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Chan Y.-C.,Max Planck Institute for Evolutionary Anthropology | Roos C.,German Primate Center | Inoue-Murayama M.,Kyoto University | Inoue E.,Kyoto University | And 2 more authors.
BMC Evolutionary Biology | Year: 2012

Background: The evolutionary relationships of closely related species have long been of interest to biologists since these species experienced different evolutionary processes in a relatively short period of time. Comparison of phylogenies inferred from DNA sequences with differing inheritance patterns, such as mitochondrial, autosomal, and X and Y chromosomal loci, can provide more comprehensive inferences of the evolutionary histories of species. Gibbons, especially the genus Hylobates, are particularly intriguing as they consist of multiple closely related species which emerged rapidly and live in close geographic proximity. Our current understanding of relationships among Hylobates species is largely based on data from the maternally-inherited mitochondrial DNAs (mtDNAs). Results: To infer the paternal histories of gibbon taxa, we sequenced multiple Y chromosomal loci from 26 gibbons representing 10 species. As expected, we find levels of sequence variation some five times lower than observed for the mitochondrial genome (mtgenome). Although our Y chromosome phylogenetic tree shows relatively low resolution compared to the mtgenome tree, our results are consistent with the monophyly of gibbon genera suggested by the mtgenome tree. In a comparison of the molecular dating of divergences and on the branching patterns of phylogeny trees between mtgenome and Y chromosome data, we found: 1) the inferred divergence estimates were more recent for the Y chromosome than for the mtgenome, 2) the species H. lar and H. pileatus are monophyletic in the mtgenome phylogeny, respectively, but a H. pileatus individual falls into the H. lar Y chromosome clade. Conclusions: Based on the ∼6.4 kb of Y chromosomal DNA sequence data generated for each of the 26 individuals in this study, we provide molecular inferences on gibbon and particularly on Hylobates evolution complementary to those from mtDNA data. Overall, our results illustrate the utility of comparative studies of loci with different inheritance patterns for investigating potential sex specific processes on the evolutionary histories of closely related taxa, and emphasize the need for further sampling of gibbons of known provenance. © 2012 Chan et al.; licensee BioMed Central Ltd. Source

Jang-Liaw N.-H.,Taipei Zoo | Jang-Liaw N.-H.,National Taiwan Ocean University | Wen Z.-H.,National Taiwan Ocean University | Chen I.-S.,National Taiwan Ocean University
Mitochondrial DNA | Year: 2016

Here we describe the complete mitochondrial genome sequence of endangered minnow, Metzia mesembrinum, which collected from Kimnen island, Fujian Province of Taiwan. The circular mitogenome (16,603 bp) consists of 13 protein coding, 22 tRNA, 2 rRNA genes and 1 control region. It has the typical vertebrate mitochondrial gene arrangement. The overall base composition in descending order is A (32.0%), T (27.1%), C (25.2%), G (15.7%) with rather higher AT content as 59.1%. Yuan et al. reported the complete mitogenome (KF997093) of M. mesembrimum from southern China that may belong to other congeneric species, but not exactly M. mesembrinum collected from either southern Fujian or Taiwan. The well-identified species sequence data of Metzia mesembrinum would be rather beneficial for further phlyogenetic approach for congeneric species in East and Southeast Asia. © 2014 Informa UK Ltd. Source

Chan Y.-C.,Max Planck Institute for Evolutionary Anthropology | Roos C.,German Primate Center | Inoue-Murayama M.,Kyoto University | Inoue E.,Kyoto University | And 3 more authors.
BMC Evolutionary Biology | Year: 2013

Background: Gibbons (Hylobatidae) are the most diverse group of living apes. They exist as geographically-contiguous species which diverged more rapidly than did their close relatives, the great apes (Hominidae). Of the four extant gibbon genera, the evolutionary histories of two polyspecific genera, Hylobates and Nomascus, have been the particular focus of research but the DNA sequence data used was largely derived from the maternally inherited mitochondrial DNA (mtDNA) locus. Results: To investigate the evolutionary relationships and divergence processes of gibbon species, particularly those of the Hylobates genus, we produced and analyzed a total of 11.5 kb DNA of sequence at 14 biparentally inherited autosomal loci. We find that on average gibbon genera have a high average sequence diversity but a lower degree of genetic differentiation as compared to great ape genera. Our multilocus species tree features H. pileatus in a basal position and a grouping of the four Sundaic island species (H. agilis, H. klossii, H. moloch and H. muelleri). We conducted pairwise comparisons based on an isolation-with-migration (IM) model and detect signals of asymmetric gene flow between H. lar and H. moloch, between H. agilis and H. muelleri, and between N. leucogenys and N. siki. Conclusions: Our multilocus analyses provide inferences of gibbon evolutionary histories complementary to those based on single gene data. The results of IM analyses suggest that the divergence processes of gibbons may be accompanied by gene flow. Future studies using analyses of multi-population model with samples of known provenance for Hylobates and Nomascus species would expand the understanding of histories of gene flow during divergences for these two gibbon genera. © 2013 Chan et al.; licensee BioMed Central Ltd. Source

Chang C.-H.,National Chiao Tung University | Chang C.-H.,Academia Sinica, Taiwan | Shao K.-T.,Academia Sinica, Taiwan | Lin Y.-S.,National Chiao Tung University | And 2 more authors.
Mitochondrial DNA | Year: 2014

Here we describe the complete mitochondrial genome sequence of the megamouth shark, Megachasma pelagios, which is an extremely rare species of deepwater shark. The circle genome (16,694 bp) consists of 13 protein coding, 22 tRNA, 2 rRNA genes and 1 control region. It has the typical vertebrate mitochondrial gene arrangement. © 2014 Informa UK Ltd. Source

Wu P.C.,Academia Sinica, Taiwan | Wu P.C.,National Tsing Hua University | Chen J.-B.,Academia Sinica, Taiwan | Kawamura S.,University of Tokyo | And 6 more authors.
Immunogenetics | Year: 2012

Membrane-bound IgE (mIgE) on B lymphocytes is essential for IgE production. Earlier studies showed that the ε chain of mIgE (mε) on human B cells has a "long" isoform, with an extra "CεmX" domain of 52 amino acid (aa) residues between the CH4 domain and the membrane-anchor segment, as compared to the conventional "short" isoform. Because CεmX provides an antigenic site for targeting IgE-expressing B cells to down-regulate IgE production in patients with allergy, analysis of CεmX in various animals is of great interest. Hence, we analyzed the ε Ig gene, in particular, its membrane exon regions encoding the membrane anchor peptide segment and CεmX domain, of 26 species of the order Primates and 12 species of seven non-Primate orders using data obtained experimentally or retrieved from GenBank. Our analyses reveal the unexpected finding that the genes of three extant tarsier species do not contain the membrane exons for mIgE. Another striking finding is that early evolved Strepsirhini primates such as lemurs and lorises do not have gene segments for the long isoform, whereas New World monkeys such as marmosets and squirrel monkeys allow the transcription of only the long isoform. In Old World monkeys and apes, including humans, the ε gene allows the transcription of both isoforms. This work thus reveals the dramatic differences in the gene segment encoding the mε C terminal region among the four major primate lineages: the Strepsirhini primates, the tarsiers, New World monkeys, and Old World monkeys and apes/humans. © Springer-Verlag 2011. Source

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