Phylogenetic relationships of toads of the Rhinella granulosa group (Anura: Bufonidae): a molecular perspective with comments on hybridization and introgression

Comparative molecular and conventional cytogenetic analyses of three species of Rhinella (Anura; Bufonidae)

The genus Rhinella corresponds to a group of anurans characterized by numerous taxonomic and systemic challenges, leading to their organization into species complexes. Cytogenetic data for this genus thus far are limited to the diploid number and chromosome morphology, which remain highly conserved among the species. In this study, we analyse the karyotypes of three species of the genus Rhinella (Rhinella granulosa, Rhinella margaritifera, and Rhinella marina) using both classical (conventional staining and C-banding) and molecular (FISH-fluorescence in situ hybridization with 18S rDNA, telomeric sequences, and microsatellite probes) cytogenetic approaches. The aim of this study is to provide data that can reveal variations in the distribution of repetitive sequences that can contribute to understanding karyotypic diversification in these species. The results revealed a conserved karyotype across the species, with 2n = 22 and FN = 44, with metacentric and submetacentric chromosomes. C-banding revealed heterochromatic blocks in the pericentromeric region for all species, with a proximal block on the long arms of pairs 3 and 6 in R. marina and on the short arms of pairs 4 and 6 in R. margaritifera. Additionally, 18S rDNA probes hybridized to pair 5 in R. granulosa, to pair 7 in R. marina, and to pair 10 in R. margaritifera. Telomeric sequence probes displayed signals exclusively in the distal region of the chromosomes, while microsatellite DNA probes showed species-specific patterns. These findings indicate that despite a conserved karyotypical macrostructure, chromosomal differences exist among the species due to the accumulation of repetitive sequences. This variation may be attributed to chromosome rearrangements or differential accumulation of these sequences, highlighting the dynamic role of repetitive sequences in the chromosomal evolution of Rhinella species. Ultimately, this study emphasizes the importance of the role of repetitive DNAs in chromosomal rearrangements to elucidate the evolutionary mechanisms leading to independent diversification in the distinct phylogenetic groups of Rhinella.

A new species of terrestrial toad of the Rhinellafestae group (Anura, Bufonidae) from the highlands of the Central Cordillera of the Andes of Colombia

The genus Rhinella (Bufonidae) comprises 92 species of Neotropical toads. In Colombia, Rhinella is represented by 22 recognized species, of which nine belong to the Rhinellafestae group. Over the past decade, there has been increasing evidence of cryptic diversity within this group, particularly in the context of Andean forms. Specimens of Rhinella collected in high Andean forests on both slopes of the Central Cordillera in Colombia belong to an undescribed species, Rhinellakumandaysp. nov. Genetic analyses using the mitochondrial 16S rRNA gene indicated that the individuals belong to the festae species group. However, they can be distinguished from other closely related species such as Rhinellaparaguas and Rhinellatenrec by a combination of morphological traits including the presence of tarsal fold, a moderate body size, and substantial genetic divergence in the 16S rRNA gene (> 5%). Through this integrative approach, the specimens from the Central Cordillera of Colombia are considered an evolutionary divergent lineage that is sister to R.paraguas, and described as a new species. Rhinellakumandaysp. nov. is restricted to the Central Cordillera of Colombia inhabiting both slopes in the departments of Caldas and Tolima, in an elevational range between 2420 and 3758 m. With the recognition of this new species, the genus Rhinella now comprises 93 species with 23 of them found in Colombia, and ten species endemic to the country.

An overview of the osseous palmar sesamoid in Anura, with the particular case of some Rhinella species

Background

Sesamoids are generally regarded as structures that are not part of the tetrapod body plan. The presence of a palmar sesamoid is assumed to serve as a distribution point for the forces of the flexor digitorum communis muscle to the flexor tendons of the digits, which are embedded in the flexor plate. It has been considered that the palmar sesamoid is present in most anuran groups, and it has been suggested that it acts by inhibiting the closing of the palm, preventing grasping. Typical arboreal anuran groups lack a palmar sesamoid and flexor plate, a pattern shared with other tetrapod groups, which can retain a reduced sesamoid and flexor plate. We focus on the anatomical structure of the Rhinella group, which includes species that present an osseous palmar sesamoid and climb bushes or trees to avoid depredation or escape dangerous situations, and can exhibit scansorial and arboreal behaviors. We also add data on the bony sesamoids of 170 anuran species to study the anatomy and evolution of the osseous palmar sesamoid within this amphibian group. Our objective is to bring an overview of the osseous palmar sesamoid in anurans, unveiling the relationship between this element of the manus, its phylogeny, and the anuran habitat use.

Methods

Skeletal whole-mount specimens of Rhinella were cleared and double-dyed to describe the sesamoid anatomy and related tissues. We review and describe the palmar sesamoid of 170 anuran species from CT images downloaded from Morphosource.org, representing almost all Anuran families. We performed an standard ancestral state reconstruction by optimizing two selected characters (osseous palmar sesamoid presence, distal carpal palmar surface) along with the habitat use of the sampled taxa, using parsimony with Mesquite 3.7.

Results

Our primary finding is that sesamoid optimization in the anuran phylogeny revealed that its presence is associated with certain clades and not as widespread as previously anticipated. Additionally, we will also be delving into other important outcomes of our study that are relevant to those working in the field of anuran sesamoids. The osseous palmar sesamoid is present in the clade Bufonidae-Dendrobatidae-Leptodactylidae-Brachicephalidae that we named as PS clade, and also in the archeobatrachian pelobatoid Leptobranchium, all strongly terrestrial and burrowing species, though with exceptions. The osseous palmar sesamoid is always present in Bufonidae, but varies in form and size, depending on the mode that they use their manus, such as in the Rhinella margaritifera which has a cylindrical one and also grasping abilities that involve closing the manus. The scattered presence of the bony palmar sesamoid among anuran clades raises the question whether this sesamoid can be present with a different tissular composition in other groups.

Hybridization despite elaborate courtship behavior and female choice in Neotropical tree frogs

The mechanisms of hybridization can be elucidated by analyzing genotypes as well as phenotypes that could act as premating barriers, as the reproductive interactions among heterospecifics can alter the evolutionary history of species. In frogs, hybrids typically occur among species that reproduce explosively (in dense aggregations) with few opportunities for mate selection but are rare in species with elaborate courtship behaviors that may prevent erroneous mating. Using 21 microsatellite markers, we examined hybridization in the prolonged-breeding tree frogs Bokermannohyla ibitiguara and B. sazimai sampled within a contact zone in the Brazilian savanna (72 tadpoles; 74 adults). We also compared acoustic and morphological data. We confirmed both parental species genetically; STRUCTURE results confirmed 14 hybrids, 11 of which were second-generation according to NEWHYBRIDS, all with intermediate values of genetic dissimilarities compared to the parentals. Morphological and acoustic analyses revealed that hybrids showed variable but not necessarily intermediate phenotypes. Moreover, 2 hybrids exhibited call types different from parentals. The reproduction of B. ibitiguara involves territorial and aggressive males, elaborate courtships with acoustic and tactile stimuli, choosy females, and opportunistic strategies. Our study uncovers a rare case of viable hybridization among closely related frogs with such a combination of complex courtship behaviors and mate choice. We discuss the likely directionality and mechanisms behind this phenomenon, and highlight the importance of investigating hybridization even in species that show elaborate reproduction and female choice to advance our understanding of animal diversification.

Testing assertions of widespread introgressive hybridization in a clade of neotropical toads with low mate selectivity (Rhinella granulosa species group)

Discordance between different genomic regions, often identified through multilocus sequencing of selected markers, presents particular difficulties in identifying historical processes which drive species diversity and boundaries. Mechanisms causing discordance, such as incomplete lineage sorting or introgression due to interspecific hybridization, are better identified based on population-level genomic datasets. In the toads of the Rhinella granulosa species group, patterns of mito-nuclear discordance and potential hybridization have been reported by several studies. However, these patterns were proposed based on few loci, such that alternative mechanisms behind gene-tree heterogeneity cannot be ruled out. Using genome-wide ddRADseq loci from a subset of species within this clade, we found only partial concordance between currently recognized species-level taxon boundaries and patterns of genetic structure. While most taxa within the R. granulosa group correspond to clades, genetic clustering analyses sometimes grouped distinct taxonomic units into a single cluster. Moreover, levels of admixture between inferred clusters were limited and restricted to a single taxon pair which is best explained by incomplete lineage sorting as opposed to introgressive hybridization, according to D-statistics results. These findings contradict previous assertions of widespread cryptic diversity and gene flow within the R. granulosa clade. Lastly, our analyses suggest that diversification events within the Rhinella granulosa group mostly dated back to the early Pliocene, being generally younger than species divergences in other closely related clades that present high levels of cross-species gene flow. This finding uniquely contradicts common assertions that this young clade of toads exhibits interspecific hybridization.

Combined phylogenetic analysis of Pleurodema (Anura: Leptodactylidae: Leiuperinae)

The genus Pleurodema comprises 15 species distributed through the Neotropical region, from sea level up to 5000 m.a.s.l. A total-evidence analysis of Pleurodema is provided based on the parsimony criterion. The combined dataset included morphometric, phenotypic, and DNA evidence (34 taxa, 4441 characters). The parsimony analysis yielded one most-parsimonious tree. Pleurodema was recovered as a well-supported clade composed of two major subclades. One subclade has an identical topology to that of previous analyses, the P. brachyops Clade (P. alium, P. borellii, P. brachyops, P. cinereum, P. diplolister, and P. tucumanum). The other subclade includes the remaining nine species of the genus, exhibiting a topology different from that of previous studies. According to the present phylogeny, this second lineage is formed by the P. nebulosum Clade (P. guayapae + P. nebulosum), P. marmoratum, the re-defined P. thaul Clade (P. bufoninum, P. somuncurense, P. thaul) and the P. bibroni Clade (P. bibroni, P. cordobae, P. kriegi). The reproductive modes of Pleurodema represent a unique combination of features within Leiuperinae, including three egg-clutch structures, two types of amplexus, and lack of vocalization. Also, some species of Pleurodema have been considered fossorial, because they are capable of digging with their hind-limbs and remaining in self-made burrows during dry seasons. The evolution of characters associated with reproductive biology and fossoriality is discussed in light of the obtained results.

Phylogenomics, introgression, and demographic history of South American true toads (Rhinella)

The effects of genetic introgression on species boundaries and how they affect species' integrity and persistence over evolutionary time have received increased attention. The increasing availability of genomic data has revealed contrasting patterns of gene flow across genomic regions, which impose challenges to inferences of evolutionary relationships and of patterns of genetic admixture across lineages. By characterizing patterns of variation across thousands of genomic loci in a widespread complex of true toads (Rhinella), we assess the true extent of genetic introgression across species thought to hybridize to extreme degrees based on natural history observations and multi-locus analyses. Comprehensive geographic sampling of five large-ranged Neotropical taxa revealed multiple distinct evolutionary lineages that span large geographic areas and, at times, distinct biomes. The inferred major clades and genetic clusters largely correspond to currently recognized taxa; however, we also found evidence of cryptic diversity within taxa. While previous phylogenetic studies revealed extensive mito-nuclear discordance, our genetic clustering analyses uncovered several admixed individuals within major genetic groups. Accordingly, historical demographic analyses supported that the evolutionary history of these toads involved cross-taxon gene flow both at ancient and recent times. Lastly, ABBA-BABA tests revealed widespread allele sharing across species boundaries, a pattern that can be confidently attributed to genetic introgression as opposed to incomplete lineage sorting. These results confirm previous assertions that the evolutionary history of Rhinella was characterized by various levels of hybridization even across environmentally heterogeneous regions, posing exciting questions about what factors prevent complete fusion of diverging yet highly interdependent evolutionary lineages.

A role of asynchrony of seasons in explaining genetic differentiation in a Neotropical toad

The process of diversification can be studied at the phylogeographic level by attempting to identify the environmental features that promote and maintain population divergence. Here we investigate diversification in Rhinella granulosa, a Neotropical toad from northeastern Brazil, by testing a range of hypotheses that encompass different putative mechanisms reducing gene flow among populations. We sequenced single nucleotide polymorphisms and examined individual predictions related to the role of geographic barriers (rivers), ecological gradients, historical habitat stability, and spatial variation in climate seasonality, also known as the asynchrony of seasons hypothesis. This hypothesis postulates that temporal asynchrony of wet and dry seasons over short distances causes parapatric populations to become isolated by time. After determining genetic structure, inferring past distributions, ranking demographic models, and estimating the power of monthly climatic variables, our results identified two populations that are not associated with geographic barriers, biome gradients, or historical refugia. Instead, they are predicted by spatial variation in monthly rainfall and minimum temperature, consistent with the asynchrony of seasons hypothesis, supported also by our comparative framework using multiple matrix regression and linear mixed effects modeling. Due to the toad's life history, climate likely mediates gene flow directly, with genetic differentiation being provoked by neutral mechanisms related to climate driven population isolation, and/or by natural selection against migrants from populations with different breeding times. The asynchrony of seasons hypothesis is seldom considered in phylogeographic studies, but our results indicate that it should be tested in systems where breeding is tightly coupled with climate.

Extensive Cryptic Diversity Within the Physalaemus cuvieri-Physalaemus ephippifer Species Complex (Amphibia, Anura) Revealed by Cytogenetic, Mitochondrial, and Genomic Markers

Previous cytogenetic and phylogenetic analyses showed a high variability in the frog taxa Physalaemus cuvieri and Physalaemus ephippifer and suggested the presence of undescribed diversity in this species complex. Here, by 1) adding specimens from the Brazilian Amazon region, 2) employing sequence-based species delimitation approaches, and 3) including RADseq-style markers, we demonstrate that the diversity in the P. cuvieri-P. ephippifer species complex is even greater than previously suspected. Specimens from Viruá and Western Pará, located at the Guiana Amazonian area of endemism, were recovered as distinct from all previously identified lineages by the phylogenetic analyses based on mitochondrial DNA and RAD markers, a PCA from RAD data, and cytogenetic analysis. The sequence-based species delimitation analyses supported the recognition of one or two undescribed species among these Amazonian specimens and also supported the recognition of at least three other species in the P. cuvieri-P. ephippifer species complex. These new results reinforce the need for a comprehensive taxonomic revision.

Comparative cytogenetics of nine populations of the Rhinella genus (Anura, Bufonidae) with a highlight on their conservative karyotype

The genus Rhinella is one of the most diverse groups of bufonid toads, currently composed by 93 valid species and naturally distributed throughout different Neotropical ecoregions. Here, we analyze nine Brazilian populations of toads representing species of the Rhinella margaritifera and Rhinella marina groups. These new data include the first description of the R. hoogmoedi and R. proboscidae karyotypes, as well as other taxonomically unresolved forms. Chromosomal analysis of the populations revealed pronounced chromosomal uniformity (2n=22), including the diploid number and chromosomal morphology. Three different NOR-bearing chromosomes were identified: in the subterminal region of pair 10q in R. hoogmoedi, Rhinella sp. 1 and Rhinella sp. 2, in subterminal region of 7p in R. proboscidae and Rhinella cf. margaritifera while in R. henseli and R. icterica was detected in interstitial region of 7p. Karyotypic uniformity of the genus permits the inference of interspecific chromosome homologies and evolutionary changes in the NOR-bearing chromosome may represent an informative character in species group level. The review of the cytogenetic data of the Rhinella species together with the new karyotypes reported here contributes to the understanding of the chromosomal evolution of these toads, which karyotypes are highly conserved despite the ample distribution of many forms.

A new species of Pseudopaludicola (Anura, Leiuperinae) from Espírito Santo, Brazil

We describe a new anuran species of the genus Pseudopaludicola that inhabits sandy areas in resting as associated to the Atlantic Forest biome in the state of Espírito Santo, Brazil. The new species is characterized by: SVL 11.7-14.6 mm in males, 14.0-16.7 mm in females; body slender; fingertips knobbed, with a central groove; hindlimbs short; abdominal fold complete; arytenoid cartilages wide; prepollex with base and two segments; prehallux with base and one segment; frontoparietal fontanelle partially exposed; advertisement call with one note composed of two isolated pulses per call; call dominant frequency ranging 4,380-4,884 Hz; diploid chromosome number 22; and Ag-NORs on 8q subterminal. In addition, its 16S rDNA sequence shows high genetic distances when compared to sequences of related species, which provides strong evidence that the new species is an independent lineage.

Evolution of a complex phenotype with biphasic ontogeny: Contribution of development versus function and climatic variation to skull modularity in toads

The theory of morphological integration and modularity predicts that if functional correlations among traits are relevant to mean population fitness, the genetic basis of development will be molded by stabilizing selection to match functional patterns. Yet, how much functional interactions actually shape the fitness landscape is still an open question. We used the anuran skull as a model of a complex phenotype for which we can separate developmental and functional modularity. We hypothesized that functional modularity associated to functional demands of the adult skull would overcome developmental modularity associated to bone origin at the larval phase because metamorphosis would erase the developmental signal. We tested this hypothesis in toad species of the Rhinella granulosa complex using species phenotypic correlation pattern (P-matrices). Given that the toad species are distributed in very distinct habitats and the skull has important functions related to climatic conditions, we also hypothesized that differences in skull trait covariance pattern are associated to differences in climatic variables among species. Functional and hormonal-regulated modules are more conspicuous than developmental modules only when size variation is retained on species P-matrices. Without size variation, there is a clear modularity signal of developmental units, but most species have the functional model as the best supported by empirical data without allometric size variation. Closely related toad species have more similar climatic niches and P-matrices than distantly related species, suggesting phylogenetic niche conservatism. We infer that the modularity signal due to embryonic origin of bones, which happens early in ontogeny, is blurred by the process of growth that occurs later in ontogeny. We suggest that the species differing in the preferred modularity model have different demands on the orbital functional unit and that species contrasting in climate are subjected to divergent patterns of natural selection associated to neurocranial allometry and T3 hormone regulation.

A new species of semiarboreal toad of the Rhinella festae group (Anura, Bufonidae) from the Cordillera Azul National Park, Peru

A new semiarboreal species of the Rhinella festae group is described from montane forests of the Cordillera Azul National Park between 1245 and 1280 m a.s.l. in the Cordillera Oriental, San Martín region, northern Peru. The new species is morphologically and genetically compared with members of the Rhinella acrolopha group (former genus Rhamphophryne) and members of the R. festae group. The new species is characterized by its large size (female SVL 47.1-58.3 mm, n = 4), eight presacral vertebrae, fusion of the sacrum and coccyx, long protuberant snout, snout directed slightly anteroventral in lateral view, cranial crests moderately developed, absence of occipital crest, presence of tympanic membrane, dorsolateral rows of small conical tubercles extending from parotoid gland to groin, hands and feet with long digits, fingers basally webbed and toes moderately webbed. Phylogenetically it is a member of the R. festae group which is most closely related to R. chavin and R. yanachaga from Peru. Morphologically the new species shares similarities with R. tenrec and R. truebae, members of the R. acrolopha group from Colombia.

Evaluating the diversity of Neotropical anurans using DNA barcodes

This study tested the effectiveness of COI barcodes for the discrimination of anuran species from the Amazon basin and other Neotropical regions. Barcodes were determined for a total of 59 species, with a further 58 species being included from GenBank. In most cases, distinguishing species using the barcodes was straightforward. Each species had a distinct COI barcode or codes, with intraspecific distances ranging from 0% to 9.9%. However, relatively high intraspecific divergence (11.4-19.4%) was observed in some species, such as Ranitomeya ventrimaculata, Craugastor fitzingeri, Hypsiboas leptolineatus, Scinax fuscomarginatus and Leptodactylus knudseni, which may reflect errors of identification or the presence of a species complex. Intraspecific distances recorded in species for which samples were obtained from GenBank (Engystomops pustulosus, Atelopus varius, Craugastor podiciferus, and Dendropsophus labialis) were greater than those between many pairs of species. Interspecific distances ranged between 11-39%. Overall, the clear differences observed between most intra- and inter-specific distances indicate that the COI barcode is an effective tool for the identification of Neotropical species in most of the cases analyzed in the present study.

High evolutionary constraints limited adaptive responses to past climate changes in toad skulls

Interactions among traits that build a complex structure may be represented as genetic covariation and correlation. Genetic correlations may act as constraints, deflecting the evolutionary response from the direction of natural selection. We investigated the relative importance of drift, selection, and constraints in driving skull divergence in a group of related toad species. The distributional range of these species encompasses very distinct habitats with important climatic differences and the species are primarily distinguished by differences in their skulls. Some parts of the toad skull, such as the snout, may have functional relevance in reproductive ecology, detecting water cues. Thus, we hypothesized that the species skull divergence was driven by natural selection associated with climatic variation. However, given that all species present high correlations among skull traits, our second prediction was of high constraints deflecting the response to selection. We first extracted the main morphological direction that is expected to be subjected to selection by using within- and between-species covariance matrices. We then used evolutionary regressions to investigate whether divergence along this direction is explained by climatic variation between species. We also used quantitative genetics models to test for a role of random drift versus natural selection in skull divergence and to reconstruct selection gradients along species phylogeny. Climatic variables explained high proportions of between-species variation in the most selected axis. However, most evolutionary responses were not in the direction of selection, but aligned with the direction of allometric size, the dimension of highest phenotypic variance in the ancestral population. We conclude that toad species have responded to selection related to climate in their skulls, yet high evolutionary constraints dominated species divergence and may limit species responses to future climate change.

The complex evolutionary history of the tympanic middle ear in frogs and toads (Anura)

Most anurans possess a tympanic middle ear (TME) that transmits sound waves to the inner ear; however, numerous species lack some or all TME components. To understand the evolution of these structures, we undertook a comprehensive assessment of their occurrence across anurans and performed ancestral character state reconstructions. Our analysis indicates that the TME was completely lost at least 38 independent times in Anura. The inferred evolutionary history of the TME is exceptionally complex in true toads (Bufonidae), where it was lost in the most recent common ancestor, preceding a radiation of >150 earless species. Following that initial loss, independent regains of some or all TME structures were inferred within two minor clades and in a radiation of >400 species. The reappearance of the TME in the latter clade was followed by at least 10 losses of the entire TME. The many losses and gains of the TME in anurans is unparalleled among tetrapods. Our results show that anurans, and especially bufonid toads, are an excellent model to study the behavioural correlates of earlessness, extratympanic sound pathways, and the genetic and developmental mechanisms that underlie the morphogenesis of TME structures.