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.