Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on “standards” for data selection, curation and tree inference. We use jawed vertebrates (Gnathostomata) as model to address these issues. Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full phylogenetic diversity of gnathostomes and some relationships remain controversial. We tested a novel bioinformatic pipeline to assemble large and accurate phylogenomic datasets from RNA sequencing and find this phylotranscriptomic approach successful and highly cost-effective. Increased sequencing effort up to ca. 10Gbp allows recovering more genes, but shallower sequencing (1.5Gbp) is sufficient to obtain thousands of full-length orthologous transcripts. We reconstruct a robust and strongly supported timetree of jawed vertebrates using 7,189 nuclear genes from 100 taxa, including 23 new transcriptomes from previously unsampled key species. Gene jackknifing of genomic data corroborates the robustness of our tree and allows calculating genome-wide divergence times by overcoming gene sampling bias. Mitochondrial genomes prove insufficient to resolve the deepest relationships because of limited signal and among-lineage rate heterogeneity. Our analyses emphasize the importance of large curated nuclear datasets to increase the accuracy of phylogenomics and provide a reference framework for the evolutionary history of jawed vertebrates.

Although the initial growth and development of most multicellular animals depends on the provision of yolk, there are many varied contrivances by which animals provide additional or alternative investment in their offspring. Providing offspring with additional nutrition should be favoured by natural selection when the consequent increased fitness of the young offsets any corresponding reduction in fecundity. Alternative forms of nutrition may allow parents to delay and potentially redirect their investment. Here we report a remarkable form of parental care and mechanism of parent-offspring nutrient transfer in a caecilian amphibian. Boulengerula taitanus is a direct-developing, oviparous caecilian, the skin of which is transformed in brooding females to provide a rich supply of nutrients for the developing offspring. Young animals are equipped with a specialized dentition, which they use to peel and eat the outer layer of their mother's modified skin. This new form of parental care provides a plausible intermediate stage in the evolution of viviparity in caecilians. At independence, offspring of viviparous and of oviparous dermatotrophic caecilians are relatively large despite being provided with relatively little yolk. The specialized dentition of skin-feeding (dermatophagous) caecilians may constitute a preadaptation to the fetal feeding on the oviduct lining of viviparous caecilians.

This chapter reviews patterns of sexual dimorphism in amphibians and discusses their proximal causes and possible adaptive significance. Amphibians are diverse organisms that live in aquatic or terrestrial ecosystems. Female-biased sexual size dimorphism (SSD) is the common pattern in frogs and salamanders, and male-biased SSD is only present in few lineages. Preliminary SSD data for caecilians indicate that many are monomorphic in body size, while others exhibit female-biased dimorphism. The typical female-biased SSD may be partly explained by sex-specific growth trajectories and delayed maturity of females. Male-biased SSD is associated with sexual selection for large males through territoriality and male-male combat. In comparison with other vertebrates, our understanding of SSD in amphibians is still incomplete. Phylogenetic comparative analyses are needed to describe more fully the evolutionary patterns of amphibian SSD and to test hypotheses based on fecundity and sexual selection, life history theory, and ecological divergence.

Maternal dermatophagy, the eating of maternal skin by offspring, is an unusual form of parental investment involving co-evolved specializations of both maternal skin and offspring dentition, which has been recently discovered in an African caecilian amphibian. Here we report the discovery of this form of parental care in a second, distantly related Neotropical species Siphonops annulatus, where it is characterized by the same syndrome of maternal and offspring specializations. The detailed similarities of skin feeding in different caecilian species provide strong evidence of its homology, implying its presence in the last common ancestor of these species. Biogeographic considerations, the separation of Africa and South American land masses and inferred timescales of amphibian diversification all suggest that skin feeding is an ancient form of parental care in caecilians, which has probably persisted in multiple lineages for more than 100 Myr. These inferences support the hypotheses that (i) maternal dermatophagy is widespread in oviparous direct-developing caecilians, and (ii) that viviparous caecilians that feed on the hypertrophied maternal oviduct evolved from skin-feeding ancestors. In addition to skin-feeding, young S. annulatus were observed to congregate around, and imbibe liquid exuded from, the maternal cloacal opening.

The late Paleogene to early Neogene salamander Chelotriton paradoxus is redescribed on the basis of new and excellent material from two deposits, the late Oligocene Enspel locality and the Miocene Randeck Maar. C. paradoxus is characterised by the following features: (1) skull outline broad and parabolic, (2) snout abbreviated, with nasal only half the length of the frontal, (3) quadratojugal with a series of 3-5 spikes on the lateral margin, and (4) osteoderms larger than in other genera. Like extant Echinotriton, its trunk ribs bear extensive spikes (epipleural processes), with an elongated one on the 3rd rib. The Enspel sample of C. paradoxus shows greater variation in the size and number of quadratojugal spikes, whereas the best-preserved Randeck specimen bears exceptionally tall tubercles on all dermal bones and osteoderms and has a larger quadratojugal. Based on preliminary taphonomical data, we suggest that C. paradoxus probably led a predominantly aquatic life.