Exploring the effects of weighting against homoplasy in genealogies of palaeontological phylogenetic matrices

Although simulations have shown that implied weighting (IW) outperforms equal weighting (EW) in phylogenetic parsimony analyses, weighting against homoplasy lacks extensive usage in palaeontology. Iterative modifications of several phylogenetic matrices in the last decades resulted in extensive genealogies of datasets that allow the evaluation of differences in the stability of results for alternative character weighting methods directly on empirical data. Each generation was compared against the most recent generation in each genealogy because it is assumed that it is the most comprehensive (higher sampling), revised (fewer misscorings) and complete (lower amount of missing data) matrix of the genealogy. The analyses were conducted on six different genealogies under EW and IW and extended implied weighting (EIW) with a range of concavity constant values (k) between 3 and 30. Pairwise comparisons between trees were conducted using Robinson-Foulds distances normalized by the total number of groups, distortion coefficient, subtree pruning and regrafting moves, and the proportional sum of group dissimilarities. The results consistently show that IW and EIW produce results more similar to those of the last dataset than EW in the vast majority of genealogies and for all comparative measures. This is significant because almost all of these matrices were originally analysed only under EW. Implied weighting and EIW do not outperform each other unambiguously. Euclidean distances based on a principal components analysis of the comparative measures show that different ranges of k-values retrieve the most similar results to the last generation in different genealogies. There is a significant positive linear correlation between the optimal k-values and the number of terminals of the last generations. This could be employed to inform about the range of k-values to be used in phylogenetic analyses based on matrix size but with the caveat that this emergent relationship still relies on a low sample size of genealogies.

Turtle skull development unveils a molecular basis for amniote cranial diversity

Amniote skulls display diverse architectural patterns including remarkable variations in the number of temporal arches surrounding the upper and lower temporal fenestrae. However, the cellular and molecular basis underlying this diversification remains elusive. Turtles are a useful model to understand skull diversity due to the presence of secondarily closed temporal fenestrae and different extents of temporal emarginations (marginal reduction of dermal bones). Here, we analyzed embryos of three turtle species with varying degrees of temporal emargination and identified shared widespread coexpression of upstream osteogenic genes Msx2 and Runx2 and species-specific expression of more downstream osteogenic genes Sp7 and Sparc in the head. Further analysis of representative amniote embryos revealed differential expression patterns of osteogenic genes in the temporal region, suggesting that the spatiotemporal regulation of Msx2, Runx2, and Sp7 distinguishes the temporal skull morphology among amniotes. Moreover, the presence of Msx2- and/or Runx2-positive temporal mesenchyme with osteogenic potential may have contributed to their extremely diverse cranial morphology in reptiles.

Climatic controls on the ecological ascendancy of dinosaurs

The ascendancy of dinosaurs to become dominant components of terrestrial ecosystems was a pivotal event in the history of life, yet the drivers of their early evolution and biodiversity are poorly understood.^1,2,3 During their early diversification in the Late Triassic, dinosaurs were initially rare and geographically restricted, only attaining wider distributions and greater abundance following the end-Triassic mass extinction event.^4,5,6 This pattern is consistent with an opportunistic expansion model, initiated by the extinction of co-occurring groups such as aetosaurs, rauisuchians, and therapsids.^4,7,8 However, this pattern could instead be a response to changes in global climatic distributions through the Triassic to Jurassic transition, especially given the increasing evidence that climate played a key role in constraining Triassic dinosaur distributions.^{7,9,10,11,12,13,14,15,16} Here, we test this hypothesis and elucidate how climate influenced early dinosaur distribution by quantitatively examining changes in dinosaur and tetrapod "climatic niche space" across the Triassic-Jurassic boundary. Statistical analyses show that Late Triassic sauropodomorph dinosaurs occupied a more restricted climatic niche space than other tetrapods and dinosaurs, being excluded from the hottest, low-latitude climate zones. A subsequent, earliest Jurassic expansion of sauropodomorph geographic distribution is linked to the expansion of their preferred climatic conditions. Evolutionary model-fitting analyses provide evidence for an important evolutionary shift from cooler to warmer climatic niches during the origin of Sauropoda. These results are consistent with the hypothesis that global abundance of sauropodomorph dinosaurs was facilitated by climatic change and provide support for the key role of climate in the ascendancy of dinosaurs.

Pendraig milnerae, a new small-sized coelophysoid theropod from the Late Triassic of Wales

We describe a new small-bodied coelophysoid theropod dinosaur, Pendraig milnerae gen. et sp. nov, from the Late Triassic fissure fill deposits of Pant-y-ffynnon in southern Wales. The species is represented by the holotype, consisting of an articulated pelvic girdle, sacrum and posterior dorsal vertebrae, and an associated left femur, and by two referred specimens, comprising an isolated dorsal vertebra and a partial left ischium. Our phylogenetic analysis recovers P. milnerae as a non-coelophysid coelophysoid theropod, representing the first-named unambiguous theropod from the Triassic of the UK. Recently, it has been suggested that Pant-y-ffynnon and other nearby Late Triassic to Early Jurassic fissure fill faunas might have been subjected to insular dwarfism. To test this hypothesis for P. milnerae, we performed an ancestral state reconstruction analysis of body size in early neotheropods. Although our results indicate that a reduced body size is autapomorphic for P. milnerae, some other coelophysoid taxa show a similar size reduction, and there is, therefore, ambiguous evidence to indicate that this species was subjected to dwarfism. Our analyses further indicate that, in contrast with averostran-line neotheropods, which increased in body size during the Triassic, coelophysoids underwent a small body size decrease early in their evolution.