Molecular Phylogenetics and Evolution 133 (2019) 198–213

Contents lists available at ScienceDirect

Molecular Phylogenetics and Evolution

journal homepage: www.elsevier.com/locate/ympev

Phylogeographic variation within the Buff-browed Foliage-gleaner (Aves: T

Furnariidae: Syndactyla rufosuperciliata) supports an Andean-Atlantic forests
connection via the Cerrado
Gustavo S. Cabannea, , Leonardo Campagnab,c, Natalia Trujillo-Ariasa,d, Kazuya Naokie,
⁎

Isabel Gómezf, Cristina Y. Miyakig, Fabricio R. Santosh, Giselle P.M. Dantasi, Alexandre Aleixoj,
Santiago Claramuntk,l, Amanda Rocham, Renato Caparrozm, Irby J. Lovetteb,c, Pablo L. Tubaroa
a
Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” – CONICET, Av. Ángel Gallardo 470, Buenos Aires C1405DJR, Argentina
b
Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, NY, USA
c
Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
d
Escuela de Biología, Universidad Industrial de Santander, Bucaramanga, Colombia
e
Instituto de Ecología, Universidad Mayor de San Andrés, La Paz, Bolivia
f
Colección Boliviana de Fauna – Museo Nacional de Historia Natural, La Paz, Bolivia
g
Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
h
Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
i
Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, Brazil
j
Museu Paraense Emılio Goeldi, Caixa Postal 399, Belém, PA, Brazil
k
Department of Ornithology, American Museum of Natural History, NY, USA
l
Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
m
Departamento de Genética e Morfologia, Instituto de Ciências Biológicas da Universidade de Brasília, Brazil

ARTICLE INFO ABSTRACT

Keywords: We evaluated whether the Andean and the Atlantic forests acted as refugia during the Quaternary, and tested
Andean tropical forests biogeographic hypotheses about the regions involved in the connectivity between those biomes (through the
Atlantic Forest Chaco or the Cerrado). To achieve these goals we selected the Buff-browed Foliage-gleaner Syndactyla rufosu-
Birds perciliata (Aves, Furnariidae) as a study system, a taxon distributed between the Andean and Atlantic forest. We
Approximate Bayesian Computation
first explored the historical connectivity between regions through niche modeling. We subsequently used DNA
ddRADseq
Population genomics
sequences (n = 71 individuals) and genomic analyses (ddRADseq, n = 33 individuals) to evaluate population
genetic structure and gene flow within this species. Finally, we performed population model selection using
Approximate Bayesian Computation. Our findings indicate that the Andean and the Atlantic forests acted as
refugia, and that the populations of the focal species from both regions contacted through the Cerrado region,
thus suggesting that the historical dynamics of Andean and Atlantic forests are important for the evolution of
forest birds in the region. The results are in agreement with studies of other organisms and may indicate a more
general pattern of connectivity among biomes in the Neotropics. Finally, we recommend recognizing both the
Andean and the Altantic forests lineages of S. rufosuperciliata as independent species.

1. Introduction phenomena with evolutionary consequences occurring across biomes

Pleistocene climate cycles are thought to have driven the diversifi-
cation of Neotropical forest organisms by promoting isolation and di-
vergence of populations in islands of habitat (Forest refugia, e.g.,
Haffer, 1969; Moritz et al., 2000). This hypothesis is derived from case
studies concerning processes taking place within biomes (e.g., Amazon
forest, Haffer and Prance, 2001). However, our understanding of
(e.g., between the Andean and the Atlantic tropical forests), remains
limited (e.g., Batalha-Filho et al., 2013; Prates et al., 2017; Trujillo-
Arias et al., 2017).
The Andean and the Atlantic tropical forests (Fig. 1A) are currently
isolated from each other by xerophytic forests and open-vegetation
regions: the Chaco and the Cerrado biomes. Despite being isolated,
these tropical forests share species and closely related lineages of

⁎
Corresponding author.
E-mail addresses: gscsss10@gmail.com, gscabanne@yahoo.com (G.S. Cabanne).

https://doi.org/10.1016/j.ympev.2019.01.011
Received 4 May 2018; Received in revised form 21 December 2018; Accepted 10 January 2019
Available online 17 January 2019
1055-7903/ © 2019 Elsevier Inc. All rights reserved.
 G.S. Cabanne et al.

199
Fig. 1. Study area for the phylogeographic study of Syndactyla rufosuperciliata and working hypotheses. (A) Study area, working hypotheses on the historical connectivity between the Atlantic and the Andean forests, and
(B) sampling localities for the phylogeographic study. Sampling localities for the sister species S. dimidiata are also shown. Underlined locality IDs indicate samples included in the genomic study. See full ID of localities in
Table A.1.
Molecular Phylogenetics and Evolution 133 (2019) 198–213
G.S. Cabanne et al.
rainforest organisms (Nores, 1992; Olrog, 1963), which suggest that
they have been connected in the past (Chapman, 1926; Trujillo-Arias
et al., 2017). For instance, according to geographic distributions
mapped in Ridgely and Tudor (2009), as well as in Erize et al. (2006),
there are 23 rainforest bird species shared between these tropical for-
ests. The link between the Andean and the Atlantic regions could have
allowed for secondary contacts and gene flow, as well as could have
promoted colonization of new areas. This connection is supported by
palynological studies as well as by niche models of forest biomes and of
the taxa that inhabit them, suggesting that wet forests expanded tran-
siently in some locations (e.g., Cerrado) towards the Andes and during
the glacial maxima of the Pleistocene, a phenomenon that could have
connected these forest domains in the past (e.g., Cabanne et al., 2016;
Ledo and Colli, 2017; Ledru, 1993; Sobral-Souza et al., 2015; Thomé
et al., 2010; Trujillo-Arias, 2017). The tropical Andean and Atlantic
forests, as tropical rainforests, are commonly thought to have con-
tracted during cold and dry phases of the global climate (i.e., glacial
maxima) (Anderson et al., 2007). However, there is a growing body of
evidence indicating that the fate of tropical forests during glacial phases
also depended on local climatic conditions, instead of solely global
climate, and that in some locations tropical forests actually expanded
during glacial maxima; for instance in northeastern Brazil (Cabanne
et al., 2016, 2008) and in the southern Cerrado (Ledo and Colli, 2017;
Ledru, 1993).
Under this historical biogeographic scenario, the Andean and the
Atlantic forests could have acted as refugia, and their dynamic history
(i.e., cycles of connection and isolation) could have been an important
driver of speciation in the Neotropics (Nores, 1992; Trujillo-Arias et al.,
2017). In the present interglacial period, these forested biomes re-
present forest refugia (Interglacial refugia, Bennett and Provan, 2008),
where isolated organisms in either biome are expected to become dif-
ferentiated (e.g., by drift or divergent selection). During other climatic
phases both forests would have been connected, allowing for gene flow
between forest domains. A prediction of this hypothesis states that
species shared by both domains should show their deepest phylogeo-
graphic gap between these forested biomes. Alternatively, if the forest
dynamism allowed for high and constant rates of historical gene flow,
enough to preclude differentiation, the shared species should show si-
milar levels of differentiation between and within regions. Further-
more, under this hypothesis we would expect to find evidence of past
geographic expansions of the forest biomes into the area that currently
separates them, for example through palynological studies or indirectly
using species distribution models (SDM).
Many aspects of the connection between the Andean and Atlantic
forests remain unknown, such as the geographic areas where these
connections took place. One biogeographic hypothesis states that the
contact between these forests occurred in the region occupied in the
present by the Chaco (hereafter termed the “Chaco connection”),
through gallery forests along the main rivers in the region (e.g.,
Bermejo and Pilcomayo Rivers, Fig. 1A) (Nores, 1992; Olrog, 1963;
Smith, 1962). These gallery forests are currently not continuous be-
tween the Andean and the Atlantic regions, but the hypothesis states
that they expanded during interglacial periods, allowing migration of
forest taxa between regions. The Chaco connection hypothesis is mostly
based on present distribution patterns of forest birds along these gallery
forests (i.e., Nores, 1992). However, there is no evidence supporting
extensive expansions of evergreen forest in the Chaco during the
Pleistocene (Trujillo-Arias et al., 2017; Zurita et al., 2014). Silva (1994)
extensively criticized the Chaco connection model, mostly on the base
of geological, palaeoecological and zoogeographical information. Silva
(1996) also documented the occurrence of Atlantic Forest birds in the
gallery forests of the Cerrado, arguing that gallery forests in that region
are more stable than in the Chaco (see also Adamoli et al., 1990).
Following Silva (1994) and Silva (1996), we propose the alternative
hypothesis that the connection between the Andean and the Atlantic
regions occurred through past forest expansions (i.e., gallery and or
200
Molecular Phylogenetics and Evolution 133 (2019) 198–213
semideciduous) in the Cerrado region (hereafter the “Cerrado connec-
tion”) (Trujillo-Arias et al., 2017). As mentioned above, transient forest
expansions in the Cerrado are supported by palynological studies, as
well as by niche models of forest taxa and biomes.
These hypotheses of connectivity between biomes can be tested by
studying SDM and phylogeographic patterns of species present in both
the Andean and the Atlantic forests. SDM can be useful for evaluating
the effect of repetitive phenomena, such as glacial cycles. The five most
recent glacial cycles were similar in duration and intensity (Lisiecki and
Raymo, 2005), thus scenarios modeled for a specific period such as the
Last Glacial Maximum (i.e., 21,000 years ago) could also represent
scenarios that occurred during earlier glacial maxima. These modeled
distributions can help generate hypotheses that can be further tested
with genetic data. Moreover, the populations that occur in-between
both regions could help shed light on the biogeographic history of the
Andean and the Atlantic forests, because different histories of con-
nectivity should result in unique evolutionary relationships among
populations and patterns of relative historical gene flow across regions.
For instance, if wet forest taxa populations that exist in gallery forest in
the Chaco (i.e., along the rivers Pilcomayo and Bermejo, Fig. 1A) are
genetically intermediate (i.e., show admixture) between the Andes and
the Atlantic Forest, a connection through the Chaco would be sup-
ported. To our knowledge there have only been two phylogeographic
studies designed to test the connectivity between the Andes and
Atlantic forests. Through the study of two forest passerines, Trujillo-
Arias et al. (2018, 2017) concluded that the tropical biotas of both
forests interacted cyclically through a main Cerrado corridor, even
though a Chaco corridor could not be excluded.
Here we study the Buff-browed Foliage-gleaner (Syndactyla rufosu-
perciliata; Aves, Furnariidae) to evaluate connectivity between forest
domains. This species is an appropriate model with which to explore
the Andean-Atlantic forests connection because it inhabits both the
main forest domains and the areas that could have been directly in-
volved in bridging them: the gallery forests of the eastern Chaco and
some regions in the southern Cerrado (Fig. 1B). There are five sub-
species in this taxon: the nominal subspecies, oleaginea Sclater, 1884;
cabanisi Taczanowski, 1875; similis Chapman, 1927; acrita Oberholser,
1901 (Fig. 1B) (Remsen, 2003). However, it is unknown if they re-
present independent evolutionary lineages.
The general aim of this study was to evaluate if the Andean and the
Atlantic forests acted as refugia during the Quaternary, as well as to test
hypotheses of historical connections between those regions (Fig. 1A).
We first explored the possible connection routes by means of SDM in the
present and in the past; second, we used DNA sequences and genomic
analyses to evaluate population structure and patterns of gene flow; and
third, we performed population model selection using Approximate
Bayesian Computation (ABC). We aimed to answer the following
questions: (1) Is the main phylogeographic gap of the focal species lo-
cated between the Andean and the Atlantic forests?; (2) What is the
phylogenetic position of samples from the southern Cerrado and from
the Chaco?; and (3) Where and when did the main connection between
these regions occur? In addition, we also investigated whether the
different subspecies in S. rufosuperciliata are independent evolutionary
lineages.
2. Material and methods
A full description of methods is presented in Supplementary
Material.
2.1. Species distribution models
To explore the Andean-Atlantic forests connection we modeled the
distribution of S. rufosuperciliata using MAXENT (Phillips et al., 2006)
and 128 specimen records (MAXENT infile available with
Supplementary Material). We first studied niche divergence between
G.S. Cabanne et al.
both regions (Andes and Atlantic Forest) by performing the PCA-en-
vironmental ordination test (Broennimann et al., 2012) in ecospat (Cola
et al., 2017) for R (R Core Team, 2016). For this test, occurrence re-
cords were organized into the two studied regions (Andes, and Atlantic
plus Cerrado and Chaco). Because niche conservatism was not rejected,
we performed a final model considering all species records. For the
model we used the climate variables available at WordClim 1.4
(Hijmans et al., 2005), where BIO 1, BIO 3, BIO 8, BIO 9, BIO 12, BIO
13, BIO 14 and BIO16 were selected for the final model (Supplementary
Material). We projected the niche model of the present to three past
periods: (1) mid-Holocene (6000 years before present –ybp-), with two
climate models: CCSM4 (Community Climate System Model) and
MIROC-ESM (http://www.worldclim.org/paleo-climate); (2) Last Gla-
cial Maximum (LGM; 21,000 ybp), past climate models: CCSM3 (Com-
munity Climate System Model, available at: http://www.ccsm.ucar.
edu) and MIROC (Model of Interdisciplinary Research on Climate,
available at: http://www.ccsr.utokyo.ac.jp/kyosei/hasumi/MIROC/
tech-repo.pdf); and (3) Last Interglacial (LIG; 120,000 ybp) (Otto-
Bliesner et al., 2006). We obtained a stability model by summing binary
maps of all six models.
2.2. Samples for genetic analyses
We sampled the range of S. rufosuperciliata comprehensively, in-
cluding localities in between the Andean and the Atlantic forests that
are in the hypothesized corridors between regions: locality 23 (Cerrado;
Fig. 1B); and localities 32–34, which are associated to the gallery forests
of the Pilcomayo and Bermejo rivers (Chaco; Fig. 1B). The localities
from the Chaco region are key to this research because they are located
where the Andean and the Atlantic forests are at their closest point.
We studied first a set of DNA sequences obtained by Sanger se-
quencing (hereafter Sanger data-set). We sampled a total of 71 S. ru-
fosuperciliata including all subspecies and 29 localities (Fig. 1B). We
also included nine samples of outgroups, with three individuals of the
sister species of our focal taxon (Planalto Foliage-gleaner, Syndactyla
dimidiata; Derryberry et al., 2011). S. dimidiata inhabits gallery forests
and woodlands of the Cerrado region (Fig. 1A), being clearly differ-
entiated from S. rufosuperciliata by plumage color and song characters
(Ridgely and Tudor, 2009).
We also conducted a study with double-digest restriction site asso-
ciated DNA sequencing (ddRADseq, Peterson et al., 2012) with a sample
of 24 S. rufosuperciliata and 9 S. dimidiata. For this analysis we used
samples from all of the distribution of the focal species, except for
Cerrado and Perú, because these regions were represented by samples
from toed pads, or because they were not available at the time of col-
lecting RADseq data, respectively. Because our preliminary genetic re-
sults suggested introgression between S. rufosuperciliata and S. dimi-
diata, we decided to include various samples of the latter species. See
Table A.1 for information on the samples used in this study.
2.3. Molecular methods: Sanger sequencing data-set
DNA was purified from muscle, blood or toe pads from museum
study skins (Table A.1). We used Sanger sequencing to obtain DNA
sequences of Cytochrome b (CytB, ca. 1009 bp), intron 9 of the Z-linked
Low-Density Lipoprotein Receptor gene (VLDL9R, ca. 440 bp), and in-
tron 11 of Glyceraldehyde-3-Phosphodehydrogenase (G3PDH, ca.
325 bp). See samples, primers and PCR conditions in Supplementary
Material. Sequences generated in this data set are deposited in Genbank
under accession numbers MK410646-MK410882.
2.4. Molecular methods: RADseq data-set
We generated RADseq loci following the approach outlined by
Peterson et al. (2012), and described in detail in Thrasher et al. (2018)
and in Supplementary Material. Briefly, we digested each sample and
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Molecular Phylogenetics and Evolution 133 (2019) 198–213
ligated adapters that allowed for multiplexing. The libraries, each
containing approximately 20 samples, were size-selected and PCR-en-
riched, incorporating the Illumina TruSeq adapters. Finally, all groups
of samples were combined in equimolar proportions and sequenced on
an Illumina HiSeq 2500 lane.
After assessing read quality with FastQC (http://www.
bioinformatics.babraham.ac.uk/projects/fastqc/), we used FASTX-
Toolkit (http://hannonlab.cshl.edu/fastx_toolkit) to trim sequences to
97 bp to discard lower-quality base calls at the 3′ end. Subsequently, we
used FASTX-Toolkit to retain reads without a single base below a Phred
quality score of 10 and with at least 95% of bases with quality above
20. We demultiplexed reads using the ‘process_radtags’ program from
the STACKS 1.41 bioinformatics pipeline (Catchen et al., 2011), dis-
carding reads that did not pass the Illumina chastity filter, had barcode
contamination, lacked an SbfI cut site or one of the unique barcodes
used for multiplexing at the 5′ end.
We obtained an average of 1.05 ± 0.60 million quality-filtered se-
quences per individual. Three S. rufosuperciliata individuals with a low
number of reads were discarded. All reads were 90 bp in length once the
inline barcodes were removed. We assembled reads into RADseq loci
using the de novo pipeline from STACKS. The bioinformatics pipeline
consisted of ‘ustacks/cstacks/sstacks/rxstacks’ and, finally, a second
iteration of ‘cstacks/sstacks’. Parameters were set to a minimum cov-
erage of 20 (m), up to five differences between alleles of the same locus
(M), and five differences among aligned loci of different individuals (n).
This combination of parameters produced a catalogue with 23,021 loci
from which we exported SNPs and calculated summary statistics using
the program ‘populations’ from the STACKS pipeline. We retained loci
that were present in at least 80% of the individuals and exported one
SNP per RADseq locus to avoid including linked loci. These filtering
criteria produced 2386 SNPs for the S. rufosuperciliata and S. dimidiata
comparison. We also re-exported SNPs under the same filtering criteria
but excluding S. dimidiata samples, retaining 2883 SNPs. Data files used
in these analyses are deposited in Mendeley Data (https://doi.org//10.
17632/5353vbczxh.1).
2.5. Phylogeographic analysis: Sanger sequencing data-set
To explore the phylogeographic structure of S. rufosuperciliata we
performed Bayesian Inference (BI) and Maximum Likelihood (ML)
phylogenetic analyses. The concatenated alignment of DNA sequences
for the intraspecific phylogeny resulted of 1776 bp (Cyt B, VLDL9R and
G3PDH), with 68 sequences from S. rufosuperciliata and 8 from out-
groups (Fig. 4). We used ModelTest 3.7 (Posada and Crandall, 1998)
and the likelihood ratio test to select nucleotide substitution models to
be used in the phylogenetic analyses: for CytB, model TNei93+I+G;
for VLDL9R and for G3PDH, HKY+I+G. We used BEAST 1.8
(Drummond et al., 2012) to perform the BI analysis with the following
conditions: (a) unlinked molecular evolution models for each marker,
(b) with I and G optimized by the analysis, and (c) a Yule tree prior,
with constant population size for each gene tree. The analysis con-
sidered heterozygous sites in nuclear markers as polymorphic char-
acters, and not as ambiguous sites (N), and used a burn-in of 10%, of a
total of 50 million generations, sampling every 1000 generations. We
used GARLI 2.0 (Zwickl, 2006) to perform the ML phylogenetic analysis
with a search of a maximum of 5 million generations and 100 search
replicates using stepwise addition. For each marker we used the best fit
model of molecular evolution and allowed parameters to vary; how-
ever, we noted that results did not change when using GTR+G+I
(numratecats = 4) for every marker. Node support was evaluated with
a nonparametric bootstrap (500 replicates), with support values sum-
marized in Treeanotator, a companion program of BEAST.
For the population genetic analyses we studied sequences of CytB,
VLDL9R and G3PDH from 71 S. rufosuperciliata and 3 S. dimidiata. This
data-set included three S. rufosuperciliata from the Cerrado that were
not included in the previous phylogenetic analyses. We tested
G.S. Cabanne et al.
population genetic structure by means of BAPS 6.0 (Corander et al.,
2008) and by an Analysis of Molecular Variance (AMOVA, Excoffier
et al., 1992). BAPS estimated the most likely number of genetic clusters,
where for each marker we surveyed K = 1 to K = 20 by performing a
mixture analysis with and without considering information of the col-
lection locality. We estimated Fst and the proportion of genetic varia-
tion among regions by performing an AMOVA in ARLEQUIN 3.5
(Excoffier and Lischer, 2010), based on pairwise differences.
We defined subpopulations according to the genetic results con-
sidered in concert (Fig. 4); they were named as: P, Peruvian; NB,
northern Bolivia; TB, Tucumano-Boliviano forest; SE; Southeastern
Atlantic Forest; S, Southern Atlantic Forest; CE, Cerrado; and CH,
Chaco. We estimated divergence time (Tdiv), gene flow (M) and ef-
fective population size (Ne) with CytB, VLDL9R and G3PDH and the
isolation with migration method in IMa2 (Hey and Nielsen, 2004). First,
we modeled five subpopulations of S. rufosuperciliata, and dimidiata
(Sdim), assuming the topology: (((NB, TB), P), ((S + CH + CE), SE)),
Sdim). We used this analysis to explore M and Tdiv between Sdim and S.
rufosuperciliata. In a second analysis we excluded Sdim and assumed
(((NB, TB), P), (((S, CH), CE), SE)).
2.6. Phylogeographic data analysis: RADseq data-set
We assigned individuals to genetic clusters with STRUCTURE 2.3.4
(Pritchard et al., 2000). We ran STRUCTURE twice, with and without Sdim.
We selected the most likely value of k using the Evanno et al. (2005)
method implemented in STRUCTURE HARVESTER 0.6.94 (Earl and
vonHoldt, 2012). We also assessed the overall level of differentiation
among species and populations by (1) conducting a principal compo-
nent analysis (PCA) in R with the package SNPRelate 3.3 (Zheng et al.,
2012) and (2) by using haplotype information to calculate a PHI sta-
tistic (PHI-ST) value for each RADseq locus and an average PHI-ST
value per pairwise comparison in STACKS.
We estimated demographic history using the Generalized
Phylogenetic Coalescent Sampler (G-PHOCS 1.2.2) (Gronau et al.,
2011). G-PHOCS co-estimates Tdiv, Ne, and asymmetrical M using a full
coalescent isolation-with-migration model. We inferred the demo-
graphic history of S. rufosuperciliata and S. dimidiata using sequence
data from 2697 RADseq loci (including both variant and invariant loci
as long as they were present in at least 80% of the individuals). First, we
explored a full model with 33 free parameters. Because some migration
parameters within S. rufosuperciliata did not converge in this full model,
we only used this model to estimate Ne and Tdiv. Second, to estimate
gene flow rates, we conducted runs with 10 different simplified models,
which differed from the full model in that they only included bidirec-
tional migration parameters between one pair of populations at a time
(total of 15 free parameters). The number of simplified models was 10
because this is the number of pairwise population comparisons. The
subpopulation tree was: ((NB, TB), (SE, S + CH), Sdim). We converted
the model parameters to units of individuals (Ne) or generations (di-
vergence times) assuming a generation time of one year and a mutation
rate of 10−9 substitutions per site per generation (Kumar and
Subramanian, 2002).
2.7. Testing biogeographic scenarios using ABC
We used Approximate Bayesian Computation (ABC, Beaumont et al.,
2002) to evaluate the fit of the Sanger sequencing data-set to hy-
pothetical population models of the connection between the Andes and
the Atlantic Forest (Fig. 2A). Assessing these scenarios complemented
the previous population genetic analyses to evaluate the working hy-
potheses. Specifically, we applied a historical biogeography approach
based on vicariance and or dispersal to derive population models (See a
full explanation in Fig. S1, as well as in Fig 12.4 of Brown and
Lomolino, 1998), and assumed that certain subpopulations directly
descended from the ancestral population that linked regions (a relic
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Molecular Phylogenetics and Evolution 133 (2019) 198–213
population). We assumed the subpopulations delimited in Fig. 4 as
demographic units for this test, and evaluated the three simplest likely
models directly related to the working hypotheses that only varied
according to topology. Each scenario tested could have been originated
either by vicariance or dispersal events between regions. Tested models
are: (1) a Central Cerrado contact (CCerr), with subpopulations P and
SE considered as sister to all the other subpopulations of their regions;
(2) a Southern Cerrado contact (SCerr), with NB and CE as sister to the
other subpopulations of their regions and; (3) a Chaco contact (Ch),
with TB and CH as sister to the other subpopulations of their regions.
Models with CH and CE as sister to Andean populations were models
rejected a priori, because these topologies were incompatible with the
phylogeographic structure (Fig. 4). Also, we did not include S. dimidiata
in the models because migration with S. rufosuperciliata was very low
and limited to only two subpopulations (see Results).
For coalescent simulations we modeled data of the most variable
Sanger-sequenced loci (CytB and VLDL9R). For each model and marker,
we performed 100,000 simulations in BayeSSC (Anderson et al., 2005).
The model parameters (current observed migration, divergence time
between subpopulations and effective population size of each sub-
population) were estimated in IMa2 and then used as priors for the
simulations (see values in Fig. 4, Table 1 and Table S1). Priors were
entered as uniform intervals, considering a coefficient of variation (CV)
of 10%, defining the maximum and minimum limits of the interval by
adding and subtracting three CVs, respectively. For each historical
event, the sink population was the largest of the pair in the event. For
simplicity, we did not use population growth.
We selected summary statistics from the set estimated by default in
BayeSSC by generating an initial set of 10,000 simulations under each
model, by selecting candidate statistics that differed the most across
models, and by evaluating those subsets of statistics with the cross-
validation test in cv4postpr of the abc package for R (Csilléry et al.,
2012). The final set of 34 summary statistics consisted of, for each
marker: 10 pairwise Fst values and private alleles (Pv) from 7 pairwise
subpopulation comparisons (Table S3). Observed summary statistics
were estimated in ARLEQUIN.
We estimated model posterior probabilities (PP) with the algorithms
rejection and mnlogistic (Beaumont, 2010), in the package abc while
varying the degrees of tolerance (Csilléry et al., 2012). We used two
quality controls. First, a cross validation test with abc’s cv4postpr
function (Csilléry et al., 2012). The objective of this test is to evaluate
whether the model selection procedure is able to distinguish between
the proposed models by using the existing simulations. Briefly, the
summary statistics from one of the simulations are considered as
pseudo-observed summary statistics and classified using all the re-
maining simulations. Then, if the summary statistics contain sufficient
information to discriminate among models, it is expected that a large PP
should be assigned to the model that generated the pseudo-observed
summary statistics (Csilléry et al., 2012). We performed four cross-va-
lidations, testing tolerance rates tol = 0.001 and tol = 0.01. Second, we
performed an evaluation of stability of the model selection across dif-
ferent tolerance rates. It was important to evaluate the stability of the
results because ABC results might vary across tolerance rates.
3. Results
3.1. Distribution models
The test of niche divergence between the Andean and the Atlantic
forest populations did not reject niche conservatism (D = 0.0147, both
comparisons’ P-values > 0.05), which supported performing a single
model for both regions. The distribution model for S. rufosuperciliata
performed much better than a random model (Average AUC = 0.921,
Fig. 3A and Fig. S2). Modeled distributions for the Holocene matched
the current distribution, while models for the LGM and LIG denoted
expansions of habitat suitability into areas where the Cerrado and
G.S. Cabanne et al.
Chaco occur in the present, as well as further south. The SDM suggested
continuous distribution of S. rufosuperciliata between Andes and the
Atlantic forest during the LGM, and nearly continuous during the LIG.
The suitable area for S. rufosuperciliata during the present was the
smallest among all modeled periods (Fig. 3A). During the LGM, the
suitable area was 2–2.67 times larger than during the present, de-
pending on the LGM climate model used for comparison. During the
LIG, the suitable area was 1.67 times larger than during the present.
The stability map indicated high historical habitat suitability in the
Chaco, and in some portions of the Cerrado, yet the habitat suitability
was continuous between the Andes and the Atlantic area only where the
Chaco region is located in the present (Fig. 3B).
3.2. Phylogeographic analysis: Sanger sequencing data-set
The phylogenetic analysis recovered S. rufosuperciliata as mono-
phyletic, with maximum BI support, but with low ML support (Fig. 4).
Within S. rufosuperciliata we recovered two main phylogroups: an Andean
clade formed by samples from Perú, Bolivia and northwestern Argentina
(subspecies similis, oleaginea and cabanisi); and an Atlantic clade, formed
by samples from the Atlantic Forest, as well as from gallery forests in the
humid Chaco and from some isolated forest in southern Cerrado (rufosu-
perciliata and acrita). None of the recognized subspecies were mono-
phyletic. However, acrita (paraphyletic) and rufosuperciliata (polyphyletic)
were close to being monophyletic (sample LGEMA1364 assigned to sub-
species rufosuperciliata grouped together with samples assigned to acrita,
Fig. 4). Because this sample was collected in the geographic transition
between acrita and rufosuperciliata (Fig. 1B), this result denoted a contact
region between the clades associated to each subspecies. The samples
collected in the gallery forests of the Chaco (localities 32–34 in Fig. 1B) did
not form a clade sister to all the other Atlantic samples, therefore the idea
of them being part of a relictual population that was isolated after the
contact between the Atlantic Forest and the Andes is not supported. The
same is true for the Cerrado samples (locality 23, Fig. 1B).
Results of BAPS with both VLDL9R and G3PDH markers supported a
single population (results not shown), while results with CytB indicated
two and four populations, depending on whether the geographic location
of the samples was considered or not in the analysis, respectively (Fig. 4).
The BAPS assignment of samples into two clusters using CytB grouped all
Peruvian samples with the Atlantic Forest cluster, suggesting a biogeo-
graphic link through northern regions. To further evaluate population
structure and to define a population model to estimate divergence time
and gene flow between regions, as well as to test among demographic
scenarios with ABC, we grouped the samples into seven subpopulations
(inset map of Fig. 4). This set of seven subpopulations respected the
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Molecular Phylogenetics and Evolution 133 (2019) 198–213
Fig. 2. Demographic models involving subpopula-
tions of Syndactyla rufosuperciliata tested by
Approximate Bayesian Computation (ABC) and a
Sanger data-set. (A) Models are defined according to
relationships among subpopulations, and according
to the following parameters with fixed values across
models: M (gene flow, values in Table S1), Tdiv
(time of demographic events, Fig. 4), and Ne (po-
pulation effective size, Table 1). Time of demo-
graphic events (in millions of years before present
–MY-) have been taken from a uniform distribution.
The inset represents the distribution of subpopula-
tions (See details in Fig. 4). (B) Variation of posterior
probability (PP) of the ABC model selection across
tolerance levels (tol) and model selection criteria
(logistic and rejection). See details in Table 2.
phylogeographic structure, with the exception of splitting the subclade of
Southern Atlantic Forest into three geographic units (CE, CH and S). An
AMOVA, with subpopulations grouped into two regions (Andean and
Atlantic regions), indicated strong genetic structure between regions for
CytB (variation between regions –Va– = 47.7%) and VLDL9R
(Va = 42.16%), and no structure for G3PDH (Va = −3.4%, interpreted as
Va = 0). Fst values were significant for all markers (Fst-CytB = 0.75, Fst-
VLDL9R = 0.49, and Fst-G3PDH = 0.065; all with P < 0.01).
According to the IMa2 analysis, the divergence between Andean and
Atlantic forest lineages occurred in the Pleistocene (Fig. 4). IMa2 also
indicated high gene flow within regions, with the exception of gene flow
between Southeastern and all Southern Atlantic Forest subpopulations (S,
CE and CH) (Fig. 5A, Table S1). Also, IMa2 indicated a high rate of his-
torical gene flow between the northernmost population in the Atlantic
Forest (SE) and Northern Bolivia (NB), as well as low gene flow between
the Chaco (CH) and NB subpopulations. Gene flow between the south-
ernmost subpopulations of the Atlantic Forest (S and CH) and of the Andes
(TB) was zero. Results of IMa2 also suggested that the Atlantic region has
larger effective population size than the Andean region (Table 1). For
instance, the highest theta in the Atlantic lineage was 10.12 (subpopula-
tion SE), while the highest theta in the Andes was 3.57 (subpopulation P).
In a different IMa2 analysis, we explored migration with the sister
species of S. rufosuperciliata (S. dimidiata). The analysis estimated that S.
dimidiata has low gene flow with subpopulations SE and S of S. rufo-
superciliata – i.e., bidirectional migration Sdim-SE: 0.39 inds/gen
(HPD95: 0–1.9 inds/gen), and bidirectional migration Sdim-S:
0.035 inds/gen (HPD95: 0–0.5 inds/gen). All gene flow estimates be-
tween S. dimidiata and the other subpopulations of S. rufosuperciliata
were estimated to be equal to zero (results not shown).
3.3. Phylogeographic analysis: RADseq data-set
Using the full RADseq data-set, STRUCTURE separated samples into
two clusters coinciding with the species level taxonomy of S. rufosu-
perciliata and S. dimidiata, but also revealing admixture in samples from
locations near the geographic contact between these species (Fig. 6A).
The two admixed samples of S. dimidiata are from northern Paraguay
(locality 25, Fig. 1B), in the ecotone between the Cerrado and the
Atlantic Forest biomes, and the most admixed samples of S. rufosu-
perciliata are from the Southeastern Atlantic Forest (SE, localities 22
and 28, Fig. 1B). A suboptimal structuring supported three clusters
(k = 3) that consisted of S. dimidiata, and two clusters in S. rufosu-
perciliata, conformed by the Andean and the Atlantic forest and Chaco
samples. We therefore conducted a second STRUCTURE analysis re-
stricted to S. rufosuperciliata. The analysis supported two clusters,
 G.S. Cabanne et al.

Table 1
Population size parameters of subpopulations of Syndactyla rufosuperciliata and S. dimidiata estimated with a data-set obtained through Sanger sequencing in IMa2, and with a RADseq data-set in G-PHOCS. See Fig. 4 for
definitions of subpopulations of S. rufosuperciliata.
Data-set and sample size S. rufosuperciliata S. dimidiata

Current subpopulations Ancestral† Current

population
P NB TB CE CH S SE AND AF

‡
Sanger (3 loci, ns CytB, 6, 12, 8 4, 7, 8 25, 33, 34 6, 10, 12 7, 10, 14 11, 17, 20 12, 28, 30 – – 3, 5, 6
1741 bp) VLDL9R,
G3PDH
π
Theta (C.I. 3.57 3.47 0.025 (0-?)§ 0.125 0.125 (0–43) 5.625 10.13 (4.525-?)§ n.e.π n.e. 7.325
95%) (0.725–6.775) (0.625–23.88) (0–33) (2.175–13.43) (1.67–38.58)
NeN (C.I. 95%) 0.739 (0.149–1.4) 0.720 0.0512 (0-?)§ 0.026 0.026 (0–8.9) 1.164 (0.45–2.78) 2.096 (0.450-?)§ n.e.π n.e.π 1.516

204
(0.130–4.94) (0–6.8) (0.345–7.982)

RADseq (2697 loci, ni€ n.a.£ 4 6 n.a.£ 9 2 10 11 9

242730 bp)
Theta (C.I. – 0.003 0.001 – 0.004 0.003 0.001 0.009 0.002
95%) (0.002–0.003) (0.000–0.001) (0.003–0.005) (0.002–0.004) (0.001–0.002) (0.008–0.010) (0.002–0.003)
NeN (C.I. 95%) – 0.675 (0.575–0.8) 0.25 (0.2–0.295) – 1.05 0.8 (0.648–0.992) 0.32 (0.25–0.375) 2.31 (1.95–2.5) 0.554
(0.912–1.207) (0.514–0.594)

†
Ancestral populations of the model: AND, Andean population; AF, Atlantic Forest population. See Material and Methods for further details.
‡
Samples size in number of sequences (ns) of each marker of the Sanger data-set separated by commas and in the following order: CytB, VLDL9R and G3PDH.
§
Maximum value of the interval not presented because the likelihood distribution was flat at the end.
π
Not estimated by the model (n.e.).
€
Sample size in number of individuals (ni) studied in subpopulation.
N
Estimated population size in millions of diploid individuals.
£
Samples were not available (n.a.) to collect RADseq loci for this subpopulation.
Molecular Phylogenetics and Evolution 133 (2019) 198–213
G.S. Cabanne et al.
Fig. 3. Present and past distribution models of Syndactyla rufosuperciliata. (A)
Binary models for Present, Holocene (6000 years before present –ybp-), Last
Glacial Maximum (LGM, 21,000 ybp) and Last Inter-Glacial period (LIG,
130,000 ybp). For each period we report the size of the suitable range as the
total amount of pixels (px) of the model; (B) Stability model. Map of habitat
suitability across the six models.
corresponding to the regions Andes and to the Atlantic Forest and
Chaco (Fig. 6B). There were low levels of admixture between regions,
mainly in NB and the SE and S subpopulations. A principal component
analysis was consistent with the results of STRUCTURE (Fig. 6C). The
first two principal components (together explaining 26% of variation)
separated both species, as well as Andean and Atlantic forests popula-
tions of S. rufosuperciliata.
The average PHI-ST pairwise differentiation between subpopulations of S.
rufosuperciliata was 0.2, with the lowest value corresponding to the com-
parison between subpopulations SE and S (PHI-ST = 0.07), and the highest
value to the comparison between subpopulations SE and TB (PHI-ST = 0.36)
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Molecular Phylogenetics and Evolution 133 (2019) 198–213
(Fig. 6D). The lowest average PHI-ST observed between an Andean and an
Atlantic population was between (S + Ch) and NB (PHI-ST = 0.19). The
average divergence between subpopulations of S. rufosuperciliata and S. di-
midiata was PHI-ST = 0.32 (min. PHI-ST = 0.27, corresponding to the
comparison with SE; max. PHI-ST = 0.38, comparison with TB).
Finally, we estimated Ne, M between populations and Tdiv between
regions with G-PHOCS. Present and ancestral Ne values tend to be
higher in the Atlantic Forest, in agreement with the Sanger data-set
(Table 1). The Tdiv between main regions, and with S. dimdiata, oc-
curred in the Pleistocene (Fig. 4). Gene flow estimations in the set of ten
simplified models (summarized in Fig. 5B, and Table S1) conformed to
those from IMa2 qualitatively, but were generally smaller in magnitude
and with narrower confidence intervals. Gene flow values were low,
even within both the Andean and Atlantic regions. Gene flow between
the Andes and the Atlantic regions was detected only through the axis
SE-NB and S-NB, with higher values from East to West. This result,
which agrees with the IMa2 analysis, supports a Cerrado contact. The
G-PHOCS analysis supported the admixture detected by STRUCTURE
between subpopulations SE and S of S. rufosuperciliata and S. dimidiata.
3.4. Selection of biogeographic scenarios with ABC
The ABC analyses tested three demographic scenarios (Fig. 2A). The
observed summary statistics used in these tests are presented in Table S3.
Results of the cross-validation examination indicated that the approach
was able to select the correct model because posterior probability values
(PP) of correctly classified models were always higher than PP of the
misclassified models. Briefly, PPs of correct models varied from 1.05 (lo-
gistic, tol = 0.001, correct model CH) to 6.5 (logistic, tol = 0.01, correct
model CH) times larger than PPs of misclassified models, which is in ac-
cordance with other ABC empirical examples (Bidegaray-Batista et al.,
2016; Csilléry et al., 2012; Singhal and Moritz, 2012).
The final ABC analysis rejected as best fit the model of a Chaco con-
nection, a result that is stable across tolerance rates and model selection
criteria (Table 2, Fig. 2B). The best fit model with the most stringent
tolerance rate (tol = 0.0005) assumed an Andean-Atlantic Forest contact
through central Cerrado (model CCerr). Selection of a Cerrado contact
model was robust across different values of tolerance, but both Cerrado
connection models (CCerr and SCerr) were not resolved with logistic when
less stringent tolerance values were applied (Fig. 2B and Table 2), because
only Bayes factors (BF) > 3 indicate substantial evidence for a specific
model (Kass and Raftery, 1995). However, this last result did not affect the
overall outcome of rejecting a Chaco contact.
4. Discussion
Here we modeled the distribution and studied the population ge-
netic structure of a forest passerine to test whether the tropical Andes
and the Atlantic Forest acted as refugia, and whether these biomes were
once connected through the Cerrado or the Chaco. Our SDM and ge-
netic results suggest that both rainforest acted as refugia, and that the
connection between them could have occurred through the Cerrado
region. The SDM also suggested greater opportunity for a Chaco con-
tact, yet this possibility was not supported by the genetic analyses.
4.1. Biogeography of the Andean – Atlantic forests connection
Our genetic analyses of S. rufosuperciliata supported an Andean-
Atlantic forests connection through the Cerrado region. First, the samples
from Chaco (localities 32–34), which are the Atlantic forest samples geo-
graphically closest to the Andes, and which could have been a relic of the
population that contacted the regions (the local most recent common
ancestor), are neither the most genetically closest to the Andean samples
nor are involved in an unresolved polytomy at the base of the phylogenetic
tree (Figs. 4 and 5). Overall this pattern is not in agreement with the Chaco
connection model. Samples in between regions (CH and CE) were
G.S. Cabanne et al. Molecular Phylogenetics and Evolution 133 (2019) 198–213

Fig. 4. Bayesian intraspecific phylogeny of Syndactyla rufosuperciliata and allies obtained with a Sanger data-set (concatenated CytB, VLDL9R and G3PDH, total
1776 bp). Node support is indicated as BI posterior probability and maximum likelihood bootstrap scores (ML, 500 replicates). Divergence times (Tdiv) obtained in
IMa2 and in G-PHOCS (G) are in millions of years (MY). Sample labels depict tissue number, sampling locality number and subspecies. Samples collected in gallery
forest in Chaco (CH) and Cerrado (CE) are indicated. See Table A.1 for further details on samples and localities. We indicate results of BAPS clustering, with (Loc) and
without (No-Loc) considering the collection location of samples as prior. We also describe the subpopulations used in downstream analyses. Inset map indicate
subpopulations of S. rufosuperciliata used in our remaining genetic analyses.

206
G.S. Cabanne et al.
Fig. 5. Schematic representation of gene flow between subpopulations of
Syndactyla rufosuperciliata, as well as gene flow with the sister species S. dimi-
diata (Sdim). (A) Point estimation (individuals per generation, inds/gen) and
direction of gene flow obtained with IMa2 and three loci. (B) Point estimation
and direction of gene flow, obtained with 10 simplified models in G-PHOCS and
sequence data from 2697 RADseq loci. Only gene flow values equal or above
0.1 inds/gen are indicated. See full gene flow values in Supplementary Material
Tables S1 and S2. Gray areas indicate geographic distribution of the focal
species. Distribution of S. dimidiata is only schematic.
associated with samples from Southern Atlantic Forest, and because of
their phylogenetic position, they do not seem to be directly descended
from the populations that linked the regions. Also, the Peruvian and
northern Bolivian samples, which are geographically closer to certain
patches of Cerrado than to the Chaco region, are involved in the oldest
splits in the Andes, suggesting that the Andean lineage originated in the
northern portion of its geographic range and dispersed toward the Tucu-
mano-Boliviano forests of Bolivia and Argentina (Fig. 4). Furthermore,
BAPS analyses with CytB clustered the northern Andes and Atlantic forest
in a single unit (Fig. 4), in full agreement with the idea of a Cerrado
contact. Second, the population genetic structure and gene flow analyses
support a Cerrado connection because they indicate genetic connectivity
through this region of central Brazil instead of high gene flow through the
Chaco (Figs. 5 and 6). For instance, the inter-biome pairwise PHI-ST
comparisons indicated that the smallest divergence involved samples from
Southeastern Atlantic Forest and northern Bolivia (SE vs NB, Fig. 6D), as
well as from Southern Atlantic Forest plus Chaco and Northern Bolivia
(S + CH vs NB, Fig. 5D), consistent with a link through Cerrado and not
through Chaco. In addition, gene flow across Chaco was very low, while
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Molecular Phylogenetics and Evolution 133 (2019) 198–213
gene flow across routes involving the Cerrado region, and or the transition
between the Chaco and Cerrado, were higher (Fig. 5 and Tables S1 and
S2). Third, the ABC analyses rejected a model representing a Chaco con-
tact and thus supported as best-fit a model with Cerrado as corridor
(Table 2 and Fig. 2). We tested two models for a Cerrado contact, a
southern and a central Cerrado contact. Model selection with the most
stringent tolerance rate favored the scenario of contact through central
Cerrado, which assumes a contact between the northernmost subpopula-
tion of S. rufosuperciliata in the Atlantic Forest and the Peruvian sub-
population. However, when less stringent tolerance rates were applied,
connections through the southern and the central Cerrado regions were
both plausible. Regardless, this result does not invalidate the general
outcome that the Chaco contact model received the lowest posterior
probability.
The magnitude of historical gene flow from the Atlantic Forest to the
Andes was higher than in the opposite direction (Fig. 5, Tables S1 and S2).
We estimated gene flow from IMa2 and G-PHOCS, and the latter is expected
to be more accurate than the former because it’s based on a substantially
higher number of independent markers, and because IMa2 tends to over-
estimate absolute migration when a small number of loci are studied
(Cruickshank and Hahn, 2014; Hey et al., 2015). Therefore, we base our
interpretation of gene flow on the GHPOCS analysis. Differential migration
could be consequences of larger Ne in the Atlantic Forest, current and an-
cestral (Table 1), which implies a larger source population. Also, according
to the SDM, the Atlantic Forest and the gallery forests in the Cerrado and
Chaco have been historically less stable across time than the Andean forests.
In particular, the Atlantic Forest could have expanded toward a static An-
dean forest, during maxima of glaciations (i.e. LGM) through Chaco and
central Cerrado, and during interglacial periods (i.e., LIG) through regions
south of Chaco (Fig. 3B). Demographic expansions that followed sudden
habitat expansions in a specific direction might have contributed to define a
pattern of higher historical gene flow in the direction of the expanding
biome. Two recent studies also showed in two passerines (Trichothraupis
melanops and Arremon flavirostris, Trujillo-Arias et al., 2018, 2017, respec-
tively) a tendency of higher historical migration from the Atlantic Forest to
the Andes, suggesting that this pattern could be common to many of the
organisms shared between the tropical Andean and Atlantic forest (e.g.,
Batara cinerea, Phylloscartes ventralis and Pipraedea melanonota).
Our research is in agreement with other studies supporting a Cerrado
connection, such as palaeopalynological analyses (Ledru, 1993, 1991; Ledru
et al., 2015; Oliveira-Filho and Ratter, 1995), genetic studies of birds and
mammals (Batalha-Filho et al., 2013; Costa, 2003; Trujillo-Arias et al.,
2018, 2017) and by distribution models of animals and plants (Bueno et al.,
2016; Sobral-Souza et al., 2015; Werneck, 2011). These studies suggested
that rainforests expanded into the Cerrado multiple times, supporting a
scenario of recurrent contacts. Trujillo-Arias et al. (2017) found support for
a Cerrado contact in the passerine A. flavirostris, yet did not fully reject low
levels of gene flow through the Chaco. This difference with S. rufosuperci-
liata could be related to ecological differences between the focal species,
perhaps linked to their vagility or habitat preferences.
A connection between the Andean and Atlantic tropical forest biota
through the Cerrado region could have existed from the late Miocene/
early Pliocene through the Bolivian foreland basin. For at least the last
10 million years the shortest path between the Andes and the Brazilian
shield has been the Bolivian Andean foreland basin, around the Chapare
Buttress (Lundberg et al., 1998) (Fig. 1). This geological setting, together
with forest dynamics associated with global glacial cycles during the
Pleistocene, could have set up a scenario of biogeographic contact between
regions (Trujillo-Arias et al., 2017). Even though the paleodistribution
models of S. rufosuperciliata did not support continuous habitat between
the Andes and the Atlantic Forest through the Cerrado for the late Pleis-
tocene, and did support an unbroken forest bridge through Chaco, they
suggest the presence of large forest tracks in central Cerrado and around
the Chapare Buttress during the last glacial maximum (Fig. 3). Although
part of this region is covered today by grasslands and xerophytic forests
(e.g., Chiquitano forest), past climatic shifts could have driven forest
G.S. Cabanne et al. Molecular Phylogenetics and Evolution 133 (2019) 198–213

Fig. 6. Population genetic analyses in STRUCTURE of RADseq loci for (A) Syndactyla rufosuperciliata and S. dimidiata (2386 SNPs), and (B) S. rufosuperciliata alone
(2883 SNPs). The supported number of populations is indicated by k. Arrows indicate admixed individuals. Asterisks indicate individuals with robust estimations of
the ancestry coefficient, where admixture coefficients 95% CI did not overlap 0 or 1 (no admixture). (C) Principal component analysis of the RADseq data-set. (D)
Pairwise comparisons of PHI-ST (RADseq data-set) between subpopulation of S. rufosuperciliata and with S. dimidiata. The axis of PHI-ST = 0 is indicated in red. The
maps in the inset indicate the geographic distribution of both species, and of subpopulations of the focal species. (For interpretation of the references to colour in this
figure legend, the reader is referred to the web version of this article.)

transitions (i.e., from dry to humid physiognomies), a process that might
have allowed wet forest taxa to establish. Some passerines showing a ty-
pical circum-Amazonian distribution (e.g., Platyrhinchus mystaceus) present
an almost continuous distribution at the region of the shortest distance
between the Andes and the Brazilian shield (Remsen, 1991). Even though
the Andean foreland basin has been unstable in terms of river and megafan
dynamics during some periods of the Neogene (Lundberg et al., 1998;
Wilkinson et al., 2006), it has been relatively stable since the mid Pliocene,
after retraction of the Paranaense sea (Lundberg et al., 1998).
The SDM suggested a contact between the Andean and the Atlantic
forests during peaks of glacial periods, and the existence of a continuous
habitat corridor that could have facilitated dispersion through the Chaco
region (Fig. 3). However, this hypothesis was not supported by our genetic
analyses, or by other studies. Specifically, other studies suggest that the
characteristic current dry vegetation of the Chaco has been present in the
region for most of the Pleistocene (Contreras et al., 2015; Zurita et al.,
2014, 2009), and that the course of the rivers in the area (e.g., Pilcomayo
and Bermejo), and their associated gallery forests, have been very unstable
(Adamoli et al., 1990; Ramella and Spichiger, 1989; Sennhauser, 1991;
Wilkinson et al., 2006). These biogeographic aspects of the Chaco could
have precluded gene flow across the region for rainforest species like S.
rufosuperciliata. A disagreement between the history suggested by SDM
and the population genetics could have been observed if some degree of
reproductive isolation between the Andean and Atlantic populations of the
focal species existed at the moment of the potential contact. Also, the
modeled climatic scenarios could not have been representative of sce-
narios when effective connections among population actually happened
(i.e., before the modeled LIG, c.130,000 years ago). This result indicates
that niche models are helpful to propose hypotheses on population evo-
lution, but that only genetic data can indicate the actual evolutionary
history of those populations. Niche models are based on climate suitability,
but factors different than climate would prevent gene flow (i.e., genetic or
geological factors), which could generate a disagreement between popu-
lation history and estimated paleodistributions.
Few studies suggest the existence of short periods of humid and
tropical climates in the Chaco during the Pleistocene (Turchetto-Zolet

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G.S. Cabanne et al. Molecular Phylogenetics and Evolution 133 (2019) 198–213

Table 2
Approximate Bayesian Computation analysis for selecting demographic models of Syndactyla rufosuperciliata. See model details in Fig. 2. Best fit models are indicated
in bold.
Model† Posterior probability PP

tol‡ = 0.05 tol = 0.01 tol = 0.005 tol = 0.001 tol = 0.0005
(n§ = 15000) (n = 3000) (n = 1500) (n = 300) (n = 150)

Rejπ Mnlog€ Rej Mnlog Rej Mnlog Rej Mnlog Rej Mnlog

CCerr 0.725 0.750 0.797 0.575 0.805 0.337 0.800 0.844 0.813 1.00
SCerr 0.184 0.222 0.147 0.413 0.145 0.648 0.163 0.156 0.160 0.000
Ch 0.091 0.027 0.056 0.011 0.050 0.013 0.037 0.000 0.027 0.000

BFΔ 1st vs 2nd 3.93 3.40 5.421 1.40 12.58 1.92 4.89 4.26 16 > 1000
BFΔ 1st vs 3rd 7.98 28.10 14.23 50 16.10 51.16 21.79 > 1000 30.45 > 1000

†
CCerr, Central Cerrado-contact; SCerr, Southern Cerrado-contact; Ch, Chaco-contact.
‡
Tolerance rate.
§
Absolute sample size of the posterior sample after the rejection step (number of simulations retained).
π
Rejection method.
€
Logistic regression method.
Δ
Bayes factor between the first (1st) and the second (2dn), and between the first and the third (3rd) model, according to a ranking of posterior probability. When
BF < 3 we considered both models equally likely.

et al., 2016; Zurita et al., 2014), which might have allowed short per-
iods of wet forest expansions and bouts of gene flow in forest organisms
(Trujillo-Arias et al., 2017). More research on the Pleistocene history of
the Chaco are needed to fully understand the region’s paleoenviron-
ment and the generality of our results.
4.2. Andean and Atlantic forests as interglacial refugia
Our study suggest that the Andean and the Atlantic forests acted as
refugia and therefore that their dynamism was important for the evolution
of forest taxa. Our analyses supported this idea as we found the deepest
phylogeographic break in S. rufosuperciliata between these forest domains,
and because the SDM suggested that these regions were connected in the
past (i.e., during maxima of glaciations, and perhaps during some periods
of interglacial phases). Because the SDM of S. rufosuperciliata indicated
that the smallest range of forest habitat (refugia) occurred in the present –
an interglacial period-, and that the largest habitat range occurred during
the LGM, the Andean and the Atlantic forests conform well with the de-
finition of an interglacial refugia system (Bennett and Provan, 2008).
Other forest taxa with allopatric populations restricted to both the
Andean and Atlantic forests show their deepest phylogeographic gap be-
tween these regions (Faivovich et al., 2005, e.g. Faivovich et al., 2004;
Pavan et al., 2014; Percequillo et al., 2011; Rocha et al., 2014; Trujillo-
Arias et al., 2018, 2017), in agreement with our results. Even though the
number of studied taxa is small, there may be heterogeneity across taxa in
the temporal divergence between the populations restricted to each forest,
which suggests that multiple biogeographic contacts could have occurred
between these regions. For instance, in a group of five songbirds with
comparable ecological features and geographic distribution (S. rufosu-
perciliata, Elaenia obscura, Arremon flavirostris, Trichothraupis melanops and
Pipraeidea melanonota), the divergence between the Andean and the
Atlantic populations varied from about 1.47 MY to 0.15 MY (Lavinia,
2016; Rheindt et al., 2008; Trujillo-Arias et al., 2018, 2017; this study).
A scenario of multiple biogeographic contacts between the Andean
and the Atlantic forests is expected by the cyclical nature of glaciations
(Nores, 1992; Trujillo-Arias et al., 2017). Therefore, species shared
between these regions could have undergone recurrent cycles of isola-
tion, divergence and secondary contacts. These cycles could have pro-
moted diversification of these organisms and or could have allowed
colonization of new regions (Trujillo-Arias et al., 2018). However, be-
cause responses to habitat shifts are species-specific (e.g., Burney and
Brumfield, 2009; Cabanne et al., 2016; Smith et al., 2014), comparative
studies are needed to obtain a full understanding of the evolutionary
role of these biogeographic links between Neotropical forests.
4.3. Introgression and molecular systematics of S. rufosuperciliata
The SNP analysis revealed unexpected admixture between Syndactyla
dimidiata and the Atlantic population of our focal species, which could be
the product of a secondary contact between them. This result could ex-
plain the low phylogenetic support given to some nodes of the phylogeny;
i.e., the basal nodes of S. rufosuperciliata and of the SE subpopulation
(Fig. 4). The observed pattern of admixture could be associated with
shallow divergence at the time of secondary contact between species, and
does not question considering S. rufosuperciliata as an evolutionary in-
dependent unit. First, through coalescent analyses we detected introgres-
sion between species (Fig. 5, Table S2) suggesting the pattern isn’t caused
by ancestral polymorphism; second, the number of admixed individuals is
small (10–20% in each population, Fig. 6A), and the most admixed in-
dividuals were collected in regions of geographic contact between species,
i.e., within the Cerrado-Atlantic Forest ecotone in northern Paraguay,
northern Paraná and in central Minas Gerais, Brazil (localities 22, 25 and
28 in Fig. 1B and Table A.1). This pattern is in agreement with the fact that
secondary contacts are usually associated with ecotones and environ-
mental gradients (Barton and Hewitt, 1985). Third, genetic analyses
clearly distinguished both species as entities (Fig. 6), in agreement with
the clear diagnosis observed in plumage and song characters (Ridgely and
Tudor, 2009). Our results further show that genomic data are revealing
unexpected introgression between unquestioned good bird species, many
of them considered as traditional examples of divergence in full isolation
(e.g., Toews et al., 2015; Zarza et al., 2016).
We suggest to recognize both the Andean and the Atlantic lineages of
Syndactyla rufosuperciliata as full species because they are reciprocally
monophyletic and already recognized as sets of subspecific taxa (Fig. 4).
The Andean lineage has subspecies oleaginea, cabanisi and similis, while the
other lineage has the nominal and acrita (Figs. 1 and 4). Both lineages
could be recognized as full species according to different species concepts.
For instance, according to the phylogenetic concept (Cracraft, 1983), they
are full species because they represent monophyletic populations. Also,
according to the general lineage species concept (de Queiroz, 1998), they
represent independent evolutionary lineages (i.e., genomic gene flow be-
tween them M < 1) with morphological diagnosis. But, according to the
biological species concept they are allopatric and therefore cannot be
tested for reproductive isolation, although historical gene flow rates be-
tween them estimated based on the Sanger dataset are very small
(Fig. 5B). However, recent taxonomic approaches considering advances on
the genetics of speciation, reproductive isolation, directional selection, and
hybridization dynamics, support that distinct and reciprocally mono-
phyletic sister populations of birds exhibit essential reproductive isolation

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G.S. Cabanne et al. Molecular Phylogenetics and Evolution 133 (2019) 198–213

and would not interbreed freely if they were to occur in sympatry (Gill,
2014), which is in further agreement with the split we proposed herein
between Andean and Atlantic Forest populations of the Buff-browed Fo-
liage-gleaner. Therefore, the Andean populations should be referred to as
S. cabanisi (the taxon name with priority, which would also include cur-
rently recognized subspecies oleaginea and similis) (Remsen, 2003), while
the Atlantic Forest populations are all grouped under S. rufosuperciliata
(which also includes subspecies acrita). Our analyses did not support the
subspecies within the Andean and the Atlantic range as independent
evolutionary entities. Even though the phylogeny revealed acrita and ru-
fosuperciliata as nearly reciprocally monophyletic, the genomic analyses
did not suggest clear divergence between them. Preliminary results of a
study of the phenotypic variation in the species indicate that those two
subspecies are part of a morphological cline (Cabanne unpubl.).
5. Conclusions
Our study of a forest passerine supports that the Andean and the
Atlantic forests acted as a refugia system, and therefore that their dy-
namism is important for the evolution of forest biota. We also found
that the Andean and the Atlantic populations of the species contacted
through expansions of forests in the region occupied today by the biome
Cerrado. This result is in agreement with studies with other passerines
in the region and may indicate a more general pattern. Finally, our
results further show that genomic data are revealing unexpected
introgression between unquestioned good species.
Acknowledgments
We thank the staff of the institutions that loaned tissue samples used
in this study: Museo Argentino de Ciencias Naturales Bernardino
Rivadavia (Argentina), Instituto de Biociências da Universidad de São
Paulo (Brazil); Louisiana Museum of Natural History (USA), Field
Museum of Natural History (USA), Biodiversity Institute and Natural
History Museum (Kansas University, USA), Museu Paraense Emílio
Goeldi (Brazil) and Centro de Coleções Taxonômicas of the
Universidade Federal de Minas Gerais (Brazil). We thank the following
institutions for granting collection permits: Administración de Parques
Nacionales (Argentina), Ministerio de Ecología de Misiones, and en-
vironmental authorities of Bolivia and Brazil. This study was funded by:
the Consejo Nacional de Investigaciones Científicas y Tecnológicas (PIP
2011 276, PIP 2015 637, Coop. Int. CNPq-CONICET, as well as Fondo
IBOL Argentina), the Agencia Nacional de Promoción Científica y
Tecnológica from Argentina (Coop. Int. CAPES-MINCyT, PICT 2012
1924 and PICT 2014 2154), and Fundação de Amparo à Pesquisa do
Estado de São Paulo (BIOTA, 2013/50297-0) from Brazil, and by the
American Museum of Natural History through a Chapman Postdoctoral
Fellowship to SC. AA was supported by CNPq research productivity
fellowships (##308927/2016-8).

Appendix A

See Table A.1.

Table A1
Genetic samples used in the present study. Underlined samples correspond to those used in both the Sanger sequencing and the RADseq data-sets.
Locality Sample ID Institution† Species Subspecies Locality Latitude Longitude
Number

1 B32446 LSU Syndactyla similis Quebrada Lanchal, ca. 8 Km ESE Sallique, Cajamarca −5.7056330 −79.271310
rufosuperciliata Department, Perú
2 B43881 LSU S. rufosuperciliata similis-cabanisi? ca. 24 km ENE Florida, San Martín Department, Perú −5.8766300 −76.882600
3 B40154 LSU S. rufosuperciliata cabanisi ca. 86 km SE Juanjui on E bank upper Rio Pauya, Loreto −7.8209440 −76.044971
Department, Perú.
4 B8051 LSU S. rufosuperciliata cabanisi ca. 8 km NW Cushi on trail to Chaglla, Playa Pampa, −10.7913570 −75.359464
Pasco, Perú.
5 FMNH429974 FMNH S. rufosuperciliata cabanisi San Pedro, Paucartambo, Curzco, Perú −13.3219240 −71.588001
FMNH429975 FMNH S. rufosuperciliata cabanisi
6 MACN6327 MACN S. rufosuperciliata cabanisi Chulumani, Sud Yungas, La Paz, Bolivia, 2179 msnm −16.3959160 −67.558816
MACN6328 MACN S. rufosuperciliata cabanisi
MACN6369 MACN S. rufosuperciliata cabanisi
MACN7237 MACN S. rufosuperciliata cabanisi
7 B38228 LSU S. rufosuperciliata oleaginea La Pajcha, ca 28 km S Samaipata, Santa Cruz −18.4013110 −63.835477
Department, Bolivia.
8 MACN6256 MACN S. rufosuperciliata oleaginea Pedernal Provincia Tomina, Dpto. Chuquisaca, Bolivia, −19.3621100 −64.119840
1470 msnm
MACN6272 MACN S. rufosuperciliata oleaginea
MACN6278 MACN S. rufosuperciliata oleaginea
MACN6301 MACN S. rufosuperciliata oleaginea
9 MACN1116 MACN S. rufosuperciliata oleaginea 2 KM E de Ocloya, Jujuy, Argentina, 1550 msnm −23.9381800 −65.217790
MACN1135 MACN S. rufosuperciliata oleaginea
MACN894 MACN S. rufosuperciliata oleaginea
10 MACN5721 MACN S. rufosuperciliata oleaginea Parque Nacional Calilegua, La Toma, near Mesada de las −23.6979320 −64.869690
Colmenas, Jujuy, 1400 msnm
MACN5722 MACN S. rufosuperciliata oleaginea
MACN5739 MACN S. rufosuperciliata oleaginea
MACN5741 MACN S. rufosuperciliata oleaginea
MACN5647 MACN S. rufosuperciliata oleaginea
MACN5659 MACN S. rufosuperciliata oleaginea
MACN5660 MACN S. rufosuperciliata oleaginea
MACN5679 MACN S. rufosuperciliata oleaginea
MACN5690 MACN S. rufosuperciliata oleaginea
MACN5691 MACN S. rufosuperciliata oleaginea
MACN5692 MACN S. rufosuperciliata oleaginea
MACN5700 MACN S. rufosuperciliata oleaginea
MACN5701 MACN S. rufosuperciliata oleaginea
(continued on next page)

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Table A1 (continued)

Locality Sample ID Institution† Species Subspecies Locality Latitude Longitude

Number

11 MACN761 MACN S. rufosuperciliata oleaginea Sierra Santa Bárbara (East slope), Jujuy, 1975 msnm. −24.1200880 −64.455952
MACN724 MACN S. rufosuperciliata oleaginea
MACN776 MACN S. rufosuperciliata oleaginea
MACN_932 MACN S. rufosuperciliata oleaginea
12 LB3574 LBEM S. dimidiata Brejinho das Ametistas, Caetité, Bahia, Brazil −14.333333 −42.532317
LB3573 LBEM S. dimidiata
13 LB4103 LBEM S. dimidiata Córrego Capetinga, Fazenda Água Limpa, Brasilia, Brazil −15.9475000 −47.938889
14 UFG5099 (UNB17) LabGenBio S. dimidiata Reserva Ecológica do IBGE, Brasilia, Brazil −15.9399320 −47.884539
UFG5106 (UNB10) LabGenBio S. dimidiata
15 LB3670 LBEM S. dimidiata Ribeirão Furnas, Fazenda Monte Carmelo, Minas Gerais, −18.8788890 −47.915000
Indianápolis, Brazil.
LB3671 LBEM S. dimidiata
16 LB2319 LBEM S. dimidiata Turmalina, Minas Gerais, Brazil −17.1600000 −42.860000
17 LB3167 LBEM S. rufosuperciliata rufosuperciliata Alfredo Chaves, Espírito Santo, Brazil −20.5157290 −40.860620
18 LB3654 LBEM S. rufosuperciliata rufosuperciliata Gonçalves, Minas Gerais, Brazil. −22.6656110 −45.859041
LB3655 LBEM S. rufosuperciliata rufosuperciliata
19 LB3718 LBEM S. rufosuperciliata rufosuperciliata Mariana, Caraca, Minas Gerais, Brazil −20.1499550 −43.501292
20 LB3838 LBEM S. rufosuperciliata rufosuperciliata Itabirito, Minas Gerais, Brazil −20.3017020 −43.904329
LB3847 LBEM S. rufosuperciliata rufosuperciliata
LB4273 LBEM S. rufosuperciliata rufosuperciliata
21 LB636 LBEM S. rufosuperciliata rufosuperciliata Araponga, Minas Gerais, Brazil −20.6500000 −42.550000
22 LGEMA10274 LGEMA S. rufosuperciliata rufosuperciliata Mata do Jambreiro, Nova Lima, Minas Gerais, Brazil. −20.0402210 −43.854848
LB739 LBEM S. rufosuperciliata rufosuperciliata
LB945 LBEM S. rufosuperciliata rufosuperciliata
LB719 LBEM S. rufosuperciliata rufosuperciliata
23 MG51834‡ MPEG S. rufosuperciliata acrita Fazenda Harmonia, Bonito, Matto Grosso do Sul, Brazil. −21.2495310 −56.704311
MG51831‡ MPEG S. rufosuperciliata acrita
MG51835‡ MPEG S. rufosuperciliata acrita
MG52459‡ MPEG S. rufosuperciliata acrita
MG51832‡ MPEG S. rufosuperciliata acrita
MG51833‡ MPEG S. rufosuperciliata acrita
MG52460‡ MPEG S. rufosuperciliata acrita
24 FMNH395424 FMNH S. rufosuperciliata rufosuperciliata Boraceia, São Paulo, Brazil. −23.6777580 −45.798289
25 KU150 KU S. dimidiata San Luis National Park, Conceptción, Paraguay. −22.5316030 −57.511071
KU149 KU S. dimidiata
26 LGEMA1149 LGEMA S. rufosuperciliata rufosuperciliata Juquitiba, São Paulo, Brazil. −23.9274530 −47.091296
27 LGEMA11433 LGEMA S. rufosuperciliata acrita? Ortigueira, Paraná, Brazil −24.2045840 −50.91418
28 LGEMA1364 LGEMA S. rufosuperciliata rufosuperciliata? Wencenslau Braz, Paraná, Brazil. −23.9071490 −49.79504
29 LGEMA2155 LGEMA S. rufosuperciliata acrita Rancho Queimado, Santa Catarina, Brazil −27.6899180 −49.003879
LGEMA2156 LGEMA S. rufosuperciliata acrita
LGEMA2168 LGEMA S. rufosuperciliata acrita
LGEMA2172 LGEMA S. rufosuperciliata acrita
30 LGEMA2129 LGEMA S. rufosuperciliata acrita Arroio do Padre, Colonia Cerrito, Pelotas, Brazil. −31.3666600 −52.38333
LGEMA2133 LGEMA S. rufosuperciliata acrita Arroio do Padre, Colonia Cerrito, Pelotas, Brazil. −31.3666600 −52.38333
31 MACN1990 MACN S. rufosuperciliata acrita Parque Urugua-í, María Soledad, Gral. Belgrano, −25.8559880 −53.983427
Argentina, 304 msnm.
MACN2022 MACN S. rufosuperciliata acrita
32 MACN1659 MACN S. rufosuperciliata acrita Estación Biológica Corrientes, San Cayetano, Corrientes, −27.5509500 −58.68441
Argentina
MACN2487 MACN S. rufosuperciliata acrita
33 MACN4491 MACN S. rufosuperciliata acrita Parque Nacional Chaco, Capitán Solari, Chaco, −26.8079670 −59.60878
Argentina, 67 msnm.
MACN4492 MACN S. rufosuperciliata acrita
MACN4530 MACN S. rufosuperciliata acrita
34 MACN4389 MACN S. rufosuperciliata acrita Parque Nacional Mburucuyá, Mburucuyá, Corrientes, −28.0180400 −58.026493
Argentina
35 MACN4996 MACN S. rufosuperciliata acrita Parque Nacional El Palmar, Colón, Entre Ríos, Argentina, −31.8915500 −58.244332
23 msnm.
FMNH321565 FMNH S. ucayale Tono, Cuzco, Perú, 780 m.
B7410 LSU S. roraimae Cerro de la Neblina Base Camp, Amazonas, Venezuela, 140 m.
B6148 LSU S. subalaris W slope Cordillera del Cutucú, Yapitya, on Logroño-Yaupi trail, Morona-Santiago Province,
Ecuador.
B43483 LSU S. subalaris 24 km ENE Florida, San Martín, Perú.
MACN3541 MACN Philydor lichtensteini Parque Nacional Iguazú, Iguazú, Misiones, Argentina.
MACN6866 MACN Philydor atricapillus Parque Nacional Iguazú, Iguazú, Misiones, Argentina.

†
Institutions where samples are housed: LSU, Louisiana Museum of Natural History, Collection of Genetic Resources, Baton Rouge, USA; FMNH, Field Museum of
Natural History, Chicago, USA; MACN, Bird tissue collection of the Museo Argentino de Ciencias Naturales “”Bernardino Rivadavia”, Buenos Aires, Argentina; LBEM,
Centro de Coleções Taxonômicas, Universidade Federal Minas Gerais, Belo Horizonte, Brazil; LGEMA, Laboratório de Genética e Evolução Molecular de Aves,
Universidad de São Paulo, Brazil; MG, Museu Paraense Emilio Goeldi, Belém, Pará, Brazil; KU, Biodiversity Institute and Natural History Museum, Kansas University,
Lawrence, USA. LabGenBio, Departamento de Genética e Morfologia, Instituto de Ciências Biológicas da Universidade de Brasília.
‡
Sample from toe pad.

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Appendix B. Supplementary material
Supplementary data to this article can be found online at https://doi.org/10.1016/j.ympev.2019.01.011.
References
Adamoli, J., Sennhauser, E., Acero, J., Rescia, A., 1990. Stress and disturbance: vegetation
dynamics in the dry Chaco region of Argentina. J. Biogeogr. 17, 491–500.
Anderson, C., Ramakrishnan, U., Chan, Y., Hadly, E., 2005. Serial SimCoal: a population
genetics model for data from multiple populations and points in time. Bioinformatics
21, 1733–1734.
Anderson, D., Goudie, A., Parker, A., 2007. Global Environments through the Quaternary:
Exploring Environmental Change. Oxford Univ. Press, Oxford.
Barton, N.H., Hewitt, G.M., 1985. Analysis of hybrid zones. Annu. Rev. Ecol. Syst. 16,
113–148.
Batalha-Filho, H., Fjeldså, J., Fabre, P., Miyaki, C.Y., 2013. Connections between the
Atlantic and the Amazonian forest avifaunas represent distinct historical events. J.
Ornithol. 154, 41–50. https://doi.org/10.1007/s10336-012-0866-7.
Beaumont, M., 2010. Approximate Bayesian Computation in evolution and ecology.
Annu. Rev. Ecol. Evol. Syst. 41, 379–406.
Beaumont, M., Zhang, W., Balding, D., 2002. Approximate Bayesian computation in po-
pulation genetics. Genetics 162, 2025–2035.
Bennett, K.D., Provan, J., 2008. What do we mean by “refugia”? Quat. Sci. Rev. 27,
2449–2455. https://doi.org/10.1016/j.quascirev.2008.08.019.
Bidegaray-Batista, L., Sánchez-gracia, A., Santulli, G., Maiorano, L., Guisan, A., Vogler,
A.P., Arnedo, M.A., 2016. Imprints of multiple glacial refugia in the Pyrenees re-
vealed by phylogeography and palaeodistribution modelling of an endemic spider.
Mol. Ecol. 25, 2046–2064. https://doi.org/10.1111/mec.13585.
Broennimann, O., Fitzpatrick, M.C., Pearman, P.B., Petitpierre, B., Pellissier, L., Yoccoz,
N.G., Thuiller, W., Fortin, M., Randin, C., Zimmermann, N.E., Graham, C.H., Guisan,
A., 2012. Measuring ecological niche overlap from occurrence and spatial environ-
mental. Glob. Ecol. Biogeogr. 21, 481–497. https://doi.org/10.1111/j.1466-8238.
2011.00698.x.
Brown, J.H., Lomolino, M.V., 1998. Biogeography, second ed. Sinauer Associates,
Sunderland, MA.
Bueno, M.L., Pennington, R.T., Dexter, K.G., Kamino, L.H.Y., Pontara, V., Neves, D.M.,
Ratter, J.A., Oliveira-filho, A.T.D., 2016. Effects of Quaternary climatic fluctuations
on the distribution of Neotropical savanna tree species. Ecography (Cop.) 39, 1–12.
https://doi.org/10.1111/ecog.01860.
Burney, C.W., Brumfield, R.T., 2009. Ecology predicts levels of genetic differentiation in
neotropical birds. Am. Nat. 174, 358–368. https://doi.org/10.1086/603613.
Cabanne, G.S., Calderón, L., Trujillo Arias, N., Flores, P., Pessoa, R., D’Horta, F.M.,
Miyaki, C.Y., 2016. Effects of Pleistocene climate changes on species ranges and
evolutionary processes in the Neotropical Atlantic Forest. Biol. J. Linn. Soc. 119,
856–872. https://doi.org/10.1111/bij.12844.
Cabanne, G.S., d’Horta, F.M., Sari, E.H.R., Santos, F.R., Miyaki, C.Y., 2008. Nuclear and
mitochondrial phylogeography of the Atlantic forest endemic Xiphorhynchus fuscus
(Aves: Dendrocolaptidae): biogeography and systematics implications. Mol.
Phylogenet. Evol. 49, 760–773. https://doi.org/10.1016/j.ympev.2008.09.013.
Catchen, J.M., Amores, A., Hohenlohe, P., Cresko, W., Postlethwait, J.H., 2011. Stacks:
building and genotyping Loci de novo from short-read sequences. G3 Genes Genomes
Genet. 1, 171–182. https://doi.org/10.1534/g3.111.000240.
Chapman, F., 1926. The distribution of bird-life in Ecuador. Bull. Am. Mus. Nat. Hist. 55,
1–784.
Cola, V. Di, Broennimann, O., Petitpierre, B., Breiner, F.T., Amen, M.D., Randin, C.,
Engler, R., Pottier, J., Pio, D., Dubuis, A., Pellissier, L., Mateo, R.G., Hordijk, W.,
Salamin, N., Guisan, A., 2017. ecospat: an R package to support spatial analyses and
modeling of species niches and distributions. Ecography (Cop.) 40, 774–787. https://
doi.org/10.1111/ecog.02671.
Contreras, S., Lutza, L., Zucol, A., 2015. Holocene paleoagrostological impressions from
the Eastern Chaco Region (Argentina). Rev. Palaeobot. Palynol. 223, 37–49.
Corander, J., Sirén, J., Arjas, E., 2008. Bayesian spatial modeling of genetic population
structure. Comput. Stat. 23, 111–129.
Costa, L., 2003. The historical bridge between the Amazon and the Atlantic Forest of
Brazil: a study of molecular phylogeography with small mammals. J. Biogeogr. 30,
71–86. https://doi.org/10.1046/j.1365-2699.2003.00792.x.
Cracraft, J., 1983. Species concepts and speciation analysis. Curr. Ornithol. 1, 159–187.
Cruickshank, T.E., Hahn, M.W., 2014. Reanalysis suggests that genomic islands of spe-
ciation are due to reduced diversity, not reduced gene flow. Mol. Ecol. 23,
3133–3157. https://doi.org/10.1111/mec.12796.
Csilléry, K., François, O., Blum, M.G.B., 2012. Abc: an R package for approximate
Bayesian computation (ABC). Methods Ecol. Evol. 3, 475–479. https://doi.org/10.
1111/j.2041-210X.2011.00179.x.
de Queiroz, K., 1998. The general lineage concept of species, species criteria, and the
process of speciation: a conceptual unification and terminological recommendations.
In: Howard, D., Berlocher, S.H. (Eds.), Endless Forms: Species and Speciation. Oxford
Univ. Press, Oxford, pp. 57–75.
Derryberry, E.P., Claramunt, S., Derryberry, G., Chesser, R.T., Cracraft, J., Aleixo, A.,
Pérez-Emán, J., Remsen, J.V., Brumfield, R.T., 2011. Lineage diversification and
morphological evolution in a large-scale continental radiation: the neotropical
ovenbirds and woodcreepers (aves: furnariidae). Evolution (N.Y.) 65, 2973–2986.
https://doi.org/10.1111/j.1558-5646.2011.01374.x.
212
Molecular Phylogenetics and Evolution 133 (2019) 198–213
Drummond, A.J., Suchard, M.A., Xie, D., Rambaut, A., 2012. Bayesian phylogenetics with
BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969–1973.
Earl, D.A., vonHoldt, B.M., 2012. STRUCTURE HARVESTER: a website and program for
visualizing STRUCTURE output and implementing the Evanno method. Conserv.
Genet. Resour. 4, 359–361. https://doi.org/10.1007/s12686-011-9548-7.
Erize, F., Rodriguez Mata, J.R., Rumboll, M., 2006. Birds of South America. Non-
Passerines: Rheas to Woodpeckers. Princeton University Press, Princeton.
Evanno, G., Regnaut, S., Goudet, J., 2005. Detecting the number of clusters of individuals
using the software STRUCTURE: a simulation study. Mol. Ecol. 14, 2611–2620.
https://doi.org/10.1111/j.1365-294X.2005.02553.x.
Excoffier, L., Lischer, H., 2010. Arlequin suite ver 3.5: a new series of programs to per-
form population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 10,
564–567.
Excoffier, L., Smouse, P.E., Quattro, J.M., 1992. Analysis of molecular variance inferred
from metric distances among DNA haplotypes: application. Genetics 491, 479–491.
Faivovich, J., Garcia, P.C.A., Ananias, F., Lanari, L., Basso, N.G., Wheeler, W.C., 2004. A
molecular perspective on the phylogeny of the Hyla pulchella species group (Anura,
Hylidae). Mol. Phylogenet. Evol. 32, 938–950.
Faivovich, J., Haddad, C.F.B., Garcia, P.C.A., Frost, D.R., Campbell, J.A., Wheeler, W.C.,
2005. Systematic review of the frog family Hylidae, with special reference to Hylinae:
phylogenetic analysis and taxonomic revision. Bull. Am. Mus. Nat. Hist. 294, 1–240.
Gill, F.B., 2014. Species taxonomy of birds: which null hypothesis? Auk 131, 150–161.
https://doi.org/10.1642/AUK-13-206.1.
Gronau, I., Hubisz, M.J., Gulko, B., Danko, C.G., Siepel, A., 2011. Bayesian inference of
ancient human demography from individual genome sequences. Nature Genet. 43,
1031–1034. https://doi.org/10.1038/ng.937.
Haffer, J., 1969. Speciation in amazonian forest birds. Science 165, 131–137.
Haffer, J., Prance, G.T., 2001. Climatic forcing of evolution in Amazonia during the
Cenozoic: on the refuge theory of biotic differentiation. Amazoniana 16, 579–605.
Hey, J., Chung, Y., Sethuraman, A., 2015. On the occurrence of false positives in tests of
migration under an isolation-with-migration model. Mol. Ecol. 24, 5078–5083.
https://doi.org/10.1111/mec.13381.
Hey, J., Nielsen, R., 2004. Multilocus methods for estimating population sizes, migration
rates and divergence time, with applications to the divergence of Drosophila pseu-
doobscura and D. persimilis. Genetics 167, 747–760. https://doi.org/10.1534/
genetics.103.024182.
Hijmans, R.J., Cameron, S.E., Parra, J.L., Jones, P.G., Jarvis, A., 2005. Very high re-
solution interpolated climate surfaces for global land areas. Int. J. Climatol. 15,
1965–1978.
Kass, R., Raftery, A., 1995. Bayes factors. J. Am. Stat. Assoc. 90, 430.
Kumar, S., Subramanian, S., 2002. Mutation rates in mammalian genomes. Proc. Natl.
Acad. Sci. USA 99, 803–808.
Lavinia, P., 2016. Estudio de los patrones de diversificación de la avifauna neotropical a
través del análisis de especies de ambientes selváticos. PhD Thesis. Universidad de
Buenos Aires, Argentina.
Ledo, R.M.D., Colli, G.R., 2017. The historical connections between the Amazon and the
Atlantic Forest revisited. J. Biogeogr. 44, 2551–2563. https://doi.org/10.1111/jbi.
13049.
Ledru, M.P., 1993. Late Quaternary environmental and climatic changes in central Brazil.
Quat. Res. 39, 90–98.
Ledru, M.P., 1991. Etude de la pluie pollinique actuelle des forêts du Brésil Central:
climat, végétation, application à l’étude de l’évolution paléoclimatique des 30 000
dernières années. Quaternaire 2, 111.
Ledru, M.P., Montade, V., Blanchard, G., Hely, C., 2015. Long-term spatial changes in the
distribution of the Brazilian Atlantic Forest. Biotropica 48, 159–169.
Lisiecki, L., Raymo, M., 2005. Pliocene-Pleistocene stack of globally distributed benthic
stable oxygen isotope records. Paleoceanography 20, 1003.
Lundberg, J., Marshall, L., Guerrero, J., Horton, B., Malabarba, M., 1998. The stage for
Neotropical fish diversification: a history of tropical South American rivers. In:
Malabarba, L.R., Reis, R.E., Vari, R.P., Lucena, Z.M.S., Lucena, C.A.S. (Eds.),
Phylogeny and Classification of Neotropical Fishes. Edipucrs, Porto Alegre, pp.
13–48.
Moritz, C., Patton, J.L., Schneider, C.J., Smith, T.B., 2000. Diversification of rainforest
faunas: an integrated molecular approach. Annu. Rev. Ecol. Syst. 31, 533–563.
Nores, M., 1992. Bird speciation in subtropical south America in relation to forest ex-
pansion and retraction. Auk 109, 346–357.
Oliveira-Filho, A., Ratter, J.A., 1995. A study of the origin of central Brazilian Forest by
the analysis of plant species distribution patterns. Edinburgh J. Bot. 52, 141–194.
Olrog, C., 1963. Lista y distribucion de las aves argentinas. Opera Lilloana 9, 1–377.
Otto-Bliesner, B.L., Marshall, S.J., Overpeck, J.T., Miller, G.H., Hu, A., 2006. Simulating
Arctic climate warmth and icefield retreat in the last interglaciation. Science (80-.)
311, 1751–1753.
Pavan, S., Jansa, S., Voss, R., 2014. Molecular phylogeny of short-tailed opossums
(Didelphidae: Monodelphis): taxonomic implications and tests of evolutionary hy-
potheses. Mol. Phylogenet. Evol. 79, 199–214.
Percequillo, A.R., Weksler, M., Costa, L.P., 2011. A new genus and species of rodent from
the Brazilian Atlantic Forest (Rodentia: Cricetidae: Sigmodontinae: Oryzomyini),
with comments on oryzomyine biogeography. Zool. J. Linn. Soc. 161, 357–390.
https://doi.org/10.1111/j.1096-3642.2010.00643.x.
G.S. Cabanne et al.
Peterson, B.K., Weber, J.N., Kay, E.H., Fisher, H.S., Hoekstra, H.E., 2012. Double digest
RADseq: an inexpensive method for de novo SNP discovery and genotyping in model
and non-model species. PLoS ONE 7, e37135. https://doi.org/10.1371/journal.pone.
0037135.
Phillips, S.J., Anderson, R.P., Schapire, R.E., 2006. Maximum entropy modeling of species
geographic distributions. Ecol. Model. 190, 231–259.
Posada, D., Crandall, K.A., 1998. MODELTEST: testing the model of DNA substitution.
Bioinformatics 14, 817–818. https://doi.org/10.1093/bioinformatics/14.9.817.
Prates, I., Melo-Sampaio, P.R., Drummond, L. de O., Teixeira, M., Rodrigues, M.T.,
Carnaval, A.C., 2017. Biogeographic links between southern Atlantic Forest and
western South America: rediscovery, re-description, and phylogenetic relationships of
two rare montane anole lizards from Brazil. Mol. Phylogenet. Evol. 113, 49–58.
https://doi.org/10.1016/J.YMPEV.2017.05.009.
Pritchard, J.K., Stephens, M., Donnelly, P., 2000. Inference of population structure using
multilocus genotype data. Genetics 155, 945–959.
R Core Team, 2016. R: A Language and Environment for Statistical Computing. R
Foundation for Statistical Computing.
Ramella, L., Spichiger, R., 1989. Interpretación preliminar del medio físico y de la
vegetación del Chaco Boreal. Contribución al estudio de la flora y de la vegetación del
Chaco. Candollea 44, 639–680.
Remsen, 1991. Zoogeography and geographic variation of Platyrinchus mystaceus in
Bolivia and Peru, and the circum-Amazonian distribution pattern. Ornitol. Neotrop.
2, 77–83.
Remsen, J.V., 2003. Family Furnariidae. In: In: Hoyo, J. del, Elliot, A., Christie, D.A.
(Eds.), Handbook of the Birds of the Word: Broadbills to Tapaculos, vol. 8. Lynx
Edicions, Barcelona, pp. 162–357.
Rheindt, F., Christidis, L., Norman, J., 2008. Habitat shifts in the evolutionary history of a
Neotropical flycatcher lineage from forest and open landscapes. BMC Evol. Biol. 8,
1193.
Ridgely, R., Tudor, G., 2009. Field Guide to the Songbirds of South America: The
Passerines. Univ. Texas Press, Austin, TX.
Rocha, A., Rivera, L., Martinez, J., Prestes, N., 2014. Biogeography of speciation of two
sister species of neotropical Amazona (Aves, Psittaciformes) based on mitochondrial
sequence data. PLoS ONE 9, e108096.
Sennhauser, E.B., 1991. The concept of stability in connection with the gallery forests of
the Chaco region. Vegetation 94, 1–13.
Silva, J.M.C., 1996. Distribution of Amazonian and Atlantic birds in gallery forests of the
Cerrado region, South America. Ornitol. Neotrop. 7, 1–18.
Silva, J.M.C., 1994. Can avian distribution patterns in Northern Argentina be related to
retraction caused by Quaternary climatic changes? Auk 111, 495–499. https://doi.
org/10.2307/4088618.
Singhal, S., Moritz, C., 2012. Testing hypotheses for genealogical discordance in a rain-
forest lizard. Mol. Ecol. 21, 5059–5072. https://doi.org/10.1111/j.1365-294X.2012.
05747.x.
Smith, B.T., McCormack, J.E., Cuervo, A.M., Hickerson, M.J., Aleixo, A., Cadena, C.D.,
Pérez-Emán, J., Burney, C.W., Xie, X., Harvey, M.G., Faircloth, B.C., Glenn, T.C.,
Derryberry, E.P., Prejean, J., Fields, S., Brumfield, R.T., 2014. The drivers of tropical
speciation. Nature 5050, 406–409. https://doi.org/10.1038/nature13687.
Smith, L.B., 1962. Origins of the flora of Southern Brazil. Contrib. United States Natl.
Herb. 35, 215–249. https://doi.org/10.2307/23493016.
Sobral-Souza, T., Lima-Ribeiro, M.S., Solferini, V.N., 2015. Biogeography of Neotropical
Rainforests: past connections between Amazon and Atlantic Forest detected by eco-
logical niche modeling. Evol. Ecol. 29, 643–655. https://doi.org/10.1007/s10682-
213
Molecular Phylogenetics and Evolution 133 (2019) 198–213
015-9780-9.
Thomé, M.T.C., Zamudio, K.R., Giovanelli, J.G.R., Haddad, C.F.B., Baldissera, F.a.,
Alexandrino, J., 2010. Phylogeography of endemic toads and post-Pliocene persis-
tence of the Brazilian Atlantic Forest. Mol. Phylogenet. Evol. 55, 1018–1031. https://
doi.org/10.1016/j.ympev.2010.02.003.
Thrasher, D.J., Butcher, B.G., Campagna, L., Webster, M.S., Lovette, I.J., 2018. Double-
digest RAD sequencing outperforms microsatellite loci at assigning paternity and
estimating relatedness: a proof of concept in a highly promiscuous bird. Mol. Ecol.
Resour. https://doi.org/10.1111/1755-0998.12771.
Toews, D., Campagna, L., Taylor, S., Balakrishnan, C., 2015. Genomic approaches to
understanding population divergence and speciation in birds. Auk 133, 13–30.
https://doi.org/10.1642/AUK-15-51.1.
Trujillo-Arias, N., 2017. Estudio del contacto histórico entre las Yungas y la Selva
Atlántica: un enfoque filogeográfico, de paleodistribución y sistemática de aves.
Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires.
Trujillo-Arias, N., Calderón, L., Santos, F.R., Miyaki, C.Y., Aleixo, A., Witt, C.C., Tubaro,
P.L., Cabanne, G.S., 2018. Forest corridors between the central Andes and the
southern Atlantic Forest enabled dispersal and peripatric diversification without
niche divergence in a passerine. Mol. Phylogenet. Evol. 128, 221–232. https://doi.
org/10.1016/j.ympev.2018.08.005.
Trujillo-Arias, N., Dantas, G.P.M., Arbeláez-Cortés, E., Naoki, K., Gómez, M.I., Santos,
F.R., Miyaki, C.Y., Aleixo, A., Tubaro, P.L., Cabanne, G.S., 2017. The niche and
phylogeography of a passerine reveal the history of biological diversification between
the Andean and the Atlantic forests. Mol. Phylogenet. Evol. 112, 107–121. https://
doi.org/10.1016/j.ympev.2017.03.025.
Turchetto-Zolet, A.C., Salgueiro, F., Turchetto, C., Cruz, F., Veto, N.M., Barros, M.J.F.,
Segatto, A.L.A., Freitas, L.B., Margis, R., 2016. Phylogeography and ecological niche
modelling in Eugenia uniflora (Myrtaceae) suggest distinct vegetational responses to
climate change between the southern and the northern Atlantic Forest. Bot. J. Linn.
Soc. 182, 670–688. https://doi.org/10.1111/boj.12473.
Werneck, F.P., 2011. The diversification of eastern South American open vegetation
biomes: historical biogeography and perspectives. Quat. Sci. Rev. 30, 1630–1648.
https://doi.org/10.1016/j.quascirev.2011.03.009.
Wilkinson, M., Marshall, L., Lundberg, J., 2006. River behavior on megafans and potential
influences on diversification and distribution of aquatic organisms. J. S. Am. Earth
Sci. 21, 151–172.
Zarza, E., Faircloth, B.C., Tsai, W.L.E., Bryson, R.W., Klicka, J., McCormack, J.E., 2016.
Hidden histories of gene flow in highland birds revealed with genomic markers. Mol.
Ecol. 25, 5144–5157. https://doi.org/10.1111/mec.13813.
Zheng, X., Levine, D., Shen, J., Gogarten, S.M., Laurie, C., Weir, B.S., 2012. A high-per-
formance computing toolset for relatedness and principal component analysis of SNP
data. Bioinformatics 28, 3326–3328. https://doi.org/10.1093/bioinformatics/
bts606.
Zurita, A., Boilini, R., Francia, A., Erra, G., Alcaraz, M., 2014. Paleontología y cronología
del Cuaternario de las provincias de Corrientes y Formosa, Argentina. Acta Geol.
Lilloana 26, 75–86.
Zurita, A., Miño-Boilini, A., Iriondo, M., Alcaraz, M., 2009. Paleontología del Chaco
Oriental. Una nueva localidad con mamíferos fósiles pleistocenos en el río Bermejo
(Formosa, Argentina). Rev. Mex. Ciencias Geol. 26, 277–288.
Zwickl, D.J., 2006. Genetic algorithm approaches for the phylogenetic analysis of large
biological sequence datasets under the maximum likelihood criterion. Ph.D. Diss.
Univ. Texas, Austin. Available from <http://www.zo.utexas.edu/faculty/antisense/
Garli.html>.