The Gondwana Breakup and the History of the Atlantic and Indian Oceans Unveils Two New Clades for Early Neobatrachian Diversification

The largest anuran diversity belongs to the Neobatrachia, which harbor more than five thousand extant species. Here, we propose a new hypothesis for the historical aspects of the neobatrachian evolution with a formal biogeographical analysis. We selected 12 genes for 144 neobatrachian genera and four archaeobatrachian outgroups and performed a phylogenetic analysis using a maximum likelihood algorithm with the rapid bootstrap test. We also estimated divergence times for major lineages using a relaxed uncorrelated clock method. According to our time scale, the diversification of crown Neobatrachia began around the end of the Early Cretaceous. Our phylogenetic tree suggests that the first split of Neobatrachia is related to the geological events in the Atlantic and Indian Oceans. Hence, we propose names for these clades that indicate this connection, i.e., Atlanticanura and Indianura. The Atlanticanura is composed of three major neobatrachian lineages: Heleophrynidae, Australobatrachia and Nobleobatrachia. On the other hand, the Indianura consists of two major lineages: Sooglossoidea and Ranoides. The biogeographical analysis indicates that many neobatrachian splits occurred as a result of geological events such as the separation between South America and Africa, between India and the Seychelles, and between Australia and South America.     

Complete mitochondrial genomes of three neobatrachian anurans: a case study of divergence time estimation using different data and calibration settings

We sequenced the whole mitochondrial (mt) genomes of three neobatrachian species: Japanese tree frog Hyla japonica, Japanese common toad Bufo japonicus, and narrow-mouthed toad Microhyla okinavensis. The gene arrangements of these genomes diverged from that of basal anurans (suborder Archaeobatrachia), but are the same as that of the members of derived frogs (i.e., superfamily Hyloidae and Ranoidae in suborder Neobatrachia), suggesting the one-time occurrence of a gene rearrangement event in an ancestral lineage of derived anurans. Furthermore, several distinct repeat motifs including putative termination-associated sequences (TASs) and conserved sequence blocks (CSBs) were observed in the control regions (CRs) of B. japonicus and H. japonica, while no repeat motifs were found in that of M. okinavensis. Phylogenetic analyses using both nucleotide and amino acid data of mt genes support monophyly of neobatrachians. The estimated divergence time based on amino acid data with multiple reference points suggests that the three living amphibian orders may have originated in the Carboniferous period, and that the divergences of anurans had occurred between the Permian and Tertiary periods. We also checked the influence of the data types and the settings of reference times on divergence time estimation. The resultant divergence times estimated from several datasets and reference time settings suggest that the substitution saturation of nucleotide data may lead to overestimated (i.e., older) branching times, especially for early divergent taxa. We also found a highly accelerated substitution rate in neobatrachian mt genes, and fast substitution possibly resulted in overestimation. To correct this erroneous estimation, it is efficient to apply several reference points among neobatrachians.     

Phylogeny and comparative substitution rates of frogs inferred from sequences of three nuclear genes

Phylogenetic relationships among major clades of anuran amphibians were studied using partial sequences of three nuclear protein coding genes, Rag-1, Rag-2, and rhodopsin in 26 frog species from 18 families. The concatenated nuclear data set comprised 2,616 nucleotides and was complemented by sequences of the mitochondrial 12S and 16S rRNA genes for analyses of evolutionary rates. Separate and combined analyses of the nuclear markers supported the monophyly of modern frogs (Neobatrachia), whereas they did not provide support for the monophyly of archaic frog lineages (Archaeobatrachia), contrary to previous studies based on mitochondrial data. The Neobatrachia contain two well supported clades that correspond to the subfamilies Ranoidea (Hyperoliidae, Mantellidae, Microhylidae, Ranidae, and Rhacophoridae) and Hyloidea (Bufonidae, Hylidae, Leptodactylidae, and Pseudidae). Two other families (Heleophrynidae and Sooglossidae) occupied basal positions and probably represent ancient relicts within the Neobatrachia, which had been less clearly indicated by previous mitochondrial analyses. Branch lengths of archaeobatrachians were consistently shorter in all separate analyses, and nonparametric rate smoothing indicated accelerated substitution rates in neobatrachians. However, relative rate tests confirmed this tendency only for mitochondrial genes. In contrast, nuclear gene sequences from our study and from an additional GenBank survey showed no clear phylogenetic trends in terms of differences in rates of molecular evolution. Maximum likelihood trees based on Rag-1 and using only one neobatrachian and one archaeobatrachian sequence, respectively, even had longer archaeobatrachian branches averaged over all pairwise comparisons. More data are necessary to understand the significance of a possibly general assignation of short branches to basal and species-poor taxa by tree-reconstruction algorithms.     

The evolution of mitochondrial genomes in modern frogs (Neobatrachia): nonadaptive evolution of mitochondrial genome reorganization

Background

Although mitochondrial (mt) gene order is highly conserved among vertebrates, widespread gene rearrangements occur in anurans, especially in neobatrachians. Protein coding genes in the mitogenome experience adaptive or purifying selection, yet the role that selection plays on genomic reorganization remains unclear. We sequence the mitogenomes of three species of Glandirana and hot spots of gene rearrangements of 20 frog species to investigate the diversity of mitogenomic reorganization in the Neobatrachia. By combing these data with other mitogenomes in GenBank, we evaluate if selective pressures or functional constraints act on mitogenomic reorganization in the Neobatrachia. We also look for correlations between tRNA positions and codon usage.

Results

Gene organization in Glandirana was typical of neobatrachian mitogenomes except for the presence of pseudogene trnS (AGY). Surveyed ranids largely exhibited gene arrangements typical of neobatrachian mtDNA although some gene rearrangements occurred. The correlation between codon usage and tRNA positions in neobatrachians was weak, and did not increase after identifying recurrent rearrangements as revealed by basal neobatrachians. Codon usage and tRNA positions were not significantly correlated when considering tRNA gene duplications or losses. Change in number of tRNA gene copies, which was driven by genomic reorganization, did not influence codon usage bias. Nucleotide substitution rates and d_N/d_S ratios were higher in neobatrachian mitogenomes than in archaeobatrachians, but the rates of mitogenomic reorganization and mt nucleotide diversity were not significantly correlated.

Conclusions

No evidence suggests that adaptive selection drove the reorganization of neobatrachian mitogenomes. In contrast, protein-coding genes that function in metabolism showed evidence for purifying selection, and some functional constraints appear to act on the organization of rRNA and tRNA genes. As important nonadaptive forces, genetic drift and mutation pressure may drive the fixation and evolution of mitogenomic reorganizations.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-691) contains supplementary material, which is available to authorized users.     

Development of the subdigital adhesive pads of Ptyodactylus guttatus (Reptilia: Gekkonidae)

Subdigital adhesive pads play an important role in the locomotion of many species of gekkonid lizards. These pads consist of integrated components derived from the epidermis, dermis, vascular system, subcuticular tendons, and phalanges. These components become intimately associated with each other during the developmental differentiation of the digits and the sequence of this integration is outlined herein in Ptyodactylus guttatus. The pads initially appear as paired swellings at the distal tips of the digits. Subsequently, a fan-like array of naked scansors develops on the ventral surface of each digit, at about the same time that scales differentiate over the surface of the foot as a whole. At the time of appearance of the naked scansors, the vascular sinus system of the pad also differentiates, along with subcuticular connective tissue specializations. At this stage the digits, along with the rest of the body, are clad in an embryonic periderm. Only after hatching and as the periderm is shed, do the epidermal setae and spines appear. The developmental sequence described here is consistent with predictions previously advanced about the evolutionary origin and elaboration of subdigital pads in gekkonid lizards. The paucity of available staged embryonic material leaves many questions unresolved.     

A molecular perspective on the evolutionary affinities of an enigmatic neotropical frog, Allophryne ruthveni

The phylogenetic relationships of neobatrachian frogs remain poorly resolved below the subordinal level. The neotropical frog Allophryne ruthveni (Gaige) illustrates the difficulty in evaluating phylogenetic relationships within the Neobatrachia. Since its discovery in 1926, it has been variously placed within five different anuran families: Bufonidae, Leptodactylidae, Centrolenidae, Hylidae and in its own monotypic family, Allophrynidae. Here we examine the evolutionary relationships of Allophryne ruthveni using DNA sequence data from two mitochondrial genes (16S and 12S rRNA). Our analyses suggest that Allophryne ruthveni is most closely allied to the glass frogs (Centrolenidae). Both 12S and combined data partitions support an Allophryne ruthveni–Cochranella midas– Centrolene geckoideum clade, with Allophryne ruthveni basally positioned. Considered alone, analyses of the 16S partition supports the placement of Allophryne ruthveni with the centrolenids only with neighbour-joining analyses. The placement of Allophryne ruthveni with the centrolenids supports Noble's (1931 ) hypothesis that Allophryne is an edentate centrolenid. More definitive statements of the evolutionary affinities of Allophryne ruthveni in particular, and the Neobatrachia in general, await greater sampling of taxa and both molecular and phenotypic (e.g. morphological and karyotypic) characters. © 2002 The Linnean Society of London. Zoological Journal of the Linnean Society , 2002, 134 , 335–346.     

Evolutionary and developmental aspects of phalangeal formula variation in pig-nose and soft-shelled turtles (Carettochelyidae and Trionychidae)

In order to examine the evolution of the phalangeal formula in a diverse clade of turtles, including hyperphalangy as a rare condition in this group, we studied 210 specimens representing all extant genera of Trionychidae and their sister taxon, Carettochelyidae. Both groups consist of highly aquatic species with elongated autopods that are either paddle-like (Trionychidae) or transformed to flippers (Carettochelyidae). Phalangeal formulae were obtained mostly by radiographs of alcohol-preserved or dry specimens, as well as by direct counts from skeletons. All trionychids and Carettochelys are pentadactylous, but their phalangeal formulae differ. Carettochelys exhibits the turtle-plesiomorphic state (manus and pes: 2-3-3-3-3), with no variation in adults. Trionychids exhibit intraspecific variation, ranging from 2-3-3-3-2 to 2-3-3-6-5 for the manus, and from 2-3-3-3-2 to 2-3-3-5-3 for the pes. The extant Carettochelys as well as the Middle Eocene Allaeochelys crassesculpta are characterized by an elongation of phalanges, whereas trionychids consistently have shorter phalanges. All trionychid genera exhibit some degree of hyperphalangy in digits IV and V, in both the manus and pes. Phalanges of the clawed digits I–III are very robust compared to phalanges of the non-clawed digits IV and V. The latter contribute significantly to the enlargement of the paddle by their additional phalanges. We hypothesize that this phalangeal pattern is coupled with prolongation of growth processes in the non-clawed digits. The differences in autopod morphology between carettochelyids and trionychids reflect different locomotor patterns related to different natural histories (elongated flippers for high-speed escape in the mainly herbivorous Carettochelys; broad paddles for rapid turns during hunting in the mainly carnivorous trionychids). The autopod of Pelodiscus sinensis is proposed as an experimental model to examine the developmental basis of adult autopod variation.     

Ontogeny and tissue differentiation of the pelvic girdle and hind limbs of anurans

We present the ontogeny of the integrated musculoskeletal complex that comprises the pelvic girdle and hind limbs of anurans. Our histological data show that the pelvic girdle originates from a single mesenchymatic condensation. The tissue differentiation sequence is cartilage, muscle and tendon. The intrusion of the ischiadic nerve into the limb bud is produced very early in ontogeny. The pre‐cartilage appears in the pre‐motile stage. Therefore, the nerve produces a movement analogous to the ‘embryonic motility’ that would induce the emergence of the pre‐cartilage. The acetabulum is the first of all cavitation processes to form, the second one being the knee. The acetabulum appears before the muscles are mature, although it has been stressed that the muscle contraction maintains joint progenitors committed to their fate. Our data indicate an explosive differentiation of all 11 muscular masses together. We provide three new characters that support the monophyly of Hyloides, Acosmanura and Neobatrachia.     

Bambi and Sp8 Expression Mark Digit Tips and Their Absence Shows That Chick Wing Digits 2 and 3 Are Truncated

An often overlooked aspect of digit development is the special nature of the terminal phalanx, a specialized structure with characteristics distinct from other phalanges, for example the presence of ectodermal derivatives such as nails and claws. Here, we describe the unique ossification pattern of distal phalanges and characteristic gene expression in the digit tips of chick and duck embryos. Our results show that the distal phalanx of chick wing digit 1 is a genuine tip with a characteristic ossification pattern and expression of Bambi and Sp8; however, the terminal phalanx of digits 2* and 3 is not a genuine tip, and these are therefore truncated digits. Bambi and Sp8 expression in the chick wing provides a direct molecular assessment of digit identity changes after experimental manipulations of digit primordia. In contrast, digits 1 and 2 of the duck wing both possess true tips. Although chick wing-tip development was not rescued by application of Fgf8, this treatment induced the development of extra phalanges. Grafting experiments show that competence for tip formation, including nails, is latent in the interdigital tissue. Our results deepen understanding of the mechanisms of digit tip formation, highlighting its developmental autonomy and modular nature, with implications for digit reduction or loss during evolution. * Numbering of wing digits is 1, 2, 3 from anterior to posterior.     

Phylogeny of frogs as inferred from primarily larval characters (Amphibia:Anura)★

This paper presents larval evidence and evaluates its contribution to the discussion of frog phylogeny;136 larval characters,6 reproductive biology characters, and 14 adult morphology characters were scored for 81 frog and 4 caudate species.More than 90% of the data matrix entries represent original data derived from personal direct examination of specimens.Some larval characters are described for the rest time and many others have not been assessed for specic taxa or in a broad phylogenetic context before.Ho‐ moplasy appears common in this and other amphibian morphological data sets.The data supported and conrmed various well‐ known clades, among others the Anura, Bufonidae, Ceratophryinae, Discoglossidae, Dendrobatidae, Hyperoliidae, Microhylidae, South American microhylids, Phyllomedusinae, Pseudinae, Pipoidea, Pipidae, and Scoptanura.The Ascaphidae was sister group to all other anurans and the Pipoidea was placed more basally than in some previous analyses.The Eurasian pelobatids formed a clade, whereas Spea and Pelodytes did not group robustly with them.Pelobatoid frogs emerged as a paraphyletic “transitional” assemblage including Heleophryne. The resolution of basal neobatrachian splits remained labile, although some subclades within the Neobatrachia were robustly supported. The “Hylidae” was paraphyletic, and hyline species were paraphyletic with respect to the Pseudinae.Hemisus clearly was in a clade with the Hyperoliidae and is proposed to be included in that family.Scaphiophryne was conrmed as basal taxon within the Microhylidae.Compared to the larval stages of the most recent common ancestor of anurans, members of the Scoptanura (microhylids except scaphiophrynines)have accumulated the highest number of apomorphic character states in anuran evolution.     

Structural basis for binding of Plasmodium falciparum erythrocyte membrane protein 1 to chondroitin sulfate and placental tissue and the influence of protein polymorphisms on binding specificity

Chondroitin sulfate (CS) A is a key receptor for adhesion of Plasmodium falciparum-infected erythrocytes (IEs) in the placenta and can also mediate adhesion to microvascular endothelial cells. IEs that adhere to CSA express var2csa-type genes, which encode specific variants of the IE surface antigen P. falciparum erythrocyte membrane protein 1 (PfEMP1). We report direct binding of native PfEMP1, isolated from IEs and encoded by var2csa, to immobilized CSA. Binding of PfEMP1 was dependent on 4-O-sulfated disaccharides and glucuronic acid rather than iduronic acid, consistent with the specificity of intact IEs. Using immobilized CS oligosaccharides as neoglycolipid probes, the minimum chain length for direct binding of PfEMP1 was eight monosaccharide units. Similarly for IE adhesion to placental tissue there was a requirement for 4-O-sulfated GalNAc and glucuronic acid mixed with non-sulfated disaccharides; 6-O-sulfation interfered with the interaction between placental CSA and IEs. The minimum chain length for maximal inhibition of adhesion was 10 monosaccharide residues. Partially 4-O-sulfated CS oligosaccharides (45-55% sulfation) were highly effective inhibitors of placental adhesion (IC(50), 0.15 microg/ml) and may have potential for therapeutic development. We used defined P. falciparum isolates expressing different variants of var2csa in adhesion assays and found that there were isolate-specific differences in the preferred structural motifs for adhesion to CSA that correlated with polymorphisms in PfEMP1 encoded by var2csa-type genes. This may influence sites of IE sequestration or parasite virulence. These findings have significant implications for understanding the pathogenesis and biology of malaria, particularly during pregnancy, and the development of targeted interventions.     

A new frog species from the central western Ghats of India, and its phylogenetic position

Tropical evergreen forests of Indian subcontinent, especially of the Western Ghats, are known hot spots of amphibian diversity, where many new anuran species await to be identified. Here we describe from the Sharavathi River basin of central Western Ghats a new shrub-frog taxon related to the anuran family Rhacophoridae. The new frog possesses the characteristic features of rhacophorids (dilated digit tips with differentiated pads circumscribed by a complete groove, intercalary cartilages on digits, T-shaped terminal phalanges and granular belly, the adaptive characters for arboreal life forms), but also a suite of unique features that distinguish it from all known congeners in the region. Morphogenetic analysis based on morphological characteristics and diversity in the mitochondrial 12S and 16S rRNA genes revealed it to be a new Philautus species that we named Philautus neelanethrus sp. nov. The phylogenetic analysis suggests the new frog to represent a relatively early Philautus species lineage recorded from the region. The distribution pattern of the species suggests its importance as a bioindicator of habitat health. In general, this relatively widespread species was found distributed only in non-overlapping small stretches, which indirectly indicates the fragmentation of the evergreen to moist deciduous forests that characterize the Western Ghats. Thus the discovery of the new rhacophorid species described here not only further reinforces the significance of the Western Ghats as a major hotspot of amphibian biodiversity, but also brings into focus the deterioration of forest habitats in the region and the need for prioritization of their conservation.     

Patterns of carpal development among anuran amphibians

The unity and diversity of developmental processes in the vertebrate limb have singular importance in the interpretation of evolutionary hypotheses of tetrapod diversification. In anurans, the intraordinal diversity of forelimbs seems to be related to the fusion of distal carpals, whereas proximal carpals are invariable. However, there are different ontogenetic pathways involved in the differentiation of proximal carpals. This study presents a comparative analysis of early developmental features in one archeobatrachian and 23 neobatrachian species representing five families and explores the variability in the differentiation of carpal cartilages. We found new evidence supporting the presence of an embryonic intermedium that incorporates with the ulnare. Difference between the pipid Xenopus and the neobatrachians is interpreted as a change in the rate of differentiation of Distal Carpal 5 that does not affect the developmental pattern of digits. The developmental variability exhibited by the intermedium, radiale, and Element Y is combined in patterns that converge on the same adult carpal morphology among neobatrachians; these patterns appear to contain potentially useful phylogenetic information.     

Time,pattern, and heterochrony: a study of hyperphalangy in the dolphin embryo flipper

The forelimb of whales and dolphins is a flipper that shows hyperphalangy (numerous finger bones). Hyperphalangy is also present in marine reptiles, including ichthyosaurs and plesiosaurs. The developmental basis of hyper-phalangy is unclear. Kükenthal suggested that phalanx anlagen split into three pieces during cetacean development, thereby multiplying the ancestral number. Alternatively, Holder suggested that apical ectodermal ridge (AER)-directed limb outgrowth might be prolonged by a timing shift (heterochrony), leading to terminal addition of extra phalanges. We prepared a series of whole mounted and serially sectioned embryonic flipper buds of the spotted dolphin Stenella attenuata. This cetacean shows marked hyperphalangy on digits II and III. We confirm previous reports that the proximodistal laying down of phalanges is prolonged in digits II and III. Histology showed that the apical ectoderm was thickened into a cap. There was a weak ridge-like structure in some embryos. The cap or ridge formed part of a bud-like mass that persisted on digits II and III at stages when it had disappeared from other digits. Thus the dolphin differs from other mammals in showing a second period of limb outgrowth during which localized hyperphalangy develops. New phalanges only formed at the tip of the digits. These findings are consistent with a model in which heterochrony leads to the terminal addition of new phalanges. Our results are more easily reconciled with the progress zone model than one in which the AER is involved in the expansion of a prepattern. We suggest that patterning mechanisms with a temporal component (i.e., the "progress zone" mechanism) are potential targets for heterochrony during limb evolution.     

Erratum

Feet of two-toed sloths (Choloepus) are long, narrow, hook-like appendages with only three functional digits, numbers II, III, and IV; Rays I and V are represented by metatarsals. Proximal phalanges of complete digits are little more than proximal and distal articulating surfaces. All interphalangeal joints are restricted, by interlocking surfaces, to flexion and extension. Ankle and transverse tarsal joints, however, allow extreme flexion and inversion of foot. Powerful digital flexion is augmented by several muscles from extensor compartment of leg. Intrinsic foot musculature is reduced to flexors and extensors but these, with the exception of lumbricals, are large and well developed. Choloepus uses its feet much like hooks with distal phalanges and covering claws forming the “hook” element. These hook-like appendages are seemingly best suited for supports less than 50 mm in diameter suggesting that two-toed sloths may prefer supports of this size in their natural habitat.     

Evolution of Hoxa-11 Expression in Amphibians: Is the Urodele Autopodium an Innovation?

In this paper we present preliminary results on the expressionof Hoxa-11 in the frog Xenopus laevis and the newt Notophthalmusviridescens. In amniote limbs, Hoxa-11 is expressed exclusivelyin the prospective zeugopodium and is involved in the developmentof zeugopodial character identity. While the Hoxa-11 expressionpattern in Xenopus is similar to those described in mice andchick, the newt Notophthalmus has a phase of autopodial Hoxa-11expression starting with the development of digit III. Expressionis particularly strong in the buds of the postaxial digits.This Hoxa-11 expression pattern is unique among tetrapods andadds to the list of developmental peculiarities of urodele limbdevelopment, which also include an anterior to posterior polarityof digit development. We propose a scenario to explain the evolutionaryorigin of urodele limb development. We assume that recent urodelesare derived from a lineage of amphibians which underwent partialdigit reduction, leaving only two digits intact, most likelydigits III and IV according to Morse's law. This implies thaturodele digits I and II are homologous to amniote digits IIIand IV, and that the postaxial digits of urodeles are an evolutionaryinnovation (re-invention). Supporting evidence for this homologyhypothesis is found in the developmental connections betweenthe basale commune and the postaxial zeugopodial element.     

The larval hyobranchial apparatus of discoglossoid frogs: its structure and bearing on the systematics of the Anura (Amphibia: Anura)

The morphology of the larval hyobranchial apparatus of discoglossoid frog species representing the genera Ascaphus, Alytes, Bombina, and Discoglossus is described and the resulting characters were analysed cladistically. Seven species representing seven major lineages of frogs were included in the cladistic analysis of characters. Several changes in the terminology of the musculature are introduced, and a new interpretation of the subarcualis-muscle system is presented. The phylogenetic analysis suggest that the hyobranchial apparatus was substantially altered in the lineages leading to and within the Pipanura. This notably involved fusion, reduction and loss of skeletal structures and muscles, and splitting of certain muscles into muscle groups. The result confirm previous hypotheses based on the study of adults: discoglossoid species retain the most numlerous plesiomorphic characters among extant ianurans. The larval hyobranchial apparatus is in many features structrually similar to that of urodeles. Many of their character states were most likely present in the most recent common ancestor of all living forgs. The cladistic analysis of 31 characters of ithe larval hyobranchial apparatus supports major clades: Anura, Bombinanura, Pipanura, and Pelobatoidea + Neobatrachia. The cladiostic analysis and interpretation of larval characters is in part compatible with phylogenetic hypotheses based on characters of adults and rRNA sequences, but is in conflict with the Mesobatrachia and Archaeobatrachia concepts of other authors.