A new species of the porcellanid genus Raphidopus Stimpson, 1858, is described on the basis of specimens from Penang and Kuala Selangor, Peninsular Malaysia. Raphidopus brevipes n. sp. is distinguished from its allied congeners, R. indicus Henderson, 1893 and R. johnsoni Ng Nakasone, 1994, by the proportionally narrower carapace and stouter ambulatory legs, as well as the different dentition on the cutting edge of the dactylus of the larger cheliped. Raphidopus johnsoni, previously known only by the holotype from Singapore, is now also recorded from Phuket (Thailand) and Java (Indonesia). Raphidopus indicus and R. johnsoni are rediagnosed on the basis of the respective type material and other specimens. A key to species of the genus Raphidopus is provided.
Five species of the genus Polyonyx Stimpson, 1858 are reported from southern Japan, the Philippines, Singapore, and Peninsular Malaysia. All of them belong to the P. sinensis group, which is morphologically defined by having the dactyli of the ambulatory legs each with the dorsal claw being much smaller than the ventral claw. Two species are described as new to science, one each from Peninsular Malaysia and the Ryukyu Islands in Japan, and their affinities are discussed. Polyonyx boucheti Osawa, 2007, P. heok Osawa Ng, 2016, and P. thai Werding, 2001, are also newly reported from southern Japan, the Philippines, and Singapore. A key to the Indo-West Pacific species of the P. sinensis group is provided.
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.
Closely linked groups of markers on the X chromosome are very useful for testing complex kinship relationships involving X-STR transmission. The Argus X-12 kit, a unique commercially available kit, can obtain haplotypes of 4 linkage groups (LGs) consisting of 3 markers. Although many population data have been reported for forensic purposes, differences in discrimination ability exist between LG1 and LG2, 3, and 4 in East Asian populations, and the data of this kit would become more useful if the discrimination ability of the latter groups were increased. Therefore, for matches found using this kit for some linkage group data, then to increase the identification ability, we additionally introduced 13 X-STR loci and established a method allowing comparison using data from 25 loci. The 13X-STRs add two locus data to each of LG2, 3, and 4, and also add two closely linked group (CLG) data between LG2 and 3 and LG3 and 4 in one multiplex PCR. Assessment of this method for a Malay population for which data by Argus X-12 had already been reported showed that the frequencies of distinct haplotypes in LG2, 3, and 4 were increased by 33.0-42.6 %, and frequencies of unique haplotypes increased by 45.4-59.2 %. The respective haplotype diversity values of the additional 3-locus and 4-locus CLGs were 0.9838 and 0.9939, which helps to improve discriminatory power and to predict recombination locations on the X chromosome. Although we have been testing these loci with Japanese subjects, this system would also be useful for the Malay population.