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Background: Differences in morphology, ecology, and behavior through ontogeny can result in opposing selective pressures at different life stages. Most animals, however, transition through two or more distinct phenotypic phases, which is hypothesized to allow each life stage to adapt more freely to its ecological niche. How this applies to sensory systems, and in particular how sensory systems adapt across life stages at the molecular level, is not well understood. Here, we used whole-eye transcriptomes to investigate differences in gene expression between tadpole and juvenile southern leopard frogs (Lithobates sphenocephalus), which rely on vision in aquatic and terrestrial light environments, respectively. Because visual physiology changes with light levels, we also tested the effect of light and dark exposure. Results: We found 42% of genes were differentially expressed in the eyes of tadpoles versus juveniles and 5% for light/dark exposure. Analyses targeting a curated subset of visual genes revealed significant differential expression of genes that control aspects of visual function and development, including spectral sensitivity and lens composition. Finally, microspectrophotometry of photoreceptors confirmed shifts in spectral sensitivity predicted by the expression results, consistent with adaptation to distinct light environments. Conclusions: Overall, we identified extensive expression-level differences in the eyes of tadpoles and juveniles related to observed morphological and physiological changes through metamorphosis and corresponding adaptive shifts to improve vision in the distinct aquatic and terrestrial light environments these frogs inhabit during their life cycle. More broadly, these results suggest that decoupling of gene expression can mediate the opposing selection pressures experienced by organisms with complex life cycles that inhabit different environmental conditions throughout ontogeny. [ABSTRACT FROM AUTHOR]

Background: Differences in morphology, ecology, and behavior through ontogeny can result in opposing selective pressures at different life stages. Most animals, however, transition through two or more distinct phenotypic phases, which is hypothesized to allow each life stage to adapt more freely to its ecological niche. How this applies to sensory systems, and in particular how sensory systems adapt across life stages at the molecular level, is not well understood. Here, we used whole-eye transcriptomes to investigate differences in gene expression between tadpole and juvenile southern leopard frogs (Lithobates sphenocephalus), which rely on vision in aquatic and terrestrial light environments, respectively. Because visual physiology changes with light levels, we also tested the effect of light and dark exposure. Results: We found 42% of genes were differentially expressed in the eyes of tadpoles versus juveniles and 5% for light/dark exposure. Analyses targeting a curated subset of visual genes revealed significant differential expression of genes that control aspects of visual function and development, including spectral sensitivity and lens composition. Finally, microspectrophotometry of photoreceptors confirmed shifts in spectral sensitivity predicted by the expression results, consistent with adaptation to distinct light environments. Conclusions: Overall, we identified extensive expression-level differences in the eyes of tadpoles and juveniles related to observed morphological and physiological changes through metamorphosis and corresponding adaptive shifts to improve vision in the distinct aquatic and terrestrial light environments these frogs inhabit during their life cycle. More broadly, these results suggest that decoupling of gene expression can mediate the opposing selection pressures experienced by organisms with complex life cycles that inhabit different environmental conditions throughout ontogeny. [ABSTRACT FROM AUTHOR]

Surprisingly, little is known about body‐size evolution within the most diverse amphibian order, anurans (frogs and toads), despite known effects of body size on the physiological, ecological and life‐history traits of animals more generally. Here, we examined anuran body‐size evolution among 2,434 species with over 200 million years of shared evolutionary history. We found clade‐specific evolutionary shifts to new body‐size optima along with numerous independent transitions to gigantic and miniature body sizes, despite the upper limits of anuran body size remaining quite consistent throughout the fossil record. We found a weak, positive correlation between a species' body size and maximum latitude and elevation, including a dearth of small species at higher elevations and broader latitudinal and elevational ranges in larger anurans. Although we found modest differences in mean anuran body size among microhabitats, there was extensive overlap in the range of body sizes across microhabitats. Finally, we found that larger anurans are more likely to consume vertebrate prey than smaller anurans are and that species with a free‐swimming larval phase during development are larger on average than those in which development into a froglet occurs within the egg. Overall, anuran body size does not conform to geographic and ecological patterns observed in other tetrapods but is perhaps more notable for variation in body size within geographic regions, ecologies and life histories. Here, we document this variation and propose target clades for detailed studies aimed at disentangling how and why variation in body size was generated and is maintained in anurans. [ABSTRACT FROM AUTHOR]

DNA evidence is often critical for taxonomic studies; however, many historical type specimens lack corresponding genetic samples, which limits contemporary molecular research questions and may restrict conservation and management decisions. We conducted a pilot Type Locality Project to collect voucher specimens and genomic-grade samples from amphibian type localities in the state of Virginia, USA. These samples can serve as proxies for cases in which obtaining genomic data from the type specimen is not possible. Undergraduate students participated in all aspects of the project including fieldwork, DNA barcoding, and incorporating specimens into the Smithsonian Institution's National Museum of Natural History research collection. The Type Locality Project is an excellent platform for providing undergraduate students with hands-on research experience and training in taxonomy and systematics. Other institutions could easily adapt our approach to obtain genomic-quality, topotypic vouchers for other taxa and simultaneously create authentic undergraduate research experiences in field, laboratory, and natural history museum settings. [ABSTRACT FROM AUTHOR]

The Central African treefrog Leptopelis brevirostris has a characteristically short and vertically truncated snout, a tooth-like process at the centre of the mandible, and unlike most species of Leptopelis, eats terrestrial gastropods. Two morphologically similar species (L. crystallinoron and L. brevipes) have been described in sympatry with L. brevirostris, each on the basis of a single female specimen and then provisionally synonymised with L. brevirostris by subsequent authors. Here we re-examine the holotypes of the three species and collect both genetic (mtDNA and 25 nuDNA loci) and morphological data across the range of L. brevirostris and its sister species L. notatus to test the hypothesis that L. brevirostris is comprised of more than one species. We found that the diagnostic characters for L. crystallinoron (lacking a visible tympanum and having larger vomerine teeth in contact) and L. brevipes (distinctive dorsal colouration) are also present in L. brevirostris and L. notatus. Furthermore, these characters vary among individuals that share the same mitochondrial haplotype and that occur within a single locality, including the type locality of L. crystallinoron. Although all samples from the type locality of L. crystallinoron form a distinct mitochondrial lineage relative to L. brevipes and L. brevirostris, our analysis of 25 nuclear loci does not support this relationship and instead suggests that this mitochondrial divergence reflects phylogeographic structure across the range of L. brevirostris, including samples from the type localities of L. crystallinoron and L. brevipes. By contrast, the mitochondrial divergence between L. notatus and L. brevirostris is strongly supported in the nuDNA dataset. Consequently, we recognise both L. brevipes and L. crystallinoron as synonyms of L. brevirostris. Given the extensive variation in the colour pattern, the tympanic membrane, and the size and shape of the vomerine teeth among L. brevirostris collected from one locality, variation in these traits should be interpreted with caution in taxonomic research on Leptopelis. [ABSTRACT FROM AUTHOR]

Theory predicts that sexually dimorphic traits under strong sexual selection, particularly those involved with intersexual signaling, can accelerate speciation and produce bursts of diversification. Sexual dichromatism (sexual dimorphism in color) is widely used as a proxy for sexual selection and is associated with rapid diversification in several animal groups, yet studies using phylogenetic comparative methods to explicitly test for an association between sexual dichromatism and diversification have produced conflicting results. Sexual dichromatism is rare in frogs, but it is both striking and prevalent in African reed frogs, a major component of the diverse frog radiation termed Afrobatrachia. In contrast to most other vertebrates, reed frogs display female-biased dichromatism in which females undergo color transformation, often resulting in more ornate coloration in females than in males. We produce a robust phylogeny of Afrobatrachia to investigate the evolutionary origins of sexual dichromatism in this radiation and examine whether the presence of dichromatism is associated with increased rates of net diversification. We find that sexual dichromatism evolved once within hyperoliids and was followed by numerous independent reversals to monochromatism. We detect significant diversification rate heterogeneity in Afrobatrachia and find that sexually dichromatic lineages have double the average net diversification rate of monochromatic lineages. By conducting trait simulations on our empirical phylogeny, we demonstrate that our inference of trait-dependent diversification is robust. Although sexual dichromatism in hyperoliid frogs is linked to their rapid diversification and supports macroevolutionary predictions of speciation by sexual selection, the function of dichromatism in reed frogs remains unclear. We propose that reed frogs are a compelling system for studying the roles of natural and sexual selection on the evolution of sexual dichromatism across micro- and macroevolutionary timescales. [ABSTRACT FROM AUTHOR]

Although naturally heterogeneous environments can lead to mosaic hybrid zones, human-induced habitat fragmentation can also lead to environmental heterogeneity and hybridization. Here we quantify phenotypic and molecular divergence across a reed frog mosaic hybrid zone on São Tomé Island as a first step towards understanding the consequences of hybridization across this heterogeneous landscape. The São Tomé giant reed frog (Hyperolius thomensis) is strongly tied to cool, wet, forest habitats whereas the distribution of Moller's reed frog (H. molleri) spans cool, wet, forests to warm, dry, disturbed habitats. Correspondingly, hybridization is concentrated in the more forested, cool, wet sites relative to non-forested, warmer, drier habitats. Four of six sites with hybrid frogs are artificial water bodies near the forest edge, indicating that both breeding habitat and broader scale environmental variation are probably important for understanding interspecific interactions and the extent of hybridization in this system. Phenotypic variation (body size and ventral coloration) largely tracks genetic and environmental variation across the hybrid zone with larger and more pigmented frogs occurring in forested, cool, wet habitats. Understanding whether human-induced changes in habitat break down reproductive barriers will be essential for conservation management of the less abundant, forest-associated H. thomensis in the face of rampant hybridization. [ABSTRACT FROM AUTHOR]

Abstract: Aim: To investigate how putative barriers, forest refugia, and ecological gradients across the lower Guineo‐Congolian rain forest shape genetic and phenotypic divergence in the leaf‐folding frog Afrixalus paradorsalis, and examine the role of adjacent land bridge and sky‐islands in diversification. Location: The Lower Guineo‐Congolian Forest, the Cameroonian Volcanic Line (CVL), and Bioko Island, Central Africa. Taxon: Afrixalus paradorsalis (Family: Hyperoliidae), an African leaf‐folding frog. Methods: We used molecular and phenotypic data to investigate diversity and divergence among the A. paradorsalis species complex distributed across lowland rain forests, a land bridge island, and mountains in Central Africa. We examined the coincidence of population boundaries, landscape features, divergence times, and spatial patterns of connectivity and diversity, and subsequently performed demographic modelling using genome‐wide SNP variation to distinguish among divergence mechanisms in mainland (riverine barriers, forest refugia, ecological gradients) and land bridge island populations (vicariance, overwater dispersal). Results: We detected four genetically distinct allopatric populations corresponding to Bioko Island, the CVL, and two lowland rain forest populations split by the Sanaga River. Although lowland populations are phenotypically indistinguishable, pronounced body size evolution occurs at high elevation, and the timing of the formation of the high elevation population coincides with mountain uplift in the CVL. Spatial analyses and demographic modelling revealed population divergence across mainland Lower Guinea is best explained by forest refugia rather than riverine barriers or ecological gradients, and that the Bioko Island population divergence is best explained by vicariance (marine incursion) rather than overseas dispersal. Main conclusions: We provide growing support for the important role of forest refugia in driving intraspecific divergences in the Guineo‐Congolian rain forest. In A. paradorsalis, sky‐islands in the CVL have resulted in greater genetic and phenotypic divergences than marine incursions of the land bridge Bioko Island, highlighting important differences in patterns of island‐driven diversification in Lower Guinea. [ABSTRACT FROM AUTHOR]

Differences in mating signals among incipient species are an important mechanism driving reproductive isolation and speciation. Here, we investigate male advertisement call divergence across a radiation of reed frogs from the Gulf of Guinea archipelago and the most closely related species on the African continent (Hyperolius olivaceus). The two species endemic to the island of São Tomé (Hyperolius molleri and Hyperolius thomensis) differ in body size, coloration and breeding ecology, yet they hybridize where their habitats overlap. A third species, Hyperolius drewesi, is sister to H. molleri and endemic to Príncipe Island. We found significant differences in average dominant frequency and average number of pulses per call among the four species. The strong relationship between body size and dominant frequency irrespective of geographical history, breeding habitat or acoustic environment suggests that differences in this component of the mating signal may be a by-product of adaptive changes in body size among the four species. Hybrid males are intermediate in size between H. molleri and H. thomensis and produce calls at intermediate dominant frequencies. Future efforts to characterize courtship behaviour and breeding habitat preference in allopatric and sympatric populations will provide additional insights as to the potential for reinforcement in this system. [ABSTRACT FROM AUTHOR]

Organismal traits interact with environmental variation to mediate how species respond to shared landscapes. Thus, differences in traits related to dispersal ability or physiological tolerance may result in phylogeographic discordance among co-distributed taxa, even when they are responding to common barriers. We quantified climatic suitability and stability, and phylogeographic divergence within three reed frog species complexes across the Guineo-Congolian forests and Gulf of Guinea archipelago of Central Africa to investigate how they responded to a shared climatic and geological history. Our species-specific estimates of climatic suitability through time are consistent with temporal and spatial heterogeneity in diversification among the species complexes, indicating that differences in ecological breadth may partly explain these idiosyncratic patterns. Likewise, we demonstrated that fluctuating sea levels periodically exposed a land bridge connecting Bioko Island with the mainland Guineo-Congolian forest and that habitats across the exposed land bridge likely enabled dispersal in some species, but not in others. We did not find evidence that rivers are biogeographic barriers across any of the species complexes. Despite marked differences in the geographic extent of stable climates and temporal estimates of divergence among the species complexes, we recovered a shared pattern of intermittent climatic suitability with recent population connectivity and demographic expansion across the Congo Basin. This pattern supports the hypothesis that genetic exchange across the Congo Basin during humid periods, followed by vicariance during arid periods, has shaped regional diversity. Finally, we identified many distinct lineages among our focal taxa, some of which may reflect incipient or unrecognized species. [ABSTRACT FROM AUTHOR]

I describe a new species of reed frog ( Hyperolius: Hyperoliidae) from the island of Príncipe in the Gulf of Guinea archipelago. The new species is within the Hyperolius cinnamomeoventris species complex, which includes four described species: H. cinnamomeoventris, H. veithi, H. molleri, and H. thomensis. The new species is sexually monochromatic (males and females have green dorsal coloration) and is thus distinguished from H. cinnamomeoventris, which is sexually dichromatic, and from H. veithi, in which both males and females are tan with yellow dorsolateral lines. The new species is smaller in size than H. thomensis, and differs in coloration from H. molleri and H. thomensis by lacking a black contour along the edges of the green/yellow band of coloration that extends down the dorsal side of the thigh, by lacking red/orange coloration on the dorsal and ventral sides of the thigh, and in the mitochondrial 16s and cytochrome-b genes. Furthermore, previous work indicates that the new species is distinct from H. molleri and H. thomensis in analyses of genome-wide single-nucleotide polymorphisms. This new species is the third endemic amphibian described from this small oceanic island. The type material for the closely related H. molleri and H. thomensis was destroyed or lost; therefore, I designate neotype material for these two species to enable the description of the new species. [ABSTRACT FROM AUTHOR]

Frog reproductive modes are complex phenotypes that include egg/clutch characteristics, oviposition site, larval development, and sometimes, parental care. Two evident patterns in the evolution of these traits are the higher diversity of reproductive modes in the tropics and the apparent progression fromaquatic to terrestrial reproduction, often attributed to higher fitness resulting fromdecreased predation on terrestrial eggs and tadpoles. Here, we propose that sexual selection-and not only natural selection due to predation-favors terrestrial breeding by reducing the loss of fitness due to polyandry. To examine this novel selective mechanism, we reconstructed the evolution of reproductive diversity in two frog families (Hylidae and Leptodactylidae) and tested for concerted evolution of egg and tadpole development sites with specific mating behaviors.We found that oviposition and tadpole development sites are evolving independently, do not show the same diversity and/or directionality in terms of terrestriality, and thus may be diversifying due to different selective mechanisms. In both families, terrestrial egg deposition is correlated with amplexus that is hidden from competing males, and in hylids, testes mass was significantly larger and more variable in males with exposed amplexus that are vulnerable to polyandry. Our results indicate that intrasexual selection has been an underappreciated mechanism promoting diversification of frog reproductive modes. [ABSTRACT FROM AUTHOR]

Almost 30 y ago, the field of intraspecific phylogeography laid the foundation for spatially explicit and genealogically informed studies of population divergence. With new methods and markers, the focus in phylogeography shifted to previously unrecognized geographic genetic variation, thus reducing the attention paid to phenotypic variation in those same diverging lineages. Although phenotypic differences among lineages once provided the main data for studies of evolutionary change, the mechanisms shaping phenotypic differentiation and their integration with intraspecific genetic structure have been underexplored in phylogeographic studies. However, phenotypes are targets of selection and play important roles in species performance, recognition, and diversification. Here, we focus on three questions. First, how can phenotypes elucidate mechanisms underlying concordant or idiosyncratic responses of vertebrate species evolving in shared landscapes? Second, what mechanisms underlie the concordance or discordance of phenotypic and phylogeographic differentiation? Third, how can phylogeography contribute to our understanding of functional phenotypic evolution? We demonstrate that the integration of phenotypic data extends the reach of phylogeography to explain the origin and maintenance of biodiversity. Finally, we stress the importance of natural history collections as sources of high-quality phenotypic data that span temporal and spatial axes. [ABSTRACT FROM AUTHOR]

Oceanic islands accumulate endemic species when new colonists diverge from source populations or by in situ diversification of resident island endemics. The relative importance of dispersal versus in situ speciation in generating diversity on islands varies with a number of archipelago characteristics including island size, age, and remoteness. Here, we characterize interisland dispersal and in situ speciation in frogs endemic to the Gulf of Guinea islands. Using mitochondrial sequence and genome-wide single-nucleotide polymorphism data, we demonstrate that dispersal proceeded from the younger island (São Tomé) to the older island (Príncipe) indicating that for organisms that disperse overseas on rafts, dispersal between islands may be determined by ocean currents and not island age. We find that dispersal between the islands is not ongoing, resulting in genotypically distinct but phenotypically similar lineages on the two islands. Finally, we demonstrate that in situ diversification on São Tomé Island likely proceeded in allopatry due to the geographic separation of breeding sites, resulting in phenotypically distinct species. We find evidence of hybridization between the species where their ranges are sympatric and the hybrid zone coincides with a transition from agricultural land to primary forest, indicating that anthropogenic development may have facilitated secondary contact between previously allopatric species. [ABSTRACT FROM AUTHOR]

Aim To infer the colonization history of reed frog species endemic to the oceanic islands of São Tomé and Príncipe, Hyperolius molleri and H. thomensis, we quantified phylogeographical structure in the closely related H. cinnamomeoventris species complex, which is broadly distributed across continental Central Africa. Location The Lower Guineo-Congolian Forest and the Gulf of Guinea islands of São Tomé and Príncipe, Central Africa. Methods We combined gene and species tree analyses to investigate diversity and divergence among H. cinnamomeoventris populations, to identify the most likely dispersal route to the islands, and to infer the order in which the islands were colonized. One of the endemics ( H. molleri) is distributed on both islands and we quantified genetic divergence between populations. Results We recovered three clades in H. cinnamomeoventris corresponding to West-Central, North/East-Central and South-Central Africa. The island endemics form a monophyletic group most closely related to the West-Central African H. cinnamomeoventris clade. Populations of H. molleri on São Tomé and Príncipe are reciprocally monophyletic at mitochondrial loci but nuclear gene trees do not support this divergence. Main conclusions Genetic structure in the H. cinnamomeoventris species complex coincides with biogeographical barriers identified in previous studies of Central African rain forest taxa. Individual gene tree and species tree analyses support a single dispersal event from the Ogooué or Congo river basins (West-Central Africa) to the island of São Tomé, with subsequent divergence within São Tomé and dispersal to Príncipe. [ABSTRACT FROM AUTHOR]

Aim We investigated how Pleistocene refugia and recent ( c. 12,000 years ago) sea level incursions shaped genetic differentiation in mainland and island populations of the Scinax perpusillus treefrog group. Location Brazilian Atlantic Forest, São Paulo state, south-eastern Brazil. Methods Using mitochondrial and microsatellite loci, we examined population structure and genetic diversity in three species from the S. perpusillus group, sampled from three land-bridge islands and five mainland populations, in order to understand the roles of Pleistocene forest fragmentation and sea level incursions on genetic differentiation. We calculated metrics of relatedness and genetic diversity to assess whether island populations exhibit signatures of genetic drift and isolation. Two of the three island populations in this study have previously been described as new species based on a combination of distinct morphological and behavioural characters, thus we used the molecular datasets to determine whether phenotypic change is consistent with genetic differentiation. Results Our analyses recovered three distinct lineages or demes composed of northern mainland São Paulo populations, southern mainland São Paulo populations, and one divergent island population. The two remaining island populations clustered with samples from adjacent mainland populations. Estimates of allelic richness were significantly lower, and estimates of relatedness were significantly higher, in island populations relative to their mainland counterparts. Main conclusions Fine-scale genetic structure across mainland populations indicates the possible existence of local refugia within São Paulo state, underscoring the small geographic scale at which populations diverge in this species-rich region of the Atlantic Coastal Forest. Variation in genetic signatures across the three islands indicates that the populations experienced different demographic processes after marine incursions fragmented the distribution of the S. perpusillus group. Genetic signatures of inbreeding and drift in some island populations indicate that small population sizes, coupled with strong ecological selection, may be important evolutionary forces driving speciation on land-bridge islands. [ABSTRACT FROM AUTHOR]

Globally, montane tropical diversity is characterized by extraordinary local endemism that is not readily explained by current environmental variables indicating a strong imprint of history. Montane species often exist as isolated populations under current climatic conditions and may have remained isolated throughout recent climatic cycles, leading to substantial genetic and phenotypic divergence. Alternatively, populations may have become contiguous during colder climates resulting in less divergence. Here we compare responses to historical climate fluctuation in a montane specialist skink, Lampropholis robertsi, and its more broadly distributed congener, L. coggeri, both endemic to rainforests of northeast Australia. To do so, we combine spatial modelling of potential distributions under representative palaeoclimates, multi-locus phylogeography and analyses of phenotypic variation. Spatial modelling of L. robertsi predicts strong isolation among disjunct montane refugia during warm climates, but with potential for localized exchange during the most recent glacial period. In contrast, predicted stable areas are more widespread and connected in L. coggeri. Both species exhibit pronounced phylogeographic structuring for mitochondrial and nuclear genes, attesting to low dispersal and high persistence across multiple isolated regions. This is most prominent in L. robertsi, for which coalescent analyses indicate that most populations persisted in isolation throughout the climate cycles of the Pleistocene . Morphological divergence, principally in body size, is more evident among isolated populations of L. robertsi than L. coggeri. These results highlight the biodiversity value of isolated montane populations and support the general hypothesis that tropical montane regions harbour high levels of narrow-range taxa because of their resilience to past climate change. [ABSTRACT FROM AUTHOR]

The article offers information on frog specie Hyperolius adspersus, and mentions about predation of a Leptopelis brevirostris tree frog by a wandering spider (Ctenidae), both in Cameroon.

New World mabuyine skinks are a diverse radiation of morphologically cryptic lizards with unique reproductive biologies. Recent studies examining population-level data (morphological, ecological, and genomic) have uncovered novel biodiversity and phenotypes, including the description of dozens of new species and insights into the evolution of their highly complex placental structures. Beyond the potential for this diverse group to serve as a model for the evolution of viviparity in lizards, much of the taxonomic diversity is concentrated in regions experiencing increasing environmental instability from climate and anthropogenic change. Consequently, a better understanding of genome structure and diversity will be an important tool in the adaptive management and conservation of this group. Skinks endemic to Caribbean islands are particularly vulnerable to global change with several species already considered likely extinct and several remaining species either endangered or threatened. Combining PacBio long-read sequencing, Hi-C, and RNAseq data, here we present the first genomic resources for this group by describing new chromosome-level reference genomes for the Puerto Rican Skink Spondylurus nitidus and the Culebra Skink S. culebrae. Results indicate two high quality genomes, both ∼1.4 Gb, assembled nearly telomere to telomere with complete mitochondrion assembly and annotation. [ABSTRACT FROM AUTHOR]

Uncovering convergent and divergent patterns of diversification is a major goal of evolutionary biology. On four Greater Antillean islands, Anolis lizards have convergently evolved sets of species with similar ecologies and morphologies (ecomorphs). However, it is unclear whether closely related anoles from Central and South America exhibit similar patterns of diversification. We generated an extensive morphological data set to test whether mainland Draconura -clade anoles are assignable to the Caribbean ecomorphs. Based on a new classification framework that accounts for different degrees of morphological support, we found morphological evidence for mainland representatives of all six Caribbean ecomorphs and evidence that many ecomorphs have also evolved repeatedly on the mainland. We also found strong evidence that ground-dwelling anoles from both the Caribbean and the mainland constitute a new and distinct ecomorph class. Beyond the ecomorph concept, we show that the island and mainland anole faunas exhibit exceptional morphological convergence, suggesting that they are more similar than previously understood. However, the island and mainland radiations are not identical, indicating that regional differences and historical contingencies can lead to replicate yet variable radiations. More broadly, our findings suggest that replicated radiations occur beyond island settings more often than previously recognized. [ABSTRACT FROM AUTHOR]

Frogs and toads (Amphibia: Anura) display diverse ecologies and behaviours, which are often correlated with visual capacity in other vertebrates. Additionally, anurans exhibit a broad range of relative eye sizes, which have not previously been linked to ecological factors in this group. We measured relative investment in eye size and corneal size for 220 species of anurans representing all 55 currently recognized families and tested whether they were correlated with six natural history traits hypothesized to be associated with the evolution of eye size. Anuran eye size was significantly correlated with habitat, with notable decreases in eye investment among fossorial, subfossorial and aquatic species. Relative eye size was also associated with mating habitat and activity pattern. Compared to other vertebrates, anurans have relatively large eyes for their body size, indicating that vision is probably of high importance. Our study reveals the role that ecology and behaviour may have played in the evolution of anuran visual systems and highlights the usefulness of museum specimens, and importance of broad taxonomic sampling, for interpreting macroecological patterns. [ABSTRACT FROM AUTHOR]

Frogs and toads (Amphibia: Anura) display diverse ecologies and behaviours, which are often correlated with visual capacity in other vertebrates. Additionally, anurans exhibit a broad range of relative eye sizes, which have not previously been linked to ecological factors in this group. We measured relative investment in eye size and corneal size for 220 species of anurans representing all 55 currently recognized families and tested whether they were correlated with six natural history traits hypothesized to be associated with the evolution of eye size. Anuran eye size was significantly correlated with habitat, with notable decreases in eye investment among fossorial, subfossorial and aquatic species. Relative eye size was also associated with mating habitat and activity pattern. Compared to other vertebrates, anurans have relatively large eyes for their body size, indicating that vision is probably of high importance. Our study reveals the role that ecology and behaviour may have played in the evolution of anuran visual systems and highlights the usefulness of museum specimens, and importance of broad taxonomic sampling, for interpreting macroecological patterns. [ABSTRACT FROM AUTHOR]

Species whose ranges encompass substantial environmental variation should experience heterogeneous selection, potentially resulting in local adaptation. Repeated covariation between phenotype and environment across ecologically similar species inhabiting similar environments provides strong evidence for adaptation. Lesser Antillean anoles present an excellent system in which to study repeated local adaptation because most species are widespread generalists occurring throughout environmentally heterogenous island landscapes. We leveraged this natural replication to test the hypothesis that intraspecific variation in phenotype (coloration and morphology) is consistently associated with environment across 9 species of bimaculatus series anoles. We measured dorsal coloration from 173 individuals from 6 species and 16 morphological traits from 883 individuals from 9 species, spanning their island ranges. We identified striking, but incomplete, parallelism in dorsal coloration associated with annual precipitation in our study species. By contrast, we observed significant patterns of morphological isolation-by-environment in only 2 species and no signal of parallel morphological evolution. Collectively, our results reveal strong divergent natural selection by environment on dorsal coloration but not morphology. [ABSTRACT FROM AUTHOR]

The shape and relative size of an ocular lens affect the focal length of the eye, with consequences for visual acuity and sensitivity. Lenses are typically spherical in aquatic animals with camera-type eyes and axially flattened in terrestrial species to facilitate vision in optical media with different refractive indices. Frogs and toads (Amphibia: Anura) are ecologically diverse, with many species shifting from aquatic to terrestrial ecologies during metamorphosis. We quantified lens shape and relative size using 179 micro X-ray computed tomography scans of 126 biphasic anuran species and tested for correlations with life stage, environmental transitions, adult habits and adult activity patterns. Across broad phylogenetic diversity, tadpole lenses are more spherical than those of adults. Biphasic species with aquatic larvae and terrestrial adults typically undergo ontogenetic changes in lens shape, whereas species that remain aquatic as adults tend to retain more spherical lenses after metamorphosis. Further, adult lens shape is influenced by adult habit; notably, fossorial adults tend to retain spherical lenses following metamorphosis. Finally, lens size relative to eye size is smaller in aquatic and semiaquatic species than other adult ecologies. Our study demonstrates how ecology shapes visual systems, and the power of non-invasive imaging of museum specimens for studying sensory evolution. [ABSTRACT FROM AUTHOR]

Pupil constriction has important functional consequences for animal vision, yet the evolutionary mechanisms underlying diverse pupil sizes and shapes are poorly understood. We aimed to quantify the diversity and evolution of pupil shapes among amphibians and to test for potential correlations to ecology based on functional hypotheses. Using photographs, we surveyed pupil shape across adults of 1294 amphibian species, 74 families and three orders, and additionally for larval stages for all families of frogs and salamanders with a biphasic ontogeny. For amphibians with a biphasic life history, pupil shape changed in many species that occupy distinct habitats before and after metamorphosis. In addition, non-elongated (circular or diamond) constricted pupils were associated with species inhabiting aquatic or underground environments, and elongated pupils (with vertical or horizontal long axes) were more common in species with larger absolute eye sizes. We propose that amphibians provide a valuable group within which to explore the anatomical, physiological, optical and ecological mechanisms underlying the evolution of pupil shape. [ABSTRACT FROM AUTHOR]

The spectral characteristics of vertebrate ocular lenses affect the image of the world that is projected onto the retina, and thus help shape diverse visual capabilities. Here, we tested whether amphibian lens transmission is driven by adaptation to diurnal activity (bright light) and/or scansorial habits (complex visual environments).Spectral transmission through the lenses of 79 species of frogs and six species of salamanders was measured, and data for 29 additional frog species compiled from published literature. Phylogenetic comparative methods were used to test ecological explanations of variation in lens transmission and to test for selection across traits.Lenses of diurnal (day‐active) and scansorial (climbing) frogs transmitted significantly less shortwave light than those of non‐diurnal or non‐scansorial amphibians, and evolutionary modelling suggested that these differences have resulted from differential selection.The presence of shortwave‐transparent lenses was common among the sampled amphibians, which implies that many are sensitive to shortwave light to some degree even in the absence of visual pigments maximally sensitive in the UV. This suggests that shortwave light, including UV, could play an important role in amphibian behaviour and ecology.Shortwave‐absorbing lens pigments likely provide higher visual acuity to diurnally active frogs of multiple ecologies and to nocturnally active scansorial frogs. This new mechanistic understanding of amphibian visual systems suggests that shortwave‐filtering lenses are adaptive not only in daylight conditions but also in those scotopic conditions where high acuity is advantageous. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Until recently many historical museum specimens were largely inaccessible to genomic inquiry, but high‐throughput sequencing (HTS) approaches have allowed researchers to successfully sequence genomic DNA from dried and fluid‐preserved museum specimens. In addition to preserved specimens, many museums contain large series of allozyme supernatant samples, but the amenability of these samples to HTS has not yet been assessed. Here, we compared the performance of a target‐capture approach using alternative sources of genomic DNA from 10 specimens of spring salamanders (Plethodontidae: Gyrinophilus porphyriticus) collected between 1985 and 1990: allozyme supernatants, allozyme homogenate pellets and formalin‐fixed tissues. We designed capture probes based on double‐digest restriction‐site associated sequencing (RADseq) derived loci from frozen blood samples available for seven of the specimens and assessed the success and consistency of capture and RADseq approaches. This study design enabled direct comparisons of data quality and potential biases among the different data sets for phylogenomic and population genomic analyses. We found that in phylogenetic analyses, all enrichment types for a given specimen clustered together. In principal component space all capture‐based samples clustered together, but RADseq samples did not cluster with corresponding capture‐based samples. Single nucleotide polymorphism calls were on average 18.3% different between enrichment types for a given individual, but these discrepancies were primarily due to differences in heterozygous/homozygous single nucleotide polymorphism calls. We demonstrate that both allozyme supernatant and formalin‐fixed samples can be successfully used for population genomic analyses and we discuss ways to identify and reduce biases associated with combining capture and RADseq data. [ABSTRACT FROM AUTHOR]

The Príncipe giant tree frog Leptopelis palmatus is endemic to the small oceanic island of Príncipe in the Gulf of Guinea. For several decades, this charismatic but poorly known species was confused with another large tree frog species from continental Africa, L. rufus. Phylogenetic relationships within the African genus Leptopelis are poorly understood and consequently the evolutionary history of L. palmatus and its affinity to L. rufus remain unclear. In this study, we combined mitochondrial DNA (mtDNA), morphological, and acoustic data for L. palmatus and L. rufus to assess different axes of divergence between the species. Our mtDNA gene tree for the genus Leptopelis indicated that L. palmatus is not closely related to L. rufus or other large species of Leptopelis. Additionally, we found low mtDNA diversity in L. palmatus across its range on Príncipe. We found significant morphological differences between females of L. rufus and L. palmatus, but not between males. We characterised the advertisement call of L. palmatus for the first time, which is markedly distinct from L. rufus. Finally, we summarised our observations of L. palmatus habitats and additional notes on phenotypic variation and behaviour. Our study reinforces the distinctiveness of L. palmatus and provides information important for the conservation of this endangered species. [ABSTRACT FROM AUTHOR]

A period of isolation in allopatry typically precedes local adaptation and subsequent divergence among lineages. Alternatively, locally adapted phenotypes may arise and persist in the face of gene flow, resulting in strong correlations between ecologically‐relevant phenotypic variation and corresponding environmental gradients. Quantifying genetic, ecological, and phenotypic divergence in such lineages can provide insights into the abiotic and biotic mechanisms that structure populations and drive the accumulation of phenotypic and taxonomic diversity. Low‐vagility organisms whose distributions span ephemeral geographic barriers present the ideal evolutionary context within which to address these questions. Here, we combine genetic (mtDNA and genome‐wide SNPs) and phenotypic data to investigate the divergence history of caecilians (Amphibia: Gymnophiona) endemic to the oceanic island of São Tomé in the Gulf of Guinea archipelago. Consistent with a previous mtDNA study, we find two phenotypically and genetically distinct lineages that occur along a north‐to‐south axis with extensive admixture in the centre of the island. Demographic modelling supports divergence in allopatry (~300 kya) followed by secondary contact (~95 kya). Consequently, in contrast to a morphological study that interpreted latitudinal phenotypic variation in these caecilians as a cline within a single widespread species, our analyses suggest a history of allopatric lineage divergence and subsequent hybridization that may have blurred species boundaries. We propose that late Pleistocene volcanic activity favoured allopatric divergence between these lineages with local adaptation to climate maintaining a stable hybrid zone in the centre of São Tomé Island. Our study joins a growing number of systems demonstrating lineage divergence on volcanic islands with stark environmental transitions across small geographic distances. [ABSTRACT FROM AUTHOR]

Phenotypic variation among populations, as seen in the signaling traits of many species, provides an opportunity to test whether similar factors generate repeated phenotypic patterns in different parts of a species' range. We investigated whether genetic divergence, abiotic gradients, and sympatry with closely related species explain variation in the dewlap colors of Amazon Slender Anoles, Anolis fuscoauratus. To this aim, we characterized dewlap diversity in the field with respect to population genetic structure and evolutionary relationships, assessed whether dewlap phenotypes are associated with climate or landscape variables, and tested for nonrandom associations in the distributions of A. fuscoauratus phenotypes and sympatric Anolis species. We found that dewlap colors vary among but not within sites in A. fuscoauratus. Regional genetic clusters included multiple phenotypes, while populations with similar dewlaps were often distantly related. Phenotypes did not segregate in environmental space, providing no support for optimized signal transmission at a local scale. Instead, we found a negative association between certain phenotypes and sympatric Anolis species with similar dewlap color attributes, suggesting that interactions with closely related species promoted dewlap divergence among A. fuscoauratus populations. Amazon Slender Anoles emerge as a promising system to address questions about parallel trait evolution and the contribution of signaling traits to speciation. [ABSTRACT FROM AUTHOR]

The fungal pathogen Batrachochytrium dendrobatidis (Bd) is implicated in global declines of amphibian populations and has been documented in African specimens originally collected as far back as the 1930s. Numerous recent surveys focusing on regional pathogen prevalence have greatly increased the number of known occurrences of Bd in African species, but few studies have focused on continental distribution patterns. We analyzed all known positive occurrences of Bd in African amphibians to date, including newly reported data from Cameroon, the Democratic Republic of the Congo, Gabon, Namibia, and the Republic of the Congo. Records from both Namibia and the Republic of the Congo reported herein represent first positive occurrences for these countries. With this most comprehensive sampling of the African continent to date we identified patterns of Bd-positive occurrences associated with (1) location (i.e., biogeographic region, country), (2) taxonomy, (3) life history, and (4) threat of extinction. We used fine-grained (30 arc seconds) environmental niche models (ENMs) to predict the continental distribution of Bd and identify hotspots for the pathogen, including areas not previously modeled to have high suitability for the fungus, and areas of high amphibian biodiversity from which Bd has not yet been documented. Our ENMs predicted that the environmentally suitable range of Bd encompasses vast areas of high amphibian biodiversity, including the Congo Basin and the Albertine Rift. Although our ENMs indicated that West Africa is environmentally suitable for Bd, the fungus has not been reported west of the Dahomey Gap. Likewise, the ENMs also identified regions across the Congo Basin and coastal Angola that are environmentally suitable for the pathogen but from which Bd has not yet been reported, underscoring a need for Bd surveys in these regions. Although amphibian declines in Africa have not been directly attributed to chytridiomycosis, Bd has been detected in over one fifth of the most-threatened African amphibians. Given the presence of the hypervirulent Bd global panzootic lineage (BdGPL) in Africa, we believe that the threat of Bd as a novel pathogen may be underestimated and that focused research is urgently needed to identify which species are susceptible to Bd-driven declines. [ABSTRACT FROM AUTHOR]

Aim: Species with wide distributions spanning the African Guinean and Congolian rain forests are often composed of genetically distinct populations or cryptic species with geographic distributions that mirror the locations of the remaining forest habitats. We used phylogeographic inference and demographic model testing to evaluate diversification models in a widespread rain forest species, the African foam‐nest treefrog Chiromantis rufescens. Location: Guinean and Congolian rain forests, West and Central Africa. Taxon: Chiromantis rufescens. Methods: We collected mitochondrial DNA (mtDNA) and single‐nucleotide polymorphism (SNP) data for 130 samples of C. rufescens. After estimating population structure and inferring species trees using coalescent methods, we tested demographic models to evaluate alternative population divergence histories that varied with respect to gene flow, population size change and periods of isolation and secondary contact. Species distribution models were used to identify the regions of climatic stability that could have served as forest refugia since the last interglacial. Results: Population structure within C. rufescens resembles the major biogeographic regions of the Guinean and Congolian forests. Coalescent‐based phylogenetic analyses provide strong support for an early divergence between the western Upper Guinean forest and the remaining populations. Demographic inferences support diversification models with gene flow and population size changes even in cases where contemporary populations are currently allopatric, which provides support for forest refugia and barrier models. Species distribution models suggest that forest refugia were available for each of the populations throughout the Pleistocene. Main conclusions: Considering historical demography is essential for understanding population diversification, especially in complex landscapes such as those found in the Guineo–Congolian forest. Population demographic inferences help connect the patterns of genetic variation to diversification model predictions. The diversification history of C. rufescens was shaped by a variety of processes, including vicariance from river barriers, forest fragmentation and adaptive evolution along environmental gradients. [ABSTRACT FROM AUTHOR]

Biodiversity loss is one major outcome of human-mediated ecosystem disturbance. One way that humans have triggered wildlife declines is by transporting disease-causing agents to remote areas of the world. Amphibians have been hit particularly hard by disease due in part to a globally distributed pathogenic chytrid fungus (Batrachochytrium dendrobatidis [Bd]). Prior research has revealed important insights into the biology and distribution of Bd; however, there are still many outstanding questions in this system. Although we know that there are multiple divergent lineages of Bd that differ in pathogenicity, we know little about how these lineages are distributed around the world and where lineages may be coming into contact. Here, we implement a custom genotyping method for a global set of Bd samples. This method is optimized to amplify and sequence degraded DNA from noninvasive skin swab samples. We describe a divergent lineage of Bd, which we call BdASIA3, that appears to be widespread in Southeast Asia. This lineage co-occurs with the global panzootic lineage (BdGPL) in multiple localities. Additionally, we shed light on the global distribution of BdGPL and highlight the expanded range of another lineage, BdCAPE. Finally, we argue that more monitoring needs to take place where Bd lineages are coming into contact and where we know little about Bd lineage diversity. Monitoring need not use expensive or difficult field techniques but can use archived swab samples to further explore the history--and predict the future impacts--of this devastating pathogen. [ABSTRACT FROM AUTHOR]

The fungal pathogen Batrachochytrium dendrobatidis ( Bd) infects hundreds of amphibian species and is implicated in global amphibian declines. Bd is comprised of several lineages that differ in pathogenicity, thus, identifying which Bd strains are present in a given amphibian community is essential for understanding host-pathogen dynamics. The presence of Bd has been confirmed in Central Africa, yet vast expanses of this region have not yet been surveyed for Bd prevalence, and the genetic diversity of Bd is largely unknown in this part of the world. Using retrospective surveys of museum specimens and contemporary field surveys, we estimated the prevalence of Bd in Central African island and continental amphibian assemblages, and genotyped strains of Bd present in each community. Our sampling of museum specimens included just a few individuals collected in the Gulf of Guinea archipelago prior to 1998, yet one of these individuals was Bd-positive indicating that the pathogen has been on Bioko Island since 1966. We detected Bd across all subsequent sample years in our study and found modest support for a relationship between host life history and Bd prevalence, a positive relationship between prevalence and host community species richness, and no significant relationship between elevation and prevalence. The Global Panzootic Lineage ( Bd GPL) was present in all the island and continental amphibian communities we surveyed. Our results are consistent with a long-term and widespread distribution of Bd in amphibian communities of Gabon and the Gulf of Guinea archipelago. [ABSTRACT FROM AUTHOR]

[Display omitted] • We identified five independent transitions to pueriparity in the genus Salamandra. • Transitions to pueriparity occurred at different evolutionary timescales. • We confirm pueriparity as the prevailing reproductive mode in S. s. bernardezi. • Introgression is common, but reproductive mode follows nuclear history. • Exome-capture and previously published RAD-data reveal similar evolutionary histories. The ability to bear live offspring, viviparity, has evolved multiple times across the tree of life and is a remarkable adaptation with profound life-history and ecological implications. Within amphibians the ancestral reproductive mode is oviparity followed by a larval life stage, but viviparity has evolved independently in all three amphibian orders. Two types of viviparous reproduction can be distinguished in amphibians; larviparity and pueriparity. Larviparous amphibians deliver larvae into nearby ponds and streams, while pueriparous amphibians deliver fully developed juveniles and thus do not require waterbodies for reproduction. Among amphibians, the salamander genus Salamandra is remarkable as it exhibits both inter- and intraspecific variation in the occurrence of larviparity and pueriparity. While the evolutionary relationships among Salamandra lineages have been the focus of several recent studies, our understanding of how often and when transitions between modes occurred is still incomplete. Furthermore, in species with intraspecific variation, the reproductive mode of a given population can only be confirmed by direct observation of births and thus the prevalence of pueriparous populations is also incompletely documented. We used sequence capture to obtain 1,326 loci from 94 individuals from across the geographic range of the genus, focusing on potential reproductive mode transition zones. We also report additional direct observations of pueriparous births for 20 new locations and multiple lineages. We identify at least five independent transitions from the ancestral mode of larviparity to pueriparity among and within species, occurring at different evolutionary timescales ranging from the Pliocene to the Holocene. Four of these transitions occurred within species. Based on a distinct set of markers and analyses, we also confirm previous findings of introgression between species and the need for taxonomic revisions in the genus. We discuss the implications of our findings with respect to the evolution of this complex trait, and the potential of using five independent convergent transitions for further studies on the ecological context in which pueriparity evolves and the genetic architecture of this specialized reproductive mode. [ABSTRACT FROM AUTHOR]

Highlights: [•] First phylogeny of African torrent frogs throughout the distribution range. [•] Description of a new genus (Odontobatrachus) for West African taxa. [•] Resurrection of the genus Arthroleptides for East African taxa. [•] Recognition of a hitherto overseen diversity in all biogeographic realms. [Copyright &y& Elsevier]