Introduction
The main factors that have promoted the diversification of the Neotropical avifauna include the Andes Mountains (Weir 2006, Brumfield and Edwards 2007, Sedano and Burns 2010, Weir and Price 2011), wide rivers (Ribas et al. 2012, Naka and Brumfield 2018, Kopuchian et al. 2020, Thom et al. 2020) and the closure of the Isthmus of Panama (Weir et al. 2009, Smith and Klicka 2010). Although with a more prominent role in the Northern Hemisphere and the southern extreme of South America, the Pleistocene glacial cycles also played a relevant role as avian diversification drivers throughout the Neotropics (Lessa et al. 2003, Weir and Schluter 2004, Lovette 2005, Campagna et al. 2012, Kopuchian et al. 2016, Acosta et al. 2020, Bukowski et al. 2023). This is clearly the case for highland Andean taxa (Weir 2006, Jetz et al. 2012), but also in the lowlands Pleistocene climatic oscillations have driven speciation by promoting cycles of contraction, fragmentation and expansion of forest ranges, which generated vicariance, divergence and in some cases secondary contact of both forest and dry habitat species (Rull et al. 2011, Trujillo-Arias et al. 2017, 2020, Silva et al. 2019, Bolívar-Leguizamón et al. 2020, Thom et al. 2020).
Another relevant driver of diversification in the Neotropical region, which until recently has been less studied than those mentioned above, is the open vegetation corridor. This dry strip formed by the Caatinga, Cerrado and Chaco biomes isolates the Amazon and Andean forests from the Atlantic Forest, thus affecting the connectivity of three of the most biodiverse rainforests in the world (Orme et al. 2005). Either by vicariance due to the establishment of the open vegetation corridor in the Neogene in a previously continuous forest or as a consequence of dispersion through these dry habitats after its formation, multiple species of birds are disjunctly codistributed in these forests, with varying degrees of differentiation between forests (Lavinia et al. 2015, 2019, Trujillo-Arias et al. 2017, 2018, 2020, Cabanne et al. 2019, Bocalini et al. 2023).
Even though the Andean and Atlantic forests are currently isolated, they have experienced cycles of connection and isolation associated with the geotectonic processes and climatic fluctuations of the Neogene and the Quaternary (Nores 1992, Silva 1994), adding more complexity to this system and its effect on the avifauna of the region (Trujillo-Arias et al. 2017, 2018, 2020, Cabanne et al. 2019, Lavinia et al. 2019). The cyclic connection between these rainforests could have occurred during glacial maxima through the expansions of forests into the Cerrado (Silva 1994), a possibility supported by palynological studies (Ledru 1991, 1993, Oliveira-Filho and Ratter 1995) and avian data (Carnaval and Moritz 2008, Cabanne et al. 2016, 2019, Trujillo-Arias et al. 2017). The contact could have also occurred during interglacial periods through gallery forests in the Chaco region (Olrog 1963, Nores 1992), a hypothesis based mainly on forest bird distribution patterns but without clear evidence (Zurita et al. 2014, Trujillo-Arias et al. 2017). Irrespective of their differences in timing and location, these proposed connections could have acted in combination (Trujillo-Arias et al. 2017, 2018, 2020).
As shown with other geographic barriers or habitat mosaics in the Neotropics (Smith et al. 2014, Naka and Brumfield 2018, van Els et al. 2021), the effect of this dynamic rainforest history also depends on species-specific ecological characteristics and dispersal abilities (Trujillo-Arias et al. 2018, 2020, Lavinia et al. 2019). Several studies have focused on the evolutionary history of species that inhabit exclusively the Amazon forest or the Atlantic Forest, providing insights into the historical diversification processes operating within these regions (e.g. Ribas et al. 2012, Maldonado-Coelho et al. 2013, Cabanne et al. 2016, Silva et al. 2019). Fewer comprehensive evolutionary studies have been performed on species that inhabit both the Atlantic and the Andean or Amazonian forests (Lavinia et al. 2015, 2019, Trujillo-Arias et al. 2017, 2018, 2020, Cabanne et al. 2019, Bolívar-Leguizamón et al. 2020).
The Rufous-capped Antshrike (Thamnophilus ruficapillus ) has three disjunct areas of distribution, one of them in the Atlantic Forest and the other two in the Andean forest (Figure 1a). In the latter, it inhabits humid and semi-humid forests (with different degrees of human alteration) and patches of dense shrubs bordering watercourses in predominantly open areas east of the Andes (Brumfield and Edwards 2007, del Hoyo et al. 2020). In the Atlantic Forest it occurs in low elevation areas of northern Argentina and southern Brazil (Brumfield and Edwards 2007, del Hoyo et al. 2020). T. ruficapillus belongs to the group of suboscine passerines and it is an insectivorous, monogamous and sexually dichromatic species (del Hoyo et al. 2020). Currently, five subspecies are recognized (del Hoyo et al. 2020, Clements et al. 2022):T. r. jaczewskii (in the Andean forest of northern Peru),T. r. marcapatae (in southeastern Peru, particularly Puno and Cusco departments), T. r. subfasciatus (in the Yungas of northwestern Bolivia), T. r. cochabambae (in southern Bolivia to northwestern Argentina) and T. r. ruficapillus (in the Atlantic Forest of southeastern Brazil and northeastern Argentina) (see Figure 1a). Consistent with these designations, previous analyses of mitochondrial DNA have shown intraspecific divergences of around 4% in the cytochrome c oxidase subunit I (COI) gene between T. r. cochabambae in the Andean forest and T. r. ruficapillus in the Atlantic Forest (Kerr et al. 2009).
Here we leverage the distribution of T. ruficapillus to use this species as a model for the study of the effect of the open vegetation corridor and the Andes on the diversification of the Neotropical avifauna. For doing this, we analyzed the evolutionary history of this species using a comprehensive approach that includes both genetic and genomic analyses (mitochondrial and nuclear genomic DNA) as well as phenotypic analyses (study of vocalizations and plumage coloration) to better understand its phylogeographic patterns and the role played by the aforementioned Neotropical diversification drivers.