The Y chromosomal haplogroup determined from single nucleotide polymorphism (SNP) combinations is a valuable genetic marker to study ancestral male lineage and ethical distribution. Next-generation sequencing has been developed for widely diverse genetics fields. For this study, we demonstrate 34 Y-SNP typing employing the Ion PGM™ system to perform haplogrouping. DNA libraries were constructed using the HID-Ion AmpliSeq™ Identity Panel. Emulsion PCR was performed, then DNA sequences were analyzed on the Ion 314 and 316 Chip Kit v2. Some difficulties became apparent during the analytic processes. No-call was reported at rs2032599 and M479 in six samples, in which the least coverage was observed at M479. A minor misreading occurred at rs2032631 and M479. A real time PCR experiment using other pairs of oligonucleotide primers showed that these events might result from the flanking sequence. Finally, Y haplogroup was determined completely for 81 unrelated males including Japanese (n=59) and Malay (n=22) subjects. The allelic divergence differed between the two populations. In comparison with the conventional Sanger method, next-generation sequencing provides a comprehensive SNP analysis with convenient procedures, but further system improvement is necessary.
Macaca fascicularis fascicularis is distributed over a wide area of Southeast Asia. Thailand is located at the center of their distribution range and is the bridge connecting the two biogeographic regions of Indochina and Sunda. However, only a few genetic studies have explored the macaques in this region. To shed some light on the evolutionary history of M. f. fascicularis, including hybridization with M. mulatta, M. f. fascicularis and M. mulatta samples of known origins throughout Thailand and the vicinity were analyzed by molecular phylogenetics using mitochondrial DNA (mtDNA), including the hypervariable region 1, and Y-chromosomal DNA, including SRY and TSPY genes. The mtDNA phylogenetic analysis divided M. f. fascicularis into five subclades (Insular Indonesia, Sundaic Thai Gulf, Vietnam, Sundaic Andaman sea coast, and Indochina) and revealed genetic differentiation between the two sides of the Thai peninsula, which had previously been reported as a single group of Malay peninsular macaques. From the estimated divergence time of the Sundaic Andaman sea coast subclade, it is proposed that after M. f. fascicularis dispersed throughout Southeast Asia, some populations on the south-easternmost Indochina (eastern Thailand, southern Cambodia and southern Vietnam at the present time) migrated south-westwards across the land bridge, which was exposed during the glacial period of the late Pleistocene epoch, to the southernmost Thailand/northern peninsular Malaysia. Then, some of them migrated north and south to colonize the Thai Andaman sea coast and northern Sumatra, respectively. The SRY-TSPY phylogenetic analysis suggested that male-mediated gene flow from M. mulatta southward to M. f. fascicularis was restricted south of, but close to, the Isthmus of Kra. There was a strong impact of the geographical factors in Thailand, such as the Isthmus of Kra, Nakhon Si Thammarat, and Phuket ranges and Sundaland, on M. f. fascicularis biogeography and their hybridization with M. mulatta.
Since the early 1950’s, Singapore is internationally known as the guppy-breeding centre. At least 40 different colour varieties of guppies are cultured in Singapore, with each farm specialising in 10 to 15 varieties. These fancy varieties have been developed by skilful farmers through intensive and continual selective breeding. Genes controlling background body pigmentation such as albino (a), blond (b), gold (g) and blue (r) are autosomally inherited and recessive to their wild-type alleles which produce drab olive-brown background coloration. Colour patterns which are superimposed onto wild-type background coloration are due to genes located on the sex chromosomes. These
sex-linked colour genes are dominant and sex-limited to males as their expression requires male hormones. Y-linked colour pattern genes carried by males are inherited only along the paternal line while X-linked genes are present in both sexes. Among the guppy varieties produced locally, only two Y-linked genes, Ssb and Sst, that control snakeskin tail and body patterns, respectively, have been found in varieties with snakeskin-like reticulations. Single colour genes that are both X- and Y-linked produce red (Rdt), blue (Blt), green (Grt), black (Bt) and variegated (Var) patterns
on the caudal fin. The black caudal-peduncle of the Tuxedo variety is the result of Bcp, a gene that is both X- and Ylinked. Different combinations of colour pattern genes and background pigmentation genes as well as interactions among them give rise to various colour phenotypes. For
instance, the inclusion of Bcp in Snakeskin varieties causes black reticulations on the tail fin to be replaced by large, coarse black spots. Neon coloration is produced by interactions between the Ln (light turquoise) gene with Blt, Rdt and Bcp.