The ADH1B Arg47His polymorphism in East Asian populations and expansion of rice domestication in history

Background: The emergence of agriculture about 10,000 years ago marks a dramatic change in human evolutionary history. The diet shift in agriculture societies might have a great impact on the genetic makeup of Neolithic human populations. The regionally restricted enrichment of the class I alcohol dehydrogenase sequence polymorphism (ADH1BArg47His) in southern China and the adjacent areas suggests Darwinian positive selection on this genetic locus during Neolithic time though the driving force is yet to be disclosed. Results: We studied a total of 38 populations (2,275 individuals) including Han Chinese, Tibetan and other ethnic populations across China. The geographic distribution of the ADH1B*47His allele in these populations indicates a clear east-to-west cline, and it is dominant in south-eastern populations but rare in Tibetan populations. The molecular dating suggests that the emergence of the ADH1B*47His allele occurred about 10,000 similar to 7,000 years ago. Conclusion: We present genetic evidence of selection on the ADH1BArg47His polymorphism caused by the emergence and expansion of rice domestication in East Asia. The geographic distribution of the ADH1B*47His allele in East Asia is consistent with the unearthed culture relic sites of rice domestication in China. The estimated origin time of ADH1B*47His allele in those populations coincides with the time of origin and expansion of Neolithic agriculture in southern China.

Evolutionary history of the mtDNA 9-bp deletion in Chinese populations and its relevance to the peopling of east and southeast Asia

In total, 1218 Chinese from twelve ethnic groups and nine Han geographic groups were screened for the mtDNA 9-bp deletion motif. The frequency of the 9-bp deletion in all samples was 14.7% but ranged from 0% to 32% in the various ethnic groups. Three individuals had a triplication of the 9-bp segment. Phylogenetic and demographic analyses of the mtDNA hypervariable segment 1 (HVS1) sequences suggest that the 9-bp deletion occurred more than once in China. The majority of the Chinese deletion:haplotypes (about 90%) have a common origin as a mutational event following an initial expansion of modem humans in eastern Asia. Other deletion haplotypes and the three haplotypes with a 9-bp triplication may have arisen independently in the Chinese, presumably by replication error. HVS1 haplotype analysis suggests two possible migration routes of the 9-bp deletion in east and southeast Asia. Both migrations originated in China with one route leading to the Pacific Islands via Taiwan, the other to southeast Asia and possibly the Nicobar Islands. Along both routes of peopling, a decrease in HVS1 diversity of the mtDNA haplotypes is observed. The "Polynesian motif (16217T/C, 16247A/G, and 16261C/T)" and the 16140T/C, 16266C/A, or C/G polymorphisms appear specific to each migration route.

Genetic diversity and population history of golden monkeys (Rhinopithecus roxellana)

Golden monkey (Rhinopithecus roxellana), namely the snub-nosed monkey, is a well-known endangered primate, which distributes only in the central part of mainland China. As an effort to understand the current genetic status as well as population history of this species, we collected a sample of 32 individuals from four different regions, which cover the major habitat of this species. Forty-four allozyme loci were surveyed in our study by allozyme electrophoresis, none of which was found to be polymorphic. The void of polymorphism compared with that of other nonhuman primates is surprising particularly considering that the current population size is many times larger than that of some other endangered species. Since many independent loci are surveyed in this Study, the most plausible explanation for our observation is that the population has experienced a recent bottleneck. We used a coalescent approach to explore various scenarios of population bottleneck and concluded that the most recent bottleneck could have happened within the last 15,000 years. Moreover, the proposed simulation approach could be useful to researchers who need to analyze the non- or low-polymorphism data.

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.

New species of Doliodrilus and other Limnodriloidinae (Oligochaeta, Tubificidae) from Hainan and other parts of the north-west Pacific Ocean

Thirteen species of Limnodriloidinae (Tubificidae) are recorded from marine and brackish-water habitats of Hainan Island, southern China, including 11 species of Doliodrilus and two species belonging to Limnodriloides . Eight species are new to science: D. bisaccus sp. n. (types from Japan), D. longidentatus sp. n. (types from Hong Kong), D. ciliatus sp. n., D. adiacens sp. n., D. fibrisaccus sp. n. (also from Fiji), D. brachyductus sp. n., D. bidolium sp. n. and D. chinensis sp. n. In addition, material of D. puertoricensis Erseus and Milligan, 1988, from New Caledonia, is briefly described. This study shows that Doliodrilus is unexpectedly species-rich in Asian seas, in particular, around Hainan. Including an unnamed species from this island, the known members of this genus increase from three to 12.

Life history characteristics of three types of females in Brachionus calyciflorus Pallas (Rotifera) fed different algae

This study describes the life history characteristics of amictic, unfertilized mictic and fertilized mictic females of the rotifer Brachionus calyciflorus cultured individually on two different algae at 0.1 mg ml(-1) food concentration and 27 degreesC. The duration of the juvenile period of amictic females was significantly shorter on Chlorella pyrenoidosa Chick than on Scenedesmus obliquus Kutz or both algae together. The duration of the juvenile period of unfertilized mictic females was significantly longer, and the number of eggs produced by amictic females was significantly larger on Chlorella pyrenoidosa than on S. obliquus. When fed the same type of alga, the duration of the juvenile period of the fertilized mictic females was the longest among the three types of females, and the durations of the reproductive period of the amictic females and the post-reproductive period of the fertilized mictic females were longer than, or equal to those of the other two types of females, respectively. The number of eggs produced by an unfertilized mictic female was the largest among the three types of females, and that of amictic females was larger than or equal to that of fertilized mictic females, depending on the type of diet.

Characterization of the life history of Bangia fuscopurpurea (Bangiaceae, Rhodophyta) in connection with its cultivation in China

Bangia fuscopurpurea (Rhodophyta) was cultivated in Putian (Fujian province, China). The characteristics of the life history concerned with cultivation were investigated and the cultivation procedure was presented. The gametophytic phase (thallus) and the sporophytic phase (conchocelis) occurred alternately in the life history of B. fuscopurpurea. Young thalli produced archeospores, and the number depended on the environmental factors. Temperature affected the number of archeospore release and percent of germination, and photo flux density (PFD) mainly affected the time of spore release and germination. Thalli matured from December to February and developed into the conchocelis phase through sexual reproduction. The conchocelis grown in shells had three developmental stages: vegetative conchocelis, conchosporangiall formation and conchospore formation. Pit-connections were present in the first 2 stages but absent after conchospore formation. Vegetative conchocelis and conchosporangial. branches can transform into each other. However, conchospores only developed into the gametophytic phase. Cultivation of B. fuscopurpurea was based on characterization of the life history, consisting of 3 steps: zygotospores collection, indoor cultivation of conchocelis and outdoor cultivation of thalli. Young thalli that developed from conchospores produced numerous archeospores before December. Over 90% of the crop was from the development of archeospores. The results indicated that conchosporelings were a good source of archeospores, and the development of the large quantity of archeospores acted as a more prevailing means to increase the population size. (C) 2008 Elsevier B.V. All rights reserved.

The history of the Yangtze River entering sea since the last glacial maximum: a review and look forward

This review paper provides a brief review on the development of ideas in the fields of the sea level change of the ECS (East China Sea), the history of the Yangtze River entering the sea and paleochannels in the shelf of the ECS since the Last Glacial Maximum (LGM). The paper summarizes two opposite theories about the Yangtze River entering the sea during the LGM. One theory is that the Yangtze River input a lacustrine in the north of Jiangsu province which was defunct in middle Holocene, and the river was once dry. The other was that the Yangtze River still existed and entered into the Okinawa Trough during the LGM, but scholars share different opinions on which course the river ran across and which place the river input the trough. This paper concludes future work is to study the evolution of the Yangtze River and the paleoclimate and the corresponding events as a whole from the view of regional and even global change, and more attention should be paid to the study on mud sediment, the Yangtze River's response to the changes in climate and sea-level, and the channel metamorphosis.

Genetic variation and phylogeographic history of Picea likiangensis revealed by RAPD markers

Repeated cycles of retreat and recolonization during the Quaternary ice ages are thought to have greatly influenced current species distributions and their genetic diversity. It remains unclear how this climatic oscillation has affected the distribution of genetic diversity between populations of wind-pollinated conifers in the Qinghai-Tibetan region. In this study, we investigated the within-species genetic diversity and phylogenetic relationships of Picea likiangensis, a dominant forest species in this region using polymorphic DNA (RAPD) markers. Our results suggest that this species has high overall genetic diversity, with 85.42% of loci being polymorphic and an average expected heterozygosity (H (E)) of 0.239. However, there were relatively low levels of polymorphism at population levels and the differences between populations were not significant, with percentages of polymorphic bands (PPB) ranging from 46.88 to 69.76%, Nei's gene diversity (H (E)) from 0.179 to 0.289 and Shannon's indices (Hpop) from 0.267 to 0.421. In accordance with our proposed hypothesis, a high level of genetic differentiation among populations was detected based on Nei's genetic diversity (G (ST) = 0.256) and AMOVA analysis (Phi (st) = 0.236). Gene flow between populations was found to be limited (Nm = 1.4532) and far lower than reported for other conifer species with wide distribution ranges from other regions. No clusters corresponding to three morphological varieties found in the south, north and west, respectively, were detected in either UPGMA or PCO analyses. Our results suggest that this species may have had different refugia during the glacial stages in the southern region and that the northern variety may have multiple origins from these different refugia.