Gene and species trees of a Neotropical group of treefrogs: Genetic diversification in the Brazilian Atlantic Forest and the origin of a polyploid species

Following the footsteps of Burmeister's leaf frog (Phyllomedusa burmeisteri) in the Atlantic forest of Brazil

Amphibians are organisms which mainly have a biphasic life cycle. When at the larval stage, their habitat is generally aquatic, and when adults, they become terrestrial. Pond-breeding amphibians are sensitive to some disturbances in their environment which lead to the decline of a population. The interactions between the species and their environment are performed through movement. Movement ecology combines and explains the movement data of organisms with biotic and abiotic factors and because of this, knowing the movement of these creatures is of great ecological importance. We used the spool-and-line methodology in individuals of the treefrog Phyllomedusa burmeisteri, at the Reserva Ecologica Michelin, located in the southern region of Bahia in Brazil to study their movement patterns in different environments inside and outside of the forest. We monitored 19 P. burmeisteri individuals that presented a mean total movement distance of 2160.76 cm (S.D. 1152.42). We found no significant difference in the trajectories of individuals in forested and open areas, as well as a positive relationship between the distances individuals moved and their weight only in forested areas. no relationship between distance and weight of these individuals. We observed that individuals followed non-linear paths and the number of steps from one place to another varied among individuals. Our movement ecology data allows us to answer questions about short-term movement patterns of Phyllomedusa burmeisteri. This is the first step to start understanding the spatial cognition of treefrogs from the Atlantic Forest and to fill gaps about life habits of these frogs. Information on the movement patterns of a species, as well as its home range can help to create conservation strategies, regarding the creation or delimitation of protected areas, for example.

Performance of intron 7 of the β-fibrinogen gene for phylogenetic analysis: An example using gladiator frogs, Boana Gray, 1825 (Anura, Hylidae, Cophomantinae)

Boana, the third largest genus of Hylinae, has cryptic morphological species. The potential applicability of b-fibrinogen intron 7 – FGBI7 is explored to propose a robust phylogeny of Boana. The phylogenetic potential of FGBI7 was evaluated using maximum parsimony, MrBayes, and maximum likelihood analysis. Comparison of polymorphic sites and topologies obtained with concatenated analysis of FGBI7 and other nuclear genes (CXCR4, CXCR4, RHO, SIAH1, TYR, and 28S) allowed evaluation of the phylogenetic signal of FGBI7. Mean evolutionary rates were calculated using the sequences of the mitochondrial genes ND1 and CYTB available for Boana in GenBank. Dating of Boana and some of its groups was performed using the RelTime method with secondary calibration. FGBI7 analysis revealed high values at informative sites for parsimony. The absolute values of the mean evolutionary rate were higher for mitochondrial genes than for FGBI7. Dating of congruent Boana groups for ND1, CYTB, and FGBI7 revealed closer values between mitochondrial genes and slightly different values from those of FGBI7. Divergence times of basal groups tended to be overestimated when mtDNA was used and were more accurate when nDNA was used. Although there is evidence of phylogenetic potential arising from concatenation of specific genes, FGBI7 provides well-resolved independent gene trees. These results lead to a paradigm for linking data in phylogenomics that focuses on the uniqueness of species histories and ignores the multiplicities of individual gene histories.

Draft genome and multi-tissue transcriptome assemblies of the Neotropical leaf-frog Phyllomedusa bahiana

Amphibians are increasingly threatened worldwide, but the availability of genomic resources that could be crucial for implementing informed conservation practices lags well behind that for other vertebrate groups. Here, we describe draft de novo genome, mitogenome, and transcriptome assemblies for the Neotropical leaf-frog Phyllomedusa bahiana native to the Brazilian Atlantic Forest and Caatinga. We used a combination of PacBio long reads and Illumina sequencing to produce a 4.74-Gbp contig-level genome assembly, which has a contiguity comparable to other recent nonchromosome level assemblies. The assembled mitogenome comprises 16,239 bp and the gene content and arrangement are similar to other Neobratrachia. RNA-sequencing from 8 tissues resulted in a highly complete (86.3%) reference transcriptome. We further use whole-genome resequencing data from P. bahiana and from its sister species Phyllomedusa burmeisteri, to demonstrate how our assembly can be used as a backbone for population genomics studies within the P. burmeisteri species group. Our assemblies thus represent important additions to the catalog of genomic resources available from amphibians.

Molecular data reveal multiple lineages of Scinax nebulosus (Spix, 1824) (Anura: Hylidae) with Plio-Pleistocene diversification in different Brazilian regions

To understand the organism's history, we can start assessing the complexity of the biome where they occur. In this study, we used a region of the mitochondrial genome, the rRNA 16S, to evaluate the genetic differentiation in Scinax nebulosus along with its geographical range highlighting important Brazilian biomes as Restinga, Cerrado, Amazon, and Atlantic Forest. Geographically structured genetic divergence was observed within the species S. nebulosus. The values of the fixation index (Фst) and the pairwise Fst index were high and significant regarding this structuring. Besides, the haplotype network corroborates these results with the haplotypes arrangement found by separating the S. nebulosus populations in two major groups: North and Northeast. The lineage delimitation analyses indicate the occurrence of several lineages with divergence mainly between the samples from the Northeast group. Thus, we can suggest that S. nebulosus may present itself as a group of cryptic species due to the genetic characteristics found. The existence of a mosaic of heterogeneous habitats may explain the genetic divergence found, which justifies the existence of cryptic species in this group. However, this hypothesis needs more detail in molecular studies, including large sample sizes and other population and demographic analyses.

Modulation of the cholinergic pathway induced by skin secretion of Phyllomedusa iheringii Boulenger, 1885 in a vertebrate model

Amphibians represent one of the main natural sources of bioactive molecules of interest to biotechnological research. The Phyllomedusidae family has several species occurring in Brazil and some studies demonstrate the biological potential of poisons of these species, however many still need to be characterized. Phyllomedusa iheringii is endemic in Brazilian and Uruguayan Pampa Biome and has little data in the literature regarding the action of its poison on experimental organisms. Thus, the present work evaluates the biological activity of P. iheringii secretion on the central and peripheral nervous system of a vertebrate model. The skin secretions of P. iheringii (SSPI) were collected through manual compression and electrical stimulation of the animal's bodies. The resulting content was used in neurobiological tests searching for modulatory effects on the main pathways involved in the neurotoxicity mechanism of vertebrates. SSPI affected the contraction force of the chick biventer cervicis muscle (Gallus gallus domesticus) at some concentrations used (5, 10, and 12 μg/mL). In slices from the cerebral cortex of G. gallus domesticus an increase in cell viability was observed after treatment with SSPI (10 μg/mL) and a neuroprotective effect when treated simultaneously with hydrogen peroxide (H₂O₂), Neostigmine (NEO) and Trichlorfon (TRI). The cholinergic pathway is possibly the main pathway modulated by SSPI since assays with the cerebral cortex and biventer cervicis muscle demonstrated the increased activity of the enzyme acetylcholinesterase (AChE) (SSPI 10 μg/mL and 12 μg/mL, respectively). SSPI (10 μg/mL) also prevented the modulation of NEO and TRI, two recognized anticholinesterase agents, in AChE activity in slices of the cerebral cortex. Therefore, our results have demonstrated the unpublished biotechnological potential of P. iheringii over the vertebrate model and its modulation on the nervous system, with apparent action on the cholinergic pathway.

The Complex History of Genome Duplication and Hybridization in North American Gray Treefrogs

Polyploid speciation has played an important role in evolutionary history across the tree of life, yet there remain large gaps in our understanding of how polyploid species form and persist. Although systematic studies have been conducted in numerous polyploid complexes, recent advances in sequencing technology have demonstrated that conclusions from data-limited studies may be spurious and misleading. The North American gray treefrog complex, consisting of the diploid Hyla chrysoscelis and the tetraploid H. versicolor, has long been used as a model system in a variety of biological fields, yet all taxonomic studies to date were conducted with only a few loci from nuclear and mitochondrial genomes. Here, we utilized anchored hybrid enrichment and high-throughput sequencing to capture hundreds of loci along with whole mitochondrial genomes to investigate the evolutionary history of this complex. We used several phylogenetic and population genetic methods, including coalescent simulations and testing of polyploid speciation models with approximate Bayesian computation, to determine that H. versicolor was most likely formed via autopolyploidization from a now extinct lineage of H. chrysoscelis. We also uncovered evidence of significant hybridization between diploids and tetraploids where they co-occur, and show that historical hybridization between these groups led to the re-formation of distinct polyploid lineages following the initial whole-genome duplication event. Our study indicates that a wide variety of methods and explicit model testing of polyploid histories can greatly facilitate efforts to uncover the evolutionary history of polyploid complexes.

Phylogenetic relationships of the genus Mischonyx Bertkau, 1880, with taxonomic changes and three new species description (Opiliones: Gonyleptidae)

The type species of Mischonyx Bertkau 1880, Mischonyx squalidus, was described based on a juvenile. The holotype is lost. Based on a revision of publications, the genus includes 12 species, all in Brazil. The objectives of this research are: to propose a phylogenetic hypothesis for Mischonyx based on Total Evidence (TE); propose taxonomic changes based on the phylogeny; and analyze the phylogenetic hypothesis biogeographically. Using the exemplar approach to taxon selection, we studied 54 specimens, 15 outgroups and 39 ingroup taxa using seven molecular markers (28S, 12S and 16S ribosomal genes, citochrome oxidase subunit I gene, carbamoyl-phosphate synthetase gene, internal transcribed spacer subunit 2 and histone H3 gene), totaling 3,742 bp, and 128 morphological characters. We analyzed the dataset under three optimality criteria: Maximum likelihood (ML), Maximum parsimony (MP) and Bayesian. We discuss the transformation of character states throughout the phylogeny, the different phylogenetic hypotheses using different datasets and the congruence of evidence between the clades obtained by the phylogenetic analysis and the biogeographical hypothesis for the Atlantic Forest areas of endemism. We estimate that Mischonyx clade diverged 50.53 Mya, and inside the genus there are two major clades. One of them cointains species from Paraná, Santa Catarina, South of São Paulo and Serra do Mar Areas of Endemism and the other has species from Espinhaço, Bocaina, South coast of Rio de Janeiro and Serra dos Órgãos Areas of Endemism. The first split inside these two clades occurred at 48.94 and 44.80 Mya, respectively. We describe three new species from Brazil: Mischonyx minimus sp. nov. (type locality: Petrópolis, Rio de Janeiro), Mischonyx intervalensis sp. nov. (type locality: Ribeirão Grande, São Paulo) and Mischonyx tinguaensis sp. nov (type locality: Nova Iguaçu, Rio de Janeiro). The genus Urodiabunus Mello-Leitão, 1935 is considered a junior synonym of Mischonyx. Weyhia spinifrons Mello-Leitão, 1923; Weyhia clavifemur Mello-Leitão, 1927 and Geraeocormobius reitzi Vasconcelos, 2005 were transferred to Mischonyx. Mischonyx cuspidatus (Roewer, 1913) is a junior synonym of M. squalidus Bertkau, 1880. In the results of the phylogenetic analyses, Gonyleptes antiquus Mello-Leitão, 1934 (former Mischonyx antiquus) does not belong in Mischonyx and its original combination is re-established. As it is now defined, Mischonyx comprises 17 species, with seven new combinations.

Systematics and phylogeography of the Brazilian Atlantic Forest endemic harvestmen Neosadocus Mello-Leitão, 1926 (Arachnida: Opiliones: Gonyleptidae)

Neosadocus harvestmen are endemic to the Southern Brazilian Atlantic Forest. Although they are conspicuous and display great morphological variation, their evolutionary history and the biogeographical events underlying their diversification and distribution are still unknown. This contribution about Neosadocus includes the following: a taxonomic revision; a molecular phylogenetic analysis using mitochondrial and nuclear markers; an investigation of the genetic structure and species' diversity in a phylogeographical framework. Our results show that Neosadocus is a monophyletic group and comprises four species: N. bufo, N. maximus, N. robustus and N. misandrus (which we did not find on fieldwork and only studied the female holotype). There is astonishing male polymorphism in N. robustus, mostly related to reproductive strategies. The following synonymies have resulted from this work: "Bunoweyhia" variabilis Mello-Leitão, 1935 = Neosadocus bufo (Mello-Leitão, 1926); and "Bunoweyhia" minor Mello-Leitão, 1935 = Neosadocus maximus (Giltay, 1928). Most divergences occurred during the Miocene, a geological epoch marked by intense orogenic and climatic events in the Brazilian Atlantic Forest. Intraspecific analyses indicate strong population structure, a pattern congruent with the general behavior and physiological constraints of Neotropical harvestmen.

North-south and climate-landscape-associated pattern of population structure for the Atlantic Forest White Morpho butterflies

Atlantic Forest White Morpho butterflies, currently classified as Morpho epistrophus and M. iphitus, are endemic to the Atlantic Forest, where they are widely distributed throughout heterogeneous environmental conditions. Studies with endemic butterflies allow to elucidate questions on both patterns of diversity distribution and current and past processes acting on insect groups in this biodiversity hotspot. In the present study, we characterized one mtDNA marker (COI sequences) and developed 11 polymorphic loci of microsatellite for 22 sampling locations distributed throughout the entire Atlantic Forest domain. We investigated both the taxonomic limits of taxa classified as White Morpho and the structure and distribution of the genetic diversity throughout their populations. Genetic markers and distribution data failed to identify species diversification, population structure, or isolation among subpopulations attributed to different taxa proposed for the White Morpho, suggesting that the current distinction between two species is unreasonable. The Bayesian coalescent tree based on COI sequences also failed to recover monophyletic clades for the putative species, and pointed instead to a north-south oriented pattern of genetic structure, with the northern clade coalescing later than the southern clade. Northern samples also showed more intragroup structure than southern samples based on mtDNA data. Clustering tests based on microsatellites indicated the existence of three genetic clusters, with turnover between the states of Paraná and São Paulo. The north-south pattern found for the White Morpho populations is showed for the first time to a endemic AF insect and coincides with the two different bioclimatic domains previously described for vertebrates and plants. Population structure observed for these butterflies is related to climate- and landscape-associated variables, mainly precipitation and elevation.

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.

Revisiting the evolution of the North American tetraploid treefrog (Hyla versicolor)

Hyla chrysoscelis and H. versicolor are common treefrogs in eastern North America and are a cryptic diploid-tetraploid species pair. They are morphologically identical but H. versicolor is a tetraploid. They can be identified acoustically by the male's advertisement mating call, which has a pulse repetition rate that has twice as many pulses per second in the diploid species, H. chrysoscelis. We used isozymes, microsatellite DNA alleles, and mitochondrial cytochrome b sequences to test the hypothesis that gene exchange occurs between the diploid and tetraploid species in sympatric populations. Each method provided results that are best explained by occasional hybridization of female H. versicolor and male H. chrysoscelis. We propose that H. versicolor first arose from an autotriploid H. chrysoscelis female that produced unreduced triploid eggs. After H. versicolor became established, genes could be passed from H. chrysoscelis to H. versicolor in sympatric populations when these species hybridize. Their F₁ female progeny produce unreduced triploid eggs that are fertilized by haploid H. chrysoscelis sperm to reconstitute H. versicolor. Genes can be passed from diploid H. chrysoscelis to tetraploid H. versicolor in sympatric populations.

Areas of endemism of land planarians (Platyhelminthes: Tricladida) in the Southern Atlantic Forest

Areas of endemism (AoE) are the main study units in analytical biogeographic methods, and are often defined as an area with two or more endemic species living in them, presenting substantial congruence among their range limits. We explored the distribution of land planarians (Geoplanidae, Platyhelminthes) across the southern region of the Brazilian Atlantic forest (from the state of Rio de Janeiro, to the state of Rio Grande do Sul) utilizing DaSilva's et al. (2015) protocol. We used two methods, Endemicity Analysis (EA), and Geographical Interpolation of Endemism (GIE). We identified nine AoE of terrestrial flatworms in the Southern Atlantic forest. Performance of the methodologies is discussed. These AoE of land planarians can be explained through vicariance events combined with their physiological and ecological own limitations. Interestingly, these AoE are congruent with fine-scale approaches such as that with harvestmen. Most land planarians have revealed to present a very small distributional range evidencing their potential as a good model for fine-scale studies of AoE.

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.

Cryptic diversity and ancient diversification in the northern Atlantic Forest Pristimantis (Amphibia, Anura, Craugastoridae)

The Neotropical region is known both for its megadiverse fauna and for the significant deficiency of our knowledge on species limits. The Amazon and Atlantic Forest are the two most diverse and large rainforests in South America, and they harbor many groups of sister species and sister genera. The frog genus Pristimantis is the most speciose genus of terrestrial vertebrates with 546 species, but only three of them occur in the Atlantic forest. Herein, we investigate the diversification history and phylogenetic relationship among the Atlantic Forest Pristimantis lineages in a spatial-temporal framework, using mitochondrial and nuclear genes. Our results reveal a remarkable hidden diversity, with nine highly structure lineages that may correspond to undescribed species, with many cases of sympatry among these divergent lineages. Atlantic forest Pristimantis form a monophyletic group that started to diversify over 40 million years ago. This ancient group shows diversification events that remount the early bursts of the Atlantic Forest diversification history, as well as lineage diversification likely resulting from recent Pleistocene climatic fluctuations. Future work must concentrate in comparing these lineages under an integrative framework including morphology, advertisement calls and other ecology traits to confidently delimit species of Pristimantis in the Atlantic Forest.

Historical biogeography and multi-trait evolution in miniature toadlets of the genus Brachycephalus (Anura: Brachycephalidae)

Evolutionary changes towards a miniaturized body plan may directly affect other important phenotypic traits related to the physiology, behaviour and ecology of organisms. The frog genus Brachycephalus is an outstanding example of a radiation of miniaturized species endemic to the Brazilian Atlantic Forest. We inferred ancestral states and historical changes in body size, body colour and hyperossification to test hypotheses about diversification and selective environmental mechanisms leading to the evolution of these specialized traits. The ancestral distribution was associated with high-elevation regions in the northern Serra do Mar mountain range, and diversification in the genus was coincident with important geological and climatic events during the history of the Atlantic Forest. The dynamic historical changes provided an opportunity for multiple lowland lineages and for speciation via dispersal and vicariance in multiple invasions of the highlands. The ancestral Brachycephalus was reconstructed as miniaturized and dull coloured, without hyperossification in the skin, skull or postcranial skeleton. A parallel evolution of phenotypic traits has occurred in northern and southern Atlantic Forest lineages, beginning in the Miocene. Shifts in body size are not related to elevation range or latitude. However, we found a significant correlation between the evolution of hyperossification and aposematism with increasing body size.

Drivers of bromeliad leaf and floral bract variation across a latitudinal gradient in the Atlantic Forest

AIM

Understanding the complex interaction and relative contributions of factors involved in species and trait diversification is crucial to gain insights into the evolution of Neotropical biodiversity. Here, we investigated the drivers of morphological variation in bromeliads along a latitudinal gradient in a biodiversity hotspot.

LOCATION

Atlantic Forest, Brazil.

TAXON

A species complex in the genus Vriesea (Bromeliaceae).

METHODS

We measured shape and size variation for 208 floral bracts and 176 leaves in individuals from 14 localities using geometric morphometrics. We compiled data for two chloroplast regions (matK and trnL-F) from 89 individuals to assess genetic diversity, population structure and phylogenetic relationships. We tested the influence of climate, altitude and genetic distance on morphological traits using linear statistical models.

RESULTS

Temperature seasonality is a main driver of floral bract shape. Together with precipitation, it also explains changes in leaf size across the latitudinal gradient. Shifts in morphological traits are correlated with genetic structure and partly support the recent taxonomic delimitation proposed for the species complex. The species started to diversify in the Pliocene ca. 5 Mya. We detected a phylogeographical break in species distribution into northern and southern clades between the Bocaina region and the southern portion of the Atlantic Forest.

MAIN CONCLUSIONS

We identify how geography and environmental changes through time shape floral bracts and leaves in similar ways. At highly seasonal sites with lower annual precipitation (in the southern subtropical portion of the Atlantic Forest), leaves are larger and floral bracts are wide-elliptic, making them better suited for increased water accumulation. In contrast, at less seasonal sites (in the tropical north, where rainfall is more abundant and temperatures are higher), leaves are narrower and floral bracts are lanceolate-shaped, facilitating water drainage. The biogeographical break we identified suggests a role of tectonic activity and climatic oscillations in promoting species divergence and diversification.

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.

Fish diversification at the pace of geomorphological changes: evolutionary history of western Iberian Leuciscinae (Teleostei: Leuciscidae) inferred from multilocus sequence data

The evolutionary history of western Iberian Leuciscinae, obligatory freshwater fish, is directly linked to the evolution of the hydrographic network of the Iberian Peninsula after its isolation from the rest of Europe, which involved dramatic rearrangements such as the transition from endorheic lakes to open basins draining to the Atlantic. Previous phylogenetic research on western Iberian leuciscines, using mainly mitochondrial DNA and more recently one or two nuclear genes, has found contradictory results and there remain many unresolved issues regarding species relationships, taxonomy, and evolutionary history. Moreover, there is a lack of integration between phylogenetic and divergence time estimates and information on the timing of geomorphological changes and paleobasin rearrangements in the Iberian Peninsula. This study presents the first comprehensive fossil-calibrated multilocus coalescent species tree of western Iberian Leuciscinae (including 14 species of Achondrostoma, Iberochondrostoma, Pseudochondrostoma and Squalius endemic to the Iberian Peninsula, seven of which endemic to Portugal) based on seven nuclear genes, and from which we infer their biogeographic history by comparing divergence time estimates to known dated geological events. The phylogenetic pattern suggests slow-paced evolution of leuciscines during the Early-Middle Miocene endorheic phase of the main Iberian river basins, with the shift to exorheism in the late Neogene-Quaternary allowing westward dispersals that resulted in many cladogenetic events and a high rate of endemism in western Iberia. The results of this study also: (i) confirm the paraphyly of S. pyrenaicus with respect to S. carolitertii, and thus the possible presence of a new taxon in the Portuguese Tagus currently assigned to S. pyrenaicus; (ii) support the taxonomic separation of the Guadiana and Sado populations of S. pyrenaicus; (iii) show the need for further population sampling and taxonomic research to clarify the phylogenetic status of A. arcasii from the Minho basin and of the I. lusitanicum populations in the Sado and Tagus basins; and (iv) indicate that A. occidentale, I. olisiponensis and P. duriensis are the most ancient lineages within their respective genera.

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.

Profound genetic divergence and asymmetric parental genome contributions as hallmarks of hybrid speciation in polyploid toads

The evolutionary causes and consequences of allopolyploidization, an exceptional pathway to instant hybrid speciation, are poorly investigated in animals. In particular, when and why hybrid polyploids versus diploids are produced, and constraints on sources of paternal and maternal ancestors, remain underexplored. Using the Palearctic green toad radiation (including bisexually reproducing species of three ploidy levels) as model, we generate a range-wide multi-locus phylogeny of 15 taxa and present four new insights: (i) at least five (up to seven) distinct allotriploid and allotetraploid taxa have evolved in the Pleistocene; (ii) all maternal and paternal ancestors of hybrid polyploids stem from two deeply diverged nuclear clades (6 Mya, 3.1-9.6 Mya), with distinctly greater divergence than the parental species of diploid hybrids found at secondary contact zones; (iii) allotriploid taxa possess two conspecific genomes and a deeply diverged allospecific one, suggesting that genomic imbalance and divergence are causal for their partly clonal reproductive mode; (iv) maternal versus paternal genome contributions exhibit asymmetry, with the maternal nuclear (and mitochondrial) genome of polyploids always coming from the same clade, and the paternal genome from the other. We compare our findings with similar patterns in diploid/polyploid vertebrates, and suggest deep ancestral divergence as a precondition for successful allopolyploidization.

Historical relationships of areas of endemism of the Brazilian Atlantic rain forest: a cladistic biogeographic analysis of harvestman taxa (Arachnida: Opiliones)

Based on a cladistic biogeographic analysis of 6 species-level phylogenies of harvestman taxa, we searched for congruence in the historical relationships of 12 areas of endemism of the Brazilian Atlantic Rain Forest. We constructed general area cladograms using Primary Brooks Parsimony Analysis (BPA), BPA of nodes, and paralogy-free subtree analysis. These analyses resulted in 6 general area cladograms, that allow to infer a general pattern of the relationships among areas of endemism from the Brazilian Atlantic Rain Forest. Northern areas resulted related basally showing main disjunctions at the Doce River Valley and Todos os Santos Bay/São Francisco River Valley. The remaining areas of endemism were included in a southern and a southeastern block, separated by the Ribeira do Iguape Valley. Incongruence Length Differences tests showed no significant incongruence among the resulting cladograms and other matrix partitions. We concluded that tectonism and ancient marine transgressions were the probable processes responsible for the main disjunctions, whereas Neogene refugia seem to have caused the more recent disjunctions. The general pattern and redundancy in area relationships suggest a model of main reiterative barriers in diversification at multiple times for the evolution of the Atlantic Rain Forest. The renewal of cladistic biogeography and the search for common biogeographic patterns are discussed.

Comparative phylogeography in the Atlantic forest and Brazilian savannas: pleistocene fluctuations and dispersal shape spatial patterns in two bumblebees

Background

Bombus morio and B. pauloensis are sympatric widespread bumblebee species that occupy two major Brazilian biomes, the Atlantic forest and the savannas of the Cerrado. Differences in dispersion capacity, which is greater in B. morio, likely influence their phylogeographic patterns. This study asks which processes best explain the patterns of genetic variation observed in B. morio and B. pauloensis, shedding light on the phenomena that shaped the range of local populations and the spatial distribution of intra-specific lineages.

Results

Results suggest that Pleistocene climatic oscillations directly influenced the population structure of both species. Correlative species distribution models predict that the warmer conditions of the Last Interglacial contributed to population contraction, while demographic expansion happened during the Last Glacial Maximum. These results are consistent with physiological data suggesting that bumblebees are well adapted to colder conditions. Intra-specific mitochondrial genealogies are not congruent between the two species, which may be explained by their documented differences in dispersal ability.

Conclusions

While populations of the high-dispersal B. morio are morphologically and genetically homogeneous across the species range, B. pauloensis encompasses multiple (three) mitochondrial lineages, and show clear genetic, geographic, and morphological differences. Because the lineages of B. pauloensis are currently exposed to distinct climatic conditions (and elevations), parapatric diversification may occur within this taxon. The eastern portion of the state of São Paulo, the most urbanized area in Brazil, represents the center of genetic diversity for B. pauloensis.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0803-0) contains supplementary material, which is available to authorized users.

Geographical and altitudinal distribution of Brachycephalus (Anura: Brachycephalidae) endemic to the Brazilian Atlantic Rainforest

Mountains of the Brazilian Atlantic Forest can act as islands of cold and wet climate, leading to the isolation and speciation of species with low dispersal capacity, such as the toadlet species of the genus Brachycephalus. This genus is composed primarily by diurnal species, with miniaturized body sizes (<2.5 cm), inhabiting microhabitats in the leaf litter of montane forests. Still, little is known about the geographical distribution, altitudinal range, and ecological limits of most Brachycephalus species. In this study, we review the available data on the geographical and altitudinal distribution of Brachycephalus based on occurrence records compiled from literature and museums, both for the genus as a whole and separately for the three recently proposed groups of species (ephippium, didactylus, and pernix). The final ensemble dataset comprised 333 records, 120 localities, 28 described species, and six undescribed ones. Species were recorded in six relief units, the richest of which being the Serra do Mar, with 30 species. When the Serra do Mar is subdivided into three subunits, Northern, Central and Southern Serra do Mar, the number of species increase from north to the south, with records of six, nine, and 16 species, respectively. We were able to estimate the extent of occurrence of nearly half of the described species, and the resulting estimates indicate that many of them show remarkably small ranges, some of which less than 50 ha. Brachycephalus species are present from sea level to roughly 1,900 m a.s.l., with the highest richness being found between 751 and 1,000 m a.s.l. (21 spp.). The species with the broadest altitudinal range were B. didactylus (1,075 m) and Brachycephalus sp. 1 (1,035 m), both in the didactylus group, and B. ephippium (1,050 m), of the ephippium group. The broadest altitudinal amplitude for species of the pernix group was recorded for B. brunneus (535 m). The lowest altitudinal records for the pernix group were at 845 m a.s.l. in the state of Paraná and at 455 m a.s.l. in the state of Santa Catarina. The altitudinal occurrence in the pernixspecies group seems to decrease southward. Syntopy between species is also reviewed.

Chromosome Banding in Amphibia. XXXIV. Intrachromosomal Telomeric DNA Sequences in Anura

The mitotic chromosomes of 4 anuran species were examined by various classical banding techniques and by fluorescence in situ hybridization using a (TTAGGG)n repeat. Large intrachromosomal telomeric sequences (ITSs) were demonstrated in differing numbers and chromosome locations. A detailed comparison of the present results with numerous published and unpublished data allowed a consistent classification of the various categories of large ITSs present in the genomes of anurans and other vertebrates. The classification takes into consideration the total numbers of large ITSs in the karyotypes, their chromosomal locations and their specific distribution patterns. A new category of large ITSs was recognized to exist in anuran species. It consists of large clusters of ITSs located in euchromatic chromosome segments, which is in clear contrast to the large ITSs in heterochromatic chromosome regions known in vertebrates. The origin of the different categories of large ITSs in heterochromatic and euchromatic chromosome regions, their mode of distribution in the karyotypes and evolutionary fixation in the genomes, as well as their cytological detection are discussed.

Multilocus phylogeography of the common midwife toad, Alytes obstetricans (Anura, Alytidae): Contrasting patterns of lineage diversification and genetic structure in the Iberian refugium

Recent investigations on the evolutionary history of the common midwife toad (Alytes obstetricans) revealed high levels of geographically structured genetic diversity but also a situation where delineation of major historical lineages and resolution of their relationships are much more complex than previously thought. We studied sequence variation in one mitochondrial and four nuclear genes throughout the entire distribution range of all recognized A. obstetricans subspecies to infer the evolutionary processes that shaped current patterns of genetic diversity and population subdivision. We found six divergent, geographically structured mtDNA haplogroups diagnosing population lineages, and varying levels of admixture in nuclear markers. Given the timeframe inferred for the splits between major lineages, the climatic and environmental changes that occurred during the Pleistocene seem to have shaped the diversification history of A. obstetricans. Survival of populations in allopatric refugia through the Ice Ages supports the generality of the "refugia-within-refugia" scenario for the Iberian Peninsula. However, lineages corresponding to subspecies A. o. almogavarii, A. o. pertinax, A. o. obstetricans, and A. o. boscai responded differently to Pleistocene climatic oscillations after diverging from a common ancestor. Alytes o. obstetricans expanded northward from a northern Iberian refugium through the western Pyrenees, leaving a signal of contrasting patterns of genetic diversity, with a single mtDNA haplotype north of the Pyrenees from SW France to Germany. Both A. o. pertinax and A. o. boscai are widespread and genetically diverse in Iberia, the latter comprising two divergent lineages with a long independent history. Finally, A. o. almogavarii is mostly restricted to the north-eastern corner of Iberia north of the Ebro river, with additional populations in a small region in south-eastern France. This taxon exhibits unparalleled levels of genetic diversity and little haplotype sharing with other lineages, suggesting a process of incipient speciation.

Prediction of phylogeographic endemism in an environmentally complex biome

Phylogeographic endemism, the degree to which the history of recently evolved lineages is spatially restricted, reflects fundamental evolutionary processes such as cryptic divergence, adaptation and biological responses to environmental heterogeneity. Attempts to explain the extraordinary diversity of the tropics, which often includes deep phylogeographic structure, frequently invoke interactions of climate variability across space, time and topography. To evaluate historical versus contemporary drivers of phylogeographic endemism in a tropical system, we analyse the effects of current and past climatic variation on the genetic diversity of 25 vertebrates in the Brazilian Atlantic rainforest. We identify two divergent bioclimatic domains within the forest and high turnover around the Rio Doce. Independent modelling of these domains demonstrates that endemism patterns are subject to different climatic drivers. Past climate dynamics, specifically areas of relative stability, predict phylogeographic endemism in the north. Conversely, contemporary climatic heterogeneity better explains endemism in the south. These results accord with recent speleothem and fossil pollen studies, suggesting that climatic variability through the last 250 kyr impacted the northern and the southern forests differently. Incorporating sub-regional differences in climate dynamics will enhance our ability to understand those processes shaping high phylogeographic and species endemism, in the Neotropics and beyond.

Delimiting areas of endemism through kernel interpolation

We propose a new approach for identification of areas of endemism, the Geographical Interpolation of Endemism (GIE), based on kernel spatial interpolation. This method differs from others in being independent of grid cells. This new approach is based on estimating the overlap between the distribution of species through a kernel interpolation of centroids of species distribution and areas of influence defined from the distance between the centroid and the farthest point of occurrence of each species. We used this method to delimit areas of endemism of spiders from Brazil. To assess the effectiveness of GIE, we analyzed the same data using Parsimony Analysis of Endemism and NDM and compared the areas identified through each method. The analyses using GIE identified 101 areas of endemism of spiders in Brazil GIE demonstrated to be effective in identifying areas of endemism in multiple scales, with fuzzy edges and supported by more synendemic species than in the other methods. The areas of endemism identified with GIE were generally congruent with those identified for other taxonomic groups, suggesting that common processes can be responsible for the origin and maintenance of these biogeographic units.

Molecular cytogenetics and phylogenetic analysis of Brazilian leaf frog species of the genera Phyllomedusa and Phasmahyla (Hylidae: Phyllomedusinae)

In this study we describe the karyotypes and molecular phylogenetic relationships of the leaf frogs Phyllomedusa bahiana Lutz, 1925, Phyllomedusa burmeisteri Boulenger, 1882, Phyllomedusa nordestina Caramaschi, 2006, Phyllomedusa rohdei Mertens, 1926, Phyllomedusa hypochondrialis (Daudin, 1800), and Phasmahyla spectabilis Cruz, Feio and Nascimento, 2008. We analyzed the karyotypes using C-banding, fluorochrome staining, and fluorescence in situ hybridization of telomeric probe, and inferred phylogeny using nuclear tyrosinase and mitochondrial 16S rDNA sequences. Heterochromatin distribution in P. nordestina diverged from the other species, and P. bahiana and P. rohdei showed evident interstitial telomere sequences. Molecular analyzes confirmed the current taxonomic classification, grouping mitochondrial DNA sequences of each species, and usually without haplotype sharing in the nuclear gene. We also extended the distribution of P. burmeisteri to northern Bahia state and restricted P. bahiana to southern Bahia state, with a discrete extension of the range of P. bahiana to the north and northeast of Minas Gerais state. The tyrosinase haplotype network showed a haplotype shared between P. bahiana and P. burmeisteri from Porto Seguro, Bahia. Based on this, we suggest a new distribution in the overlapping area between these two species, which according to our data ranges between Porto Seguro and Camacan, in Bahia state.

Cryptic genetic diversity is paramount in small-bodied amphibians of the genus Euparkerella (Anura: Craugastoridae) endemic to the Brazilian Atlantic forest

Morphological similarity associated to restricted distributions and low dispersal abilities make the direct developing “Terrarana” frogs of the genus Euparkerella a good model for examining diversification processes. We here infer phylogenetic relationships within the genus Euparkerella, using DNA sequence data from one mitochondrial and four nuclear genes coupled with traditional Bayesian phylogenetic reconstruction approaches and more recent coalescent methods of species tree inference. We also used Bayesian clustering analysis and a recent Bayesian coalescent-based approach specifically to infer species delimitation. The analysis of 39 individuals from the four known Euparkerella species uncovered high levels of genetic diversity, especially within the two previously morphologically-defined E. cochranae and E. brasiliensis. Within these species, the gene trees at five independent loci and trees from combined data (concatenated dataset and the species tree) uncovered six deeply diverged and geographically coherent evolutionary units, which may have diverged between the Miocene and the Pleistocene. These six units were also uncovered in the Bayesian clustering analysis, and supported by the Bayesian coalescent-based species delimitation (BPP), and Genealogical Sorting Index (GSI), providing thus strong evidence for underestimation of the current levels of diversity within Euparkerella. The cryptic diversity now uncovered opens new opportunities to examine the origins and maintenance of microendemism in the context of spatial heterogeneity and/or human induced fragmentation of the highly threatened Brazilian Atlantic forest hotspot.

Cytogenetic analysis of Phyllomedusa distincta Lutz, 1950 (2n = 2x = 26), P. tetraploidea Pombal and Haddad, 1992 (2n = 4x = 52), and their natural triploid hybrids (2n = 3x = 39) (Anura, Hylidae, Phyllomedusinae)

Background

Natural polyploidy has played an important role during the speciation and evolution of vertebrates, including anurans, with more than 55 described cases. The species of the Phyllomedusa burmeisteri group are mostly characterized by having 26 chromosomes, but a karyotype with 52 chromosomes was described in P. tetraploidea. This species was found in sintopy with P. distincta in two localities of São Paulo State (Brazil), where triploid animals also occur, as consequence of natural hybridisation. We analyse the chromosomes of P. distincta, P. tetraploidea, and their triploid hybrids, to enlighten the origin of polyploidy and to obtain some evidence on diploidisation of tetraploid karyotype.

Results

Phyllomedusa distincta was 2n = 2x = 26, whereas P. tetraploidea was 2n = 4x = 52, and the hybrid individuals was 2n = 3x = 39. In meiotic phases, bivalents were observed in the diploid males, whereas both bivalents and tetravalents were observed in the tetraploid males. Univalents, bivalents or trivalents; metaphase II cells carrying variable number of chromosomes; and spermatids were detected in the testis preparations of the triploid males, indicating that the triploids were not completely sterile. In natural and experimental conditions, the triploids cross with the parental species, producing abnormal egg clutches and tadpoles with malformations. The embryos and tadpoles exhibited intraindividual karyotype variability and all of the metaphases contained abnormal constitutions. Multiple NORs, detected by Ag-impregnation and FISH with an rDNA probe, were observed on chromosome 1 in the three karyotypic forms; and, additionally, on chromosome 9 in the diploids, mostly on chromosome 8 in the tetraploids, and on both chromosome 8 and 9 in the triploids. Nevertheless, NOR-bearing chromosome 9 was detected in the tetraploids, and chromosome 9 carried active or inactive NORs in the triploids. C-banding, base-specific fluorochrome stainings with CMA₃ and DAPI, FISH with a telomeric probe, and BrdU incorporation in DNA showed nearly equivalent patterns in the karyotypes of P. distincta, P. tetraploidea, and the triploid hybrids.

Conclusions

All the used cytogenetic techniques have provided strong evidence that the process of diploidisation, an essential step for stabilising the selective advantages produced by polyploidisation, is under way in distinct quartets of the tetraploid karyotype.