Peer-reviewed articles and pre-prints

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

Acero-Murcia A. C., Amaral F. R, Barros F. C., Ribeiro T. S., Miyaki C. Y., Coelho M. M. In press. 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.

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. 

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. In press. Seeing the forest through many trees: multi-taxon patterns of phylogenetic diversity in the Atlantic Forest hotspot. Diversity and Distributions 26 (9), 1160-1176

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