Peripheral isolation and demographic stability are reflected in the genetic diversity of the populations of the Helmeted Manakin: a bird endemic to the gallery forests

Abstract

The Cerrado encompasses a complex network of hydrographic basins, which is responsible for the formation and maintenance of the riparian and gallery forests. Alterations in the vegetation resulting from the paleoclimatic changes that occurred during the Pleistocene influenced the current distribution of these humid forests. To understand of the evolutionary dynamics of this landscape on the population structure of the associated organisms, we studied the population genetics of the Antilophia galeata (Pipridae), a bird endemic to the gallery forests of the Cerrado. For this, we evaluated the variability of the mitochondrial control region of 71 A. galeata specimens from 18 localities distributed throughout the Cerrado. The results indicated the existence of significant substructure among the populations located in the peripheral areas of the Cerrado, in comparison with the populations found in the central portion, reflecting historical changes in the environment. We also found high levels of diversity in all the populations, while the analysis of the demographic history revealed a scenario of stability. Overall, then, these findings indicate that the historical modifications of the gallery forest distribution may have been most accentuated in the peripheral zones, with a greater stability and connectivity persisting in the central portion of the biome.

Key words
Antilophia galeata; Cerrado; Late Pleistocene; population structure; paloeclimatic events; South America

INTRODUCTION

The central Brazilian plateau forms the core area of the Cerrado savanna domain and encompasses the headwaters of a number of important South American hydrographic basins (Oliveira et al. 2019). The hydrographic basins located within the Cerrado are associated with a typical vegetation classified as riparian and gallery forests, which are extremely important for the species richness and composition of the biome (Ribeiro & Marinho-Filho 2005). The five principal basins are those of the Araguaia-Tocantins, Paraná, Paraguay, Parnaíba, and São Francisco rivers (Figure 1). These riparian and gallery forests function as an important repository of the domain’s biodiversity (Felfili et al. 2005), acting as “ecological corridors” which interlink and connect the forest elements of the other ecological formations within the region (Aquino et al. 2012). The organisms that inhabit and transit through the Cerrado matrix also depend on these forest environments to feed, reproduce, and nest (Ribeiro et al. 2005).

Figure 1
The five principal hydrographic basins of the Cerrado domain. The geographic distribution of Antilophia galeata (black line) and the sampling points are differentiated by hydrographic basin. The map of each basin shows the distribution of the haplotypes of Hypervariable Domain I of the mitochondrial Control Region. Each haplotype is represented by a distinct color and the numbers indicate the quantity of specimens that had the respective haplotype.

Paleoenvironmental records of the evolution of the Cerrado landscape indicate that the associated vegetation has had a dynamic history (Ledru 2002, Ledru et al. 2006). The occurrence of the forest formations in this domain has been molded by both temporal (over geological and ecological time) and spatial processes (local variation, such as topography, hydrography, and the depth of the water table), in particular, the major climatic pulses of the Quaternary, with long periods of low temperatures (glaciations) alternating with shorter intervals of higher temperatures, that is, the interglacial periods (Salgado-Labouriau 1994, Ribeiro & Walter 1998). The climatic fluctuations that occurred during the Pleistocene were fundamental to the formation of the present-day phytogeographic configuration of the central Brazilian plateau, with the available evidence indicating that the areas currently covered with savanna underwent multiple modifications of their phytophysiognomy and the distribution of different vegetation types (Salgado-Labouriau et al. 1997). However, the changes in climatic conditions that occurred during the Last Glaciation Maximum (LGM) had a more intense effect throughout the tropical region, characterized by a marked decline in both precipitation and temperatures (van der Hammen et al. 1992, Ledru 2002). This cool, dry period, between 20,000 and 18,000 years ago (the Late Pleistocene) resulted in the progressive isolation of humid forests due to the expansion of savannas into areas that are now covered by forest, forming what are known as the Pleistocene refugia (van der Hammen & Hooghiemstra 2000). The available phylogeographic evidence indicates that these processes molded the demographic history and population structure of the species dependent on the forested environments located within the Cerrado, which makes these taxa excellent models for the understanding of the evolutionary processes that formed this environment (Prado et al. 2012, Santos et al. 2014). Studies of plants, reptiles, and birds endemic to the Cerrado indicate that the greatest genetic diversity and the lowest differentiation among populations are found in the central portion of the biome, decreasing toward its edges (Telles et al. 2007, Diniz-Filho et al. 2009, Santos et al. 2014).

One species endemic to the gallery forests of the Cerrado is the helmeted manakin, Antilophia galeata (Lichtenstein 1823), which currently has a Least Concern conservation status (BirdLife International 2018). This bird occurs throughout central Brazil, extending to the west as far as the Pantanal, northeastern Paraguay, and Bolivia (Sick 1997, del Hoyo et al. 2004). Leite (2006) found a clear pattern of geographic variation in the morphometric parameters of A. galeata, which indicates that the populations restricted to the gallery forests of different hydrographic basins are more or less isolated from each other, leading to intraspecific variation in morphology.

The present-day division of the hydrographic basins of the Cerrado indicates that the biota found in its gallery forests may have also suffered certain limitations of connectivity during the final paleoclimatic alterations of the LGM, which would have triggered population subdivisions in species associated with these forests that are still poorly studied or understood. Given its ample distribution in central Brazil, A. galeata is an ideal model for the evaluation of population structure and the distribution of the genetic variability among populations on an ample spatial scale, based on the analysis of a hypervariable mitochondrial region. This analysis elucidated part of the evolutionary history of the species and provided evidence of the probable effects of the most recent climate fluctuations in the region, which has determined so much of the biodiversity of the Neotropics. Based on the analyses, we tested two hypotheses: (i) Events during the Pleistocene (climatic fluctuations) provoked historical shifts in the connectivity of the gallery forests, resulting in the isolation of the A. galeata populations, which is reflected in their genetic differentiation, and (ii) the gallery forests formed refugia for the A. galeata populations on the central Brazilian plateau during the climate shifts of the Pleistocene, establishing systematic differences in the genetic diversity of the populations found in the principal hydrographic basins.

MATERIALS AND METHODS

Sampling

A total of 71 A. galeata specimens were sampled in the present study, collected from 18 localities in the five principal hydrographic basins of the Cerrado biome (of the Araguaia-Tocantins, Paraguay, Paraná, Parnaíba, and São Francisco rivers - Figure 1). Twenty-seven of these samples were obtained in the field between 2015 and 2017 (IBAMA collecting license 48380/2015) at eight points distributed throughout the range of the species in the Cerrado (Supplementary Material - Table SI). These specimens were captured in mist-nets set in gallery forests in the vicinity of river headwaters, with blood samples being collected from each individual and stored in 70% ethanol. The other samples (n=44) represent 10 other Cerrado localities (Table SI) and were obtained on loan from the following institutions: the Federal University of Mato Grosso (n=1), Museum of Natural Science at Louisiana State University (n=9), Zoology Museum of the University of São Paulo (n=14), the National Museum at the University Federal of Rio de Janeiro (n=4), the Goeldi Museum (MPEG) in Belém (n=3), the University of Brasília (n=9), and the Federal University of São Carlos (n=4). The samples (muscle tissue and/or blood) were conserved in 95% ethanol at -20°C.

Laboratory procedures

The genetic material was extracted using the Wizard® Genomic DNA Purification kit (Promega) following the maker’s protocol. The Polymerase Chain Reaction (PCR) was used to amplify Hypervariable Domain I (HDI) of the mitochondrial Control Region, a segment commonly used in studies of population genetics for the evaluation of levels of genetic diversity (Sammler et al. 2012, Jackson et al. 2013, Luna et al. 2017a, Almeida et al. 2019) and the population structure of species (Roukonen & Svist 2002). The Dloop H-739 (Sorenson et al. 1999) and CytB-End (Bensch & Harlid 2000) primers were used to amplify the sequence in a cycle consisting of initial denaturation at 94°C for 5 minutes, followed by 35 cycles of denaturation at 94°C for 40 seconds, hybridization at 57°C for 30 seconds, and extension at 72°C for 2 minutes, with a final extension at 72°C for 5 minutes. The PCR products were purified using Polyethylene Glycol 8000 (PEG, 1g/mL) and sequenced in an ABI 3500XL (Applied Biosystems™) automatic sequencer using the BigDye® Terminator v3.1 CycleSequencing kit (Applied Biosystems™).

Population structure analysis

The sequences were aligned in Clustal-W (Thompson et al. 1994) and edited in BIOEDIT (Hall 1999). As previous studies have shown that the hydrographic basins of the Cerrado may be a factor segregating populations dependent on gallery forest, the fixation index (F_ST) was calculated to determine the level of genetic differentiation among the A. galeata populations occurring in the five principal hydrographic basins of the Brazilian Cerrado (Araguaia-Tocantins, Paraguay, Paraná, Parnaíba, and São Francisco). A priori, the F_ST index with 1,000 permutations and the Analysis of Molecular Variance (AMOVA) were applied to the populations assumed to be confined to these five hydrographic basins. Both these analyses were run in ARLEQUIN 3.5.2.2 (Excoffier & Lischer 2010), which was also used to apply the Mantel test to evaluate the potential existence of isolation by distance among the populations, based on the correlation between geographic and genetic distances.

The genetic structure was also evaluated using a Bayesian analysis of the potential formation of genetic groups, run in BAPS v 6.0 (Bayesian Analysis of Population Structure - Corander et al. 2003, 2008). This analysis applies a search algorithm that calculates the posterior distribution of the parameters of the model established by the observed data, that is, the haplotypes of the DNA sequences. To determine the most probable number of groups (K), the analysis was based on the assumption that genetic mixing was not spatially hierarchical at an individual level. The probable number of genetic groups was included as a parameter to be estimated, and the best partition (number of groups) was considered to be the arrangement with the greatest probability.

Genetic parameters and demography history

The genetic diversity of the populations was calculated in ARLEQUIN 3.5.2.2 (Excoffier & Lischer 2010), and included the indices of holotype (h) and nucleotide (π) diversity, the number of polymorphic sites, and the number of haplotypes, and their frequency and distribution among the five groups delimited a priori. The haplotype network was compiled in Haploviewer (Salzburger et al. 2011) using the Maximum Likelihood algorithm, providing a visual representation of the genealogical relationships among the different haplotypes.

Historical changes in the size of the A. galeata population were evaluated using two approaches. The first approach analyzed the deviations from neutral evolution based on Tajima’s D (Tajima 1989) and Fu’s Fs (Fu 1997), which were applied to determine whether the A. galeata populations are in equilibrium, expansion or have passed through a bottleneck (Rogers & Harpending 1992). These tests were also computed in ARLEQUIN 3.5.2.2. The second approach consisted of the evaluation of historical fluctuations in population size estimated by the Bayesian Skyline Plot (BSP), run in BEAST 1.8 (Drummond & Rambaut 2007). This analysis was run over 200 × 10⁸ generations, with the genealogy being sampled every 10,000 generations, with the first 10% of generations being discarded as burn-in. The molecular clock was calibrated based on the intraspecific mutation rate estimated for the HDI by Norman et al. (2014), that is, 0.0348 substitutions per site per million years in a given lineage. A generation time of one year was assumed for the calculation of the effective number of females (Nef – Luna et al. 2017a). The Bayesian Skyline Plot (BSP) and Effective Sample Size (ESS) were determined in Tracer 1.6 (Rambaut & Drummond 2007). The HKY model was the best model of nucleotide evolution, based on the Bayesian Information Criterion (BIC), which was used to compile the BSP. The best model of nucleotide evolution was identified in MEGA 7 (Tamura et al. 2013).

RESULTS

Population structure

A total of 355 base pairs (bps) of the Hypervariable Domain I (HDI) of the mitochondrial Control Region were sequenced in the 71 A. galeata specimens, with no evidence being found of the presence of indels. A total of 26 polymorphic sites were identified, being used to define 25 haplotypes (Table SII, Figure 2). The GenBank accession numbers of the sequences recorded in the present study are MZ028975 - MZ029045.

Figure 2
Haplotype network based on the Maximum Likelihood analysis of Hypervariable Domain I of the mitochondrial Control Region of Antilophia galeata. The different colors represent each of the five hydrographic basins shown in Figure 1.

The pairwise analysis of the F_ST values indicated that the A. galeata populations of the São Francisco basin are differentiated significantly from the other population groups (Table I). The population of the Paraguay basin was also differentiated from that of the Paraná basin. No evidence was found of any correlation between geographic and genetic distances (Mantel test: r = 0.0320; p = 0.1768), which indicates that the geographic distance does not influence the genetic differentiation found among the study populations. The AMOVA indicated that most (88.9%) of the observed variability exists within the groups that represent each hydrographic basin (Table II).

Table I
Pairwise fixation indices f (F _ST) between the Antilophia galeata populations sampled in the gallery forests of the five hydrographic basins of the Cerrado.

	Araguaia-Tocantins	Paraguai	Paraná	Parnaíba	São Francisco
Araguaia-Tocantins	----------
Paraguai	0,02297	----------
Paraná	0,03090	0,12433*	----------
Parnaíba	-0,02113	-0,01264	0,05902	----------
São Francisco	0,12014*	0,16116*	0,14986*	0,15215*	----------

• *p<0.05.

Table II
Results of the Analysis of Molecular Variance (AMOVA), considering the groups of Antilophia galeata populations present in the gallery forests of the five principal hydrographic basins of the Cerrado domain and the global fixation index (ΦST) values.

	Sum of squares	Components of variability	% of variation
Among groups	6.148	0.12553	10.02
Among populations within groups	2.688	0.01302	1.04
Within groups	73.558	1.11452	88.94
Total	82.394	1.25307
ΦSC=0.11055 (p=0.17009)
ΦST=0.11057 (p=0.00587)
ΦCT=0.10018 (p=0)

The haplotype network reveals that the most common haplotypes are amply distributed in all five hydrographic basins (Table SII, Figure 2). Exclusive haplotypes were identified in each hydrographic basin, although most were rare (Table SII). The BAPS analysis of population structure indicated the presence of three genetic groups (K=3, marginal probability = -328.2651; Supplementary Material - Figure S1) based on the haplotype sequences. This analysis is consistent with the F_ST values, with the geographic substructuring of the individuals revealing differences in the frequencies of the three genetic profiles in the populations of the five hydrographic basins, with the populations of the Paraguay and São Francisco basins presenting a higher level of differentiation in their composition in comparison with the other three populations, which are located more centrally.

Genetic parameters and demography history

High levels of haplotype and nucleotide diversity were found in the populations of the five hydrographic basins, when analyzed separately (Table III), with the population of the São Francisco basin presenting the highest diversity values (h = 0.929; π = 0.14011) and the Araguaia-Tocantins population, the lowest values (h = 0.848; π = 0.08547). High levels of diversity (h = 0.910; π = 0.09054) were also found for the whole A. galeata dataset, without the division by hydrographic basin.

Table III
Summary of genetic diversity and neutrality tests to assess changes in the population size of Antilophia galeata in the Cerrado. The samples were grouped to observe the diversity of populations as a single evolutionary unit and also populations within the gallery forests present in the river basins.

	N	NH	h	π	D	P (D)	Fs	P (Fs)
Araguaia-Tocantins	19	9	0.848	0.08547	-0.79196	0.22800	-3.05710	0.02800
Paraguai	10	7	0.867	0.10341	-1.38129	0.09900	-2.36149	0.04700
Paraná	18	8	0.856	0.05807	-0.44281	0.35300	-3.56113	0.01200
Parnaíba	16	10	0.900	0.08141	-0.44002	0.34800	-5.44778	0
São Francisco	8	6	0.929	0.14011	-0.70580	0.30100	-1.16498	0.18700
All populations	71	25	0.910	0.09054	-1.75786	0.0090	-18.15960	0

• N = number of samples; NH = number of haplotypes; h = haplotype diversity; π = nucleotide diversity; D = Tajima’s D; P(D)= probability of Tajima’s test; Fs = Fu’s Fs; P(Fs)= probability of Fu’s test.

The results of the neutrality tests (D) were not significant, in contrast with those of the Fs test, which presented significant negative values, which may reflect a degree of deviation from neutrality in all the populations of the different hydrographic basins, except for that of the São Francisco basin (Table III). When the tests are applied to the whole A. galeata dataset, without the subdivision by hydrographic basin (Table III), significant negative values were obtained in both cases (D = 1.75788, p < 0.05; Fs = -18.15960, p < 0.05), indicating a population in expansion, rather than in equilibrium.

The demographic history defined by the BSP (Figure 3) indicates a scenario of stability in the A. galeata populations of the five Cerrado hydrographic basins. Evidence of a pattern of growth followed by stability was found when the whole A. galeata dataset was analyzed without considering the basin subdivisions, which is consistent with the results of the previous analyses, presented above.

Figure 3
Bayesian Skyline Plot showing the effective size of the Antilophia galeata populations found in the five hydrographic basins of the Cerrado and the complete population, considering all the datasets combined. The solid line represents the variation in the effective size of the population over time.

DISCUSSION

Historical structure of the Antilophia galeata population

The variation found in certain morphological features among the A. galeata populations indicates that this species may have passed through a period of isolation based on the discontinuities of the gallery forests distributed within the hydrographic basins, which limited gene flow among these populations (Leite 2006). The analysis of the population structure of A. galeata, based on the sequences of the mitochondrial Control Region, indicate a pattern of population sub-structuring related to peripheral sampling. Populations located in the more peripheral portions of the Cerrado, that is, in the gallery forests of the Paraguay and São Francisco basins, have a more distinct genetic makeup in comparison with the populations located toward the center of the biome.

Genetic variation in the A. galeata populations may reflect past events of environmental change occurring in the Cerrado domain (Silva 1995, 1997, Werneck et al. 2012, Ribeiro et al. 2016). The interaction of global factors, such as glaciations, with regional and local elements, including differences in altitude and geomorphological conditions, have contributed to the final response of the species to the climatic modifications in each region (Sano et al. 2019). Simulations of climatic models for the genus Antilophia have revealed the successive expansion and retraction of the gallery forests of the Cerrado during the LGM (Luna et al. 2017b). Under these environmental conditions, it is likely that the gallery forests found in the peripheral portions of the Cerrado domain would have suffered more intense changes in climate which, in turn, provoked a greater degree of differentiation in the genetic profile of the A. galeata populations in these areas, in particular, in the outer limits of the distribution of the species.

The palynological data reveal modifications in the distribution and composition of the Cerrado vegetation during the Late Pleistocene and the Holocene, resulting from paleoclimatic changes (Barberi 2003). These records, together with the geomorphological evidence indicate that a single, large refugium of humid vegetation persisted in the center of the Brazilian Cerrado, in addition to a number of smaller refugia (microrefugia) in the periphery of the domain, located in the southeast, northwest (adjacent to the Amazon biome), and the northeast, in the transition zone with the Caatinga biome during the climatic fluctuations of the Pleistocene, between 20,000 and 13,000 years ago (Ab’Saber 1977, 1983, Bueno et al. 2017). These areas encompass a number of plateaus, such as the central Goiás plateau and the Guimarães plateau, where the surrounding gallery forests may have been little disturbed during the Late Pleistocene, if at all (Ab’Saber 1977, 1983).

The A. galeata populations of the gallery forests of the central portion of the Cerrado have relatively similar genetic profiles (Figure 2), with more shared haplotypes, which indicates a greater degree of connectivity and stability (Figure S1, Table SII). However, the portions of the gallery forest that retracted toward the periphery of the domain would have experienced more accentuated changes in their constitution, exerting pressures on the resident forest-dependent species (Ab’Saber 1977, 1983), which would have supported the differentiation of these populations (Leite 2006). This hypothesis of peripheral isolation is supported by the more differentiated genetic profile of the population of the Paraguay basin, and in particular by the genetic differences between the population of the São Francisco basin, in comparison with the other populations of the central Cerrado (Table I). The vegetation of this region, for example, the Central plateau that separates the São Francisco and Tocantins basins, endured profound alterations, and were at least partially replaced by the xeric vegetation that expanded from the region of the Caatinga, while others, such as the Espinhaço plateau, were invaded by the open vegetation that expanded from the cooler and drier areas of South America (Ab’Saber 1983, Bueno et al. 2017).

The unique environmental features that arose in distinct regions of the Brazilian Cerrado during the LGM may have provided preferencial habitats for forest-dependent species, with landscape structure having a fundamental influence on the community of the gallery forests of the Cerrado (Werneck et al. 2012). These distinct ecoregions are formed by well-preserved plateaus and depressions, which are considered to be separate regions, based on the hierarchical analyses of their biophysical attributes (Sano et al. 2019). These well-preserved areas may have served as refugia for A. galeata populations during specific periods, when these populations may have been more prone to genetic drift, which would have resulted in their differentiation from the populations inhabiting other regions of the Cerrado.

Genetic diversity and demographic history

The results of the present study indicate that, during the Late Pleistocene, the gallery forests of the Cerrado underwent considerable retractions, resulting in the formation of a major central core, with a number of microrefugia formed by fragments of forest in the peripheral areas of the Cerrado. However, these modifications in the configuration of the forest vegetation did not have a drastic impact on the genetic diversity of A. galeata, which remained high in all the populations, even when the diversity is analyzed separately by hydrographic basin (Table III). These significant levels of diversity may be attributed to the persistence of a large and stable population with a long evolutionary history (Grant & Bower 1998), which means that the possible occurrence of discontinuities among the gallery forests did not result in significant changes in the diversity of the A. galeata populations confined to the different hydrographic basins.

Ecological studies have shown that A. galeata is a highly versatile and adaptive species that is capable of reproducing even in small, isolated, and degraded fragments of forest habitat (Marini et al. 2007, Paniago 2016, Marçal & Lopes 2019, Silva et al. 2017, Tolentino et al. 2018). This may explain why the species was able to maintain such a stable population and preserve its genetic diversity, despite the profound shifts in the configuration of the Cerrado forests over time.

The high levels of diversity found in all the A. galeata populations is probably also related to their demographic stability. This hypothesis is supported by the results of the Bayesian Skyline Plot (Figure 3), which indicates that the populations were stable over time. The areas of endemism found within the Cerrado domain are considered to be extremely important for the evolution and maintenance of the fauna of this biome (Werneck 2011). In particular, four principal centers of endemism have been proposed to account for the distribution of the endemic Cerrado birds, resulting from their historical isolation, which has persisted to the present day (Silva 1997, Silva & Bates 2002). Three of these areas are located in the central portion of the Cerrado, on the Central Goiás Plateau, and in the valleys of the Araguaia and Paranã rivers, which are characterized by the presence of gallery forests and enclaves of tropical dry forest (Silva 1997, Silva & Bates 2002).

Two of these important areas of endemism are found in peripheral regions of the Cerrado. One is the Parecis Plateau, in the hydrographic basin of the Paraguay River, while the other is the Espinhaço Plateau, in the São Francisco basin. These areas also represent historically stable tracts of vegetation (King 1956, Braun 1970, Silva 1997, Silva & Bates 2002), which persisted as microrefugia that favored the maintenance of the species’ genetic diversity and played an important role in the diversification of the local fauna (Lima-Rezende et al. 2019). This is supported by the differentiation of these areas from the other regions of the Cerrado domain, due to their unique environmental characteristics, which are appropriate for the establishment and persistence of forest-dependent species (Haddad et al. 1988, Rodrigues 1988). These findings should be used to orientate future studies on the distribution patterns of other groups of organisms in these regions.

The genetic parameters described here for A. galeata indicate that this species, endemic to the gallery forests of the Cerrado domain, is characterized by the isolation of its peripheral populations, demographic stability, and high genetic variability throughout its distribution. These results indicate that the connectivity of the gallery forests was sustained more extensively in the central portion of the Cerrado during the climatic oscillations of the Quaternary, through “corridors” that maintained the genetic diversity and flux of individuals. This pattern further reinforces the findings of previous studies, which indicate that the dynamic interaction between climate and relief played a fundamental role in the diversification and persistence of the biodiversity of the Cerrado (Santos et al. 2014, Lima-Rezende et al. 2019). However, to test this hypothesis against potential alternative demographic scenarios (e.g., stability between micro refugia with subsequent connection by range expansion), further studies using additional genetic markers (e.g., microsatellites; Souza et al. 2019) coupled with an analysis framework based on the coalescent theory that models different historical demographic change (e.g., ABC; Beaumont et al. 2010) will be necessary.

ACKNOWLEDGMENTS

We are grateful to the following institutions for providing samples analyzed in the present study: the bird laboratory at UFMT, the Museum of Natural Science at Louisiana State University, Museu de Zoologia da USP, the Museu Nacional at UFRJ, Museu Paraense Emílio Goeldi, UnB, and UFSC. This study was supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) through Universal project 460195/2014-0, Grants 312404/2019-0 to JA, and 311539/2019-0 to PSR, and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brazil (CAPES process 88881.337398/2019-01 to PSR) and the Universidade Federal do Pará, through the Instituto de Estudos Costeiros and the Associação de Pesquisa e Preservação de Ecossistemas Aquáticos (AQUASIS), together with the Graduate Program in Environmental Biology. LWL was supported by the fellowship of the Coordenação de Aperfeiçoamento Pessoal de Nível Superior (CAPES - 88882.444617/2019-01), through the Doctoral Graduate Program in Zoology, Universidade Federal do Pará (UFPA) and Museu Paraense Emílio Goeldi (MPEG), Belém, Brazil. We thank Stephen Ferrari for the revision of the manuscript.

SUPPLEMENTARY MATERIAL

Tables SI, SII

Figure S1

REFERENCES

• AB’SABER AN. 1977. Os domínios morfoclimáticos na América do Sul. São Paulo, Universidade de São Paulo, Geomorfologia 52: 1-22.
• AB’SABER AN. 1983. O domínio dos cerrados: introdução ao conhecimento. Revista do Serviço Público 111: 41-55.
• ALMEIDA TRA, PRESTL FT, CRUZ VP & WASKO AP. 2019. Genetic analysis of the endangered Hyacinth Macaw (Anodorhynchus hyacinthinus) based on mitochondrial markers: different conservation efforts are required for different populations. J Ornithol 160: 711-720. https://doi.org/10.1007/s10336-019-01652-z.
  » https://doi.org/10.1007/s10336-019-01652-z
• AQUINO FG, ALBUQUERQUE LB, ALONSO AM, LIMA JEFW & SOUSA ES. 2012. Cerrado: Restauração de Matas de Galeria e Ciliares. Brasília, DF: Embrapa.
• BARBERI M. 2003. História Geo-Ecológica do Bioma Cerrado. Estudos 30(9): 2043-2067.
• BEAUMONT MA ET AL. 2010. In defence of model-based inference in phylogeography. Mol Ecol 19: 436-446.
• BENSCH S & HARLID A. 2000. Mitochondrial Genomic Rearrangements in Songbirds. Mol Biol Evol 17: 107-113.
• BIRDLIFE INTERNATIONAL. 2018. Antilophia galeata. The IUCN Red List of Threatened Species. http://dx.doi.org/10.2305/IUCN.UK.2018-2.RLTS.T22701068A130269766.en Downloaded on 13 May 2019.
  » http://dx.doi.org/10.2305/IUCN.UK.2018-2.RLTS.T22701068A130269766.en
• BRAUN OPG. 1970. A Formação Areado e a Formação Serra Negra. Rev Esc 28(3): 100-106.
• BUENO ML, PENNINGTON RT, DEXTER KG, KAMINO LHY, PONTARA V, NEVES DM, RATTER JA & OLIVEIRA-FILHO AT. 2017. Effects of Quaternary climatic fluctuations on the distribution of Neotropical savanna tree species. Ecography 40: 403-414.
• CORANDER J, SIRÉN J & ARJAS E. 2008. Bayesian spatial modeling of genetic population structure. Computation Stat 23: 111-129.
• CORANDER J, WALDMANN P & SILLANPÄÄ MJ. 2003. Bayesian analysis of genetic differentiation between populations. Genetics 163(1): 367-374.
• DEL HOYO J, ELLIOTT A & SARGATAL J. 2004. (Eds). Handbook of the birds of the world, v. 9 (cotingas to pipits and wagtails). Barcelona: Lynx Editions.
• DINIZ-FILHO JAF, NABOUT JC, BINI LM, SOARES TN, TELLES MPC, MARCO P & COLLEVATTI RG. 2009. Niche modelling and landscape genetics of Caryocar brasiliense (“Pequi” tree: Caryocaraceae) in Brazilian Cerrado: An integrative approach for evaluating central-peripheral population patterns. Tree Genet Genomes 5: 617-627.
• DRUMMOND AJ & RAMBAUT A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7(1): 1-8.
• EXCOFFIER L & LISCHER HEL. 2010. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Res 10: 564-567.
• FELFILI JM, SOUSE-SILVA JC & SCARIOT A. 2005. Biodiversidade, ecologia e conservação do Cerrado: avanços no conhecimento. In: SCARIOT A, SOUSA-SILVA JC & FELFILI JM. Cerrado: ecologia, biodiversidade e conservação. Brasília: Ministério do Meio Ambiente, p. 27-44
• FU YX. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915-925.
• GRANT WS & BOWER BW. 1998. Shallow population histories in deep evolutionary lineages of marine fishes: Insights from sardines and anchovies and lessons for conservation. J Hered 89: 415-426.
• HADDAD CFB, ANDRADE GV & CARDOSO AJ. 1988. Anfíbios anuros no Parque Nacional da Serra da Canastra, estado de Minas Gerais. Brasil Florestal 64: 9-20.
• HALL TA. 1999. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41: 95-98.
• JACKSON H, MORGAN BJT & GROOMBRIDGE JJ. 2013. How closely do measures of mitochondrial DNA control region diversity reflect recent trajectories of population decline in birds? Conserv Genet 14: 1291-1296.
• KING LC. 1956. A geomorphological comparison between eastern Brazil and Africa (Central and Southern). Quart J Geol Soc London 112(1-4): 445-474.
• LEDRU MP. 2002. Late Quaternary history and evolution of the Cerrados as revealed by palynological records. In: OLIVEIRA PS & MARQUIS RJ (Eds) The Cerrados of Brazil: Ecology and Natural History of a Neotropical Savanna. New York: Columbia University Press, p. 33-50.
• LEDRU MP, CECCANTINI G, GOUVEIA SEM, LOPEZ-SAEZ JÁ, PESSENDA LCR & RIBEIRO AS. 2006. Millenial-scale climatic and vegetation changes in a northern cerrado (Northeast, Brazil) since the last glacial maximum. Quat Sci Rev 25: 1110-1126.
• LEITE LO. 2006. Análise de Endemismo, Variação Geográfica e Distribuição Potencial das espécies de Aves endêmica do Cerrado. Tese. Universidade de Brasília. (Unpublished).
• LIMA-REZENDE CA, ROCHA AV, JÚNIOR AFC, SOUZA-MARTINS É, VASCONCELOS V & CAPARROZ R. 2019. Late Pleistocene climatic changes promoted demographic expansion and population reconnection of a Neotropical savanna-adapted bird, Neothraupis fasciata (Aves: Thraupidae). PLoS ONE 14(3): e0212876.
• LUNA LW, SOUZA TO, CARNEIRO LS, SILVA WAG, SCHNEIDER H, SAMPAIO I, ARARIPE J & RÊGO PS. 2017b. Molecular data and distribution dynamics indicate a recent and incomplete separation of manakins species of the genus Antilophia (Aves: Pipridae) in response to Holocene climate change. J Avian Biol 48: 1177-1188. https://doi.org/10.1111/jav.01378.
  » https://doi.org/10.1111/jav.01378
• LUNA LW, SOUZA TO, SILVA WAG, SCHNEIDER H, SAMPAIO I, ARARIPE J & RÊGO OS. 2017a. Genetic variation of the endangered Araripe Manakin (Antilophia bokermanni) indicates a history of demographic decline. Rev Bras Ornitol 25(1): 60-66.
• MARÇAL BF & LOPES LE. 2019. Breeding biology of the Helmeted Manakin Antilophia galeata in an ecotone between the Atlantic Forest and the Cerrado. Rev Bras Ornitol 27(1): 1-9.
• MARINI MÂ, AGUILAR TM, ANDRADE RD, LEITE LO, ANCIÃES M, CARVALHO CEA, DUCA C, MALDONADO-COELHO M, SEBAIO F & GONÇALVES J. 2007. Biologia da nidificação de aves do sudeste de Minas Gerais, Brasil. Rev Bras Ornitol 15(3): 367-376.
• NORMAN JA, BLACKMORE CJ, ROURKE M & CHRISTIDIS L. 2014. Effects of Mitochondrial DNA Rate Variation on Reconstruction of Pleistocene Demographic History in a Social Avian Species Pomatostomus superciliosus. PLoS ONE 9(9): e106267.
• OLIVEIRA AS, COUTO JUNIOR AF, VASCONCELOS V, SILVA FAM & MARTINS ES. 2019. Proposta Metodológica de Zoneamento Agrogeológico: Estudo de Caso na Ecorregião do Planalto Central. R Bras Geog Fis 12(1): 160-169.
• PANIAGO LPM. 2016. Aspectos ecológicos de Antilophia galeata (Passeriformes: Pipridae) e seu potencial em biomonitoramento e conservação. Dissertation. Universidade Federal de Uberlândia. (Unpublished).
• PRADO CPA, HADDAD CFB & ZAMUDIO KR. 2012. Cryptic lineages and Pleistocene populations expansion in a Brazilian Cerrado frog. Mol Ecol 21: 921-941.
• RAMBAUT A & DRUMMOND AJ. 2007. Tracer v1.4. http://beast.bio.ed.ac.uk/Tracer (accesse on 12 December 2015).
  » http://beast.bio.ed.ac.uk/Tracer
• RIBEIRO JF, BRIDGEWATER S, RATTER JÁ & SOUSA-SILVA JC. 2005. Ocupação do bioma Cerrado e conservação da sua diversidade vegetal. In: SCARIOT A, SOUSA-FILHO JC & FELFILI JM. Cerrado: ecologia, biodiversidade e conservação. Brasília: Ministério do Meio Ambiente, p. 383-399.
• RIBEIRO JF & WALTER BMT. 1998. Fitofisionomias do bioma Cerrado. In: SANO SM & ALMEIDA SP (Eds). Cerrado: Ambiente e Flora. Brasília: EMBRAPA, p. 91-166.
• RIBEIRO R & MARINHO FILHO J. 2005. Community structure of small mammals (Mammalia, Rodentia) from Estação Ecológica de Águas Emendadas, Planaltina, Distrito Federal, Brasil. Rev Bras Zool 22(4): 898-907.
• RIBEIRO V, WERNECK FP & MACHADO RB. 2016. Distribution dynamics of South American savanna birds in response to Quaternary climate change. Austral Ecol 41: 768-777.
• RODRIGUES MT. 1988. Distribution of lizards of the genus Tropidurus in Brazil (Sauria, Igaunidae). In: HEYER WR & VANZOLINI PE (Ed). Proceedings of a Workshop on Neotropical Distribution Patterns. An Acad Bras Cienc, p. 305-315.
• ROGERS AR & HARPENDING H. 1992. Population growth makes waves in the distribuition of pairwise genetic diferences. Mol Biol Evol 9: 552-569.
• ROUKONEN M & KVIST L. 2002. Structure and evolution of the avian mitochondrial control region. Mol Phylogenet Evol 23: 422-432.
• SALGADO-LABOURIAU ML. 1994. História ecológica da Terra. São Paulo: Editora Blucher.
• SALGADO-LABOURIAU ML, CASSETI V, FERRAZ-VIVENTINI KR, MARTIN L, SOUBIÈS F, SUGUIO K & TURCQ B. 1997. Late Quaternary vegetational and climatic changes in Cerrado and palm swamp from Central Brazil. Palaeogeogr Palaeoclimatol Palaeoecol 128: 215-226.
• SALZBURGER W, EWING GB & VON HEASELER A. 2011. The performance of phylogenetic algorithms in estimating haplotype genealogies with migrations. Mol Ecol 20: 1952-1963.
• SAMMLER S, KETMAIER V, HAVENSTEIN K, KRAUSE U, CURIO E & TIEDMANN R. 2012. Mitochondrial control region I and microsatellite analyses of endangered Philippine hornbill species (Aves; Bucerotidae) detect gene flow between island populations and genetic diversity loss. BMC Evol Biol 12: 203.
• SANO EE, RODRIGUES AA, MARTINS ES, BETTIOL GM, BUSTAMANTE MMC, BEZERRA AS, COUTO JR AF, VASCONCELOS V, SCHULER J & BOLFE EL. 2019. Cerrado ecoregions: A spatial framework to assess and prioritize Brazilian savanna environmental diversity for conservation. J Environ Manage 232: 818-828.
• SANTOS MG, NOGUEIRA C, GIUGLIANO LG & COLLI GR. 2014. Landscape evolution and phylogeography of Micrablepharus atticolus (Squamata, Gymnophthalmidae), an endemic lizard of the Brazilian Cerrado. J Biogeography 41: 1506-1519.
• SICK H. 1997. Ornitologia brasileira. In: PACHECO JF. (Coord). Rio de Janeiro: Nova Fronteira, 912 p.
• SILVA JMC. 1995. Biogeographic analysis of the South American Cerrado avifauna. Steenstrupia 21: 49-67.
• SILVA JMC. 1997. Endemic bird species and conservation in the Cerrado Region, South America. Biol Conserv 6: 435-450.
• SILVA JMC & BATES JM. 2002. Biogeographic patterns and conservation in the South American Cerrado: A tropical savanna hotspot. BioScience 52(3): 225-233.
• SILVA PR, SILVA AM & MELO C. 2017. Male Helmeted Manakins (Antilophia galeata) with More Colorful Crowns Have Better Body Conditions. Wilson J Ornithol 129(1): 158-163.
• SORENSON MD, AST JC, DIMCHEFF DE, YURI T & MINDELL DP. 1999. Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Mol Phylogenet Evol 12(2): 105-114.
• SOUZA TO, LUNA LW, ARARIPE J, MELO MAD, SILVA WAG, SCHNEIDER H, SAMPAIO I & RÊGO PS. 2019. Characterization of the genetic diversity and population structure of the manakin genus Antilophia through the development and analysis of microsatellite markers. J Ornithol 160: 825-830.
• TAJIMA F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
• TAMURA K, STECHER G, PETERSON D, FILIPSKI A & KUMAR S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30: 2725-2729.
• TELLES MPDC, DINIZ-FILHO JAF, BASTOS RP, SOARES TN, GUIMARÃES LDA & LIMA L. 2007. Landscape genetics of Physalaemus cuvieri in Brazilian Cerrado: Correspondence between population structure and patterns of human occupation and habitat loss. Biol Conserv 139: 37-46.
• THOMPSON JD, HIGGINS DG & GIBSON TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
• TOLENTINO VCM, BAESSE CQ & MELO C. 2018. Dominant frequency of songs in tropical bird species is higher in sites with high noise pollution. Environ Pollut 235: 983-992.
• VAN DER HAMMEN T, DUIVENVOORDEN JF, LIPS JM, YRREGO LE & ESPEJO N. 1992. Late Quaternary of the middle Caquetá River area (Colombian Amazonia). J Quaternary Sci 7(1): 45-55.
• VAN DER HAMMEN T & HOOGHIEMSTRA H. 2000. Neogene and quaternary history of vegetation, climate, and plant diversity in Amazonia. Quaternary Sci Rev 19(8): 725 742.
• WERNECK FP. 2011. The diversification of eastern South American open vegetation biomes: Historical biogeography and perspectives. Quaternary Sci Rev 30: 1630-1648.
• WERNECK FP, NOGUEIRA C, COLLI GR, SITES JR JW & COSTA GC. 2012. Climatic stability in the Brazilian Cerrado: implications for biogeographical connections of South American savannas, species richness and conservation in a biodiversity hotspot. J Biogeogr 39: 1695-1706.

Publication Dates

• Publication in this collection
  16 Dec 2022
• Date of issue
  2022

History

• Received
  31 July 2020
• Accepted
  07 June 2021