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.

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.

The Genomes of Oryza sativa: A history of duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped superscaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000 - 40,000. Only 2% - 3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism ( SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

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.

Ancient Chinese algorithm: The Ying Buzu Shu (method of surplus and deficiency) vs Newton iteration method

Air exploratory discussion of an ancient Chinese algorithm, the Ying Buzu Shu, in about 2nd century BC, known as the rule of double false position in the West is given. In addition to pointing out that the rule of double false position is actually a translation version of the ancient Chinese algorithm, a comparison with well-known Newton iteration method is also made. If derivative is introduced, the ancient Chinese algorithm reduces to the Newton method. A modification of the ancient Chinese algorithm is also proposed, and some of applications to nonlinear oscillators are illustrated.

Elastodynamic stress intensity factor history for a semi-infinite crack under three-dimensional transient loading

The dynamic stress intensity factor history for a semi-infinite crack in an otherwise unbounded elastic body is analyzed. The crack is subjected to a pair of suddenly-applied point loadings on its faces at a distance L away from the crack tip. The exact expression for the mode I stress intensity factor as a function of time is obtained. The method of solution is based on the direct application of integral transforms, the Wiener-Hopf technique and the Cagniard-de Hoop method. Due to the existence of the characteristic length in loading this problem was long believed a knotty problem. Some features of the solutions are discussed and graphical result for numerical computation is presented.

中国力学学会史 = A history of Chinese society of theoretical and applied mechanics

《中国力学学会史》是《中国学会史丛书》之一。是一部全面系统记述中国力学学会建立与发展历程的专著。 《中国力学学会史》全书30万字，书中不但重点对学会的初创情况、发展过程、组织建设、学术交流、分支机构等进行了专门介绍，还特别收录了记述学会重大活动情况的大事记、名人与学会发展的丰富资料和一些极有史料价值的历史照片，旨在反映学会在不同时期的活动概况及其在中国力学界中发挥的桥梁与纽带作用。 中国力学学会是中国科协的组成部分，也是我国著名的学术团体之一，仅以此书的编著出版，纪念中国科协成立50周年和中国力学学会成立50多周年。本书可供力学界和科技界有关部门及工作者、各学会相关人员、大专院校师生参阅，也可作为组织和开展国内外学术交流研究的参考资料。