Barriers, rather than refugia, underlie the origin of diversity in toads endemic to the Brazilian Atlantic Forest

Mitonuclear and phenotypic discordance in an Atlantic Forest frog hybrid zone

Discordance between mitochondrial and nuclear DNA is common among animals and can be the result of a number of evolutionary processes, including incomplete lineage sorting and introgression. Particularly relevant in contact zones, mitonuclear discordance is expected because the mitochondrial genome is haploid and primarily uniparentally inherited, whereas nuclear loci are evolving at slower rates. In addition, when closely related taxa come together in hybrid zones, the distribution of diagnostic phenotypic characters and their concordance with the mitochondrial or nuclear lineages can also inform on historical and ongoing dynamics within hybrid zones. Overall, genetic and phenotypic discordances provide evidence for evolutionary divergence and processes that maintain boundaries among sister species or lineages. In this study, we characterized patterns of genetic and phenotypic variation in a contact zone between Cycloramphus dubius and Cycloramphus boraceiensis, two sister species of frogs endemic to the Atlantic Coastal Forest of Brazil. We examined genomic-scale nuclear diversification across 19 populations, encompassing the two parental forms and a contact zone between them. We compared the distribution of genomic DNA variability with that of a mitochondrial locus (16S) and two morphological traits (dorsal tubercles and body size). Our results reveal multiple divergent lineages with ongoing admixture. We detected discordance in patterns of introgression across the three data types. Cycloramphus dubius males are significantly larger than C. boraceiensis males, and we posit that competition among males in the hybrid zone, coupled with mate choice by females, may be one mechanism leading to patterns of introgression observed between the species.

The dispersal between Amazonia and Atlantic Forest during the Early Neogene revealed by the biogeography of the treefrog tribe Sphaenorhynchini (Anura, Hylidae)

The Amazonia and the Atlantic Forest, separated by the diagonal of open formations, are two ecoregions that comprise the most diverse tropical forests in the world. The Sphaenorhynchini tribe is among the few tribes of anurans that occur in both rainforests, and their historical biogeographic have never been proposed. In this study, we infer a dated phylogeny for the species of the Sphaenorhynchini and we reconstructed the biogeographic history describing the diversification chronology, and possible patterns of dispersion and vicariance, providing information about how orogeny, forest dynamics and allopatric speciation affected their evolution in South America. We provided a dated phylogeny and biogeography study for the Sphaenorhynchini tribe using mitochondrial and nuclear genes. We analyzed 41 samples to estimate the ancestral areas using biogeographical analysis based on the estimated divergence times and the current geographical ranges of the species of Sphaenorhynchini. We recovered three characteristic clades that we recognize as groups of species (S. lacteus, S. planicola, and S. platycephalus groups), with S. carneus and G. pauloalvini being the sister taxa of all other species from the tribe. We found that the diversification of the tribe lineages coincided with the main climatic and geological factors that shaped the Neotropical landscape during the Cenozoic. The most recent common ancestor of the Sphaenorhynchini species emerged in the North of the Atlantic Forest and migrated to the Amazonia in different dispersion events that occurred during the connections between these ecoregions. This is the first large-scale study to include an almost complete calibrated phylogeny of Sphaenorhynchini, presenting important information about the evolution and diversification of the tribe. Overall, we suggest that biogeographic historical of Sphaenorhynchini have resulted from a combination of repeated range expansion and contraction cycles concurrent with climate fluctuations and dispersal events between the Atlantic Forest and Amazonia.

Deep Genomic Divergence and Phenotypic Admixture of the Treefrog Dendropsophus elegans (Hylidae: Amphibia) Coincide With Riverine Boundaries at the Brazilian Atlantic Forest

The Atlantic Forest (AF) domain is one of the Earth’s biodiversity hotspots, known for its high levels of species diversity and endemism. Factors related to palaeoenvironmental dynamics, such as the establishment of vegetational refugia and river basins, have different impacts on biological communities and biodiversity patterns in this domain. Here, we sample genome-wide RADseq data from a widespread treefrog (Dendropsophus elegans), inhabiting natural and human-impacted ecosystems at the Brazilian AF to test the impact of riverine boundaries and climatic refugia on population structure and diversification. We estimate divergence times and migration rate across identified genetic breaks related to the rivers Doce, Paraíba do Sul, Ribeira de Iguape, and Paraguaçu, known to represent barriers to gene flow for other AF endemic species, and test the role of climatic refugia. Finally, we investigate the impact of spatio-temporal population history on morphological variation in this species. We recovered a phylogeographic history supporting three distinct clades separated into two geographically structured populations, corresponding to the north and south of AF. In addition, we identified an admixture zone between north and south populations in the latitude close to the Doce River. Our findings support a pattern of isolation-by-distance and the existence of a secondary contact zone between populations, which might have been promoted by gene flow during population expansion. Further, we found support for models considering migration parameters for all the tested rivers with different population divergence times. Based on the species history and the AF palaeoenvironmental dynamics, we corroborate the role of forest refugia impacting population structure for this species through recent range expansion after the Last Glacial Maximum (LGM). The Doce and Paraíba do Sul Rivers coincide with the main genetic breaks, suggesting they might also have played a role in the diversification processes. Finally, despite finding subtle correlations for phenotypic data among different populations, variation is not strongly detectable and does not seem associated with speciation-level processes that could warrant taxonomic changes. Such results can be explained by phenotypic plasticity of the evaluated traits and by recent divergence times, where there has been insufficient time and weak selective pressures to accumulate enough phenotypic differences.

Ecological divergence and synchronous Pleistocene diversification in the widespread South American butter frog complex

Phylogeographic studies primarily focus on the major role of landscape topography in driving lineage diversification. However, populational phylogeographic breaks may also occur as a result of either niche conservatism or divergence, in the absence of geographic barriers to gene flow. Furthermore, these two factors are not mutually exclusive and can act in concert, making it challenging to evaluate their relative importance on explaining genetic variation in nature. Herein, we use sequences of two mitochondrial and four nuclear genes to investigate the timing and diversification patterns of species pertaining to the Leptodactylus latrans complex, which harbors four morphologically cryptic species with broad distributions across environmental gradients in eastern South America. The origin of this species complex dates back to the late Miocene (ca. 5.5 Mya), but most diversification events occurred synchronically during the late Pleistocene likely as the result of ecological divergence driven by Quaternary climatic oscillations. Further, significant patterns of environmental niche divergences among species in the L. latrans complex imply that ecological isolation is the primary mode of genetic diversification, mostly because phylogenetic breaks are associated with environmental transitions rather than topographic barriers at both species and populational scale. We provided new insights about diversification patterns and processes within a species complex of broadly and continuously distributed group of frogs along South America.

Phenotypic and genomic differences between biomes of the South America marsh rat, Holochilus brasiliensis

Abiotic factors can influence genetic and phenotypic divergence in several ways, and identifying the mechanisms responsible for generating this variation is challenging. However, when evaluated in combination, ecological characteristics and genetic and phenotypic information can help us to understand how habitat preferences can influence morphological and genetic patterns exhibited by taxa distributed between distinct biomes, such as the Atlantic Forest and Pampas biomes in South America. By combining distributional, environmental, phenotypic and genomic information from a habitat-specialist semi-aquatic rodent (Holochilus brasiliensis), we quantified the relationship between ecological niche differences and the phenotypic and genetic variation. The results demonstrate notable segregation among the ecological niches of H. brasiliensis within each biome, although we could not refute the hypothesis of niche similarity or equivalency. Such differences are consistent with a solid morphometric variation associated with the size of these rodents. However, the ecological and morphometric differentiation is not accompanied by the same pattern of genetic variation. Despite differences in the connectivity patterns in both biomes, the genetic differences corroborate a consistent level of migration history between biomes. Additionally, the association tests show that the environment explains a small and non- significant part of the genetic variation but a significant portion of the morphometric variation.

Comparative phylogeography and palaeomodelling reveal idiosyncratic responses to climate changes in Neotropical paper wasps

The impact of the broad disjunction between Amazonia and the Atlantic Forest on biodiversity has been the theme of several discussions in recent decades. Here, we evaluate the effects of dependence on humid environments and the role of historical factors on the level, distribution and structuring of genetic variation in widely distributed Neotropical insects. For such, we test whether climatically stable zones (i.e. refuges) in both Amazonia and the Atlantic Forest concentrate higher genetic diversity in the social paper wasps Angiopolybia pallens and Synoeca surinama. We found that historical events have avoided the interchange of A. pallens between both rainforests at least since the Early Pliocene and that ancient colonization in north-western Amazonia and the Bahia refuge significantly predicts genetic diversity in populations of this species. Conversely, the split between the Atlantic Forest and remaining western populations of S. surinama is more recent (Plio-Pleistocene); this species has considerably lower genetic diversity than A. pallens and such diversity is mostly concentrated in Amazonia and in the cerrado biome (savanna) than in the Atlantic Forest. Finally, we propose that the occurrence of species that exhibit such distribution patterns should be taken into consideration when establishing areas for conservation.

Comparative phylogeographic and demographic analyses reveal a congruent pattern of sister relationships between bird populations of the northern and south-central Atlantic Forest

The Pernambuco Center of Endemism (PCE) is the northernmost strip of the Atlantic Forest (AF). Biogeographic affinities among avifaunas in the PCE, the southern-central Atlantic Forest (SCAF), and Amazonia (AM) have not been studied comprehensively, and current patterns of genetic diversity in the PCE remain unclear. The interplay between species' ecological attributes and historical processes, such as Pleistocene climate fluctuations or the appearance of rivers, may have affected population genetic structures in the PCE. Moreover, the role of past connections between the PCE and AM and the elevational distribution of species in assembling the PCE avifauna remain untested. Here, we investigated the biogeographic history of seven taxa endemic to the PCE within a comparative phylogeographic framework based on a mean of 3,618 independent single nucleotide polymorphisms (SNPs) extracted from flanking regions of ultraconserved elements (UCEs) and one mitochondrial gene. We found that PCE populations were more closely related to SCAF populations than they were to those in AM, regardless of their elevational range, with divergence times placed during the Mid-Pleistocene. These splits were consistent with a pattern of allopatric divergence with gene flow until the upper Pleistocene and no signal of rapid changes in population sizes. Our results support the existence of a Pleistocene refugium driving current genetic diversity in the PCE, thereby rejecting the role of the São Francisco River as a primary barrier for population divergence. Additionally, we found that connections with Amazonia also played a significant role in assembling the PCE avifauna through subsequent migration events.

Multilocus phylogeny of Paratelmatobiinae (Anura: Leptodactylidae) reveals strong spatial structure and previously unknown diversity in the Atlantic Forest hotspot

The Brazilian Atlantic Forest harbors high levels of anuran diversity and endemism, including several taxa restricted to small geographic ranges. Here, we provide a multilocus phylogeny for Paratelmatobiinae, a leptodactylid subfamily composed of small-ranged species distributed in the Brazilian Atlantic Forest and in the campo rupestre ecosystem. We performed Bayesian inference and maximum likelihood analyses using three mitochondrial and five nuclear markers, and a matrix comprising a broad taxonomic sampling. We then delimitated independently evolving lineages within the group. We recovered Paratelmatobiinae and each of its four genera as monophyletic and robustly supported. Five putatively new species included in our analyses were unambiguously supported in the phylogenetic trees and delimitation analyses. We also recovered other deeply divergent and geographically structured lineages within the four genera of Paratelmatobiinae. Our estimation of divergence times indicates that diversification in the subfamily began in the Eocene and continued until the Pleistocene. We discuss possible scenarios of diversification for the four genera of Paratelmatobiinae, and outline the implications of our findings for taxonomy and conservation.

Outstanding diversity and microendemism in a clade of rare Atlantic Forest montane frogs

Distributed across topographically complex landscapes that vary from lowland to high elevation, the Atlantic Forest harbors one of the richest biotas worldwide. Atlantic Forest amphibians are particularly speciose, taxonomic accounts are rising and the group is used as model for biogeographic inference. Past climate-related habitat fragmentation is often invoked to explain diversification, with montane taxa expected to become more widespread during glacial times and restrained at interglacials. In this study we investigate diversification in Ischnocnema lactea and I. holti (Anura: Brachycephalidae), two rare frog species inhabiting Atlantic Forest montane regions in Southeastern Brazil. Previous phylogenetic accounts have suggested uncertain limits between these two sister species. We assembled a multilocus DNA dataset, delimited lineages in this clade, and used ecological niche modeling to explore past and future putative ranges. Assignment analyses and traditional and coalescent phylogenetic methods confirmed the existence of a species complex of Miocene origin comprising nine lineages, most of which show very narrow ranges. Lineages were fully supported as species based in coalescent species delimitation, but the phylogenetic relationships among lineages in higher elevation were unresolved. Models of past ranges suggest extensive suitable areas at the last glacial maximum which, along with phylogenetic uncertainty, are consistent with a hypothesis that climate driven vicariance at higher elevation areas resulted in hard polytomies. Species distribution models under future climates suggest narrower ranges of the lineages relative to now, but no species are currently considered endangered. Overall, our results argue in favor for the reassessment of the taxonomic and conservation status of the I. holti - I. lactea species complex.

Areas of endemism in the Brazilian Atlantic Forest based on the distribution of dung beetles (Coleoptera, Scarabaeidae, Scarabaeinae)

ABSTRACT Our goals were to determine whether the pattern of geographical distribution of dung beetles in the Brazilian Atlantic Forest (BAF), Southeast Brazil, supports the identification of the areas of endemism in this biome, how the number and boundaries of the areas of endemism vary with the spatial scale used in the analysis, if the areas of endemism identified here are consistent with previous proposals described in the literature. We used the analysis of endemicity (NDM) on the distributional patterns of 198 species and subspecies of dung beetles in order to identify areas of endemism into grids of 0.25°x0.25°, 0.5°x0.5° and 1°x1°. A total of 15 consensus areas (CA) were identified with the different grid sizes employed (two of 0.25°, three of 0.5° and 10 of 1°). Our results support the assumptions about the influence of the grid size, since a smaller number of CA were identified for the 0.25° grids (02 CA), whereas by increasing the size of the units, there was an increase in the number of the areas of endemism (10 CA of 1°). Despite different levels of geographical congruence, the areas of endemism located in the BAF described elsewhere are corroborate, all or part of them. The overlap of these CA allowed the definition of three generalized areas of endemism: Southeast, Central and Southwest. These generalized areas encompassed habitats with great environmental variety, potentially influencing the levels of endemism of species of dung beetles. Furthermore, they were corroborated by other areas of endemism described in the literature, allowing us to argue that processes forming these regions have influenced dung beetle species as described for other groups of organisms.

Dual influence of terrestrial and marine historical processes on the phylogeography of the Brazilian intertidal red alga Gracilaria caudata

In this study, we explored how past terrestrial and marine climate changes have interacted to shape the phylogeographic patterns of the intertidal red seaweed Gracilaria caudata, an economically important species exploited for agar production in the Brazilian north-east. Seven sites were sampled along the north-east tropical and south-east sub-tropical Brazilian coast. The genetic diversity and structure of G. caudata was inferred using a combination of mitochondrial (COI and cox2-3), chloroplast (rbcL) and 15 nuclear microsatellite markers. A remarkable congruence between nuclear, mitochondrial and chloroplast data revealed clear separation between the north-east (from 03° S to 08° S) and the south-east (from 20° S to 23° S) coast of Brazil. These two clades differ in their demographic histories, with signatures of recent demographic expansions in the north-east and divergent populations in the south-east, suggesting the maintenance of several refugia during the last glacial maximum due to sea-level rise and fall. The Bahia region (around 12° S) occupies an intermediate position between both clades. Microsatellites and mtDNA markers showed additional levels of genetic structure within each sampled site located south of Bahia. The separation between the two main groups in G. caudata is likely recent, probably occurring during the Quaternary glacial cycles. The genetic breaks are concordant with (i) those separating terrestrial refugia, (ii) major river outflows and (iii) frontiers between tropical and subtropical regions. Taken together with previously published eco-physiological studies that showed differences in the physiological performance of the strains from distinct locations, these results suggest that the divergent clades in G. caudata correspond to distinct ecotypes in the process of incipient speciation and thus should be considered for the management policy of this commercially important species.

Signature of the Paleo-Course Changes in the São Francisco River as Source of Genetic Structure in Neotropical Pithecopus nordestinus (Phyllomedusinae, Anura) Treefrog

Historical processes that have interrupted gene flow between distinct evolutionary lineages have played a fundamental role in the evolution of the enormous diversity of species found in the Neotropical region. Numerous studies have discussed the role of geographic barriers and Pleistocene forest refugia in the diversification of the region's biodiversity. In the present study, we investigated the relative contribution of these different factors to the evolutionary history of Pithecopus nordestinus, a Neotropical tree frog, which is amply distributed in the Brazilian Atlantic Forest and adjacent areas of the Caatinga biome. We used an extensive sample and multilocus DNA sequences to provide an overview of the intraspecific genetic diversity of P. nordestinus, characterize historical diversification patterns, and identify possible phylogenetic splits. We tested different scenarios of diversification based on Pleistocene Refugia and river barrier models using approximate Bayesian computation (ABC) and ecological niche modeling (ENM). The phylogenetic approach indicate the occurrence of processes of phylogeographic divergence in both time and space, related to historical shifts in the course of the São Francisco River during Plio-Pleistocene period, resulting in two principal, highly divergent clades. The ABC model provided strong statistical support for this scenario, confirming the hypothesis that the São Francisco River acted as an effective geographical barrier during vicariant events in the evolutionary history of P. nordestinus. We believe that the climatic changes that occurred during the Pleistocene also played a secondary role in the genetic signatures identified, reinforcing the divergence of populations isolated by physical barriers. These findings reinforce the conclusion that the two models of diversification (geographic barriers and refugia) are not mutually exclusive in the Neotropical domain but may interact extensively during the diversification of species on a regional scale.

Historical signatures in the alpha and beta diversity patterns of Atlantic Forest harvestman communities (Arachnida: Opiliones)

The integration of ecology and historical biogeography is fostering the investigation of diversity patterns. We studied alpha and beta diversity patterns of Brazilian Atlantic Forest harvestman (Arachnida: Opiliones) communities and related them to environmental and historical factors. Our data bank contains 508 species from 63 sites, encompassing almost the entire latitudinal range of Atlantic Forest. Alpha diversity was higher in coastal sites in the south and southeast regions and decreased in sites inland, as well as in sites in the coastal northeast region, especially in northern Bahia state. Alpha diversity was positively influenced by precipitation and altitudinal range, but the low number of species in northeastern coastal sites seems to be more related to the historical distribution of Neotropical harvestman lineages than to recent environmental factors. Geographic distance was the most influential factor for beta diversity. Compositional changes were also remarkably congruent with areas of endemism delimited for Atlantic Forest harvestmen. The percentage of protected areas for each area of endemism was very unbalanced, and Espírito Santo and Pernambuco states were the least protected areas. The turnover process observed in the compositional changes indicates that conservation strategies should include as many reserves as possible because every community presents a unique set of species.

Historical climate changes and hybridization shaped the evolution of Atlantic Forest spinetails (Aves: Furnariidae)

Combining phylogeographic approaches and hybrid zone inference in a single framework is a robust way to depict respectively the biogeographic history of lineages and the evolutionary processes responsible for speciation. Here, we studied the spatiotemporal patterns of diversification and characterize the hybrid zone between two Atlantic Forest spinetails (Synallaxis ruficapilla and Synallaxis cinerea) using mitochondrial DNA and nuclear (autosomal and Z-linked) genes. We consistently recovered divergence between and within the two species during the late Pliocene and Pleistocene using an isolation with migration model. Also, our results indicate distinct levels of introgression among lineages. Ecological niche models and demographic inferences, used to infer range distributions throughout the late Quaternary, were not consistent with the hypothesis of a large river as a primary barrier responsible for the divergence of the two species. Instead, a scenario of isolation and divergence followed by geographic expansion and admixture as a consequence of Quaternary climatic oscillations was supported. Paleomodels also were not consistent with the idea that the hybrid zone originated in primary differentiation and favor a secondary contact scenario. Model fitting indicated that clines of different loci spanning the hybrid zone are coincident and concordant. The narrow cline for one Z-linked locus could be indicative of some form of post-zygotic selection hindering genetic homogenization between the two species.

Phylogeography of plastid DNA sequences suggests post-glacial southward demographic expansion and the existence of several glacial refugia for Araucaria angustifolia

Despite the high diversity of the Southern South American environments, the patterns and processes driving both their species diversity and demographic history are still poorly known and are a challenging task. In this study, we evaluate plastid DNA sequences of the conifer species Araucaria angustifolia aiming to (i) assess the species genetic structure within its main range of occurrence, (ii) infer its population demographic history, looking for evidence of southward expansion, (iii) search for evidence of glacial refugia within the species distribution area and (iv) discuss some conservation and management strategies for this species. Twenty haplotypes were identified, revealing the presence of three distinct genetic groups across the geographic range of the species and structuring the populations into Northern, Central and Southern groups. Our results suggest the occurrence of post-glacial expansion of A. angustifolia towards the south, as well as the existence of at least three refugia within the species occurrence area. Testing the occurrence of historical demographic expansion, we suggest that genetic groups experienced fluctuations in effective size, associated to a structured distribution of populations. The identification of three genetic groups in this study corroborates the proposition of using the geographic distribution of A. angustifolia for selecting in situ conservation areas, for planning seed collection for ex situ conservation, as well as for the delineation of seed zones.

Phylogeography of Atlantic Forest glassfrogs (Vitreorana): when geography, climate dynamics and rivers matter

Recent advances in the field of landscape genetics provide ways to jointly analyze the role of present-day climate and landscape configuration in current biodiversity patterns. Expanding this framework into a phylogeographic study, we incorporate information on historical climatic shifts, tied to descriptions of the local topography and river configuration, to explore the processes that underlie genetic diversity patterns in the Atlantic Forest hotspot. We study two montane, stream-associated species of glassfrogs: Vitreorana eurygnatha and V. uranoscopa. By integrating species distribution modeling with geographic information systems and molecular data, we find that regional patterns of molecular diversity are jointly explained by geographic distance, historical (last 120 ky) climatic stability, and (in one species) river configuration. Mitochondrial DNA genealogies recover significant regional structure in both species, matching previous classifications of the northern and southern forests in the Atlantic Forest, and are consistent with patterns reported in other taxa. Yet, these spatial patterns of genetic diversity are only partially supported by nuclear data. Contrary to data from lowland taxa, historical climate projections suggest that these montane species were able to persist in the southern Atlantic Forest during glacial periods, particularly during the Last Glacial Maximum. These results support generally differential responses to climatic cycling by northern (lowland) and southern (montane) Atlantic Forest species, triggered by the joint impact of regional landscape configuration and climate change.

Historical connections among river basins and climatic changes explain the biogeographic history of a water rat

Background

The water ratNectomys squamipes(Cricetidae: Sigmodontinae) is a semiaquatic rodent from eastern South America that shows shallow genetic structure across space, according to some studies. We tested the influence of hydrography and climatic changes on the genetic and phylogeographic structure of this semiaquatic small mammal.

Methods

DNA sequences of two mitochondrial genetic markers (Cyt b and D-loop) and six microsatellite loci from water rats were collected at 50 localities in five river basins in the Atlantic Forest along the eastern coast of South America. We evaluated the genetic structure within and among river basins, and we estimated divergence dates. Species distribution models for the present and past were built to identify possible gene flow paths.

Results

Mitochondrial data and species distribution models showed coherent results. Microsatellite loci showed a more complex pattern of genetic differentiation. The diversification ofN. squamipeshaplotypes occurred during the Pleistocene and the river basin cannot explain most of the genetic structure. We found evidence of population expansion during the last glacial maximum, and gene flow paths indicate historical connections among rivers in the Atlantic Forest.

Discussion

Historical connections among rivers in the Atlantic Forest may have allowedN. squamipesto disperse farther across and within basins, leading to shallow genetic structure. Population expansions and gene flow through the emerged continental shelf during glacial period support the Atlantis forest hypothesis, thus challenging the forest refuge hypothesis.

Neither barriers nor refugia explain genetic structure in a major biogeographic break: phylogeography of praying mantises in the Brazilian Atlantic Forest

The Atlantic Forest is one of the world's top biodiversity hotspots, but the diversification processes of its biota are still poorly known, with competing models attributing dominant roles to either Quaternary climatic changes or geographic barriers. Many studies identify the Doce river as a major phylogeographic break, but the reasons for this phenomenon are highly debated. Here we test the predictions of the refugial and barrier models for a common species of praying mantis, Miobantia fuscata, focusing in the areas immediately south and north of the Doce river. Our analyses show high intraspecific genetic diversity, deep coalescence times and no evidence for recent population expansion. Phylogeographic structure is inconsistent with a refugial hypothesis. Significant gene flow between northern and southern populations also conflicts with a strong role for geographic barriers. This study highlights the need for considering invertebrate taxa to infer recent landscape changes, and points towards a more complex picture of genetic diversification in the Atlantic Forest.

Bayesian estimation of scaled mutation rate under the coalescent: a sequential Monte Carlo approach

BACKGROUND

Samples of molecular sequence data of a locus obtained from random individuals in a population are often related by an unknown genealogy. More importantly, population genetics parameters, for instance, the scaled population mutation rate Θ=4N _e μ for diploids or Θ=2N _e μ for haploids (where N _e is the effective population size and μ is the mutation rate per site per generation), which explains some of the evolutionary history and past qualities of the population that the samples are obtained from, is of significant interest.

RESULTS

In this paper, we present the evolution of sequence data in a Bayesian framework and the approximation of the posterior distributions of the unknown parameters of the model, which include Θ via the sequential Monte Carlo (SMC) samplers for static models. Specifically, we approximate the posterior distributions of the unknown parameters with a set of weighted samples i.e., the set of highly probable genealogies out of the infinite set of possible genealogies that describe the sampled sequences. The proposed SMC algorithm is evaluated on simulated DNA sequence datasets under different mutational models and real biological sequences. In terms of the accuracy of the estimates, the proposed SMC method shows a comparable and sometimes, better performance than the state-of-the-art MCMC algorithms.

CONCLUSIONS

We showed that the SMC algorithm for static model is a promising alternative to the state-of-the-art approach for simulating from the posterior distributions of population genetics parameters.

The xeric side of the Brazilian Atlantic Forest: The forces shaping phylogeographic structure of cacti

In order to investigate biogeographic influences on xeric biota in the Brazilian Atlantic Forest (BAF), a biodiversity hotspot, we used a monophyletic group including three cactus taxa as a model to perform a phylogeographic study: Cereus fernambucensis subsp. fernambucensis, C. fernambucensis subsp. sericifer, and C. insularis. These cacti are allopatric and grow in xeric habitats along BAF, including isolated granite and gneiss rock outcrops (Inselbergs), sand dune vegetation (Restinga forest), and the rocky shore of an oceanic archipelago (islands of Fernando de Noronha). The nucleotide information from nuclear gene phytochrome C and plastid intergenic spacer trnS-trnG was used to perform different approaches and statistical analyses, comprising population structure, demographic changes, phylogenetic relationships, and biogeographic reconstruction in both spatial and temporal scales. We recovered four allopatric population groups with highly supported branches in the phylogenetic tree with divergence initiated in the middle Pleistocene: southern distribution of C. fernambucensis subsp. fernambucensis, northern distribution of C. fernambucensis subsp. fernambucensis together with C. insularis, southern distribution of C. fernambucensis subsp. sericifer, and northern distribution of C. fernambucensis subsp. sericifer. Further, the results suggest that genetic diversity of population groups was strongly shaped by an initial colonization event from south to north followed by fragmentation. The phylogenetic pattern found for C. insularis is plausible with peripatric speciation in the archipelago of Fernando de Noronha. To explain the phylogeographic patterns, the putative effects of both climatic and sea level changes as well as neotectonic activity during the Pleistocene are discussed.

The roles of barriers, refugia, and chromosomal clines underlying diversification in Atlantic Forest social wasps

Phylogeographic studies have sought to explain the genetic imprints of historical climatic changes and geographic barriers within the Brazilian Atlantic Forest (AF) biota, and consequently two processes of diversification (refugia and barriers) have been proposed. Additionally, there is evidence that eustatic changes influenced the biogeographic history of the AF. Here we evaluate these contrasting diversification processes using two AF social wasp species – the mid-montane Synoeca cyanea and the lowland Synoeca aff. septentrionalis. We analyzed several sources of data including multilocus DNA sequence, climatic niche models and chromosomal features. We find support for idiosyncratic phylogeographic patterns between these wasps, involving different levels of population structure and genetic diversity, contrary suitable climatic conditions during the last glaciation, and contrasting historical movements along the AF. Our data indicate that neotectonics and refugia played distinct roles in shaping the genetic structure of these wasps. However, we argue that eustatic changes influenced the demographic expansion but not population structure in AF biota. Notably, these wasps exhibited chromosomal clines, involving chromosome number and decreasing of GC content, latitudinally oriented along the AF. Together, these results reinforce the need to consider individual organismal histories and indicate that barriers and refugia are significant factors in understanding AF evolution.

Environmental constraints on the compositional and phylogenetic beta-diversity of tropical forest snake assemblages

The ongoing biodiversity crisis increases the importance and urgency of studies addressing the role of environmental variation on the composition and evolutionary history of species assemblages, but especially the tropics and ectotherms remain understudied. In regions with rainy summers, coexistence of tropical ectothermic species may be determined by the partitioning of the climatic niche, as ectotherms can rely on water availability and thermoregulatory behaviour to buffer constraints along their climatic niche. Conversely, tropical ectotherms facing dry summers would have fewer opportunities to climatic niche partitioning and other processes rather than environmental filtering would mediate species coexistence. We used 218 snake assemblages to quantify the compositional (CBD) and phylogenetic (PBD) beta-diversity of snakes in the Atlantic Forest (AF) hotspot, South America. We identify two AF regions with distinct climatological regimes: dry summers in the northern-AF and rainy summers in the southern-AF. While accounting for the influence of multiscale spatial processes, we disentangle the relative contribution of thermal, water-related and topographic conditions in structuring the CBD and PBD of snake assemblages, and determine the extent in which snake assemblages under distinct climatological regimes are affected by environmental filtering. Thermal conditions best explain CBD and PBD of snakes for the whole AF, whereas water-related factors best explain the structure of snake assemblages within a same climatological regime. CBD and PBD patterns are similarly explained by spatial factors but snake assemblages facing dry summers are more affected by spatial processes operating at fine to intermediate spatial scale, whereas those assemblages in regions with rainy summers have a stronger signature of coarse-scale processes. As expected, environmental filtering plays a stronger role in southern-AF than northern-AF, and the synergism between thermal and water-related conditions is the key cause behind this difference. Differences in climatological regimes within the tropics affect processes mediating species coexistence. The influence of broad-scale gradients (e.g. temperature and precipitation) in structuring tropical ectothermic assemblages is greater in regions with rainy summers where climatic niche partitioning is more likely. Our findings highlight the potential stronger role of biotic interactions and neutral processes in structuring ectothermic assemblages facing changes towards warmer and dryer climates.

Multilocus Phylogeography of the Treefrog Scinax eurydice (Anura, Hylidae) Reveals a Plio-Pleistocene Diversification in the Atlantic Forest

We aim to evaluate the genetic structure of an Atlantic Forest amphibian species, Scinax eurydice, testing the congruence among patterns identified and proposed by the literature for Pleistocene refugia, microrefugia, and geographic barriers to gene flow such as major rivers. Furthermore, we aim to evaluate predictions of such barriers and refugia on the genetic structure of the species, such as presence/absence of dispersal, timing since separation, and population expansions/contractions. We sequenced mitochondrial and nuclear genetic markers on 94 tissue samples from 41 localities. We inferred a gene tree and estimated genetic distances using mtDNA sequences. We then ran population clustering and assignment methods, AMOVA, and estimated migration rates among populations identified through mtDNA and nDNA analyses. We used a dated species tree, skyline plots, and summary statistics to evaluate concordance between population's distributions and geographic barriers and Pleistocene refugia. Scinax eurydice showed high mtDNA divergences and four clearly distinct mtDNA lineages. Species tree and population assignment tests supported the existence of two major clades corresponding to northeastern and southeastern Atlantic Forest in Brazil, each one composed of two other clades. Lineage splitting events occurred from late Pliocene to Pleistocene. We identified demographic expansions in two clades, and inexistent to low levels of migrations among different populations. Genetic patterns and demographic data support the existence of two northern Refuge and corroborate microrefugia south of the Doce/Jequitinhonha Rivers biogeographic divide. The results agree with a scenario of recent demographic expansion of lowland taxa. Scinax eurydice comprises a species complex, harboring undescribed taxa consistent with Pleistocene refugia. Two rivers lie at the boundaries among populations and endorse their role as secondary barriers to gene flow.

Neotropical forest expansion during the last glacial period challenges refuge hypothesis

The forest refuge hypothesis (FRH) has long been a paradigm for explaining the extreme biological diversity of tropical forests. According to this hypothesis, forest retraction and fragmentation during glacial periods would have promoted reproductive isolation and consequently speciation in forest patches (ecological refuges) surrounded by open habitats. The recent use of paleoclimatic models of species and habitat distributions revitalized the FRH, not by considering refuges as the main drivers of allopatric speciation, but instead by suggesting that high contemporary diversity is associated with historically stable forest areas. However, the role of the emerged continental shelf on the Atlantic Forest biodiversity hotspot of eastern South America during glacial periods has been ignored in the literature. Here, we combined results of species distribution models with coalescent simulations based on DNA sequences to explore the congruence between scenarios of forest dynamics through time and the genetic structure of mammal species cooccurring in the central region of the Atlantic Forest. Contrary to the FRH predictions, we found more fragmentation of suitable habitats during the last interglacial (LIG) and the present than in the last glacial maximum (LGM), probably due to topography. We also detected expansion of suitable climatic conditions onto the emerged continental shelf during the LGM, which would have allowed forests and forest-adapted species to expand. The interplay of sea level and land distribution must have been crucial in the biogeographic history of the Atlantic Forest, and forest refuges played only a minor role, if any, in this biodiversity hotspot during glacial periods.

Speciation with gene flow in whiptail lizards from a Neotropical xeric biome

Two main hypotheses have been proposed to explain the diversification of the Caatinga biota. The riverine barrier hypothesis (RBH) claims that the São Francisco River (SFR) is a major biogeographic barrier to gene flow. The Pleistocene climatic fluctuation hypothesis (PCH) states that gene flow, geographic genetic structure and demographic signatures on endemic Caatinga taxa were influenced by Quaternary climate fluctuation cycles. Herein, we analyse genetic diversity and structure, phylogeographic history, and diversification of a widespread Caatinga lizard (Cnemidophorus ocellifer) based on large geographical sampling for multiple loci to test the predictions derived from the RBH and PCH. We inferred two well-delimited lineages (Northeast and Southwest) that have diverged along the Cerrado-Caatinga border during the Mid-Late Miocene (6-14 Ma) despite the presence of gene flow. We reject both major hypotheses proposed to explain diversification in the Caatinga. Surprisingly, our results revealed a striking complex diversification pattern where the Northeast lineage originated as a founder effect from a few individuals located along the edge of the Southwest lineage that eventually expanded throughout the Caatinga. The Southwest lineage is more diverse, older and associated with the Cerrado-Caatinga boundaries. Finally, we suggest that C. ocellifer from the Caatinga is composed of two distinct species. Our data support speciation in the presence of gene flow and highlight the role of environmental gradients in the diversification process.