Anuran radiations and the evolution of tadpole morphospace

Larval morphology and natural history in two Minervarya species from Andaman Islands, with comments on a new phytotelmonous larval morphotype for the genus

We studied the larval morphology and natural history of two species of Minervarya from the Andaman Islands of India. A recent assignment of Charles Darwins frog to the genus Minervarya opened up new questions on the systematic affinities and natural history of its enigmatic tadpoles. Originally described as Rana charlesdarwini Das, 1998, and long considered as Ingerana charlesdarwini, the tadpoles of this species were poorly understood and incomparable to those of other presumed close relatives based on an original brief description of its phytotelmonous tadpoles. Here we present a detailed redescription of the larval morphology of M. charlesdarwini based on genetically confirmed tadpoles. At the same time, we compared the external morphology of M. charlesdarwini tadpoles to that of its closest phylogenetic and sympatric congener, M. andamanensis, consequently reporting the first-ever larval description for M. andamanensis. For the first time also for minervaryan frogs, we record that M. charlesdarwini lays eggs on the inner walls of tree holes, and the tadpoles possess morphological adaptations for a phytotelmonous life. Their unique features, such as tail-to-body ratio >2.2, reduced labial tooth rows (LTRF 1/1), acutely pointed serrations in the jaw sheath, and the medial portion of the upper sheath broadly arched and that of the lower sheath U-shaped, justify adding a new larval morphotype to the genus Minervarya. In contrast, M. andamanensis breeds and undergoes development in ground water puddles and ponds, a common trait for other known minervaryan species. Furthermore, our study generates new knowledge on the amplexus, oviposition site, and early embryonic development in these species. The deeper understanding of the biology and habitat requirements contributes additional traits for future systematic and evolutionary studies, and helps guide conservation assessments for these two species endemic to a handful of islands in the Andaman Archipelago.

Phylogeny and historical biogeography of the water boatmen (Insecta: Hemiptera: Heteroptera: Nepomorpha: Corixoidea)

The water boatmen of Corixoidea, a group of aquatic bugs with more than 600 extant species, is one of the largest superfamilies of Nepomorpha. Contrary to the other nepomorphan lineages, the Corixoidea are most diverse in the Laurasian remnant Holarctic region. To explicitly test whether the present-day Holarctic distribution of diverse corixids is associated with the arising of the Laurasian landmass that was separated from Gondwana, we investigated the phylogeny, divergence times and historical biogeography of Corixoidea based on morphological and molecular characters sampled from 122 taxa representing all families, subfamilies, tribes and approximately 54 % of the genera. Our results were largely congruent with the phylogenetic relationships within the established nepomorphan phylogenetic context. The fossil calibrated chronogram, diversification analysis and ancestral ranges reconstruction indicated that Corixoidea began to diversify in Gondwana in the late Triassic approximately at 224 Ma and the arising of the most diverse subfamily Corixinae in Corixidae in the Holarctic region was largely congruent with the time of separation of Laurasia from Gondwana. The large-scale expansion of the temperate and cold zones on the northward-moving Laurasian landmass after the breakup of the Pangea provided new aquatic niches and ecological opportunities for promoting rapid diversification for the Holarctic corixid lineage.

Larval morphology of Amazonia foam-nesting frogs of the genus Engystomops (Anura: Leptodactylidae: Leiuperinae)

The highly differentiated anuran larvae make them an interesting and complementary source of information to understand anuran evolution. Among neotropical foam-nesting frogs, the available information on tadpole morphology for the subfamily Leiuperinae remains largely incomplete and variably reported among genera; in the monophyletic genus Engystomops it is still incipient. Herein, we summarize available information on larval morphology for five of the nine known species of Engystomops, three of them for the first time, reporting external morphology, buccopharyngeal cavity, and skeleton. The tadpoles of the genus have an overall generalized morphology and many traits are conserved across species. Nevertheless, many characters are systematically informative and some are diagnostic for some species, as the paravertebral gland in E. petersi and the dorsally directed spiracle in E. puyango. Other characters provide support for some subclades within the genus. Moreover, some traits, such as the direction of the vent tube, supports the close relationship between Engystomops and Physalaemus, whereas other support the existence of these two as distinct genera, such as the overall shape of the lateral ridge papillae and the presence of a processus pseudopterygoideus. This article is protected by copyright. All rights reserved.

Finding a pathway through the rocks: the role of development on the evolution of quasi-terrestriality and the origin of endotrophism in cycloramphids (Anura)

Anurans have served as models in evolutionary studies on reproduction and development. Several generalizations have emerged but it is unclear whether they represent the diversity of the entire group. We studied the development of two species of the Neotropical family Cycloramphidae. Frogs in this family have peculiar spawning sites and developmental biologies. Whereas some cycloramphid tadpoles are exotrophic, quasi-terrestrial and thrive in films of water that flow over rocky outcrops, others are endotrophic, terrestrial and complete their development outside the eggs laid on the forest floor, under logs or in crevices. Cycloramphid tadpoles have aspects of their morphology distinct from those of pond and stream dwellers; they hatch in more advanced stages of development and have typical tadpole structures, either in a modified form or absent. Herein we present a study of the tadpoles of C. lithomimeticus and T. miliaris, in order to document and discuss alterations in the ontogeny of several larval structures. These changes seem to be associated with adaptations to life in the peculiar habitats where the tadpoles thrive. We infer that the observations we present are explained by development being associated with aspects of terrestrialization and endotrophism.

Transcriptomic evidence for visual adaptation during the aquatic to terrestrial metamorphosis in leopard frogs

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.

Phenotypic Variation Through Ontogeny: Thyroid Axis Disruption During Larval Development in the Frog Pleurodema borellii

Studies of the effects of thyroid hormones on larval development in the frog Xenopus spp. have provided baseline information to identify developmental constraints and elucidate genetic and hormonal mechanisms driving development, growth, and life history transitions. However, this knowledge requires data based on other anurans to complete a comprehensive approach to the understanding of larval developmental diversity and phenotypic variation through ontogeny. Mesocosm experiments provide realistic data about environmental conditions and timing; this information is useful to describe anuran larval development and/or analyze endocrine disruption. In this study, mesocosm experiments of the larval development of the frog Pleurodema borellii were conducted to explore the consequences of thyroid axis disruption; the sensitivity of tadpoles to the methimazole (2.66 mg/l) and thyroxine (T4) (1.66 μg/l) was compared. These concentrations were selected based on previous studies in Pleurodema borellii. We test the effects of methimazole and thyroxine on development in early exposure (from beginning of larval development) and late exposure, 18 days after hatching, with doses administered every 48 h. Tadpoles were evaluated 31 days after hatching. Methimazole caused moderate hypertrophy of the thyroid gland, alteration in the growth rates, differentiation without inhibition of development, and an increase of developmental variability. Thyroxine produced slight atrophy of the thyroid gland, accelerated growth rates and differentiation, and minor developmental variability. In tadpoles at stages previous to metamorphose, skull development (differentiation of olfactory capsules, appearance of dermal bones, and cartilage remodeling) seemed to be unaltered by the disruptors. Moreover, similar abnormal morphogenesis converged in specimens under methimazole and thyroxine exposures. Abnormalities occurred in pelvic and pectoral girdles, and vent tube, and could have been originated at the time of differentiation of musculoskeletal tissues of girdles. Our results indicate that premetamorphic stages (Gosner Stages 25–35) are sensitive to minimal thyroid axis disruption, which produces changes in developmental rates; these stages would also be critical for appendicular musculoskeletal morphogenesis to achieve the optimal condition to start metamorphosis.

Eye‐body allometry across biphasic ontogeny in anuran amphibians

Animals with biphasic lifecycles often inhabit different visual environments across ontogeny. Many frogs and toads (Amphibia: Anura) have free-living aquatic larvae (tadpoles) that metamorphose into adults that inhabit a range of aquatic and terrestrial environments. Ecological differences influence eye size across species, but these relationships have not yet been explored across life stages in an ontogenetic allometric context. We examined eye-body size scaling in a species with aquatic larvae and terrestrial adults, the common frog Rana temporaria, using a well-sampled developmental series. We found a shift in ontogenetic allometric trajectory near metamorphosis indicating prioritized growth in tadpole eyes. To explore the effects of different tadpole and adult ecologies on eye-body scaling, we expanded our taxonomic sampling to include developmental series of eleven additional anuran species. Intraspecific eye-body scaling was variable among species, with 8/12 species exhibiting a significant change in allometric slope between tadpoles and adults. Traits categorizing both tadpole ecology (microhabitat, eye position, mouth position) and adult ecology (habitat, activity pattern) across species had significant effects on allometric slopes among tadpoles, but only tadpole eye position had a significant effect among adults. Our study suggests that relative eye growth in the preliminary stages of biphasic anuran ontogenies is somewhat decoupled and may be shaped by both immediate ecological need (i.e. tadpole visual requirements) and what will be advantageous during later adult stages.

The remarkable larval anatomy of Proceratophrys minuta Napoli, Cruz, Abreu and Del-Grande, 2011 (Amphibia: Anura: Odontophrynidae)

The free living larvae of anurans (i.e., tadpoles) are a key element in the evolution and diversification of this group, and as such, their morphology is an important element to understand the phylogenetic relationships of frogs. However, the lack of data on larval morphology prevents us from fully understanding larval evolution in several lineages. The Neotropical genus Proceratophrys currently comprises 39 species, but descriptions of the internal morphology of larvae in this group are rare and restricted to few aspects of their buccopharyngeal cavity, chondrocranium, and muscles. In the present study, I describe the internal anatomy of the tadpole of P. minuta and report a new remarkable myological character state for the species. Given the rarity of this material, the description of this species' buccopharyngeal and musculo-skeletal elements is based on two tadpoles in developmental stages 30 and 31. Several new apomorphic character states are described: (a) the presence of a conical papilla in the interior of the nostril; (b) a row of five short, conical papilla preceding the tall, postnarial papilla; and (c) the m. mandibulolabialis inserting in the gular skin. This latter feature is a remarkable, newly discovered character state that had never been reported in the literature before and is probably related to a particular feeding habit of the tadpoles of this species. The function of the m. mandibulolabialis in P. minuta is unknown.

Olfaction across the water-air interface in anuran amphibians

Extant anuran amphibians originate from an evolutionary intersection eventually leading to fully terrestrial tetrapods. In many ways, they have to deal with exposure to both terrestrial and aquatic environments: (i) phylogenetically, as derivatives of the first tetrapod group that conquered the terrestrial environment in evolution; (ii) ontogenetically, with a development that includes aquatic and terrestrial stages connected via metamorphic remodeling; and (iii) individually, with common changes in habitat during the life cycle. Our knowledge about the structural organization and function of the amphibian olfactory system and its relevance still lags behind findings on mammals. It is a formidable challenge to reveal underlying general principles of circuity-related, cellular, and molecular properties that are beneficial for an optimized sense of smell in water and air. Recent findings in structural organization coupled with behavioral observations could help to understand the importance of the sense of smell in this evolutionarily important animal group. We describe the structure of the peripheral olfactory organ, the olfactory bulb, and higher olfactory centers on a tissue, cellular, and molecular levels. Differences and similarities between the olfactory systems of anurans and other vertebrates are reviewed. Special emphasis lies on adaptations that are connected to the distinct demands of olfaction in water and air environment. These particular adaptations are discussed in light of evolutionary trends, ontogenetic development, and ecological demands.

Geographic variation in shape and size of anuran tadpoles: Interpopulation comparisons in Scinax fuscovarius (Anura, Hylidae)

Among anuran species with biphasic life cycle, the occurrence of intraspecific larval morphotypes has been related to variations in developmental time, diet, geographical variation, or response to predators. Here, we evaluated the external morphological variation of larvae among three populations, located more than 270 km apart, of the anuran hylid Scinax fuscovarius by linear and geometric methods, to elucidate the presence of geographically different morphs. Comparisons targeted development, growth, and external morphology. Studied populations exhibited differences in reproductive seasonality, growth rate, timing of development, shape, and size. Shape and size comparisons revealed two well-differentiated morphs, one of them shared by the two closest populations. Morphological differences evidenced a smaller and depressed form of the entire body plan in the most distant population, which showed continuous reproduction throughout the rainy season and under more unpredictable conditions. We interpret the occurrence of the two different larval morphs in S. fuscovarius as a by-product of local geographical conditions, and discuss on possible associations with biotic and abiotic factors cues.

Conservation of Glomerular Organization in the Main Olfactory Bulb of Anuran Larvae

The glomerular array in the olfactory bulb of many vertebrates is segregated into molecularly and anatomically distinct clusters linked to different olfactory functions. In anurans, glomerular clustering is so far only described in Xenopus laevis. We traced olfactory projections to the bulb in tadpoles belonging to six distantly related anuran species in four families (Pipidae, Hylidae, Bufonidae, Dendrobatidae) and found that glomerular clustering is remarkably conserved. The general bauplan consists of four unequally sized glomerular clusters with minor inter-species variation. During metamorphosis, the olfactory system undergoes extensive remodeling. Tracings in metamorphotic and juvenile Dendrobates tinctorius and Xenopus tropicalis suggest a higher degree of variation in the glomerular organization after metamorphosis is complete. Our study highlights, that the anatomical organization of glomeruli in the main olfactory bulb (MOB) is highly conserved, despite an extensive ecomorphological diversification among anuran tadpoles, which suggests underlying developmental constraints.

Morphological characterization and taxonomic key of tadpoles (Amphibia: Anura) from the northern region of the Atlantic Forest

Abstract: Although anuran tadpoles are widely distributed and abundant in tropical aquatic habitats, there is a lack of taxonomic keys for the Atlantic Forest. Herein, we developed a dichotomous key for identifying the tadpoles for all species with known larval phase and already recorded in the Atlantic Forest north of the São Francisco River. We analyzed discrete characteristics of 1,042 tadpoles encompassing 63 species of 28 genera from 32 localities. The user-friendly key includes illustration and pictures, and it is a significant step towards improving our knowledge of tadpoles of the Atlantic Forest.

The MHC Class Ia Genes in Chenfu's Treefrog (Zhangixalus chenfui) Evolved via Gene Duplication, Recombination, and Selection

Simple Summary

Amphibians, the first terrestrial vertebrates, provide materials for adaptive evolutionary studies, such as the evolution of the major histocompatibility complex (MHC). To date, various MHC evolutionary mechanisms have been identified in frogs, but more research is needed to determine the evolutionary mechanisms of the frog MHC. The main purpose of this study was to evaluate polymorphisms in the MHC class Ia genes of the Chenfu’s Treefrog. The MHC class Ia genes of the Chenfu’s Treefrog have high polymorphism. The mechanisms responsible for the formation of the polymorphisms include gene duplication, recombination, and selection.

Abstract

The molecular mechanisms underlying the evolution of adaptive immunity-related proteins can be deduced by a thorough examination of the major histocompatibility complex (MHC). Currently, in vertebrates, there is a relatively large amount of research on MHCs in mammals and birds. However, research related to amphibian MHC genes and knowledge about the evolutionary patterns is limited. This study aimed to isolate the MHC class I genes from Chenfu’s Treefrog (Zhangixalus chenfui) and reveal the underlying evolutionary processes. A total of 23 alleles spanning the coding region of MHC class Ia genes were identified in 13 individual samples. Multiple approaches were used to test and identify recombination from the 23 alleles. Amphibian MHC class Ia alleles, from NCBI, were used to construct the phylogenetic relationships in MEGA. Additionally, the partition strategy was adopted to construct phylogenetic relationships using MrBayes and MEGA. The sites of positive selection were identified by FEL, PAML, and MEME. In Chenfu’s Treefrog, we found that: (1) recombination usually takes place between whole exons of MHC class Ia genes; (2) there are at least 3 loci for MHC class Ia, and (3) the diversity of genes in MHC class Ia can be attributed to recombination, gene duplication, and positive selection. We characterized the evolutionary mechanisms underlying MHC class Ia genes in Chenfu’s Treefrog, and in so doing, broadened the knowledge of amphibian MHC systems.

From cryptic to colorful: Evolutionary decoupling of larval and adult color in butterflies

Many animals undergo complete metamorphosis, where larval forms change abruptly in adulthood. Color change during ontogeny is common, but there is little understanding of evolutionary patterns in these changes. Here, we use data on larval and adult color for 246 butterfly species (61% of all species in Australia) to test whether the evolution of color is coupled between life stages. We show that adults are more variable in color across species than caterpillars and that male adult color has lower phylogenetic signal. These results suggest that sexual selection is driving color diversity in male adult butterflies at a broad scale. Moreover, color similarities between species at the larval stage do not predict color similarities at the adult stage, indicating that color evolution is decoupled between young and adult forms. Most species transition from cryptic coloration as caterpillars to conspicuous coloration as adults, but even species with conspicuous caterpillars change to different conspicuous colors as adults. The use of high‐contrast coloration is correlated with body size in caterpillars but not adults. Taken together, our results suggest a change in the relative importance of different selective pressures at different life stages, resulting in the evolutionary decoupling of coloration through ontogeny.

Phylogeny of spiny frogs Nanorana (Anura: Dicroglossidae) supports a Tibetan origin of a Himalayan species group

Recent advances in the understanding of the evolution of the Asian continent challenge the long-held belief of a faunal immigration into the Himalaya. Spiny frogs of the genus Nanorana are a characteristic faunal group of the Himalaya-Tibet orogen (HTO). We examine the phylogeny of these frogs to explore alternative biogeographic scenarios for their origin in the Greater Himalaya, namely, immigration, South Tibetan origin, strict vicariance. We sequenced 150 Nanorana samples from 62 localities for three mitochondrial (1,524 bp) and three nuclear markers (2,043 bp) and complemented the data with sequence data available from GenBank. We reconstructed a gene tree, phylogenetic networks, and ancestral areas. Based on the nuDNA, we also generated a time-calibrated species tree. The results revealed two major clades (Nanorana and Quasipaa), which originated in the Lower Miocene from eastern China and subsequently spread into the HTO (Nanorana). Five well-supported subclades are found within Nanorana: from the East, Central, and Northwest Himalaya, the Tibetan Plateau, and the southeastern Plateau margin. The latter subclade represents the most basal group (subgenus Chaparana), the Plateau group (Nanorana) represents the sister clade to all species of the Greater Himalaya (Paa). We found no evidence for an east-west range expansion of Paa along the Himalaya, nor clear support for a strict vicariance model. Diversification in each of the three Himalayan subclades has probably occurred in distinct areas. Specimens from the NW Himalaya are placed basally relative to the highly diverse Central Himalayan group, while the lineage from the Tibetan Plateau is placed within a more terminal clade. Our data indicate a Tibetan origin of Himalayan Nanorana and support a previous hypothesis, which implies that a significant part of the Himalayan biodiversity results from primary diversification of the species groups in South Tibet before this part of the HTO was uplifted to its recent heights.

Running in circles in phylomorphospace: host environment constrains morphological diversification in parasitic wasps

Understanding phenotypic diversification and the conditions that spur morphological novelty or constraint is a major theme in evolutionary biology. Unequal morphological diversity between sister clades can result from either differences in the rate of morphological change or in the ability of clades to explore novel phenotype ranges. We combine an existing phylogenetic framework with new phylogenomic data and geometric morphometrics to explore the relative roles of rate versus mode of morphological evolution for a hyperdiverse group: cryptine ichneumonid wasps. Data from genomic ultraconserved elements confirm that cryptines are divided into two large clades: one specialized in the use of hosts that are deeply concealed under hard substrates, and another with a much more diversified host range. Using a phylomorphospace approach, we show that both clades have experienced similar rates of morphological evolution. Nonetheless, the more specialized group is much more restricted in morphospace occupation, indicating that it repeatedly evolved morphological change through the same morphospace regions. This is in agreement with our prediction that host use imposes constraints in the morphospace available to lineages, and reinforces an important distinction between evolutionary stasis as opposed to a scenario of continual morphological change restricted to a certain range of morphotypes.

A gyroscopic advantage: phylogenetic patterns of compensatory movements in frogs

Head and eye compensatory movements known as vestibulo-ocular and vestibulo-cervical reflexes are essential to stay orientated in space while moving. We have used a previously developed methodology focused on the detailed mathematical description of head compensatory movements in frogs without the need for any surgical procedures on the examined specimens. Our comparative study comprising 35 species of frogs from different phylogenetic backgrounds revealed species-specific head compensatory abilities ensuring gaze stabilization. Moreover, we found a strong phylogenetic signal highlighting the great ability of compensatory head movements in families of Pyxicephalidae and Rhacophoridae from the Natatanura group. By contrast, families of Dendrobatidae and Microhylidae exhibited only poor or no head compensatory movements. Contrary to our expectation, the results did not corroborate an ecomorphological hypothesis anticipating a close relationship between ecological parameters and the head compensatory movements. We did not find any positive association between more complex (3D structured, arboreal or aquatic) habitats or more saltatory behavior and elevated abilities of head compensatory movements. Moreover, we found compensatory movements in most basal Archeobatrachia, giving an indication of common ancestry of these abilities in frogs that are variously pronounced in particular families. We hypothesize that the uncovered proper gaze stabilization during locomotion provided by the higher head compensatory abilities can improve or even enable visual perception of the prey. We interpret this completely novel finding as a possible gyroscopic advantage in a foraging context. We discuss putative consequences of such advanced neuromotor skills for diversification and ecological success of the Natatanura group.

Ecomorphological diversity of Australian tadpoles

Ecomorphology is the association between an organism's morphology and its ecology. Larval anuran amphibians (tadpoles) are classified into distinct ecomorphological guilds based upon morphological features and observations of their ecology. The extent to which guilds comprise distinct morphologies resulting from convergent evolution, the degree of morphological variability within each guild, and the degree of continuity in shape between guilds has not previously been examined in a phylogenetically informed statistical framework. Here, we examine tadpole ecomorphological guilds at a macroevolutionary scale by examining morphological diversity across the Australian continent. We use ecological data to classify species to guilds, and geometric morphometrics to quantify body shape in the tadpoles of 188 species, 77% of Australian frog diversity. We find that the ecomorphological guilds represented by Australian species are morphologically distinct, but there is substantial morphological variation associated with each guild, and all guilds together form a morphological continuum. However, in a phylogenetic comparative context, there is no significant difference in body shape among guilds. We also relate the morphological diversity of the Australian assemblage of tadpoles to a global sample and demonstrate that ecomorphological diversity of Australian tadpoles is limited with respect to worldwide species. Our results demonstrate that general patterns of ecomorphological variation are upheld in Australian tadpoles, but tadpole body shape is more variable and possibly generalist than generally appreciated.

Phylogenetic, ecological and biomechanical constraints on larval form: A comparative morphological analysis of barnacle nauplii

Barnacle naupliar larvae are differentiated from other zooplankton by their unique pair of frontal lateral horns, frontal filaments, and a pear-shaped cephalic shield. Their morphology impose constraints on their ecological functions and reflect their evolutionary history. To explore the potential functional basis underlying the similarities and differences in barnacle larval form, we conducted a meta-analysis on the shape of the barnacle nauplii's cephalic shield and examined its relation to larval size, trophic mode, pelagic larval duration and habitat. Nauplii cephalic shield morphology of 102 species were quantified with normalized elliptic Fourier analysis. Most of the species were distributed around the center of the morphospace but a few extreme groups occupied the periphery: nauplii that were large and lecithotrophic. Subsequent principal component regression analyses showed that larval size was a good predictor of the first shape variations axis (aspect ratio). After allometry adjustment, nauplii from different trophic modes differentiated along the second axis of the major shape variations (relative frontal horn length). Habitat was a poor predictor of variations in naupliar body form, but it could be used to differentiate extreme morphology groups from other nauplii. Our result suggests that size-related biomechanical or developmental constraints and feeding requirements are important in shaping the evolution of the naupliar body form. Within the limitations of these functional constraints, habitat drives the divergence of extreme morphology groups from the majority of species. Our comparative morphometrics analysis demonstrated how variations in larval body form can be quantitatively linked to the functional needs that constrain or drive their diversity, and inform further empirical experiments on larval functional morphology.

The evolution, distribution and diversity of endogenous circoviral elements in vertebrate genomes

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Sequences derived from circoviruses occur sporadically in vertebrate genomes.

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The vast majority of fixed circovirus sequences in vertebrate genomes are derived from rep genes.

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Some ancient circoviruses were closely related to modern circoviruses.

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Integrated circovirus sequences are highly duplicated in some carnivore lineages.

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Sequences in the Mus spretus genome are closely related to modern canine circoviruses.

Circoviruses (family Circoviridae) are small, non-enveloped viruses that have short, single-stranded DNA genomes. Circovirus sequences are frequently recovered in metagenomic investigations, indicating that these viruses are widespread, yet they remain relatively poorly understood. Endogenous circoviral elements (CVe) are DNA sequences derived from circoviruses that occur in vertebrate genomes. CVe are a useful source of information about the biology and evolution of circoviruses. In this study, we screened 362 vertebrate genome assemblies in silico to generate a catalog of CVe loci. We identified a total of 179 CVe sequences, most of which have not been reported previously. We show that these CVe loci reflect at least 19 distinct germline integration events. We determine the structure of CVe loci, identifying some that show evidence of potential functionalization. We also identify orthologous copies of CVe in snakes, fish, birds, and mammals, allowing us to add new calibrations to the timeline of circovirus evolution. Finally, we observed that some ancient CVe group robustly with contemporary circoviruses in phylogenies, with all sequences within these groups being derived from the same host class or order, implying a hitherto underappreciated stability in circovirus-host relationships. The openly available dataset constructed in this investigation provides new insights into circovirus evolution, and can be used to facilitate further studies of circoviruses and CVe.

Genetic variation and selection of MHC class I loci differ in two congeneric frogs

Major histocompatibility complex (MHC) genes encode proteins in the acquired immune response pathway that often show distinctive selection-driven patterns in wild vertebrate populations. We examined genetic variation and signatures of selection in the MHC class I alpha 1 (A1)- and alpha 2 (A2)-domain encoding exons of two frog congeners [Agalychnis callidryas (n = 20) and A. lemur (n = 20)] from a single locality in Panama. We also investigated how historical demographic processes may have impacted MHC genetic diversity by analyzing a neutral mitochondrial marker. We found that both MHC domains were highly variable in both species, with both species likely expressing three loci. Our analyses revealed different signatures of selection between the two species, most notably that the A. callidryas A2 domain had experienced positive selection while the A2 domain of A. lemur had not. Diversifying selection acted on the same number of A1 and A2 allelic lineages, but on a higher percentage of A1 sites compared to A2 sites. Neutrality tests of mitochondrial haplotypes predominately indicated that the two species were at genetic equilibrium when the samples were collected. In addition, two historical tests of demography indicated both species have had relatively stable population sizes over the past 100,000 years; thus large population size changes are unlikely to have greatly influenced MHC diversity in either species during this time period. In conclusion, our results suggest that the impact of selection on MHC diversity varied between these two closely related species, likely due to a combination of distinct ecological conditions and past pathogenic pressures.

Transcriptomic and macroevolutionary evidence for phenotypic uncoupling between frog life history phases

Anuran amphibians undergo major morphological transitions during development, but the contribution of their markedly different life-history phases to macroevolution has rarely been analysed. Here we generate testable predictions for coupling versus uncoupling of phenotypic evolution of tadpole and adult life-history phases, and for the underlying expression of genes related to morphological feature formation. We test these predictions by combining evidence from gene expression in two distantly related frogs, Xenopus laevis and Mantidactylus betsileanus, with patterns of morphological evolution in the entire radiation of Madagascan mantellid frogs. Genes linked to morphological structure formation are expressed in a highly phase-specific pattern, suggesting uncoupling of phenotypic evolution across life-history phases. This gene expression pattern agrees with uncoupled rates of trait evolution among life-history phases in the mantellids, which we show to have undergone an adaptive radiation. Our results validate a prevalence of uncoupling in the evolution of tadpole and adult phenotypes of frogs.

Multiple major histocompatibility complex class I genes in Asian anurans: Ontogeny and phylogeny

Amphibians, as the first terrestrial vertebrates, offer a window into early major histocompatibility complex (MHC) evolution. We characterized the MHC class I of two Korean amphibians, the Asiatic toad (Bufo gargarizans) and the Japanese tree frog (Hyla japonica). We found at least four transcribed MHC class I (MHC I) loci, the highest number confirmed in any anuran to date. Furthermore, we identified MHC I transcripts in terrestrial adults, and possibly in aquatic larvae, of both species. We conducted a phylogenetic analysis based on MHC I sequence data and found that B. gargarizans and H. japonica cluster together in the superfamily Nobleobatrachia. We further identified three supertypes shared by the two species. Our results reveal substantial variation in the number of MHC I loci in anurans and suggest that certain supertypes have particular physiochemical properties that may confer pathogen resistance.

Tectonic blocks and molecular clocks

Evolutionary timescales have mainly used fossils for calibrating molecular clocks, though fossils only really provide minimum clade age constraints. In their place, phylogenetic trees can be calibrated by precisely dated geological events that have shaped biogeography. However, tectonic episodes are protracted, their role in vicariance is rarely justified, the biogeography of living clades and their antecedents may differ, and the impact of such events is contingent on ecology. Biogeographic calibrations are no panacea for the shortcomings of fossil calibrations, but their associated uncertainties can be accommodated. We provide examples of how biogeographic calibrations based on geological data can be established for the fragmentation of the Pangaean supercontinent: (i) for the uplift of the Isthmus of Panama, (ii) the separation of New Zealand from Gondwana, and (iii) for the opening of the Atlantic Ocean. Biogeographic and fossil calibrations are complementary, not competing, approaches to constraining molecular clock analyses, providing alternative constraints on the age of clades that are vital to avoiding circularity in investigating the role of biogeographic mechanisms in shaping modern biodiversity.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.

Para-allopatry in hybridizing fire-bellied toads (Bombina bombina and B. variegata): Inference from transcriptome-wide coalescence analyses

Ancient origins, profound ecological divergence, and extensive hybridization make the fire‐bellied toads Bombina bombina and B. variegata (Anura: Bombinatoridae) an intriguing test case of ecological speciation. Previous modeling has proposed that the narrow Bombina hybrid zones represent strong barriers to neutral introgression. We test this prediction by inferring the rate of gene exchange between pure populations on either side of the intensively studied Kraków transect. We developed a method to extract high confidence sets of orthologous genes from de novo transcriptome assemblies, fitted a range of divergence models to these data and assessed their relative support with analytic likelihood calculations. There was clear evidence for postdivergence gene flow, but, as expected, no perceptible signal of recent introgression via the nearby hybrid zone. The analysis of two additional Bombina taxa (B. v. scabra and B. orientalis) validated our parameter estimates against a larger set of prior expectations. Despite substantial cumulative introgression over millions of years, adaptive divergence of the hybridizing taxa is essentially unaffected by their lack of reproductive isolation. Extended distribution ranges also buffer them against small‐scale environmental perturbations that have been shown to reverse the speciation process in other, more recent ecotypes.

The geometry of morphospaces: lessons from the classic Raup shell coiling model

Morphospaces are spatial depictions of morphological variation among biological forms that have become an integral part of the analytical toolkit of evolutionary biologists and palaeobiologists. Nevertheless, the term morphospace brings together a great variety of spaces with different geometries. In particular, many morphospaces lack the metric properties underlying the notions of distance and direction, which are, however, central to the analysis of morphological differences and evolutionary transitions. The problem is illustrated here with the iconic morphospace of coiled shells implemented by Raup 50 years ago. The model, which allows the description of shell coiling geometry of various invertebrate taxa, is a seminal reference in theoretical morphology and morphospace theory, but also a morphometric framework frequently used in empirical studies, particularly of ammonoids. Because of the definition of its underlying parameters, Raup's morphospace does not possess a Euclidean structure and a meaningful interpretation of the spread and spacing of taxa within it is not guaranteed. Focusing on the region of the morphospace occupied by most ammonoids, I detail a landmark-based morphospace circumventing this problem and built from the same input measurements required for the calculation of Raup's parameters. From simulations and a reanalysis of Palaeozoic ammonoid shell disparity, the properties of these morphospaces are compared and their algebraic and geometric relationships highlighted. While Raup's model remains a valuable tool for describing ammonoid shells and relating their shapes to the coiling process, it is demonstrated that quantitative analyses of morphological patterns should be carried out within the landmark-based framework. Beyond this specific case, the increasing use and diversity of morphospaces in evolutionary morphology call for caution when interpreting patterns and comparing results drawn from different types of morphospaces.

Ontogenetic Development of the Derived Olfactory System of the Mantellid Frog Mantidactylus betsileanus

The nasal cavity of Mantidactylus betsileanus, a frog of the Madagascar-Comoroan endemic family Mantellidae, is characterized by a unique internal architecture. Unlike the state commonly observed in anurans, the two discernible olfactory subsystems of M. betsileanus (the main olfactory organ and the vomeronasal organ) are anatomically separated from each other, suggesting an enhanced functional differentiation. Here we evaluate the ontogenetic formation of this extraordinary anatomical state based on a histological study of a developmental series of M. betsileanus. The olfactory system of premetamorphic tadpoles, and most of its changes during metamorphosis, resembles that of other anurans. At the end of metamorphosis however, a growing obstruction of the passage between main olfactory organ and vomeronasal organ takes place, leading to the deviant morphological state previously described for adults. The late appearance of this atypical anatomical feature in the course of ontogeny agrees with the phylogenetic hypothesis of the observed obstruction representing a derived state for these frogs. From a functional point of view, the apparent autonomy of the vomeronasal organ is possibly linked to the presence of clade-specific femoral glands that are known to produce pheromones and that likewise are fully expressed in adults only. Anat Rec, 299:943-950, 2016. © 2016 Wiley Periodicals, Inc.

Developmental changes and novelties in ceratophryid frogs

The Neotropical frog genera Ceratophrys, Chacophrys and Lepidobatrachus form the monophyletic family Ceratophryidae. Although in- and out-group relationships are not fully resolved, the monophyly of the three genera is well supported by both morphological and molecular data. Much is known about the morphology of the ceratophryids, but there is little comparative information on how modification of a common ancestral developmental pathway played a role in shaping their particular body plans. Herein, we review morphological variation during ceratophryid ontogeny in order to explore the role of development in their evolution. The ceratophryids are collectively characterized by rapid larval development with respect to other anurans, yet the three genera differ in their postmetamorphic growth rates to sexual maturity. Derived traits in the group can be divided into many homoplastic features that evolved in parallel with those of anurans with fossorial/burrowing behaviors in semiarid environments, and apomorphies. Morphological novelties have evolved in their feeding mechanism, which makes them capable of feeding on exceptional large prey. Lepidobatrachus is unusual in having reduced the ecomorphological differences between its larvae and adults. As a result, both the larvae and the frog are similarly able to capture large prey underwater. Some unique features in Lepidobatrachus are differentiated in the tadpole and then exaggerated in the adult (e.g., the posterior displaced jaw articulation) in a manner unobserved in any other anurans.

Acute Toxic Effects of the Herbicide Formulation Focus(®) Ultra on Embryos and Larvae of the Moroccan Painted Frog, Discoglossus scovazzi

For regulatory and scientific purposes, there is a need to understand the sensitivity of a wider variety of wild species of amphibians and the sensitivities within their life stages to chemicals of widespread use such as herbicides. We investigated the acute toxic effects of the herbicide formulation Focus Ultra [with the active ingredient (a.i.) cycloxydim plus solvent naphtha and sodium dioctylsulphosuccinate as added substances] on embryos and early stage larvae of the Moroccan painted frog (Discoglossus scovazzi). Different clinical signs (twitching, convulsion, and narcosis) occurred at 40 and 80 mg/L in embryos (4 and 8 mg a.i./L) and narcotic effects (total immobilization or irregular escape responses) at 10, 15, and 20 mg/L in larvae (1, 1.5, and 2 mg a.i./L). Growth inhibition (total length), starting at 20 mg/L in embryos and 2.5 mg/L in larvae (2 and 0.25 mg a.i./L, respectively) was understood as sign of toxicity (retardation) and not as sign of teratogenicity. However, the connection to teratogenesis remained unclear though total length reduction occurred at concentrations <20 % of the 96-h LC50 value and at a minimum concentration that inhibits growth of only 17 % of the 96-h LC50 value. Starting at 20 mg/L, mortality in embryos significantly increased and at 15 mg/L in early larvae (2 and 1.5 mg a.i./L, respectively). Mortality of larvae was enhanced during the first 24 h of exposure to 15 and 20 mg/L (1.5 and 2 mg a.i./L). Morphology of the embryos remained unobtrusive. In contrary, axial malformations significantly increased in the early larvae starting at 10 mg/L (1 mg a.i./L), a concentration free of lethal effects. In all considered end points, larvae were significantly more sensitive than embryos, probably because of developmental and physiological properties or different exposure and bioavailability of the compound. Focus Ultra induced comparable lethal and immobilization effects in D. scovazzi as it does to standard test organisms in pesticide approval. However, to validate the apparent safety in the field, which is based on calculated surface water concentrations of the a.i., more data on real contamination levels is necessary (e.g., peak concentrations, concentrations of added substances). Furthermore, sufficient buffer strips between the farmland and amphibian ponds must be considered, and the effects of the substance on terrestrial life stages have not been assessed yet.

Effects of an environmentally relevant temporal application scheme of low herbicide concentrations on larvae of two anuran species

Cultivation of herbicide-tolerant crops involves repeated applications of the complementary herbicide throughout the growing season, while in conventional corn production, herbicide application is restricted to the beginning of cultivation. Repeated application of herbicides increases both the likelihood an organism will be exposed to the herbicide and the concentration it may be exposed to. We examined effects of short and pulsed exposure of the cycloxydim-based herbicide formulation Focus® Ultra at doses close to the calculated LC5 (0.01 and 0.5 mg a.i. L(-1)) and LC10 values (0.05 and 1.0 mg a.i. L(-1)) on early premetamorphic and prometamorphice larvae of two anuran model organisms, Xenopus laevis and Discoglossus scovazzi. In addition, larvae were repeatedly exposed, i.e. at all considered developmental stages. The herbicide did not induce effects on body size at and time to metamorphosis or increase deformation rates in both species. Exposure to calculated LC5 values did not increase mortality or cause clinical signs in both species. At calculated LC10 values, narcotic effects were seen in all developmental stages. There was no clear evidence of developmental-specific mortality. Metamorphic success was independent of time point and duration of application in X. laevis. Only repeated exposure significantly increased mortality at metamorphosis in D. scovazzi. Narcosis may result in increased mortality under field conditions due to rise of predation risk. Different sensitivity of the test species to the compound was attributed to their physiological properties. Different filtering rates were understood as an accompanying factor influencing exposition.

The floral morphospace--a modern comparative approach to study angiosperm evolution

Morphospaces are mathematical representations used for studying the evolution of morphological diversity and for the evaluation of evolved shapes among theoretically possible ones. Although widely used in zoology, they--with few exceptions--have been disregarded in plant science and in particular in the study of broad-scale patterns of floral structure and evolution. Here we provide basic information on the morphospace approach; we review earlier morphospace applications in plant science; and as a practical example, we construct and analyze a floral morphospace. Morphospaces are usually visualized with the help of ordination methods such as principal component analysis (PCA) or nonmetric multidimensional scaling (NMDS). The results of these analyses are then coupled with disparity indices that describe the spread of taxa in the space. We discuss these methods and apply modern statistical tools to the first and only angiosperm-wide floral morphospace published by Stebbins in 1951. Despite the incompleteness of Stebbins’ original dataset, our analyses highlight major, angiosperm-wide trends in the diversity of flower morphology and thereby demonstrate the power of this previously neglected approach in plant science.

The lateral line system in anuran tadpoles: neuromast morphology, arrangement, and innervation

Anuran larvae have been classified into four morphological types which reflect intraordinal macroevolution. At present, complete characterizations of the lateral line system are only available for Xenopus laevis (Type I) and Discoglossus pictus (Type III). We analyzed the morphology, arrangement, and innervation of neuromasts related to the anterodorsal and anteroventral lateral line nerves in 10 anuran species representing Types I, II, and IV with the aim of interpreting the existing variation and discussing the evolution of the lateral line in anuran larvae. We found: (1) the presence of two orbital and three mandibular neuromast lines in all anuran larvae studied, (2) the ventral arrangement of mandibular neuromast lines appears to have evolved convergently in Larval Types I and II, and the lateroventral arrangement of mandibular lines of neuromasts appears to have evolved in Larval Types III and IV; (3) interspecific variation in the organization, size, and number of sensory cells per neuromast within the lines; and (4) the supralabial extension of the Angular line in Lepidobatrachus spp. and the tentacular location of the Oral neuromasts in X. laevis are concomitant with their particular morphologies. Based on the variation described we find that the lateral line system in anuran larvae seems to have been maintained without significant changes, with the exception of Lepidobatrachus spp. and Xenopus. These unique features added to other of Lepidobatrachus tadpoles are sufficient to propose a new Larval Type (V).

Evolution by selection, recombination, and gene duplication in MHC class I genes of two Rhacophoridae species

BACKGROUND

Comparison of major histocompatibility complex (MHC) genes across vertebrate species can reveal molecular mechanisms underlying the evolution of adaptive immunity-related proteins. As the first terrestrial tetrapods, amphibians deserve special attention because of their exposure to probably increased spectrum of microorganisms compared with ancestral aquatic fishes. Knowledge regarding the evolutionary patterns and mechanisms associated with amphibian MHC genes remains limited. The goal of the present study was to isolate MHC class I genes from two Rhacophoridae species (Rhacophorus omeimontis and Polypedates megacephalus) and examine their evolution.

RESULTS

We identified 27 MHC class I alleles spanning the region from exon 2 to 4 in 38 tree frogs. The available evidence suggests that these 27 sequences all belong to classical MHC class I (MHC Ia) genes. Although several anuran species only display one MHC class Ia locus, at least two or three loci were observed in P. megacephalus and R. omeimontis, indicating that the number of MHC class Ia loci varies among anuran species. Recombination events, which mainly involve the entire exons, played an important role in shaping the genetic diversity of the 27 MHC class Ia alleles. In addition, signals of positive selection were found in Rhacophoridae MHC class Ia genes. Amino acid sites strongly suggested by program to be under positive selection basically accorded with the putative antigen binding sites deduced from crystal structure of human HLA. Phylogenetic relationships among MHC class I alleles revealed the presence of trans-species polymorphisms.

CONCLUSIONS

In the two Rhacophoridae species (1) there are two or three MHC class Ia loci; (2) recombination mainly occurs between the entire exons of MHC class Ia genes; (3) balancing selection, gene duplication and recombination all contribute to the diversity of MHC class Ia genes. These findings broaden our knowledge on the evolution of amphibian MHC systems.

Molecular phylogeny of microhylid frogs (Anura: Microhylidae) with emphasis on relationships among New World genera

BACKGROUND

Over the last ten years we have seen great efforts focused on revising amphibian systematics. Phylogenetic reconstructions derived from DNA sequence data have played a central role in these revisionary studies but have typically under-sampled the diverse frog family Microhylidae. Here, we present a detailed phylogenetic study focused on expanding previous hypotheses of relationships within this cosmopolitan family. Specifically, we placed an emphasis on assessing relationships among New World genera and those taxa with uncertain phylogenetic affinities (i.e., incertae sedis).

RESULTS

One mitochondrial and three nuclear genes (about 2.8 kb) were sequenced to assess phylogenetic relationships. We utilized an unprecedented sampling of 200 microhylid taxa representing 91% of currently recognized subfamilies and 95% of New World genera. Our analyses do not fully resolve relationships among subfamilies supporting previous studies that have suggested a rapid early diversification of this clade. We observed a close relationship between Synapturanus and Otophryne of the subfamily Otophryninae. Within the subfamily Gastrophryninae relationships between genera were well resolved.

CONCLUSION

Otophryninae is distantly related to all other New World microhylids that were recovered as a monophyletic group, Gastrophryninae. Within Gastrophryninae, five genera were recovered as non-monophyletic; we propose taxonomic re-arrangements to render all genera monophyletic. This hypothesis of relationships and updated classification for New World microhylids may serve as a guide to better understand the evolutionary history of this group that is apparently subject to convergent morphological evolution and chromosome reduction. Based on a divergence analysis calibrated with hypotheses from previous studies and fossil data, it appears that microhylid genera inhabiting the New World originated during a period of gradual cooling from the late Oligocene to mid Miocene.

The origin of modern frogs (Neobatrachia) was accompanied by acceleration in mitochondrial and nuclear substitution rates

Background

Understanding the causes underlying heterogeneity of molecular evolutionary rates among lineages is a long-standing and central question in evolutionary biology. Although several earlier studies showed that modern frogs (Neobatrachia) experienced an acceleration of mitochondrial gene substitution rates compared to non-neobatrachian relatives, no further characterization of this phenomenon was attempted. To gain new insights on this topic, we sequenced the complete mitochondrial genomes and nine nuclear loci of one pelobatoid (Pelodytes punctatus) and five neobatrachians, Heleophryne regis (Heleophrynidae), Lechriodus melanopyga (Limnodynastidae), Calyptocephalella gayi (Calyptocephalellidae), Telmatobius bolivianus (Ceratophryidae), and Sooglossus thomasseti (Sooglossidae). These represent major clades not included in previous mitogenomic analyses, and most of them are remarkably species-poor compared to other neobatrachians.

Results

We reconstructed a fully resolved and robust phylogeny of extant frogs based on the new mitochondrial and nuclear sequence data, and dated major cladogenetic events. The reconstructed tree recovered Heleophryne as sister group to all other neobatrachians, the Australasian Lechriodus and the South American Calyptocephalella formed a clade that was the sister group to Nobleobatrachia, and the Seychellois Sooglossus was recovered as the sister group of Ranoides. We used relative-rate tests and direct comparison of branch lengths from mitochondrial and nuclear-based trees to demonstrate that both mitochondrial and nuclear evolutionary rates are significantly higher in all neobatrachians compared to their non-neobatrachian relatives, and that such rate acceleration started at the origin of Neobatrachia.

Conclusions

Through the analysis of the selection coefficient (ω) in different branches of the tree, we found compelling evidence of relaxation of purifying selection in neobatrachians, which could (at least in part) explain the observed higher mitochondrial and nuclear substitution rates in this clade. Our analyses allowed us to discard that changes in substitution rates could be correlated with increased mitochondrial genome rearrangement or diversification rates observed in different lineages of neobatrachians.