Molecular systematics and evolution of the Synallaxis ruficapilla complex (Aves: Furnariidae) in the Atlantic Forest Henrique Batalha-Filho a,⇑ , Martin Irestedt b , Jon Fjeldså c , Per G.P. Ericson b , Luis F. Silveira d , Cristina Y. Miyaki a a Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil b Molecular Systematics Laboratory, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden c Center for Macroecology, Evolution and Climate at the Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark d Museu de Zoologia, Universidade de São Paulo, São Paulo, Brazil article info Article history: Received 21 August 2012 Revised 7 January 2013 Accepted 9 January 2013 Available online 20 January 2013 Keywords: Passeriformes Neotropics Species tree Plio–Pleistocene Diversification abstract The Neotropical Synallaxis ruficapilla complex is endemic to the Atlantic Forest and is comprised of three species: S. ruficapilla, S. whitneyi, and S. infuscata. This group is closely related to the Synallaxis moesta complex that occurs in the Andes, Tepuis, and Guianan shield. Here we used mitochondrial and nuclear gene sequences to infer the phylogeny and the time of diversification of the S. ruficapilla and S. moesta complexes. We also included samples of an undescribed population of Synallaxis that resembles other populations of the S. ruficapilla complex. Our results showed that different geographical lineages within the S. ruficapilla complex are reciprocally monophyletic, but the northern form (S. infuscata) grouped with an Andean taxon. This suggests that at least two lineages of this group independently colonized the Atlantic Forest. Specimens of the undescribed population formed a monophyletic clade with deep diver- gence. Estimated diversification dates were within the late Pliocene to Pleistocene (2.75–0.16 million of years ago). This suggests that at this time there was a higher connectivity between habitats in the rugged landscapes of the circum-Amazonian bioregions. The observed Pleistocene diversification within the Atlantic Forest is congruent in space and time with studies of other co-distributed organisms, and may be associated with climate changes and tectonic activity during this period. Ó 2013 Elsevier Inc. All rights reserved. 1. Introduction The genus Synallaxis Vieillot (Spinetails) is endemic to the Neo- tropical region and occurs from southern Mexico to Argentina. This is the most species-rich genus in the family Furnariidae, with 33 recognized species (Remsen, 2003). Recently, an additional species of Synallaxis was described (Hilty and Ascanio, 2009). Overall, the systematics of the genus is rather obscure, as many species are similar in morphology (Ridgely and Tudor, 1994), and some species include two to ten subspecies that could represent full species themselves (Remsen, 2003). Most Synallaxis species inhabit dense understory vegetation in riparian thickets, edge habitat and sec- ondary forest, with some exceptions occurring inside continuous forest (Ridgely and Tudor, 1994; Sick, 1997). Remsen (2003) suggests a close relationship between Synallaxis and the genera Certhiaxis, Schoeniophylax, Gyalophylax, and Siptornopsis. Recent phylogenetic hypotheses (Irestedt et al., 2009; Derryberry et al., 2011) confirm these relationships. The S. ruficapilla complex (Fig. 1) comprises S. ruficapilla, S. whit- neyi, and S. infuscata (Pacheco and Gonzaga, 1995) and is endemic to the highly endangered and megadiverse Atlantic Forest – AF (Myers et al., 2000; Ribeiro et al., 2009). Pacheco and Gonzaga (1995) suggested that this species complex is monophyletic based on similarities in plumage and song and notably their nearly identical scolding call. In a recent near-complete species-level phy- logeny of the Furnariidae (Derryberry et al., 2011) the S. ruficapilla and S. moesta complexes are placed together as a monophyletic clade, but with low node supports for the relationships within the clade. However, this phylogeny only included one species from the S. ruficapilla complex (S. ruficapilla) while the S. moesta complex was represented by all three species (S. moesta, S. macconnelli, and S. cabanisi), which occur in the Andes, Tepuis, and Guianan shield (Fig. 1; Ridgely and Tudor, 1994; Remsen, 2003). Recently Stopiglia et al. (2012) suggested that S. whitneyi is a ju- nior synonym of S. ruficapilla based on plumage, morphometric, and song characters. Thus, according to these authors, there are only two species in the S. ruficapilla complex: S. ruficapilla and S. infuscata. They also argued that only the number of rectrices is 1055-7903/$ - see front matter Ó 2013 Elsevier Inc. All rights reserved. http://dx.doi.org/10.1016/j.ympev.2013.01.007 ⇑ Corresponding author. Address: Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, Cidade Universitária, 05508-090 São Paulo, SP, Brazil. Fax: +55 11 3091 7553. E-mail addresses: henrique.batalha@usp.br, rickbio@hotmail.com (H. Batalha-Filho). Molecular Phylogenetics and Evolution 67 (2013) 86–94 Contents lists available at SciVerse ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev