.identifier.citedreferenceHubert, N., & Renno, J. F. ( 2006 ). Historical biogeography of South American freshwater fishes. Journal of Biogeography, 33, 1414 – 1436.
dc.identifier.citedreferenceHudson, R. R. ( 2002 ). Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics, 18, 337 – 338.
dc.identifier.citedreferenceIrion, G., de Mello, J. A. S. N., Morais, J., Piedade, M. T. F., Junk, W. J., & Garming, L. ( 2010 ). Development of the Amazon valley during the middle to late quaternary: Sedimentological and climatological observations. In W. J. Junk, M. T. F. Piedade, F. Wittmann, J. Schöngart, & P. Parolin (Eds.), Ecology studies 210 (pp. 27 – 42 ). Springer.
dc.identifier.citedreferenceIrion, G., Junk, W. J., & de Mello, J. A. S. N. ( 1997 ). The large Central Amazonian river floodplains near Manaus: Geological, climatological, hydrological, and geomorphological aspects. In W. J. Junk (Ed.), The Central Amazon floodplain. Ecology of a pulsing system (pp. 23 – 46 ). Springer.
dc.identifier.citedreferenceJombart, T. ( 2008 ). adegenet: A R package for the multivariate analysis of genetic markers. Bioinformatics, 24, 1403 – 1405.
dc.identifier.citedreferenceJunk, W. J., Piedade, M. T. F., Schöngart, J., Cohn-Haft, M., Adency, J. M., & Wittmann, F. ( 2011 ). A classification of major naturally-occurring Amazonian lowland wetlands. Wetlands, 31, 623 – 640.
dc.identifier.citedreferenceJunk, W. J., Piedade, M. T. F., Schöngart, J., & Wittmann, F. ( 2012 ). A classification of major natural habitats of Amazonian white-water river floodplains ( várzeas ). Wetlands Ecology and Management, 20, 461 – 475.
dc.identifier.citedreferenceJunk, W. J., Wittmann, F., Schöngart, J., & Piedade, M. T. F. ( 2015 ). A classification of the major habitats of Amazonian black-water river floodplains and a comparison with their white-water counterparts. Wetlands Ecology and Management, 23, 677 – 693.
dc.identifier.citedreferenceKalliola, R., Salo, J., Puhakka, M., & Rajasilta, M. ( 1991 ). New site formation and colonizing vegetation in primary succession on the western Amazon floodplains. Journal of Ecology, 79, 877 – 901.
dc.identifier.citedreferenceKalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A., & Jermiin, L. S. ( 2017 ). ModelFinder: Fast model selection for accurate phylogenetic estimates. Nature Methods, 14, 587 – 589.
dc.identifier.citedreferenceKatoh, K., & Standley, D. M. ( 2013 ). MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution, 30, 772 – 780.
dc.identifier.citedreferenceKopuchian, C., Campagna, L., Lijtmaer, D. A., Cabanne, G. S., García, N. C., Lavinia, P. D., Tubaro, P. L., Lovette, I., & Di Giacomo, A. S. ( 2020 ). A test of the riverine barrier hypothesis in the largest subtropical river basin in the Neotropics. Molecular Ecology, 29, 2137 – 2149.
dc.identifier.citedreferenceKuhn, M., Wing, J., Weston, S., Williams, A., Keefer, C., Engelhardt, A., Cooper, T., Mayer, Z., Kenkel, B., the R Core Team, Benesty, M., Lescarbeau, R., Ziem, A., Scrucca, L., Tang, Y., Candan, C., & Hunt, T. ( 2017 ) Caret: Classification and regression training. R package version 4.
dc.identifier.citedreferenceLaranjeiras, T. O., Naka, L. N., & Cohn-Haft, M. ( 2019 ). Using river colorcolour to predict Amazonian floodplain forest avifaunas in the world’s largest blackwater river basin. Biotropica, 51, 330 – 341.
dc.identifier.citedreferenceLaranjeiras, T. O., Naka, L. N., Leite, G. A., & Cohn-Haft, M. ( 2020 ). Effects of a major Amazonian river confluence on the distribution of floodplain forest avifauna. Journal of Biogeography, 48, 847 – 860.
dc.identifier.citedreferenceLatrubesse, E. M., & Franzinelli, E. ( 2005 ). The late Quaternary Evolution of the Negro River, Amazon, Brazil: Implications for Island and floodplain formation in large anabranching tropical systems. Geomorphology, 70, 372 – 397.
dc.identifier.citedreferenceLeaché, A. D., Oaks, J. R., Ofori-Boateng, C., & Fujita, M. ( 2020 ). Comparative phylogeography of West African amphibians and reptiles. Evolution, 74, 716 – 724.
dc.identifier.citedreferenceLi, H., & Durbin, R. ( 2009 ). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754 – 1760.
dc.identifier.citedreferenceLuna, L. W., Ribas, C. C., & Aleixo, A. ( 2022 ). Genomic differentiation with gene flow in a widespread Amazonian floodplain-specialist bird species. Journal of Biogeography, 49, 1670 – 1682.
dc.identifier.citedreferenceMarske, K. A., Thomaz, A. T., & Knowles, L. L. ( 2020 ). Dispersal barriers and opportunities drive multiples levels of phylogeographical concordance in the Southern Alps of New Zealand. Molecular Ecology, 29, 4665 – 4679.
dc.identifier.citedreferenceMcKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., & DePristo, M. A. ( 2010 ). The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20, 1297 – 1303.
dc.identifier.citedreferenceMelo, T. N., Cerqueira, M. C., d’Horta, F. M., Toumisto, H., Doninck, J. V., & Ribas, C. C. ( 2021 ). Impacts of a large hydroelectric dam on the Madeira River (Brazil) on floodplain avifauna. Acta Amazonica, 51, 298 – 310.
dc.identifier.citedreferenceMinh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., von Haeseler, A., & Lanfear, R. ( 2020 ). IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution, 37, 1530 – 1534.
dc.identifier.citedreferenceMyers, E. A., Xue, A. T., Gehara, M., Cox, C. L., Rabosky, A. R. D., Lemos-Espinal, J., Martínez-Gómez, J. E., & Burbrink, F. T. ( 2019 ). Environmental heterogeneity and not vicariant biogeographic barriers generate community-wide population structure in desert-adapted snakes. Molecular Ecology, 28, 4535 – 4548.
dc.identifier.citedreferenceNaka, L. N., & Brumfield, R. T. ( 2018 ). The dual role of Amazonian rivers in the generation and maintenance of avian diversity. Science Advances, 4, eaar8575.
dc.identifier.citedreferenceNaka, L. N., Cohn-Haft, M., Whittaker, A., Barnett, J. M., & Torres, M. F. ( 2007 ). Avian biogeography of Amazonian flooded forest in the Rio Branco basin, Brazil. The Wilson Journal of Ornithology, 119, 439 – 449.
dc.identifier.citedreferenceNaka, L. N., Costa, B. M. S., Lima, G. R., & Claramunt, S. ( 2022 ). Riverine barriers as obstacles to dispersal in Amazonian birds. Frontiers in Ecology and Evolution, 10, 846975.
dc.identifier.citedreferenceNaka, L. N., Laranjeiras, T. O., Lima, G. R., Plaskeivicz, A., Pinto, F., & Gonçalves-Souza, T. ( 2020 ). Climate as a major driver of avian diversity in riparian Amazonian habitats along an environmental gradient. Journal of Biogeography, 47, 2328 – 2340.
dc.identifier.citedreferenceNazareno, A. G., Knowles, L. L., Dick, C. W., & Lohmann, L. G. ( 2021 ). By animal, water, or wind: Can dispersal mode predict genetic connectivity in riverine plant species? Frontiers in Plant Science, 12, 626405.
dc.identifier.citedreferenceNguyen, L. T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. ( 2015 ). IQ-TREE: A fast and effective stochastic algorithm for estimatinga maximum-likelihood phylogenies. Molecular Biology and Evolution, 32, 268 – 274.
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Remediation of Harmful Language

The University of Michigan Library aims to describe its collections in a way that respects the people and communities who create, use, and are represented in them. We encourage you to Contact Us anonymously if you encounter harmful or problematic language in catalog records or finding aids. More information about our policies and practices is available at Remediation of Harmful Language.

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