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Peer-reviewed articles and pre-prints

Thom G, Gehara M, Smith B, Miyaki C, Amaral FR. 2021. Microevolutionary dynamics show tropical valleys are deeper for montane birds of the Atlantic Forest. Nature Communications, 12 (6269).

Amaral FR, Thom G, Lima-Ribeiro MS, Serrano DA, Montesanti JAC, Pellegrino KCM, Miyaki CY, Hickerson ML, Coelho MM. 2021. Rugged relief and climate promote isolation and divergence between two neotropical cold-associated birds. Evolution 75: 2371-2387. PDF

Acero-Murcia A. C., Amaral F. R, Barros F. C., Ribeiro T. S., Miyaki C. Y., Coelho M. M. 2021. Ecological and evolutionary drivers of geographic variation in songs of a Neotropical suboscine bird: The Drab-breasted Bamboo Tyrant (Hemitriccus diops, Rhynchocyclidae). Ornithology 138,ukab003. PDF.

Paz, A., Brown, J.L., Cordeiro, C.L.O., Aguirre-Santoro, J., Assis, C., Amaro, R.C., Raposo do Amaral, F., Bochorny, T., Bacci, L.F., Caddah, M.K., d’Horta, F., Kaehler, M., Lyra, M., Grohmann, C.H., Reginato, M., Silva-Brandão, K.L., Freitas, A.V.L., Goldenberg, R., Lohmann, L.G., Michelangeli, F.A., Miyaki, C., Rodrigues, M.T., Silva, T.S. and Carnaval, A.C. (2021), Environmental correlates of taxonomic and phylogenetic diversity in the Atlantic Forest. Journal of Biogeography, 48: 1377-1391. PDF.

Brown J.L., Paz A., Reginato, M., Amaro, R.C., Assis, C., Lyra, M., Caddah, M.K., Aguirre-Santoro, J., D'Horta, F., Amaral, F.R., Goldeberg, R., Silva-Brandão, K.L., Freitas, A.V.L., Rodrigues, M.T., Michelangeli, F.A., Miyaki, C.Y., Carnaval, A.C. 2020. Seeing the forest through many trees: multi-taxon patterns of phylogenetic diversity in the Atlantic Forest hotspot. Diversity and Distributions 26 (9), 1160-1176. PDF

Thom, G., Smith, B. T., Gehara, M., Montesanti, J., Lima-Ribeiro, M. S., Piacentini, V. Q., Miyaki, CY, Amaral, FR 2020. Climatic dynamics and topography control genetic variation in Atlantic Forest montane birds. Molecular Phylogenetics and Evolution, v. 148, 1-11. PDF

Macedo G, Silva M, Amaral, FR, Coelho MM. 2019. Symmetrical discrimination despite weak song differentiation in two Suboscine sister species. Behavioral Ecology, v. 30, 1205-1215. PDF 

Amaral FR, Maldonado-Coelho M, Aleixo A, Luna L, Rego PS, Araripe J, Souza TO, Silva WAG, Thom G. 2018. Recent chapters of Neotropical history overlooked in phylogeography: shallow divergence explains phenotype and genotype uncoupling in Antilophia manakins. Molecular Ecology, v. 27, 4108-4120. Cover article  PDF 

Amaral FR, Alvarado-Serrano D., Maldonado-Coelho M, Pellegrino KCM, Miyaki CY, Montesanti JAC, Lima-Ribeiro MS, Hickerson M, Thom G. 2018. Climate explains recent population divergence, introgression and persistence in tropical mountains: phylogenomic evidence from Atlantic Forest warbling finches. BioRxiv. PDF

Thom G, Amaral FR, Hickerson MJ, Aleixo A, Araujo-Silva LE, Ribas CC, Choueri E, Miyaki CY. 2018. Phenotypic and Genetic Structure Support Gene Flow Generating Gene Tree Discordances in an Amazonian Floodplain Endemic Species. Systematic Biology, v.64, 700-718. PDF

Coelho MM, Marini M, Amaral FR,  Ribon R. Accepted. 2017. Invasive Species Rules? A Possible Case of Competitive Exclusion in Avian Mixed-species Flocks in a Fragmented Landscape. Revista Brasileira De Ornitologia, v.25, 54-59. PDF

Amaral FR, Macedo G, Maldonado-Coelho M, Piacentini VQ,  Keuroghlian A,  Biondo C. 2017. Bluffing in the Forest: Neotropical Ground-cuckoos and Peccaries in a Possible Case of Acoustic Mimicry. Journal of Avian Biology, v.48, 1471-1474. PDF

Nacer D, Amaral FR . 2017. Striking Pseudogenization in Avian Phylogenetics: Numts Are Large and Common in Falcons. Molecular Phylogenetics and Evolution, v. 115, 1-6. PDF


Biancalana RN, Biondo C, Amaral FR. 2017. The mitochondrial genome of the Sooty Swift (Cypseloides fumigatus). Mitochondrial DNA, v.2, 198-200. PDF


Ceríaco LMP , Gutierrez E, Dubois A. et al (493 authors, including Amaral FR). 2016. Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences. Zootaxa 4196 (3): 435-445. PDF


Amaral F.R., Edwards S.V., Pie M.R., Jennings W.B., Svensson-Coelho M., d´Horta F.M., Schmitt C.J., Maldonado-Coelho M. 2016. The “Atlantis Forest hypothesis" does not explain Atlantic Forest phylogeography. Proceedings of the National Academy of Sciences. doi: 10.1073/pnas.1602213113. PDF


Piacentini V. Q, et al. 2015. Annotated checklist of the birds of Brazil by the Brazilian Ornithological Records Committee / Lista comentada das aves do Brasil pelo Comitê Brasileiro de Registros Ornitológicos. Revista Brasileira de Ornitologia, v. 23, 91–298.  PDF


Amaral, F. R.; Neves, L. G.; Resende Jr, M. F. R.; Mobili, F.; Miyaki, C. Y.; Pellegrino, K. C. M.; Biondo, C. 2015. Ultraconserved elements sequencing as a low-cost source of complete mitochondrial genomes and microsatellite markers in non-model amniotes. Plos OnePDF


Amaral, FR; Albers, PK; Edwards, SV; Miyaki, CY. 2013. Multilocus tests of Pleistocene refugia and ancient divergence in a pair of Atlantic Forest antbirds (Myrmeciza). Molecular Ecology, v. 22, 3996-4013. Cover article PDF  


Amaral, FR; Piacentini, VQ; Brito, GRR; Curcio, FF. 2012. A simple and effective air shotgun for collecting small birds and other vertebrates at close range. Journal of Field Ornithology, v. 83, p. 403-406. PDF


Amaral, FR; Edwards, SV; Miyaki, CY. 2012. Eight anonymous nuclear loci for the squamate antbird (Myrmeciza squamosa), cross-amplifiable in other species of typical antbirds (Aves, Thamnophilidae). Conservation Genetics Resources, v.4, p. 645-647. PDF


Batalha-Filho, H, Amaral, FR; Firme, DH. 2011. New specimens extend by 200 kilometers north the range of the Serra Antwren. Cotinga, v. 33, p. 145-147. PDF


Amaral, FR, Sheldon, FH, Gamauf, A, Haring, E, Riesing, M, Silveira, LF, Wajntal, A. 2010. Priority of Geranoaetus Kaup, 1844 over Tachytriorchis Kaup, 1844 (Aves: Accipitridae) based on the first reviser principle. Zootaxa, v. 2534, p. 67-68. PDF


Amaral, FR, Sheldon, FH, Wajntal, A. 2010. Towards an assessment of character interdependence in avian RNA phylogenetics: a general secondary structure model for the avian mitochondrial 16S rRNA. Molecular Phylogenetics and Evolution, v. 56, p. 498-506. PDF


Amaral, FR, Sheldon, FH, Gamauf, A, Haring, E, Riesing, M, Silveira, LF, Wajntal, A. 2009. Patterns and processes of diversification in a widespread and ecologically diverse avian group, the buteonine hawks (Aves, Accipitridae). Molecular Phylogenetics and Evolution, v. 53, p. 703-715. PDF


Miller, MJ, Berminghan, E, Klicka, J, Escalante, P, Amaral, FR, Weir, J, Winker, K. 2008. Out of Amazonia again and again: episodic crossing of the Andes promotes diversification in a lowland forest flycatcher. Proceedings of the Royal Society of London. Biological Sciences, v. 275, p. 1133-1142. PDF


Amaral, FR, Silveira, LF, Whitney,B. 2007. New Localities For The Black-Faced hawk (Leucopternis melanops) south of the Amazon River and description of the immature plumage of the White-Browed Hawk (Leucopternis kuhli). The Wilson Journal of Ornithology, v. 119, p. 450-454. PDF


Amaral, FR, Miller, MJ, Silveira, LF, Bermingham, E, Wajntal, A. 2006. Polyphyly of the hawk genera Leucopternis and Buteogallus (Aves, Accipitridae): multiple habitat shifts during the Neotropical buteonine diversification. BMC Evolutionary Biology, 6:10.  Highly accessed PDF


Amaral, FR, Silveira, LF. 2004. Tinamus solitarius pernambucensis Berla, 1946 é sinônimo de Tinamus solitarius (Vieillot, 1819). Ararajuba: Revista Brasileira de Ornitologia, 12:1, p.33-41. PDF


Book chapters


Amaral, FR. Leucopternis lacernulatus. In: Bressan, PM; Kierulff, MCM; Sugieda, AM. (Org.). Fauna ameaçada de extinção no Estado de São Paulo - Vertebrados. São Paulo: Fundação Parque Zoológico de São Paulo, 2010, p. 133-133. PDF


Amaral, FR. Leucopternis polionotus.  In: Bressan, PM; Kierulff, MCM; Sugieda, AM. (Org.). Fauna ameaçada de extinção no Estado de São Paulo - Vertebrados. São Paulo: Fundação Parque Zoológico de São Paulo, 2010, p. 134-134. PDF


Amaral, FR; Cabanne, GS. 2008. Leucopternis lacernulata. In: Machado, AB; Drummond, GM, Paglia, AP. (Org.). Livro vermelho da fauna brasileira ameaçada de extinção. 1 ed. Brasília: Ministério do Meio Ambiente, v2, p. 426-427. PDF


Cabanne, GS; Amaral, FR. 2008. Circus cinereus. In: Machado, AB; Drummond, GM, Paglia, AP. (Org.). Livro vermelho da fauna brasileira ameaçada de extinção. 1 ed. Brasília: Ministério do Meio Ambiente, v2, p. 422-423. PDF




Soares, ES; Amaral, FR; Carvalho-Filho, EPM; Granzinolli, MA; Albuquerque, JLB; Lisboa, JS; Azevedo, MAG; Moraes, W; Sanaiotti, T; Guimarães, IG. 2008. Plano de ação nacional para a conservação de aves de rapina: série espécies ameaçadas n. 5. Brasília: Ministério do Meio Ambiente, 136 p. PDF

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