Modeling body size evolution in Felidae under alternative phylogenetic hypotheses

The use of phylogenetic comparative methods in ecological research has advanced during the last twenty years, mainly due to accurate phylogenetic reconstructions based on molecular data and computational and statistical advances. We used phylogenetic correlograms and phylogenetic eigenvector regression (PVR) to model body size evolution in 35 worldwide Felidae (Mammalia, Carnivora) species using two alternative phylogenies and published body size data. The purpose was not to contrast the phylogenetic hypotheses but to evaluate how analyses of body size evolution patterns can be affected by the phylogeny used for comparative analyses (CA). Both phylogenies produced a strong phylogenetic pattern, with closely related species having similar body sizes and the similarity decreasing with increasing distances in time. The PVR explained 65% to 67% of body size variation and all Moran's I values for the PVR residuals were non-significant, indicating that both these models explained phylogenetic structures in trait variation. Even though our results did not suggest that any phylogeny can be used for CA with the same power, or that “good” phylogenies are unnecessary for the correct interpretation of the evolutionary dynamics of ecological, biogeographical, physiological or behavioral patterns, it does suggest that developments in CA can, and indeed should, proceed without waiting for perfect and fully resolved phylogenies

Can sexual selection drive female life histories? A comparative study on Galliform birds

Sexual selection is an important driver of many of the most spectacular morphological traits that we find in the animal kingdom (for example see Andersson, 1994). As such, sexual selection is most often emphasized as

Automated removal of noisy data in phylogenomic analyses

Noisy data, especially in combination with misalignment and model misspecification can have an adverse effect on phylogeny reconstruction; however, effective methods to identify such data are few. One particularly important class of noisy data is saturated positions. To avoid potential errors related to saturation in phylogenomic analyses, we present an automated procedure involving the step-wise removal of the most variable positions in a given data set coupled with a stopping criterion derived from correlation analyses of pairwise ML distances calculated from the deleted (saturated) and the remaining (conserved) subsets of the alignment. Through a comparison with existing methods, we demonstrate both the effectiveness of our proposed procedure for identifying noisy data and the effect of the removal of such data using a well-publicized case study involving placental mammals. At the least, our procedure will identify data sets requiring greater data exploration, and we recommend its use to investigate the effect on phylogenetic analyses of removing subsets of variable positions exhibiting weak or no correlation to the rest of the alignment. However, we would argue that this procedure, by identifying and removing noisy data, facilitates the construction of more accurate phylogenies by, for example, ameliorating potential long-branch attraction artefacts

The genome of Oryctes rhinoceros nudivirus provides novel insight into the evolution of nuclear arthropod-specific large circular double-tranded DNA viruses

The Oryctes rhinoceros nudivirus (OrNV) is a dsDNA virus with enveloped, rod-shaped virions. Its genome is 127,615 bp in size and contains 139 predicted protein-coding open reading frames (ORFs). In-depth genome sequence comparisons revealed a varying number of shared gene homologues, not only with other nudiviruses (NVs) and baculoviruses, but also with other arthropod-specific large dsDNA viruses, including the so-called Monodon baculovirus (MBV), the salivary gland hypertrophy viruses (SGHVs) and white spot syndrome virus (WSSV). Nudivirus genomes contain 20 baculovirus core gene homologues associated with transcription (p47, lef-8, lef-9, lef-4, vlf-1, and lef-5), replication (dnapol and helicase), virus structure (p74, pif-1, pif-2, pif-3, 19kda/pif- 4, odv-e56/pif-5, vp91, vp39, and 38K), and unknown functions (ac68, ac81, and p33). Most strikingly, a set of homologous genes involved in peroral infection (p74, pif-1, pif-2, and pif-3) are common to baculoviruses, nudiviruses, SGHVs, and WSSV indicating an ancestral mode of infection in these highly diverged viruses. A gene similar to polyhedrin/granulin encoding the baculovirus occlusion body protein was identified in non-occluded NVs and in Musca domestica SGHV evoking the question of the evolutionary origin of the baculovirus polyhedrin/granulin gene. Based on gene homologies, we further propose that the shrimp MBV is an occluded member of the nudiviruses. We conclude that baculoviruses, NVs and the shrimp MBV, the SGHVs and WSSV share the significant number of conserved genetic functions, which may point to a common ancestry of these viruse

CONDENSED MATTER RESEARCH USING PULSED NEUTRON SOURCES: A BIBLIOGRAPHY

Supertree methods allow to reconstruct large phylogenetic trees by combining smaller trees with overlapping leaf sets into one, more comprehensive supertree. The most commonly used supertree method, matrix representation with parsimony (MRP), produces accurate supertrees but is rather slow due to the underlying hard optimization problem. In this paper, we present an extensive simulation study comparing the performance of MRP and the polynomial supertree methods MinCut Supertree, Modified MinCut Supertree, Build-with-distances, PhySIC, PhySIC_IST, and super distance matrix. We consider both quality and resolution of the reconstructed supertrees. Our findings illustrate the tradeoff between accuracy and running time in supertree construction, as well as the pros and cons of voting- and veto-based supertree approaches. Based on our results, we make some general suggestions for supertree methods yet to come

Dinosaurs and the Cretaceous Terrestrial Revolution

The observed diversity of dinosaurs reached its highest peak during the mid- and Late Cretaceous, the 50 Myr that preceded their extinction, and yet this explosion of dinosaur diversity may be explained largely by sampling bias. It has long been debated whether dinosaurs were part of the Cretaceous Terrestrial Revolution (KTR), from 125–80 Myr ago, when flowering plants, herbivorous and social insects, squamates, birds and mammals all underwent a rapid expansion. Although an apparent explosion of dinosaur diversity occurred in the mid-Cretaceous, coinciding with the emergence of new groups (e.g. neoceratopsians, ankylosaurid ankylosaurs, hadrosaurids and pachycephalosaurs), results from the first quantitative study of diversification applied to a new supertree of dinosaurs show that this apparent burst in dinosaurian diversity in the last 18 Myr of the Cretaceous is a sampling artefact. Indeed, major diversification shifts occurred largely in the first one-third of the group's history. Despite the appearance of new clades of medium to large herbivores and carnivores later in dinosaur history, these new originations do not correspond to significant diversification shifts. Instead, the overall geometry of the Cretaceous part of the dinosaur tree does not depart from the null hypothesis of an equal rates model of lineage branching. Furthermore, we conclude that dinosaurs did not experience a progressive decline at the end of the Cretaceous, nor was their evolution driven directly by the KTR