Pitfalls in the analysis of ancient human mtDNA

The retrieval of DNA from ancient human specimens is not always successful owing to DNA deterioration and contamination although it is vital to provide new insights into the genetic structure of ancient people and to reconstruct the past history. Normally, only short DNA fragments can be retrieved from the ancient specimens. How to identify the authenticity of DNA obtained and to uncover the information it contained are difficult. We employed the ancient mtDNAs reported from Central Asia (including Xinjiang, China) as an example to discern potentially extraneous DNA contamination based on the updated mtDNA phylogeny derived from mtDNA control region, coding region, as well as complete sequence information. Our results demonstrated that many mtDNAs reported are more or less problematic. Starting from a reliable mtDNA phylogeney and combining the available modern data into analysis, one can ascertain the authenticity of the ancient DNA, distinguish the potential errors in a data set, and efficiently decipher the meager information it harbored. The reappraisal of the mtDNAs with the age of more than 2000 years from Central Asia gave support to the suggestion of extensively (pre)historical gene admixture in this region.

A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae

Background: The Galliformes is a well-known and widely distributed Order in Aves. The phylogenetic relationships of galliform birds, especially the turkeys, grouse, chickens, quails, and pheasants, have been studied intensively, likely because of their close association with humans. Despite extensive studies, convergent morphological evolution and rapid radiation have resulted in conflicting hypotheses of phylogenetic relationships. Many internal nodes have remained ambiguous. Results: We analyzed the complete mitochondrial (mt) genomes from 34 galliform species, including 14 new mt genomes and 20 published mt genomes, and obtained a single, robust tree. Most of the internal branches were relatively short and the terminal branches long suggesting an ancient, rapid radiation. The Megapodiidae formed the sister group to all other galliforms, followed in sequence by the Cracidae, Odontophoridae and Numididae. The remaining clade included the Phasianidae, Tetraonidae and Meleagrididae. The genus Arborophila was the sister group of the remaining taxa followed by Polyplectron. This was followed by two major clades: ((((Gallus, Bambusicola) Francolinus) (Coturnix, Alectoris)) Pavo) and (((((((Chrysolophus, Phasianus) Lophura) Syrmaticus) Perdix) Pucrasia) (Meleagris, Bonasa)) ((Lophophorus, Tetraophasis) Tragopan))). Conclusions: The traditional hypothesis of monophyletic lineages of pheasants, partridges, peafowls and tragopans was not supported in this study. Mitogenomic analyses recovered robust phylogenetic relationships and suggested that the Galliformes formed a model group for the study of morphological and behavioral evolution.

Reconstructing the evolutionary history of China: A caveat about inferences drawn from ancient DNA

The decipherment of the meager information provided by short fragments of ancient mitochondrial DNA (mtDNA) is notoriously difficult but is regarded as a most promising way toward reconstructing the past from the genetic perspective. By haplogroup-specific hypervariable segment (HVS) motif search and matching or near-matching with available modem data sets, most of the ancient mtDNAs can be tentatively assigned to haplogroups, which are often subcontinent specific. Further typing for mtDNA haplogroup-diagnostic coding region polymorphisms, however, is indispensable for establishing the geographic/genetic affinities of ancient samples with less ambiguity. In the present study, we sequenced a fragment (similar to 982 bp) of the mtDNA control region in 76 Han individuals from Taian, Shandong, China, and we combined these data with previously reported samples from Zibo and Qingdao, Shandong. The reanalysis of two previously published ancient mtDNA population data sets from Linzi (same province) then indicates that the ancient populations had features in common with the modem populations from south China rather than any specific affinity to the European mtDNA pool. Our results highlight that ancient mtDNA data obtained under different sampling schemes and subject to potential contamination can easily create the impression of drastic spatiotemporal changes in the genetic structure of a regional population during the past few thousand years if inappropriate methods of data analysis are employed.

Moderate energy impact analysis combining phenomenological contact law with localised damage and integral equation method

A computational impact analysis methodology has been developed, based on modal analysis and a local contact force-deflection model. The contact law is based on Hertz contact theory while contact stresses are elastic, defines a modified contact theory to take account of local permanent indentation, and considers elastic recovery during unloading. The model was validated experimentally through impact testing of glass-carbon hybrid braided composite panels. Specimens were mounted in a support frame and the contact force was inferred from the deceleration of the impactor, measured by high-speed photography. A Finite Element analysis of the panel and support frame assembly was performed to compute the modal responses. The new contact model performed well in predicting the peak forces and impact durations for moderate energy impacts (15 J), where contact stresses locally exceed the linear elastic limit and damage may be deemed to have occurred. C-scan measurements revealed substantial damage for impact energies in the range of 30-50 J. For this regime the new model predictions might be improved by characterisation of the contact law hysteresis during the unloading phase, and a modification of the elastic vibration response in line with damage levels acquired during the impact. © 2011 Elsevier Ltd. All rights reserved.

A general mass law for broadband energy harvesting

It is well known that the power absorbed by a linear oscillator when excited by white noise base acceleration depends only on the mass of the oscillator and the spectral density of the base motion. This places an upper bound on the energy that can be harvested from a linear oscillator under broadband excitation, regardless of the stiffness of the system or the damping factor. It is shown here that the same result applies to any multi-degree-of-freedom nonlinear system that is subjected to white noise base acceleration: for a given spectral density of base motion the total power absorbed is proportional to the total mass of the system. The only restriction to this result is that the internal forces are assumed to be a function of the instantaneous value of the state vector. The result is derived analytically by several different approaches, and numerical results are presented for an example two-degree-of-freedom-system with various combinations of linear and nonlinear damping and stiffness. © 2013 The Author.

Independent adaptation to riverine habitats allowed survival of ancient cetacean lineages

The four species of "river dolphins" are associated with six separate great river systems on three subcontinents and have been grouped for more than a century into a single taxon based on their similar appearance. However, several morphologists recently questioned the monophyly of that group. By using phylogenetic analyses of nucleotide sequences from three mitochondrial and two nuclear genes, we demonstrate with statistical significance that extant river dolphins are not monophyletic and suggest that they are relict species whose adaptation to riverine habitats incidentally insured their survival against major environmental changes in the marine ecosystem or the emergence of Delphinidae.

Nanoadhesion of a Power-Law Graded Elastic Material

The Dugdale-Barenblatt model is used to analyze the adhesion of graded elastic materials at the nanoscale with Young's modulus E varying with depth z according to a power law E = E-0(z/c(0))(k) (0 < k < 1) while Poisson's ratio v remains a constant, where E-0 is a referenced Young's modulus, k is the gradient exponent and c(0) is a characteristic length describing the variation rate of Young's modulus. We show that, when the size of a rigid punch becomes smaller than a critical length, the adhesive interface between the punch and the graded material detaches due to rupture with uniform stresses, rather than by crack propagation with stress concentration. The critical length can be reduced to the one for isotropic elastic materials only if the gradient exponent k vanishes.