Limb reduction in squamate reptiles correlates with the reduction of the chondrocranium: A case study on serpentiform anguids

Genomic data are rapidly resolving the tree of living species calibrated to time, the timetree of life, which will provide a framework for research in diverse fields of science. Previous analyses of taxonomically restricted timetrees have found a decline in the rate of diversification in many groups of organisms, often attributed to ecological interactions among species. Here, we have synthesized a global timetree of life from 2,274 studies representing 50,632 species and examined the pattern and rate of diversification as well as the timing of speciation. We found that species diversity has been mostly expanding overall and in many smaller groups of species, and that the rate of diversification in eukaryotes has been mostly constant. We also identified, and avoided, potential biases that may have influenced previous analyses of diversification including low levels of taxon sampling, small clade size, and the inclusion of stem branches in clade analyses. We found consistency in time-to-speciation among plants and animals, ∼2 My, as measured by intervals of crown and stem species times. Together, this clock-like change at different levels suggests that speciation and diversification are processes dominated by random events and that adaptive change is largely a separate process.

Two common approaches for estimating phylogenies in species-rich groups are to: (i) sample many loci for few species (e.g. phylogenomic approach), or (ii) sample many species for fewer loci (e.g. supermatrix approach). In theory, these approaches can be combined to simultaneously resolve both higher-level relationships (with many genes) and species-level relationships (with many taxa). However, fundamental questions remain unanswered about this combined approach. First, will higher-level relationships more closely resemble those estimated from many genes or those from many taxa? Second, will branch support increase for higher-level relationships (relative to the estimate from many taxa)? Here, we address these questions in squamate reptiles. We combined two recently published datasets, one based on 44 genes for 161 species, and one based on 12 genes for 4161 species. The likelihood-based tree from the combined matrix (52 genes, 4162 species) shared more higher-level clades with the 44-gene tree (90% vs. 77% shared). Branch support for higher level-relationships was marginally higher than in the 12-gene tree, but lower than in the 44-gene tree. Relationships were apparently not obscured by the abundant missing data (92% overall). We provide a time-calibrated phylogeny based on extensive sampling of genes and taxa as a resource for comparative studies.

We have used the quail-chick chimera technique to study the origin of the bones of the skull in the avian embryo. Although the contribution of the neural crest to the facial and visceral skeleton had been established previously, the origin of the vault of the skull (i.e. frontal and parietal bones) remained uncertain. Moreover formation of the occipito-otic region from either the somitic or the cephalic paraxial mesoderm had not been experimentally investigated. The data obtained in the present and previous works now allow us to assign a precise embryonic origin from either the mesectoderm, the paraxial cephalic mesoderm or the five first somites, to all the bones forming the avian skull. We distinguish a skull located in front of the extreme tip of the notochord which reaches the sella turcica and a skull located caudally to this boundary. The former ('prechordal skull') is derived entirely from the neural crest, the latter from the mesoderm (cephalic or somitic) in its ventromedial part ('chordal skull') and from the crest for the parietal bone and for part of the otic region. An important point enlighten in this work concerns the double origin of the corpus of the sphenoid in which basipresphenoid is of neural crest origin and the basipostsphenoid is formed by the cephalic mesoderm. Formation of the occipito-otic region of the skeleton is particularly complex and involves the cooperation of the five first somites and the paraxial mesoderm at the hind-brain level. The morphogenetic movements leading to the initial puzzle assembly could be visualized in a reproducible way by means of small grafts of quail mesodermal areas into chick embryos. The data reported here are discussed in the evolutionary context of the 'New Head' hypothesis of Gans and Northcutt (1983, Science, 220, 268-274).