Cultivated rice, Oryza sativa L., represents the world's most important staple food crop, feeding more than half of the human population. Despite this essential role in world agriculture, the history of cultivated rice's domestication from its wild ancestor, Oryza rufipogon, remains unclear. In this study, DNA sequence variation in three gene regions is examined in a phylogeographic approach to investigate the domestication of cultivated rice. Results indicate that India and Indochina may represent the ancestral center of diversity for O. rufipogon. Additionally, the data suggest that cultivated rice was domesticated at least twice from different O. rufipogon populations and that the products of these two independent domestication events are the two major rice varieties, Oryza sativa indica and Oryza sativa japonica. Based on this geographical analysis, O. sativa indica was domesticated within a region south of the Himalaya mountain range, likely eastern India, Myanmar, and Thailand, whereas O. sativa japonica was domesticated from wild rice in southern China.

The vegetation of the northeast Qinghai-Tibetan Plateau is dominated by alpine meadow and desert-steppe with sparse forests scattered within it. To obtain a better understanding of the phylogeography of one constituent species of the forests in this region, we examined chloroplast trnT-trnF and trnS-trnG sequence variation within Juniperus przewalskii, a key endemic tree species. Sequence data were obtained from 392 trees in 20 populations covering the entire distribution range of the species. Six cpDNA haplotypes were identified. Significant population subdivision was detected (G(ST) = 0.772, N(ST) = 0.834), suggesting low levels of recurrent gene flow among populations and significant phylogeographic structure (N(ST) > G(ST), P < 0.05). Eight of the nine disjunct populations surveyed on the high-elevation northeast plateau were fixed for a single haplotype (A), while the remaining, more westerly population, contained the same haplotype at high frequency together with two low frequency haplotypes (C and F). In contrast, most populations that occurred at lower altitudes at the plateau edge were fixed or nearly fixed for one of two haplotypes, A or E. However, two plateau edge populations had haplotype compositions different from the rest. In one, four haplotypes (A, B, D and E) were present at approximately equivalent frequencies, which might reflect a larger refugium in the area of this population during the last glacial period. Phylogenetic analysis indicated that the most widely distributed haplotype A is not ancestral to other haplotypes. The contrasting phylogeographic structures of the haplotype-rich plateau edge area and the almost haplotype-uniform plateau platform region indicate that the plateau platform was recolonized by J. przewalskii during the most recent postglacial period. This is supported by the findings of a nested clade analysis, which inferred that postglacial range expansion from the plateau edge followed by recent fragmentation is largely responsible for the present-day spatial distribution of cpDNA haplotypes within the species.

Next-generation-sequencing (NGS) has revolutionized the field of genome assembly because of its much higher data throughput and much lower cost compared with traditional Sanger sequencing. However, NGS poses new computational challenges to de novo genome assembly. Among the challenges, GC bias in NGS data is known to aggravate genome assembly. However, it is not clear to what extent GC bias affects genome assembly in general. In this work, we conduct a systematic analysis on the effects of GC bias on genome assembly. Our analyses reveal that GC bias only lowers assembly completeness when the degree of GC bias is above a threshold. At a strong GC bias, the assembly fragmentation due to GC bias can be explained by the low coverage of reads in the GC-poor or GC-rich regions of a genome. This effect is observed for all the assemblers under study. Increasing the total amount of NGS data thus rescues the assembly fragmentation because of GC bias. However, the amount of data needed for a full rescue depends on the distribution of GC contents. Both low and high coverage depths due to GC bias lower the accuracy of assembly. These pieces of information provide guidance toward a better de novo genome assembly in the presence of GC bias.

The hepatitis D virus (HDV) genotypes in 46 HDVinfected patients and 12 prostitutes were screened with XhoI restriction fragment length polymorphism (RFLP) analysis of reverse transcription PCR products of viral genomes and verified by phylogenetic analysis. The amplificates of three (6n5 %) patients and two (17 %) prostitutes showed a novel RFLP pattern different from those of the three known

Taiwan and Ryukyus constitute an archipelago lying on the western rim of the Pacific Ocean. In contrast to volcanic islands that often arise sequentially, these continental islands emerged almost simultaneously as the Luzon arc collided with the Eurasian margin some 9 million years ago (Mya). Taiwan and Ryukyus attained their modern features and their current flora and fauna from the adjacent mainland and from tropical Asia only 5–6 Mya. Quaternary glaciation led to a drop in sea level of the South China Sea and a land bridge that connected the Taiwan‐Ryukyu Archipelago to the mainland, which allowed plants and animals to migrate across what was previously ocean. These islands provided refugia for northern species that migrated south during glacial periods, as indicated by unanticipated high levels of genetic diversity in island populations of plants like Cunninghamia and Pinus. For most insect‐pollinated species, allozymes and nuclear DNA markers indicate significant genetic differentiation between populations and between geographical regions of the archipelago. In contrast, organelle based DNA markers suggest a migrant‐pool model, where colonists are recruited from a random sample of source populations. Consistent with this model, low elevation species have high genetic heterogeneity within populations and low levels of genetic differentiation between populations. In contrast, colonization of alpine species appeared to follow a phalanx model due to the limited availability of high elevation habitats. Genetic differentiation was detected between fragmented populations of the alpine species. A scenario of stepwise colonization from the mainland to near and then distant islands remains to be tested, although several studies indicate no such pattern. These conflicting results challenge the ability to define clear conservation criteria for the rare plant species of the archipelago.