Mitochondrial introgression obscures phylogenetic relationships among manakins of the genus Lepidothrix (Aves: Pipridae)

Bandeira, R.S., Rêgo, P.S., Aleixo, A., Schneider, H., Sampaio, I., Vallinoto, M., 2008. Lepidothrix vilasboasi (Sick, 1959): espécie válida? Uso de marcadores moleculares no estudo de uma ave amazônica, endêmica e ameaçada. Resumos 54° Congresso Brasileiro de Genética, 148.

Banker, 2017, The confounding effects of hybridization on phylogenetic estimation in the New Zealand cicada genus Kikihia, Mol. Phylogenet. Evol., 116, 172, 10.1016/j.ympev.2017.08.009

Barrera-Guzmán, 2018, Hybrid speciation leads to novel male secondary sexual ornamentation of an Amazonian bird, Proc. Natl. Acad. Sci., 115, E218, 10.1073/pnas.1717319115

Bates, 1989, Notes on bird distribution in northeastern Dpto. Santa Cruz, Bolivia, with 15 species new to Bolivia, Bull. Brit. Ornithological Club, 109, 236

BirdLife International and Handbook of the Birds of the World (2016), 2016a. Lepidothrix iris. The IUCN Red List of Threatened Species. Version 2017-1. Downloaded on 29 March 2017.

BirdLife International and Handbook of the Birds of the World (2016), 2016b. Lepidothrix nattereri. The IUCN Red List of Threatened Species. Version 2017-1. Downloaded on 29 March 2017.

BirdLife International and Handbook of the Birds of the World (2016), 2016c. Lepidothrix vilasboasi. The IUCN Red List of Threatened Species. Version 2017-1. Downloaded on 29 March 2017.

Britski, 2011, New species of Trachycorystes Bleeker, with comments on other species of the genus (Ostariophysi: Siluriformes: Auchenipteridae), Neotrop. Ichthyol., 9, 273, 10.1590/S1679-62252011000200004

Brumfield, 2001, Evolutionary implications of divergent clines in an avian (Manacus: Aves) hybrid zone, Evolution, 55, 2070, 10.1111/j.0014-3820.2001.tb01322.x

Cheviron, 2005, Complex evolutionary history of a Neotropical lowland forest bird (Lepidothrix coronata) and its implications for historical hypotheses of the origin of Neotropical avian diversity, Mol. Phylogenet. Evol., 36, 338, 10.1016/j.ympev.2005.01.015

Dun, 1987, Charons 36 to 40: multi enzyone, high capacity, recombination deficient replacement vectors with polylinkers and ploystuffers, Nucleic Acids Res., 15, 2677, 10.1093/nar/15.6.2677

Felsenstein, J., 2005. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.

Fernandes, 2014, Rivers acting as barriers for bird dispersal in the Amazon, Revista Brasileira de Ornitologia, 22, 363, 10.1007/BF03544273

Fernandes, 2013, Fine-scale endemism of Amazonian birds in a threatened landscape, Biodivers. Conserv., 22, 2683, 10.1007/s10531-013-0546-9

Fernandes, 2012, Phylogeography of the chestnut-tailed antbird (Myrmeciza hemimelaena) clarifies the role of rivers in Amazonian biogeography, J. Biogeogr., 39, 1524, 10.1111/j.1365-2699.2012.02712.x

Fernandes, 2014, Multiple speciation across the Andes and throughout Amazonia: the case of the spot-backed antbird species complex (Hylophylax naevius/Hylophylax naevioides), J. Biogeogr., 41, 1094, 10.1111/jbi.12277

Ferreira, 2017, Biogeography of the Neotropical genus Malacoptila (Aves: Bucconidae): the influence of the Andean orogeny, Amazonian drainage evolution and palaeoclimate, J. Biogeogr., 44, 748, 10.1111/jbi.12888

Haffer, J., 1997. Species concepts and species limits in ornithology. Handbook of the Birds of the World 4, 11–24.

Hall, 1999, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids Sympos. Series, 95

Harrigan, 2008, Computation vs. cloning: evaluation of two methods for haplotype determination, Mol. Ecol. Resour., 8, 1239, 10.1111/j.1755-0998.2008.02241.x

Hayakawa, 2015, Late quaternary dyhnamics in the Madeira river basin, southern Amazonia (Brazil), as revealed by paleomorphological analysis, Anais da Academia Brasileira de Ciências, 87, 29, 10.1590/0001-3765201520130506

Holder, 2001, Difficulties in detecting hybridization, Syst. Biol., 50, 978, 10.1080/106351501753462911

Huelsenbeck, 2001, MRBAYES: Bayesian inference of phylogenetic trees, Bioinformatics, 17, 754, 10.1093/bioinformatics/17.8.754

Lanfear, 2012, PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses, Mol. Biol. Evol., 29, 1695, 10.1093/molbev/mss020

Librado, 2009, DnaSP v5: a software for comprehensive analysis of DNA polymorphism data, Bioinformatics, 25, 1451, 10.1093/bioinformatics/btp187

McDonald, 2001, Sexual selection on plumage and behavior in an avian hybrid zone: experimental tests of male-male interactions, Evolution, 55, 1443, 10.1111/j.0014-3820.2001.tb00664.x

McKay, 2010, A molecular phylogenetic hypothesis for the manakins (Aves: Pipridae), Mol. Phylogenet. Evol., 55, 733, 10.1016/j.ympev.2010.02.024

Ohlson, 2013, Molecular phylogeny of the manakins (Aves: Passeriformes: Pipridae), with a new classification and the description of a new genus, Mol. Phylogenet. Evolut., 69, 796, 10.1016/j.ympev.2013.06.024

Olmos, 2003, Rediscovery of Golden-crowned Manakin Lepidotrix vilasboasi, Cotinga, 20, 48

Pessenda, 1988, Catalytic determination of molybdenum in plants by flow-injection spectrophotometry with ion-exchange separation, Analytica Chimica Acta, 214, 239, 10.1016/S0003-2670(00)80445-6

Prance, 1996, Islands in Amazonia, Philos. Trans. Roy. Soc. London B: Biol. Sci., 351, 823, 10.1098/rstb.1996.0077

Prum, R.O., 1992. Syringeal morphology, phylogeny, and evolution of the Neotropical manakins (Aves: Pipridae). American Museum of Natural History.

Prum, 1997, Phylogenetic tests of alternative intersexual selection mechanisms: trait macroevolution in a polygynous clade (Aves: Pipridae), Am. Nat., 149, 668, 10.1086/286014

Pulido-Santacruz, 2018, Morphologically cryptic Amazonian bird species pairs exhibit strong postzygotic reproductive isolation, Proc. Royal Soc. B, 285, 20172081, 10.1098/rspb.2017.2081

Qu, 2012, Incomplete lineage sorting or secondary admixture: disentangling historical divergence from recent gene flow in the Vinous-throated parrotbill (Paradoxornis webbianus), Mol. Ecol., 21, 6117, 10.1111/mec.12080

Rêgo, 2007, Phylogenetic analyses of the genera Pipra, Lepidothrix and Dixiphia (Pipridae, Passeriformes) using partial cytochrome b and 16S mtDNA genes, Zoologica Scripta, 36, 565, 10.1111/j.1463-6409.2007.00301.x

Rheindt, 2011, Genetic introgression: an integral but neglected component of speciation in birds, Auk, 128, 620, 10.1525/auk.2011.128.4.620

Ridgely, R.S., Tudor, G., 1994. The birds of South America. Volume II. The suboscine passerines. University of Texas Press, Austin, TX(USA).

Rocha, 2008, A new species of Gladioglanis Ferraris & Mago-Leccia from rio Aripuanã, Amazonas, Brazil (Siluriformes: Heptapteridae), Neotropical Ichthyol., 6, 433, 10.1590/S1679-62252008000300017

Salzburger, 2011, The performance of phylogenetic algorithms in estimating haplotype genealogies with migration, Mol. Ecol., 20, 1952, 10.1111/j.1365-294X.2011.05066.x

Sanger, 1977, DNA sequencing with chain-terminating inhibitors, Proc. Natl. Acad. Sci., 74, 5463, 10.1073/pnas.74.12.5463

Sick, 1997

Sigrist, 2009, 305p

Snow, D., 2017. Manakins (Pipridae). In: del Hoyo, J., Elliott, A., Sargatal, J., Christie, D.A. & de Juana, E. (Eds.). Handbook of the Birds of the World Alive. Lynx Edicions, Barcelona. (retrieved from <http://www.hbw.com/node/52296> on 22 August 2017).

Snow, D. & Sharpe, C.J. 2017. Opal-crowned Manakin (Lepidothrix iris). In: del Hoyo, J., Elliott, A., Sargatal, J., Christie, D.A. & de Juana, E. (Eds.). Handbook of the Birds of the World Alive. Lynx Edicions, Barcelona. (retrieved from <http://www.hbw.com/node/57075> on 17 August 2017).

Sousa-Neves, 2013, Cryptic patterns of a widespread Amazonian Woodcreeper species complex (Aves: Dendrocolaptidae) inferred from multilocus phylogenetic analysis: Implications for historical biogeography and taxonomy, Mol. Phylogenet. Evol., 68, 410, 10.1016/j.ympev.2013.04.018

Stamatakis, 2014, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, 30, 1312, 10.1093/bioinformatics/btu033

Stein, 2006, Unidirectional introgression of a sexually selected trait across an avian hybrid zone: a role for female choice?, Evolution, 60, 1476

Stephens, 2001, A new statistical method for haplotype reconstruction from population data, Am. J. Human Genetics, 68, 978, 10.1086/319501

Sullivan, 2014, Divergence with gene flow within the recent chipmunk radiarion (Tamias), Heredity, 113, 185, 10.1038/hdy.2014.27

Tamura, 2013, MEGA6: molecular evolutionary genetics analysis version 6.0, Mol. Biol. Evol., 30, 2725, 10.1093/molbev/mst197

Tello, 2009, Phylogeny and phylogenetic classification of the tyrant flycatchers, cotingas, manakins, and their allies (Aves: Tyrannides), Cladistics, 25, 429, 10.1111/j.1096-0031.2009.00254.x

Thom, 2015, Cryptic speciation in the white-shouldered antshrike (Thamnophilus aethiops, Aves – Thamnophilidae): the tale of a transcontinental radiation across rivers in lowland Amazonia and the Northeastern Atlantic Forest, Mol. Phylogenet. Evolut., 82, 95, 10.1016/j.ympev.2014.09.023

Thompson, 1997, The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools, Nucleic Acids Res., 25, 4876, 10.1093/nar/25.24.4876

van Roosmalen, 2007, A new species of living peccary (Mammalia: Tayassuidae) from the Brazilian Amazon, Bonner Zoologische Beiträge, 55, 105

van Roosmalen, 2003, The description of a new marmoset genus, Callibella (Callitrichinae, Primates), including its molecular phylogenetic status, Neotropical Primates, 11, 1, 10.62015/np.2003.v11.525

Weir, 2015, Hybridization in headwater regions, and the role of rivers as drivers of speciation in Amazonian birds, Evolution, 69, 1823, 10.1111/evo.12696

Whitney, B., Cohn-Haft, M., Bravo, G.A., Silveira, L.F., 2013. A new species of Herpsilochmus antwren from the Aripuanã-Machado interfluvium in central Amazonian Brazil. In: del Hoyo, J., Elliot, A., Sargatal, J., Christie, D. (Eds.), Handbook of the Birds of the World. Special volume: new species and global index. Lynx Edicions, Barcelona, pp. 277–281.