Phylogeny of snakes (Serpentes): combining morphological and molecular data in likelihood Bayesian and parsimony analyses

Copyright © 2007 The Natural history MuseumThe phylogeny of living and fossil snakes is assessed using likelihood and parsimony approaches and a dataset combining 263 morphological characters with mitochondrial (2693 bp) and nuclear (1092 bp) gene sequences. The ‘no common mechanism’ (NCMr) and ‘Markovian’ (Mkv) models were employed for the morphological partition in likelihood analyses; likelihood scores in the NCMr model were more closely correlated with parsimony tree lengths. Both models accorded relatively less weight to the molecular data than did parsimony, with the effect being milder in the NCMr model. Partitioned branch and likelihood support values indicate that the mtDNA and nuclear gene partitions agree more closely with each other than with morphology. Despite differences between data partitions in phylogenetic signal, analytic models, and relative weighting, the parsimony and likelihood analyses all retrieved the following widely accepted groups: scolecophidians, alethinophidians, cylindrophiines, macrostomatans (sensu lato) and caenophidians. Anilius alone emerged as the most basal alethinophidian; the combined analyses resulted in a novel and stable position of uropeltines and cylindrophiines as the second-most basal clade of alethinophidians. The limbed marine pachyophiids, along with Dinilysia and Wonambi, were always basal to all living snakes. Other results stable in all combined analyses include: Xenopeltis and Loxocemus were sister taxa (fide morphology) but clustered with pythonines (fide molecules), and Ungaliophis clustered with a boine-erycine clade (fide molecules). Tropidophis remains enigmatic; it emerges as a basal alethinophidian in the parsimony analyses (fide molecules) but a derived form in the likelihood analyses (fide morphology), largely due to the different relative weighting accorded to data partitions.Michael S. Y. Lee, Andrew F. Hugall, Robin Lawson & John D. Scanlo

A multiscale model of grain boundary structure and energy : from atomistics to a continuum description

Grain boundaries play an important role in the mechanical and physical properties of polycrystalline metals. While continuum macroscale simulations are appropriate for modeling grain boundaries in coarse-grained materials, only atomistic simulations provide access to the details of the grain boundary (GB) structure and energy. Hence, a multiscale description is required to capture these GB details. The objective of this paper is to consolidate various approaches for characterizing grain boundaries in an effort to develop a multiscale model of the initial GB structure and energy. The technical approach is detailed using various ; and symmetric tilt grain boundaries in copper and aluminum. Characteristic features are: (i) GB energies obtained from atomistic simulations and boundary period vectors from crystallography, (ii) structural unit and dislocation descriptions of the GB structure and (iii) the Frank–Bilby equation to determine the dislocation content. The proposed approach defines an intrinsic net defect density scalar that is used to accurately compute the GB energy for these GB systems. The significance of the present work is that the developed atomistic-to-continuum approach is suitable for realistically inserting the initial GB structure and energy into continuum level frameworks