Phylogeny of caecilian amphibians (Gymnophiona) based on complete mitochondrial genomes and nuclear RAG1

We determined the complete nucleotide sequence of the mitochondrial (mt) genome of five individual caecilians (Amphibia: Gymnophiona) representing five of the six recognized families: Rhinatrema bivittatum (Rhinatrematidae), Ichthyophis glutinosus (Ichthyophiidae), Uraeotyphlus cf. oxyurus (Uraeotyphlidae), Scolecomorphus vittatus (Scolecomorphidae), and Gegeneophis ramaswamii (Caeciliidae). The organization and size of these newly determined mitogenomes are similar to those previously reported for the caecilian Typhlonectes natans (Typhlonectidae), and for other vertebrates. Nucleotide sequences of the nuclear RAG1 gene were also determined for these six species of caecilians, and the salamander Mertensiella luschani atifi. RAG1 (both at the amino acid and nucleotide level) shows slower rates of evolution than almost all mt protein-coding genes (at the amino acid level). The new mt and nuclear sequences were compared with data for other amphibians and subjected to separate and combined phylogenetic analyses (Maximum Parsimony, Minimum Evolution, Maximum Likelihood, and Bayesian Inference). All analyses strongly support the monophyly of the three amphibian Orders. The Batrachia hypothesis (Gymnophiona, (Anura, Caudata) receives moderate or good support depending on the method of analysis. Within Gymnophiona, the optimal tree (Rhinatrema, (Ichthyophis, Uraeotyphlus), (Scolecomorphus, (Gegeneophis Typhlonectes) agrees with the most recent morphological and molecular studies. The sister group relationship between Rhinatrematidae and all other caecilians, that between Ichthyophiidae and Uraeotyphlidae, and the monophyly of the higher caecilians Scolecomorphidae+Caeciliidae+Typhlonectidae, are strongly supported, whereas the relationships among the higher caecilians are less unambiguously resolved. Analysis of RAG1 is affected by a spurious local rooting problem and associated low support that is ameliorated when outgroups are excluded. Comparisons of trees using the non-parametric Templeton, Kishino-Hasegawa, Approximately Unbiased, and Shimodaira-Hasegawa tests suggest that the latter may be too conservative.     

Cellular migration and morphological complexity in the caecilian brain

The morphology of the tectum mesencephali and the medial pallium is studied in species representing the six families of caecilians (Amphibia: Gymnophiona) in order to determine whether differences in brain morphology are related to function, phylogenetic history, or life history strategies. In general, the caecilian tectum is characterized by simplification in having little to no lamination and few migrated cells. The degree of morphological complexity differs between species and between brain regions. Our data suggest that changes in brain morphology are due to a mosaic of different influences. We did not find a strict correlation between visual system reduction and tectal morphologies. However, phylogenetic effects exist. The greatest degree of morphological complexity is found in members of the Rhinatrematidae, a family that is considered basal to the lineage. Thus, simplification of brain morphology in caecilians must be considered a secondary or derived rather than a primitive feature. Direct development and miniaturization are correlated with the greatest simplification in the tectum mesencephali and medial pallium. There is a relationship between differences in brain morphology and heterochrony in caecilians, as in other amphibians. J. Morphol. 231:11–27, 1997. © 1997 Wiley-Liss, Inc.     

The evolution of parental investment in caecilian amphibians: a comparative approach

Parental care is widespread among vertebrates and the observed patterns of parental care and investment are extremely diverse. Among amphibians, caecilians (Gymnophiona) exhibit considerable variation in reproductive modes, including both oviparity and viviparity, combined with highly unusual investment strategies (e.g. skin‐feeding and intrauterine feeding). In the present study, current knowledge on the reproductive modes is integrated into an analysis of the evolutionary scenario of parental investment of caecilians. Phylogenetically basal caecilians possessing a biphasic life cycle that includes an aquatic larval stage invest in macrolecithal eggs directly corresponding to size at hatching. Some phylogenetically derived caecilians (i.e. the Teresomata) have a smaller clutch size and show a reduction to either medium‐yolked (mesolecithal) or small‐yolked (microlecithal) eggs. Via alternative pathways of parental investment, such as intrauterine feeding in viviparous taxa and maternal dermatotrophy in oviparous taxa, teresomatan caecilians increase both offspring size and quality. However, more data regarding reproductive biology are needed to obtain a fully resolved understanding of the evolution of reproduction in caecilian amphibians.     

Global patterns of body size evolution are driven by precipitation in legless amphibians

Body size shapes ecological interactions across and within species, ultimately influencing the evolution of large‐scale biodiversity patterns. Therefore, macroecological studies of body size provide a link between spatial variation in selection regimes and the evolution of animal assemblages through space. Multiple hypotheses have been formulated to explain the evolution of spatial gradients of animal body size, predominantly driven by thermal (Bergmann's rule), humidity (‘water conservation hypothesis’) and resource constraints (‘resource rule’, ‘seasonality rule’) on physiological homeostasis. However, while integrative tests of all four hypotheses combined are needed, the focus of such empirical efforts needs to move beyond the traditional endotherm–ectotherm dichotomy, to instead interrogate the role that variation in lifestyles within major lineages (e.g. classes) play in creating neglected scenarios of selection via analyses of largely overlooked environment–body size interactions. Here, we test all four rules above using a global database spanning 99% of modern species of an entire Order of legless, predominantly underground‐dwelling amphibians (Gymnophiona, or caecilians). We found a consistent effect of increasing precipitation (and resource abundance) on body size reductions (supporting the water conservation hypothesis), while Bergmann's, the seasonality and resource rules are rejected. We argue that subterranean lifestyles minimize the effects of aboveground selection agents, making humidity a dominant selection pressure – aridity promotes larger body sizes that reduce risk of evaporative dehydration, while smaller sizes occur in wetter environments where dehydration constraints are relaxed. We discuss the links between these principles with the physiological constraints that may have influenced the tropically‐restricted global radiation of caecilians.     

Rotational feeding in caecilians: putting a spin on the evolution of cranial design

Caecilians are a poorly known group of amphibians with a highly derived skull and cranial musculature that has evolved in response to their specialized head-first burrowing lifestyle. They possess a unique jaw-closing system, which is shown to be capable of generating considerable bite forces for its head width (1.09+/-0.34 and 0.62+/-0.31 N for Schistometopum thomense and Boulengerula taitanus, respectively). However, comprehensive dietary studies indicate that there is no need for large bite forces, since most caecilians appear to be generalist predators of subterranean macrofauna. Here, we demonstrate, based on in vivo external and X-ray video recordings of animals feeding, that long-axis body rotations are used independent of prey size by these two species of caeciliid caecilians when feeding underground. Further, we show that individuals are capable of generating a substantial spinning force, which is greater than their bite force (1.35+/-0.26 and 1.02+/-0.18 N, respectively). These observations shed light on the functional and the evolutionary significance of several unique features of the cranial design in derived caecilians; spinning may allow the individuals to judge prey size and subsequently reduce oversized prey within gape limits.     

A mitogenomic perspective on the phylogeny and biogeography of living caecilians (Amphibia: Gymnophiona)

The caecilians, members of the amphibian Order Gymnophiona, are the least known Order of tetrapods, and their intra-relationships, especially within its largest group, the Family Caeciliidae (57% of all caecilian species), remain controversial. We sequenced thirteen complete caecilian mitochondrial genomes, including twelve species of caeciliids, using a universal primer set strategy. These new sequences, together with eight published caecilian mitochondrial genomes, were analyzed by maximum parsimony, partitioned maximum-likelihood and partitioned Bayesian approaches at both nucleotide and amino acid levels, to study the intra-relationships of caecilians. An additional multiple gene dataset including most of the caecilian nucleotide sequences currently available in GenBank produced phylogenetic results that are fully compatible with those based on the mitogenomic data. Our phylogenetic results are summarized as follow. The caecilian family Rhinatrematidae is the sister taxon to all other caecilians. Beyond Rhinatrematidae, a clade comprising the Ichthyophlidae and Uraeotyphlidae is separated from a clade containing all remaining caecilians (Scolecomorphidae, Typhlonectidae and Caeciliidae). Within this large clade, Scolecomorphidae is the sister taxon of Typhlonectidae and Caeciliidae but this placement did not receive strong support in all analyses. Caeciliidae is paraphyletic with regard to Typhlonectidae, and can be divided into three well-supported groups: Caeciliidae group 1 contains the African caeciliids Boulengerula and Herpele; Caeciliidae group 2 contains Caecilia and Oscaecilia and it is the sister taxon of Typhlonectidae; Caeciliidae group 3 comprises the remaining species of caeciliids. The mitochondrial genome data were also used to calculate divergence times for caecilian evolution using the penalized likelihood method implemented in the program R8S. The newly obtained dating results are compatible with (but a little older than) previous time estimates mainly based on nuclear gene data. The mitogenomic time tree of caecilians suggests that the initial diversification of extant caecilians most probably took place in Late Triassic about 228 (195–260) Ma. Caeciliids currently distributed in India and the Seychelles diverged from their African and American relatives most probably in Late Jurassic about 138 (112–165) Ma, fairly close to the time (130 Ma) when Madagascar–India–Seychelles separated from Africa and South America. The split between the Indian caeciliid Gegeneophis and Seychellean caeciliids occurred about 103 (78–125) Ma, predated the rifting of India and the Seychelles (65 Ma).     

Evolutionary morphology of the caecilian urogenital system. I. The gonads and the fat bodies

The comparative morphology of the gonads and fat bodies of members of 17 genera and 46 species of caecilians (Amphibia: Gymnophiona) is described and analyzed. Comparison is made with the morphology of salamanders and frogs in order to elucidate evolutionary trends and relationships within the order Gymnophiona and within the class Amphibia. The structure of the testis lobes and transverse and longitudinal ducts is described based on gross dissection and histological investigation. The pattern of spermatogenesis and interstitial tissue changes are described and compared with those of other amphibians. A trend toward fusion of testis lobes is analyzed. The characteristics of the seasonal reproductive cycle of male Gymnopis m. proxima are described, and evidence for cyclic reproductive activity in other forms is presented. The morphology of the ovaries and ova is described. Size of ovary and size and number of ova is dependent on the state of maturation of the ova. Some evidence for seasonal ovum production and breeding is presented. Fat body morphology is found to be correlated with size, nutrition, and gonad condition, as in other amphibians.     

Novel modification of the tetrapod cardiovascular system in the West African caecilian Herpele squalostoma (Amphibia: Gymnophiona: Caeciliaidae)

Aspects of the cardiovascular system of Herpele squalostoma are described and compared to other caecilians. Novel modifications of the systemic arches, anterior vertebral arteries and vertebral structures associated with the systemic arches are identified. The evolution of aortic arch diversity in caecilians is considered from the perspective of efficiency of the cardiovascular system. A speculative hypothesis is advanced concerning the evolutionary history of the systemic arches in H. squalostoma . It is argued that modification of vertebral structures is the result of epigenetic interaction between the vertebral column and the evolving systemic arch.     

A stem-group caecilian (Lissamphibia: Gymnophiona) from the Lower Cretaceous of North Africa

Of living amphibian groups, the limbless burrowing caecilians are amongst the most highly specialised, but are the least known. Their fossil record is extremely poor, leaving unresolved questions as to their origins, relationships and early distribution. We describe here caecilian remains from a Lower Cretaceous (Berriasian) microfossil locality near Anoual, Morocco. This material represents the second oldest record for the group, after the Jurassic Eocaecilia of North America, and the earliest caecilian record for Gondwana. It forms the basis of a new genus, Rubricacaecilia , which appears slightly more derived than Eocaecilia , but lacks major features of crown-group taxa. We support the use of Apoda Oppel, 1811 for the crown-group alone, and Gymnophiona Rafinesque 1814 for the clade comprising stem-group taxa + Apoda.     

Mitochondrial evidence on the phylogenetic position of caecilians (Amphibia: Gymnophiona)

The complete nucleotide sequence (17,005 bp) of the mitochondrial genome of the caecilian Typhlonectes natans (Gymnophiona, Amphibia) was determined. This molecule is characterized by two distinctive genomic features: there are seven large 109-bp tandem repeats in the control region, and the sequence for the putative origin of replication of the L strand can potentially fold into two alternative secondary structures (one including part of the tRNA(Cys)). The new sequence data were used to assess the phylogenetic position of caecilians and to gain insights into the origin of living amphibians (frogs, salamanders, and caecilians). Phylogenetic analyses of two data sets-one combining protein-coding genes and the other combining tRNA genes-strongly supported a caecilian + frog clade and, hence, monophyly of modern amphibians. These two data sets could not further resolve relationships among the coelacanth, lungfishes, and tetrapods, but strongly supported diapsid affinities of turtles. Phylogenetic relationships among a larger set of species of frogs, salamanders, and caecilians were estimated with a mitochondrial rRNA data set. Maximum parsimony analysis of this latter data set also recovered monophyly of living amphibians and favored a frog + salamander (Batrachia) relationship. However, bootstrap support was only moderate at these nodes. This is likely due to an extensive among-site rate heterogeneity in the rRNA data set and the narrow window of time in which the three main groups of living amphibians were originated.     

Frequency of independent origins of viviparity among caecilians (Gymnophiona): evidence from the first 'live-bearing' Asian amphibian

Viviparity is reported for Gegeneophis seshachari (Gymnophiona: Caeciliidae) from a gravid female containing four oviductal foetuses. The oviducts are highly vascularized and contain patches of thickened, layered tissue similar to foetal gut contents. Gegeneophis seshachari probably resemble other viviparous caecilians in having foetuses that ingest thickened oviduct lining using specialized deciduous teeth. This is the first report of viviparity in Asian amphibians and Indo-Seychellean caeciliids. Gegeneophis is the only caecilian genus known to include oviparous and viviparous species, and G. seshachari is the smallest known viviparous caecilian. Phylogenetic analysis of mitochondrial DNA sequences supports assignment of G. seshachari to a monophyletic Gegeneophis. Character optimization indicates that viviparity has evolved independently at least four times within Gymnophiona--a rate of incidence relative to the number of extant species that is higher than for other vertebrate groups except squamate reptiles. Our findings strengthen the proposal that caecilian reproduction demands further attention.     

Copulation and egg retention in an oviparous Caecilian (Amphibia: Gymnophiona)

Viviparity (i.e., the bearing of live young) has evolved from oviparity (egg laying) independently in various major vertebrate lineages, and several transitional stages have been described. The transition from oviparity to viviparity requires the retention of fertilised eggs in the female reproductive tract. Caecilian amphibians (Gymnophiona) display a considerable diversity of reproductive modes, including oviparity and viviparity. Among amphibians, caecilians have also modified the process of internal fertilisation through a special intromittent organ, or phallus, in males. Here we report the oviposition of “embryonated” eggs ranging from various gastrula-to-neurula stages by female Ichthyophis cf. kohtaoensis (Ichthyophiidae) from North-eastern Thailand. In addition, we describe a copulation resulting in an oviposition of embryonated eggs. Our findings will have implications for the further understanding of the evolutionary reproductive biology of amphibians.     

Patterns of peripheral innervation of the tongue and hyobranchial apparatus in caecilians (Amphibia: Gymnophiona).

The innervation of the musculature of the tongue and the hyobranchial apparatus of caecilians has long been assumed to be simple and to exhibit little interspecific variation. A study of 14 genera representing all six families of caecilians demonstrates that general patterns of innervation by the trigeminal, facial, glossopharyngeal, and vagus nerves are similar across taxa but that the composition of the "hypoglossal" nerve is highly variable. Probably in all caecilians, spinal nerves 1 and 2 contribute to the hypoglossal. In addition, in certain taxa, an "occipital," the vagus, and/or spinal 3 appear to contribute fibers to the composition of the hypoglossal nerve. These patterns, the lengths of fusion of the contributing elements, and the branching patterns of the hypoglossal are assessed according to the currently accepted hypothesis of phylogenetic relationships of caecilians, and of amphibians. An hypothesis is proposed that limblessness and a simple tongue, with concomitant reduced complexity of innervation of muscles associated with limbs and the tongue, has released a constraint on pattern of innervation. As a consequence, a greater diversity and, in several taxa, greater complexity of neuroanatomical associations of nerve roots to form the hypoglossal are expressed.     

Batrachochytrium dendrobatidis Infection and Lethal Chytridiomycosis in Caecilian Amphibians (Gymnophiona)

Batrachochytrium dendrobatidis (Bd) is commonly termed the ‘amphibian chytrid fungus’ but thus far has been documented to be a pathogen of only batrachian amphibians (anurans and caudatans). It is not proven to infect the limbless, generally poorly known, and mostly soil-dwelling caecilians (Gymnophiona). We conducted the largest qPCR survey of Bd in caecilians to date, for more than 200 field-swabbed specimens from five countries in Africa and South America, representing nearly 20 species, 12 genera, and 8 families. Positive results were recovered for 58 specimens from Tanzania and Cameroon (4 families, 6 genera, 6+ species). Quantities of Bd were not exceptionally high, with genomic equivalent (GE) values of 0.052–17.339. In addition, we report the first evidence of lethal chytridiomycosis in caecilians. Mortality in captive (wild-caught, commercial pet trade) Geotrypetes seraphini was associated with GE scores similar to those we detected for field-swabbed, wild animals.     

Evolutionary morphology of the caecilian urogenital system. IV. The cloaca

The gross and microscopic anatomy of male and female cloacae of caecilians (Amphibia: Apoda or Gymnophiona) is described and analyzed in terms of structure and function. The arrangement of musculature and cloacal accessory structures is species-specific in males. Contraction of certain cloacal and body wall musculature facilitates eversion of the male cloaca for use as an intromittent organ. The cloacae of females show less marked morphological differences from species to species, and are modified as receptors of male phallodea.     

用线粒体tRNA基因探讨现存两栖动物三个目间系统发生关系

现存两栖类3个目的系统发生关系仍然没有统一意见,最广泛被接受的假说是单系起源,并且无尾类和有尾类为姐妹群关系而排斥蚓螈类(蛙类假说)。然而,这一假说一直存在争议。我们在测定了泽蛙线粒体基因组全序列的基础上,与已知其他的6种两栖类进行详细的比较分析,同时选择了11种高等脊椎动物的线粒体全基因序列,以硬骨鱼类作外群,用22个tRNA基因合并数据进行系统发生重建分析,结果表明MP、ML树都强力地支持现生两栖类动物为单系群,并且有尾目和蚓螈目为姐妹群关系。这个结果与蛙类假说是相矛盾的,与Bolt(1991)在形态学基础上提出的有尾类和蚓螈类为姐妹群关系的假说相一致,并得到建立在线粒体和核rRNA基因数据基础上的许多分子研究的支持。另外还探讨了本结果与前人的研究不一致的原因,以及利用线粒体全基因序列进行系统发生分析可能存在的偏差。     

Development of the tectum in Gymnophiones,with comparison to other amphibians

Tectal development in a number of caecilian (Gymnophiona: Amphibia) species was examined and compared with that in frogs and salamanders. The caecilian optic tectum develops along the same rostrocaudal and lateromedial gradients as those of frogs and salamanders. However, differences exist in the time course of development. Our data suggest that, as in salamanders, simplification of morphological complexity in caecilians is due to a retardation or loss of late developmental stages. Differences in the time course of development (heterochrony) among different caecilian species are correlated with phylogenetic history as well as with variation in life histories. The most pronounced differences in development occur between the directly developing Hypogeophis rostratus and all other species examined. In this species, the increase in the degree of morphological complexity is greatly accelerated. J. Morphol. 236:233–246, 1998. © 1998 Wiley-Liss, Inc.