Journal of Phylogenetics & Evolutionary Biology

Bats are well known for their role as reservoirs of viral diseases. Previous studies have reported the presence of endogenous gamma and betaretrovirus in diverse species of bats. Here, we characterize one of these lineages- Pteropus vampyrus endogenous betaretrovirus namely PvEB in depth describing the genomic organization, age estimation and phylogenetic approaches to examine the origin and history of this virus. Phylogenetic analysis of gag, pol and full genome sequence has placed PvEB robustly within the betaretrovirus genus. Subsequently, PvEB was estimated to invade the bat genome since 1.5-8.8mya. The results of bioinformatics analysis were verified through amplification of the PvEB reverse transcriptase gene with the size of 700bp. With these findings together with the previous report, it is evident that PvEB is a member of type D betaretrovirus group.

Aquaporins are a super family of major intrinsic proteins, which facilitate the fast and passive movement of water across the cell membrane. This study presented genome-wide identification, characterization and functional prediction of aquaporins in maize using bioinformatics. A total of 41 non-redundant putative aquaporins were identified and were classified into four subfamilies: 18 TIPs, 12 PIPs, 8 NIPs and 3 SIPs. The finding reveals that exon-intron organization were conserved within subfamilies. Several transmembrane domains(TM1-TM6) were predicted by analyzing of conserved domains and motifs, along with various selectivity filters(ar/R). The functional prediction demonstrated ZmAQPs roles in regulation of multiple compounds i.e. water, glycerol, carbohydrates, metal ions and others small solutes. Furthermore, ZmAQPs were the crucial constituent of membranous structure such as plasma membrane and vacuolar membrane etc. These results deliver valuable information to address function of ZmAQPs as well as provide basic data for the improvement of plant growth and development.

Ancistrus is one of the most diverse genera in the Ancistrini tribe, with 64 nominal species. The group is characterized by high cytogenetic variability; the diploid number of chromosomes ranges from 2n = 34 to 2n = 54. Ancistrus is widely distributed in the basins of the Uruguay, Paraguay, and Amazonian rivers; the latter two regions show the greatest diversity of Ancistrus species and karyotypes. Despite these characteristics, the group includes species for which taxonomic identification is difficult, and phylogenetic relationships and phylogeographic patterns, especially in the Paraguay and Amazon basins, have not yet been revealed. In this study, we determined the phylogenetic and phylogeographic relationships among the Ancistrus lineages in these regions. In particular, 93 concatenated sequences of mitochondrial ATPase 6/8 and COI as well as nuclear Rag2 were used for a phylogenetic analysis, and ATPase 6/8 were used for a phylogeographic analysis. The topology generated by the Bayesian method included three distinct clades subdivided into 21 groups. The clades indicated a monophyletic relationship among the lineages from the Amazon and Paraguay basins. The 21 groups had a high average genetic distance (8.4%) and were structured genetically. In the haplotype network, eight large groups were observed, seven belonging to the Paraguay basin and one corresponding to the Amazon basin, and no haplotypes were shared between the two basins. These results indicate that Ancistrus lineages form a monophyletic unit in the Paraguay and Amazon basins, and these lineages have a high level of divergence and genetic isolation. These results corroborate the existence of cryptic species in the region and emphasize the need for a taxonomic revision of the genus in these basins.

There is a consensus that gene flow characterizing modern Mainland Chinese arrived in Taiwan during the last 400 years, mostly from East China. However, primary genetic studies of ancient human remains of the middle Neolithic era, revealing inconsistencies between the archaic genes profile and that of modern Mainland Chinese, raised debates about the time of arrival of modern Chinese in Taiwan.

To resolve this problem, this study focuses on the analysis of 3000 years BP human remains excavated from the Neolithic east coast archeological Ling-Ding site II near Hualien in Taiwan. The mitochondrial DNA (mtDNA) recovered from five archeological human remains was analyzed to elucidate their genealogy, and to characterize their genetic relationship with the present-day aboriginal and non-aboriginal people of Taiwan.

Five mtDNA haplogroups were characterized from the Ling-Ding site II skeletons, C4a2, N9a1, B4c1b2a, Z, and B4b. Except for mtDNA haplogroups B4c1b2a, commonly seen among the present-day central Taiwan Aborigines and scarce in the heavily sinicised Taiwan western plain tribes, all other haplogroups were common to urban Taiwanese and modern Mainland Chinese. It is proposed that a middle Neolithic gene flow, characterizing Modern Mainland East Asians, was introduced to Taiwan by settlers who reached the East coast of Taiwan in Hualien (Ling- Ding site II) and co-habited with Taiwan Mountain tribe Aborigines. The findings of this study may be relevant for the understanding of the middle Neolithic peopling of Taiwan by non-Austronesian speakers.