Evolutionary and Ecological Processes Underlying Geographic Variation in Innate Bird Songs.

AbstractEcological and evolutionary processes underlying spatial variation in signals involved in mate recognition and reproductive isolation are crucial to understanding the causes of population divergence and speciation. Here, to test hypotheses concerning the causes of song divergence, we examine how songs of two sister species of Atlantic Forest suboscine birds with innate songs, the Pyriglena fire-eye antbirds, vary across their ranges. Specifically, we evaluated the influence of isolation by distance and introgressive hybridization, as well as morphological and environmental variation, on geographic variation in male songs. Analyses based on 496 male vocalizations from 63 locations across a 2,200-km latitudinal transect revealed clinal changes in the structure of songs and showed that introgressive hybridization increases both the variability and the homogenization of songs in the contact zone between the two species. We also found that isolation by distance, morphological constraints, the environment, and genetic introgression independently predicted song variation across geographic space. Our study shows the importance of an integrative approach that investigates the roles of distinct ecological and evolutionary processes that influence acoustic signal evolution.

Vicariance, dispersal, extinction and hybridization underlie the evolutionary history of Atlantic forest fire-eye antbirds (Aves: Thamnophilidae).

In order to gain insights into the biogeographic processes underlying biotic diversification in the Atlantic Forest (AF), we used a multi-locus approach to examine the evolutionary history of the White-shouldered Fire-eye (Pyriglena leucoptera) and the Fringe-backed Fire-eye (Pyriglena atra), two parapatric sister species endemic to the AF. We sequenced one mitochondrial, three Z chromosome-linked and three anonymous markers of 556 individuals from 66 localities. We recovered four lineages throughout the AF: P. atra and three populations within P. leucoptera. All populations diverged during the late Pleistocene and presented varying levels of admixture. One Z-linked locus showed the highest level of differentiation between the two species. On the other hand, a mitochondrial haplotype was shared extensively between them. Our data supported vicariance driving speciation along with extinction and dispersal as processes underlying intraspecific diversification. Furthermore, signatures of demographic expansion in most populations and areas of genetic admixture were recovered throughout the AF, suggesting that forest fragmentation was also important in differentiation. Genetic admixture areas are located between large rivers suggesting that AF rivers may diminish gene flow. Our results indicated a complex and dynamic biogeographic history of Pyriglena in the AF, with vicariance, extinction, dispersal and secondary contact followed by introgression likely influencing the current patterns of genetic distribution.

Evolution between forest macrorefugia is linked to discordance between genetic and morphological variation in Neotropical passerines.

The central Andean rainforests and the Atlantic Forest are two similar biomes that are fully isolated by xerophytic and open-vegetation regions (the Chaco and Cerrado, respectively). Even though there is evidence suggesting that these rainforests have been connected in the past, their dynamics of connection, the geographic areas that bridged these regions, and the biological processes that have promoted diversification between them remain to be studied. In this research, we used three passerine species (Poecilotriccus plumbeiceps, Phylloscartes ventralis and Cacicus chrysopterus) as models to address whether the Andean and the Atlantic forests have acted as a refugia system (macrorefugia), and to evaluate biogeographic hypotheses of diversification and connection between them. In order to achieve these goals, we performed traditional phylogeographic analyses and compared alternative biogeographic scenarios by using Approximate Bayesian Computation. Additionally, we performed morphological analyses to evaluate phenotypic divergence between these regions. Our findings support that both rainforest regions acted as refugia, but that the impact of their isolation was stronger on the genetic than on the morphologic characters. Our results provided evidence that both geographic isolation as well as ecological factors have modeled the external traits of forest organisms in the region. Regarding the connection routes between the Andes and the Atlantic Forest, the genetic data rejected the hypothesis of a Chaco connection in the tested species, providing evidence for a connection through the Cerrado or through the transition between the Cerrado and Chaco, in a process that could have started as early as the Late Miocene.

Climatic dynamics and topography control genetic variation in Atlantic Forest montane birds.

Montane organisms responded to Quaternary climate change by tracking suitable habitat along elevational gradients. However, it is unclear whether these past climatic dynamics generated predictable patterns of genetic diversity in co-occurring montane taxa. To test if the genetic variation is associated with historical changes in the elevational distribution of montane habitats, we integrated paleoclimatic data and a model selection approach for testing the demographic history of five co-distributed bird species occurring in the southern Atlantic Forest sky islands. We found that changes in historical population sizes and current genetic diversity are attributable to habitat dynamics among time periods and the current elevational distribution of populations. Taxa with populations restricted to the more climatically dynamic southern mountain block (SMB) had, on average, a six-fold demographic expansion, whereas the populations from the northern mountain block (NMB) remained constant. In the current configuration of the southern Atlantic Forest montane habitats, populations in the SMB have more widespread elevational distributions, occur at lower elevations, and harbor higher levels of genetic diversity than NMB populations. Despite the apparent coupling of demographic and climatic oscillations, our data rejected simultaneous population structuring due to historical habitat fragmentation. Demographic modeling indicated that the species had different modes of differentiation, and varied in the timing of divergence and the degree of gene flow across mountain blocks. Our results suggest that the heterogeneous distribution of genetic variation in birds of the Atlantic Forest sky islands is associated with the interplay between topography and climate of distinct mountains, leading to predictable patterns of genetic diversity.

Isolation and characterization of 15 new microsatellite markers for the globally endangered Lear's macaw Anodorhynchus leari.

A set of 16 microsatellite markers was characterized for Lear's macaw (Anodorhynchus leari) using DNA samples from captive individuals. Extending this molecular toolkit, including the use of samples from wild individuals, is expected to provide the required power of resolution for pedigree inference of both wild and captive individuals, and could support research on the genetic structure of wild populations. We characterize a set of 15 microsatellite markers optimized for the Lear's macaw, developed from a microsatellite-enriched library in a three-step procedure. Primer pairs were initially designed for 62 microsatellites with > 7 tandem repetitions. After amplification of DNA of five wild individuals from different localities, 22 loci seemed to be polymorphic and were further tested on 12 wild nestling samples. Fifteen unlinked loci showed unambiguous peaks and low to moderate polymorphism levels. The combination of the four most polymorphic markers allowed individual identification even of putative sibs.These markers complement previously described microsatellites developed for A. leari and constitute a fundamental genetic toolkit for the investigation of the genetics of both wild and captive populations, thus assisting integrated management plans for the conservation of this globally endangered species.

Diversification history in the Dendrocincla fuliginosa complex (Aves: Dendrocolaptidae): Insights from broad geographic sampling.

Dendrocincla woodcreepers are ant-following birds widespread throughout tropical America. Species in the genus are widely distributed and show little phenotypic variation. Notwithstanding, several subspecies have been described, but the validity of some of these taxa and the boundaries among them have been discussed for decades. Recent genetic evidence based on limited sampling has pointed to the paraphyly of D. fuliginosa, showing that its subspecies constitute a complex that also includes D. anabatina and D. turdina. In this study we sequenced nuclear and mitochondrial markers for over two hundred individuals belonging to the D. fuliginosa complex to recover phylogenetic relationships, describe intraspecific genetic diversity and provide historical biogeographic scenarios of diversification. Our results corroborate the paraphyly of D. fuliginosa, with D. turdina and D. anabatina nested within its recognized subspecies. Recovered genetic lineages roughly match the distributions of described subspecies and congruence among phylogenetic structure, phenotypic diagnosis and distribution limits were used to discuss current systematics and taxonomy within the complex, with special attention to Northern South America. Our data suggest the origin of the complex in western Amazonia, associated with the establishment of upland forests in the area during the early Pliocene. Paleoclimatic cycles and river rearrangements during the Pleistocene could have, at different times, both facilitated dispersal across large Amazonian rivers and the Andes and isolated populations, likely playing an important role in differentiation of extant species. Previously described hybridization in the headwaters of the Tapajós river represents a secondary contact of non-sister lineages that cannot be used to test the role of the river as primary source of diversification. Based on comparisons of D. fuliginosa with closely related understory upland forest taxa, we suggest that differential habitat use could influence diversification processes in a historically changing landscape, and should be considered for proposing general mechanisms of diversification.

Phylogeographic variation within the Buff-browed Foliage-gleaner (Aves: Furnariidae: Syndactyla rufosuperciliata) supports an Andean-Atlantic forests connection via the Cerrado.

We evaluated whether the Andean and the Atlantic forests acted as refugia during the Quaternary, and tested biogeographic hypotheses about the regions involved in the connectivity between those biomes (through the Chaco or the Cerrado). To achieve these goals we selected the Buff-browed Foliage-gleaner Syndactyla rufosuperciliata (Aves, Furnariidae) as a study system, a taxon distributed between the Andean and Atlantic forest. We first explored the historical connectivity between regions through niche modeling. We subsequently used DNA 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.

Phenotypic and Genetic Structure Support Gene Flow Generating Gene Tree Discordances in an Amazonian Floodplain Endemic Species.

Before populations become independent evolutionary lineages, the effects of micro evolutionary processes tend to generate complex scenarios of diversification that may affect phylogenetic reconstruction. Not accounting for gene flow in species tree estimates can directly impact topology, effective population sizes and branch lengths, and the resulting estimation errors are still poorly understood in wild populations. In this study, we used an integrative approach, including sequence capture of ultra-conserved elements (UCEs), mtDNA Sanger sequencing and morphological data to investigate species limits and phylogenetic relationships in face of gene flow in an Amazonian endemic species (Myrmoborus lugubris: Aves). We used commonly implemented species tree and model-based approaches to understand the potential effects of gene flow in phylogenetic reconstructions. The genetic structure observed was congruent with the four recognized subspecies of M. lugubris. Morphological and UCEs data supported the presence of a wide hybrid zone between M. l. femininus from the Madeira river and M. l. lugubris from the Middle and lower Amazon river, which were recovered as sister taxa by species tree methods. When fitting gene flow into simulated demographic models with different topologies, the best-fit model indicated these two taxa as non-sister lineages, a finding that is in agreement with the results of mitochondrial and morphological analyses. Our results demonstrated that failing to account for gene flow when estimating phylogenies at shallow divergence levels can generate topological uncertainty, which can nevertheless be statistically well supported, and that model testing approaches using simulated data can be useful tools to test alternative phylogenetic hypotheses.

Forest corridors between the central Andes and the southern Atlantic Forest enabled dispersal and peripatric diversification without niche divergence in a passerine.

The central Andean rainforests and the Atlantic Forest are separated by the Chaco and the Cerrado domains. Despite this isolation, diverse evidence suggests that these rainforests have been connected in the past. However, little is known about the timing and geographic positions of these connections, as well as their effects on diversification of species. In this study, we used the Black-goggled Tanager (Trichothraupis melanops, Thraupidae) as a model to study whether the Andean and the Atlantic forests have acted as a refugia system, and to evaluate biogeographic hypotheses of diversification and connection between these rainforests. We compared alternative biogeographic scenarios by using Approximate Bayesian Computation (ABC), modeled range shifts across time, and assessed niche divergence between regions. The results indicated that the major phylogeographic gap within T. melanops is located between these rainforests. The ABC analysis supported peripatric diversification, with initial dispersal from the Atlantic Forest to the Andes during the Mid-Pleistocene. Also, the results supported an Andean-Atlantic forests connection through the current Cerrado-Chaco transition, linking the southern Atlantic Forest with the central Andes. Our findings, taken together with other studies, support that the connection between these biomes has been recurrent, and that has occurred mostly through the Cerrado and/or the Cerrado-Chaco transition. The data also support that the connection dynamic has played an important role in the biological diversification, by promoting peripatric divergence in some forest taxa restricted to both biomes.

The niche and phylogeography of a passerine reveal the history of biological diversification between the Andean and the Atlantic forests.

The Atlantic Forest is separated from the Andean tropical forest by dry and open vegetation biomes (Chaco and Cerrado). Despite this isolation, both rainforests share closely related lineages, which suggest a past connection. This connection could have been important for forest taxa evolution. In this study, we used the Saffron-billed Sparrow (Arremon flavirostris) as a model to evaluate whether the Andean and the Atlantic forests act as a refugia system, as well as to test for a history of biogeographic connection between them. In addition, we evaluated the molecular systematic of intraspecific lineages of the studied species. We modeled the current and past distribution of A. flavirostris, performed phylogeographic analyses based on mitochondrial and nuclear genes, and used Approximate Bayesian Computation (ABC) analyses to test for biogeographic scenarios. The major phylogeographic disjunction within A. flavirostris was found between the Andean and the Atlantic forests, with a divergence that occurred during the Mid-Pleistocene. Our paleodistribution models indicated a connection between these forest domains in different periods and through both the Chaco and Cerrado. Additionally, the phylogeographic and ABC analyses supported that the Cerrado was the main route of connection between these rainforests, but without giving decisive evidence against a Chaco connection. Our study with A. flavirostris suggest that the biodiversity of the Andean and of the Atlantic forests could have been impacted (and perhaps enriched?) by cycles of connections through the Cerrado and Chaco. This recurrent cycle of connection between the Andean and the Atlantic Forest could have been important for the evolution of Neotropical forest taxa. In addition, we discussed taxonomic implications of the results and proposed to split the studied taxon into two full species.

Continental-scale analysis reveals deep diversification within the polytypic Red-crowned Ant Tanager (Habia rubica, Cardinalidae).

We explored the phylogeographic patterns of intraspecific diversity in the Red-crowned Ant Tanager (Habia rubica) throughout its continent-wide distribution, in order to understand its evolutionary history and the role of evolutionary drivers that are considered to promote avian diversification in the Neotropics. We sampled 100 individuals of H. rubica from Mexico to Argentina covering the main areas of its disjunct distribution. We inferred phylogenetic relationships through Bayesian and maximum parsimony methodologies based on mitochondrial and nuclear markers, and complemented genetic analyses with the assessment of coloration and behavioral differentiation. We found four deeply divergent phylogroups within H. rubica: two South American lineages and two Mexican and Middle American lineages. The divergence event between the northern and southern phylogroups was dated to c. 5.0 Ma, seemingly related to the final uplift of the Northern Andes. Subsequently, the two South American phylogroups split c. 3.5 Ma possibly due to the development of the open vegetation corridor that currently isolates the Amazonian and Atlantic forests. Diversification throughout Mexico and Middle America, following dispersion across the Isthmus of Panama, was presumably more recent and coincident with Pleistocene climatic fluctuations and habitat fragmentations. The analyses of vocalizations and plumage coloration showed significant differences among main lineages that were consistent with the phylogenetic evidence. Our findings suggest that the evolutionary history of H. rubica has been shaped by an assortment of diversification drivers at different temporal and spatial scales resulting in deeply divergent lineages that we recommend should be treated as different species.

Population Genetic Structure in Hyacinth Macaws (Anodorhynchus hyacinthinus) and Identification of the Probable Origin of Confiscated Individuals.

Understanding the intraspecific genetic composition of populations in different geographic locations is important for the conservation of species. If genetic variability is structured, conservation strategies should seek to preserve the diversity of units. Also, origin of individuals can be determined, which is important for guiding actions against animal trafficking. The hyacinth macaw (Anodorhynchus hyacinthinus) is located in allopatric regions, vulnerable to extinction and suffering animal trafficking pressure. Therefore, we characterized its population genetic structure based on 10 microsatellites from 98 individuals and 2123bp of mitochondrial sequence (ND5, cytochrome b, and ND2) from 80 individuals. Moderate to high levels of differentiation were observed among 3 geographic regions of Brazil: the north/northeast of the country, the north Pantanal, and the south Pantanal. Differentiation between the 2 regions within the Pantanal was not expected, as they are relatively close and there is no known barrier to macaw movement between these regions. These genetically differentiated groups were estimated to have diverged 16000 to 42000 years ago. The low genetic variability observed seems not to be the result of past bottlenecks, although a star-shaped haplotype network and the mismatch distribution suggest that there was recent demographic expansion in the north and northeast. Environmental changes in the Holocene could have caused this expansion. Given the genetic structure observed, the most probable regions of origin of 24 confiscated individuals were identified. Thus, these data helped to trace illegal traffic routes and identify natural populations that are being illegally harvested.

DNA Barcoding Identifies Illegal Parrot Trade.

Illegal trade threatens the survival of many wild species, and molecular forensics can shed light on various questions raised during the investigation of cases of illegal trade. Among these questions is the identity of the species involved. Here we report a case of a man who was caught in a Brazilian airport trying to travel with 58 avian eggs. He claimed they were quail eggs, but authorities suspected they were from parrots. The embryos never hatched and it was not possible to identify them based on morphology. As 29% of parrot species are endangered, the identity of the species involved was important to establish a stronger criminal case. Thus, we identified the embryos' species based on the analyses of mitochondrial DNA sequences (cytochrome c oxidase subunit I gene [COI] and 16S ribosomal DNA). Embryonic COI sequences were compared with those deposited in BOLD (The Barcode of Life Data System) while their 16S sequences were compared with GenBank sequences. Clustering analysis based on neighbor-joining was also performed using parrot COI and 16S sequences deposited in BOLD and GenBank. The results, based on both genes, indicated that 57 embryos were parrots (Alipiopsitta xanthops, Ara ararauna, and the [Amazona aestiva/A. ochrocephala] complex), and 1 was an owl. This kind of data can help criminal investigations and to design species-specific anti-poaching strategies, and demonstrate how DNA sequence analysis in the identification of bird species is a powerful conservation tool.

Phylogeny and historical biogeography of gnateaters (Passeriformes, Conopophagidae) in the South America forests.

We inferred the phylogenetic relationships, divergence time and biogeography of Conopophagidae (gnateaters) based on sequence data of mitochondrial genes (ND2, ND3 and cytb) and nuclear introns (TGFB2 and G3PDH) from 45 tissue samples (43 Conopophaga and 2 Pittasoma) representing all currently recognized species of the family and the majority of subspecies. Phylogenetic relationships were estimated by maximum likelihood and Bayesian inference. Divergence time estimates were obtained based on a Bayesian relaxed clock model. These chronograms were used to calculate diversification rates and reconstruct ancestral areas of the genus Conopophaga. The phylogenetic analyses support the reciprocal monophyly of the two genera, Conopophaga and Pittasoma. All species were monophyletic with the exception of C. lineata, as C. lineata cearae did not cluster with the other two C. lineata subspecies. Divergence time estimates for Conopophagidae suggested that diversification took place during the Neogene, and that the diversification rate within Conopophaga clade was highest in the late Miocene, followed by a slower diversification rate, suggesting a diversity-dependent pattern. Our analyses of the diversification of family Conopophagidae provided a scenario for evolution in Terra Firme forest across tropical South America. The spatio-temporal pattern suggests that Conopophaga originated in the Brazilian Shield and that a complex sequence of events possibly related to the Andean uplift and infilling of former sedimentation basins and erosion cycles shaped the current distribution and diversity of this genus.

Multilocus tests of Pleistocene refugia and ancient divergence in a pair of Atlantic Forest antbirds (Myrmeciza).

The Atlantic Forest (AF) harbours one of the most diverse vertebrate faunas of the world, including 199 endemic species of birds. Understanding the evolutionary processes behind such diversity has become the focus of many recent, primarily single locus, phylogeographic studies. These studies suggest that isolation in forest refugia may have been a major mechanism promoting diversification, although there is also support for a role of riverine and geotectonic barriers, two sets of hypotheses that can best be tested with multilocus data. Here we combined multilocus data (one mtDNA marker and eight anonymous nuclear loci) from two species of parapatric antbirds, Myrmeciza loricata and M. squamosa, and Approximate Bayesian Computation to determine whether isolation in refugia explains current patterns of genetic variation and their status as independent evolutionary units. Patterns of population structure, differences in intraspecific levels of divergence and coalescent estimates of historical demography fit the predictions of a recently proposed model of refuge isolation in which climatic stability in the northern AF sustains higher diversity and demographic stability than in the southern AF. However, a pre-Pleistocene divergence associated with their abutting range limits in a region of past tectonic activity also suggests a role for rivers or geotectonic barriers. Little or no gene flow between these species suggests the development of reproductive barriers or competitive exclusion. Our results suggests that limited marker sampling in recent AF studies may compromise estimates of divergence times and historical demography, and we discuss the effects of such sampling on this and other studies.

Molecular systematics and evolution of the Synallaxis ruficapilla complex (Aves: Furnariidae) in the Atlantic Forest.

The Neotropical Synallaxis ruficapilla complex is endemic to the Atlantic Forest and is comprised of three species: S. ruficapilla, S. whitneyi, and S. infuscata. This group is closely related to the Synallaxis moesta complex that occurs in the Andes, Tepuis, and Guianan shield. Here we used mitochondrial and nuclear gene sequences to infer the phylogeny and the time of diversification of the S. ruficapilla and S. moesta complexes. We also included samples of an undescribed population of Synallaxis that resembles other populations of the S. ruficapilla complex. Our results showed that different geographical lineages within the S. ruficapilla complex are reciprocally monophyletic, but the northern form (S. infuscata) grouped with an Andean taxon. This suggests that at least two lineages of this group independently colonized the Atlantic Forest. Specimens of the undescribed population formed a monophyletic clade with deep divergence. Estimated diversification dates were within the late Pliocene to Pleistocene (2.75-0.16 million of years ago). This suggests that at this time there was a higher connectivity between habitats in the rugged landscapes of the circum-Amazonian bioregions. The observed Pleistocene diversification within the Atlantic Forest is congruent in space and time with studies of other co-distributed organisms, and may be associated with climate changes and tectonic activity during this period.

Non-invasive genetic sampling for molecular sexing and microsatellite genotyping of hyacinth macaw (Anodorhynchus hyacinthinus).

Molted feather sampling is a useful tool for genetic analyses of endangered species, but it is often very laborious due to the low quality and quantity of the DNA obtained. In the present study we show the parts of feathers that resulted in better yield of DNA. In descending order these were: blood clot outside the umbilicus, umbilicus (without blood clot), tip, inner membrane, and small calamus. Compared to DNA extracted from blood samples, DNA extracted from feathers produced microsatellite alleles of poorer quality and had to be processed immediately after extraction. As expected due to the level of DNA degradation, molecular sexing protocols that result in shorter PCR products were more efficient.

A palaeobiogeographic model for biotic diversification within Amazonia over the past three million years.

Many hypotheses have been proposed to explain high species diversity in Amazonia, but few generalizations have emerged. In part, this has arisen from the scarcity of rigorous tests for mechanisms promoting speciation, and from major uncertainties about palaeogeographic events and their spatial and temporal associations with diversification. Here, we investigate the environmental history of Amazonia using a phylogenetic and biogeographic analysis of trumpeters (Aves: Psophia), which are represented by species in each of the vertebrate areas of endemism. Their relationships reveal an unforeseen 'complete' time-slice of Amazonian diversification over the past 3.0 Myr. We employ this temporally calibrated phylogeny to test competing palaeogeographic hypotheses. Our results are consistent with the establishment of the current Amazonian drainage system at approximately 3.0-2.0 Ma and predict the temporal pattern of major river formation over Plio-Pleistocene times. We propose a palaeobiogeographic model for the last 3.0 Myr of Amazonian history that has implications for understanding patterns of endemism, the temporal history of Amazonian diversification and mechanisms promoting speciation. The history of Psophia, in combination with new geological evidence, provides the strongest direct evidence supporting a role for river dynamics in Amazonian diversification, and the absence of such a role for glacial climate cycles and refugia.

Multiple independent origins of mitochondrial control region duplications in the order Psittaciformes.

Mitochondrial genomes are generally thought to be under selection for compactness, due to their small size, consistent gene content, and a lack of introns or intergenic spacers. As more animal mitochondrial genomes are fully sequenced, rearrangements and partial duplications are being identified with increasing frequency, particularly in birds (Class Aves). In this study, we investigate the evolutionary history of mitochondrial control region states within the avian order Psittaciformes (parrots and cockatoos). To this aim, we reconstructed a comprehensive multi-locus phylogeny of parrots, used PCR of three diagnostic fragments to classify the mitochondrial control region state as single or duplicated, and mapped these states onto the phylogeny. We further sequenced 44 selected species to validate these inferences of control region state. Ancestral state reconstruction using a range of weighting schemes identified six independent origins of mitochondrial control region duplications within Psittaciformes. Analysis of sequence data showed that varying levels of mitochondrial gene and tRNA homology and degradation were present within a given clade exhibiting duplications. Levels of divergence between control regions within an individual varied from 0-10.9% with the differences occurring mainly between 51 and 225 nucleotides 3' of the goose hairpin in domain I. Further investigations into the fates of duplicated mitochondrial genes, the potential costs and benefits of having a second control region, and the complex relationship between evolutionary rates, selection, and time since duplication are needed to fully explain these patterns in the mitochondrial genome.

The genetic effects of Late Quaternary climatic changes over a tropical latitudinal gradient: diversification of an Atlantic Forest passerine.

The increase in biodiversity from high to low latitudes is a widely recognized biogeographical pattern. According to the latitudinal gradient hypothesis (LGH), this pattern was shaped by differential effects of Late Quaternary climatic changes across a latitudinal gradient. Here, we evaluate the effects of climatic changes across a tropical latitudinal gradient and its implications to diversification of an Atlantic Forest (AF) endemic passerine. We studied the intraspecific diversification and historical demography of Sclerurus scansor, based on mitochondrial (ND2, ND3 and cytb) and nuclear (FIB7) gene sequences. Phylogenetic analyses recovered three well-supported clades associated with distinct latitudinal zones. Coalescent-based methods were applied to estimate divergence times and changes in effective population sizes. Estimates of divergence times indicate that intraspecific diversification took place during Middle-Late Pleistocene. Distinct demographic scenarios were identified, with the southern lineage exhibiting a clear signature of demographic expansion, while the central one remained more stable. The northern lineage, contrasting with LGH predictions, exhibited a clear sign of a recent bottleneck. Our results suggest that different AF regions reacted distinctly, even in opposite ways, under the same climatic period, producing simultaneously favourable scenarios for isolation and contact among populations.