Multiple maternal origins of chickens: Out of the Asian jungles

Domestic chickens have long been important to human societies for food, religion, entertainment, and decorative uses, yet the origins and phylogeography of chickens through Eurasia remain uncertain. Here, we assessed their origins and phylogeographic hist

MULTIPLE GENOTYPES OF MITOCHONDRIAL-DNA WITHIN A HORSE POPULATION FROM A SMALL REGION IN YUNNAN PROVINCE OF CHINA

mtDNA genotypes of six domestic horses (three adult short horses whose heights are under 1 m and three common domestic horses) from a small region of 15 km(2) in Malipo county of Yunnan province of China were investigated by the technique of restriction fragment length polymorphism (RFLP) with restriction endonucleases which recognize 6-bp sequences. An average of fragments for an individual was obtained. Unlike other domestic animals, this population of horses exhibits high mtDNA genetic diversity. Each of the six horses has a specific mtDNA genotype showing a pattern of multiple maternal origins, as suggested by fossil and literature records. We think the population of horses is an amazing seed-resource pool of horses and hence deserves to be paid more attention from the view of conservation genetics. However it is also remarkable that we did not find any typical mtDNA genetic markers which would discriminate between short horses and common domestic horses.

Molecular evidence for double maternal origins of the diploid hybrid Hippophae goniocarpa (Elaeagnaceae)

Homoploid hybrid plant species are rare, and the mechanisms of their speciation are largely unknown, especially for homoploid hybrid tree species. Two contrasting hypotheses have been proposed to explain the origin of Hippophae goniocarpa: (1) it is a diploid hybrid originating from H. rhamnoides ssp. sinensis x H. neurocarpa ssp. neurocarpa, and (2) it originated via marginal differentiation from H. rhamnoides ssp. sinensis. Regardless of which of these hypotheses is true (if either), previous studies have suggested that H. rhamnoides ssp. sinensis is the only maternal donor for this hybrid species. In this study, we aim to elucidate the maternal composition of H. goniocarpa and to test the two hypotheses. For this purpose, we sequenced the maternal chloroplast DNA trnL-F region of 75 individuals representing H. goniocarpa, H. rhamnoides ssp. sinensis, and H. neurocarpa ssp. neurocarpa in two co-occurring sites of the taxa. Seven haplotypes were identified from three taxonomic units, and their phylogenetic relationships were further constructed by means of maximum parsimony, maximum likelihood, and network analyses. These seven haplotypes clustered into two distinct, highly divergent lineages. Two haplotypes from one lineage were found in H. rhamnoides ssp. sinensis, and five (representing the other lineage) in H. neurocarpa ssp. neurocarpa. Hippophae goniocarpa shared four common haplotypes from both lineages, but the haplotypes detected from the two populations differed to some extent, and in each case were identical to local haplotypes of the putative parental species. Thus, both H. rhamnoides ssp. sinensis and H. neurocarpa ssp. neurocarpa appear to have together contributed to the maternal establishment of H. goniocarpa. These results clearly demonstrate that the marginal origin hypothesis should be rejected, and support the hybrid origin hypothesis. Hippophae goniocarpa exhibits a sympatric distribution with its two parent species, without occupying new niches or displaying complete ecological isolation. However, this species has effectively developed reproductive isolation from its sympatric parent species. Our preliminary results suggest that H. goniocarpa may provide a useful model system for studying diploid hybrid speciation in trees. (c) 2008 The Linnean Society of London.

Mitochondrial diversity and phylogeographic structure of Chinese domestic goats

China has numerous native domestic goat breeds, but so far there has been no extensive study on genetic diversity, population demographic history, and origin of Chinese goats. Here, we examined the genetic diversity and phylogeographic structure of Chinese domestic goats by determining a 481-bp fragment of the first hypervariable region of mitochondrial DNA (mtDNA) control region from 368 individuals representing 18 indigenous breeds. Phylogenetic analyses revealed that there were four mtDNA lineages (A-D) identified in Chinese goats, in which lineage A was predominant, lineage B was moderate, and lineages C and D were at low frequency. These results further support the multiple maternal origins of domestic goats. The pattern of genetic variation in goat mtDNA sequences indicated that the two larger lineages A and B had undergone population expansion events. In a combined analysis of previously reported sequences and our sequences belonging to lineage B, we detected two subclades, in which one was unique to eastern Asia and another was shared between eastern and southern Asia. A larger genetic variation in eastern Asia than southern Asia and the pattern of phylogeographic variation in lineage B suggest that at least one subclade of lineage B originated from eastern Asia. There was no significant geographical structuring in Chinese goat populations, which suggested that there existed strong gene flow among goat populations caused by extensive transportation of goats in history. (c) 2005 Elsevier Inc. All rights reserved.

Origin of mitochondrial DNA diversity of domestic yaks

Background: The domestication of plants and animals was extremely important anthropologically. Previous studies have revealed a general tendency for populations of livestock species to include deeply divergent maternal lineages, indicating that they were domesticated in multiple, independent events from genetically discrete wild populations. However, in water buffalo, there are suggestions that a similar deep maternal bifurcation may have originated from a single population. These hypotheses have rarely been rigorously tested because of a lack of sufficient wild samples. To investigate the origin of the domestic yak (Poephagus grunnies), we analyzed 637 bp of maternal inherited mtDNA from 13 wild yaks (including eight wild yaks from a small population in west Qinghai) and 250 domesticated yaks from major herding regions.Results: The domestic yak populations had two deeply divergent phylogenetic groups with a divergence time of > 100,000 yrs BP. We here show that haplotypes clustering with two deeply divergent maternal lineages in domesticated yaks occur in a single, small, wild population. This finding suggests that all domestic yaks are derived from a single wild gene pool. However, there is no clear correlation of the mtDNA phylogenetic clades and the 10 morphological types of sampled yaks indicating that the latter diversified recently. Relatively high diversity was found in Qinghai and Tibet around the current wild distribution, in accordance with previous suggestions that the earliest domestications occurred in this region. Conventional molecular clock estimation led to an unrealistic early dating of the start of the domestication. However, Bayesian estimation of the coalescence time allowing a relaxation of the mutation rateConclusion: The information gathered here and the previous studies of other animals show that the demographic histories of domestication of livestock species were highly diverse despite the common general feature of deeply divergent maternal lineages. The results further suggest that domestication of local wild prey ungulate animals was a common occurrence during the development of human civilization following the postglacial colonization in different locations of the world, including the high, arid Qinghai-Tibetan Plateau.

Investigation of high cycle and Very-High-Cycle Fatigue behaviors for a structural steel with smooth and notched specimens

The high cycle and Very-High-Cycle Fatigue (VHCF) properties of a structural steel with smooth and notched specimens were studied by employing a rotary bending machine with frequency of 52.5 Hz. For smooth specimens, VHCF failure did occur at fatigue cycles of 7.1 x 10(8) with the related S-N curve of stepwise tendency. Scanning Electron Microscopy (SEM) was used for the observations of the fracture surfaces It shows that for smooth specimens the crack origination is surface mode in the failure regime of less than 10(7) cycles While at VHCF regime, the material failed from the nonmetallic inclusion lies in the interior of material, leading to the formation of fisheye pattern. The dimensions of crack initiation region were measured and discussed with respect to the number of cycles to failure. The mechanism analysis by means of low temperature fracture technique shows that the nonmetallic inclusion in the interior of specimen tends to debond from surrounding matrix and form a crack. The crack propagates and results to the final failure. The stress intensity factor and fatigue strength were calculated to investigate the crack initiation properties. VHCF study on the notched specimens shows that the obtained S-N curve decreases continuously. SEM analysis reveals that multiple crack origins are dominant on specimen surface and that fatigue crack tends to initiate from the surface of the specimen. Based on the fatigue tests and observations, a model of crack initiation was used to describe the transition of fatigue initiation site from subsurface to surface for smooth and notched specimens. The model reveals the influences of load, grain size, inclusion size and surface notch on the crack initiation transition. (C) 2010 Elsevier Ltd. All rights reserved

Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations

Background: The phylogeography of the Y chromosome in Asia previously suggested that modern humans of African origin initially settled in mainland southern East Asia, and about 25,000 30,000 years ago, migrated northward, spreading throughout East Asia. H

More evidence for non-maternal inheritance of mitochondrial DNA?

Background: A single case of paternal co-transmission ofmitochondrial DNA (mtDNA) in humans has been reported so far. Objective: To find potential instances of non-maternal inheritance of mtDNA. Methods: Published medical case studies (of single patients) were searched for irregular mtDNA patterns by comparing the given haplotype information for different clones or tissues with the worldwide mtDNA database as known to date-a method that has proved robust and reliable for the detection of flawed mtDNA sequence data. Results: More than 20 studies were found reporting clear cut instances with mtDNAs of different ancestries in single individuals. As examples, cases are reviewed from recent published reports which, at face value, may be taken as evidence for paternal inheritance of mtDNA or recombination. Conclusions: Multiple types (or recombinant types) of quite dissimilar mitochondrial DNA from different parts of the known mtDNA phylogeny are often reported in single individuals. From re-analyses and corrigenda of forensic mtDNA data, it is apparent that the phenomenon of mixed or mosaic mtDNA can be ascribed solely to contamination and sample mix up.

Multiple Axial Cracks in A Coated Hollow Cylinder due to Thermal Shock

The transient thermal stress problem of an inner-surface-coated hollow cylinder with multiple pre-existing surface cracks contained in the coating is considered. The transient temperature, induced thermal stress, and the crack tip stress intensity factor (SIF) are calculated for the cylinder via finite element method (FEM), which is exposed to convective cooling from the inner surface. As an example, the material pair of a chromium coating and an underlying steel substrate 30CrNi2MoVA is particularly evaluated. Numerical results are obtained for the stress intensity factors as a function of normalized quantities such as time, crack length, convection severity, material constants and crack spacing. (c) 2005 Elsevier Ltd. All rights reserved.

Effective elastic moduli of two-dimensional solids with multiple cracks

An accurate method which directly accounts for the interactions between different microcracks is used for analyzing the elastic problem of multiple cracks solids. The effective elastic moduli for randomly oriented cracks and parallel cracks are evaluated for the representative volume element (RVE) with microcracks in infinite media. The numerical results are compared with those from various micromechanics models and experimental data. These results show that the present method is simple and provides a direct and efficient approach to dealing with elastic solids containing multiple cracks.

Behavior of Multiple Shear Bands in Zr-Based Bulk Metallic Glass

The deformation behavior of Zr41.2Ti13.8Cu12.5Ni10Be22.5 bulk metallic glass was studied by in situ scanning electron microscopy (SEM) quasi-static uniaxial compression tests at room temperature. Multiple shear bands were observed with a large plasticity. Microscopic examination demonstrates that slipping, branching and intersecting of multiple shear bands are the main mechanisms for enhancing the plasticity of this metallic glass. Additionally, nano/micro-scale voids and cracks at the intersecting sites of shear bands and preferential etching of shear bands were observed as well. These observations demonstrated that the formation of shear bands in bulk metallic glasses is resulted mainly from local free volume coalescence.

Interacting multiple cracks in piezoelectric materials

In this paper, a method is presented to calculate the plane electro-elastic fields in piezoelectric materials with multiple cracks. The cracks may be distributed randomly in locations, orientations and sizes. In the method, each crack is treated as a continuous distributed dislocations with the density function to be determined according to the conditions of external loads and crack surfaces. Some numerical examples are given to show the interacting effect among multiple cracks.

Concentrated-Mass Cantilever Enhances Multiple Harmonics In Tapping-Mode Atomic Force Microscopy

The natural frequencies of a cantilever probe can be tuned with an attached concentrated mass to coincide with the higher harmonics generated in a tapping-mode atomic force microscopy by the nonlinear tip-sample interaction force. We provide a comprehensive map to guide the choice of the mass and the position of the attached particle in order to significantly enhance the higher harmonic signals containing information on the material properties. The first three eigenmodes can be simultaneously excited with only one carefully positioned particle of specific mass to enhance multiple harmonics. Accessing the interaction force qualitatively based on the high-sensitive harmonic signals combines the real-time material characterization with the imaging capability. (C) 2008 American Institute of Physics.

Clemaps: Multiple Alignment Of Protein Structures Based On Conformational Letters

CLEMAPS is a tool for multiple alignment of protein structures. It distinguishes itself from other existing algorithms for multiple structure alignment by the use of conformational letters, which are discretized states of 3D segmental structural states. A letter corresponds to a cluster of combinations of three angles formed by C-alpha pseudobonds of four contiguous residues. A substitution matrix called CLESUM is available to measure the similarity between any two such letters. The input 3D structures are first converted to sequences of conformational letters. Each string of a fixed length is then taken as the center seed to search other sequences for neighbors of the seed, which are strings similar to the seed. A seed and its neighbors form a center-star, which corresponds to a fragment set of local structural similarity shared by many proteins. The detection of center-stars using CLESUM is extremely efficient. Local similarity is a necessary, but insufficient, condition for structural alignment. Once center-stars are found, the spatial consistency between any two stars are examined to find consistent star duads using atomic coordinates. Consistent duads are later joined to create a core for multiple alignment, which is further polished to produce the final alignment. The utility of CLEMAPS is tested on various protein structure ensembles.