Ryota Suzuki

Abstract Summary: Pvclust is an add-on package for a statistical software R to assess the uncertainty in hierarchical cluster analysis. Pvclust can be used easily for general statistical problems, such as DNA microarray analysis, to perform the bootstrap analysis of clustering, which has been popular in phylogenetic analysis. Pvclust calculates probability values (p-values) for each cluster using bootstrap resampling techniques. Two types of p-values are available: approximately unbiased (AU) p-value and bootstrap probability (BP) value. Multiscale bootstrap resampling is used for the calculation of AU p-value, which has superiority in bias over BP value calculated by the ordinary bootstrap resampling. In addition the computation time can be enormously decreased with parallel computing option. Availability: The program is freely distributed under GNU General Public License (GPL) and can directly be installed from CRAN (), the official R package archive. The instruction and program source code are available at Contact: ryota.suzuki@is.titech.ac.jp

To construct an East Asia mitochondrial DNA (mtDNA) phylogeny, we sequenced the complete mitochondrial genomes of 672 Japanese individuals (http://www.giib.or.jp/mtsnp/index_e.html). This allowed us to perform a phylogenetic analysis with a pool of 942 Asiatic sequences. New clades and subclades emerged from the Japanese data. On the basis of this unequivocal phylogeny, we classified 4713 Asian partial mitochondrial sequences, with <10% ambiguity. Applying population and phylogeographic methods, we used these sequences to shed light on the controversial issue of the peopling of Japan. Population-based comparisons confirmed that present-day Japanese have their closest genetic affinity to northern Asian populations, especially to Koreans, which finding is congruent with the proposed Continental gene flow to Japan after the Yayoi period. This phylogeographic approach unraveled a high degree of differentiation in Paleolithic Japanese. Ancient southern and northern migrations were detected based on the existence of basic M and N lineages in Ryukyuans and Ainu. Direct connections with Tibet, parallel to those found for the Y-chromosome, were also apparent. Furthermore, the highest diversity found in Japan for some derived clades suggests that Japan could be included in an area of migratory expansion to Continental Asia. All the theories that have been proposed up to now to explain the peopling of Japan seem insufficient to accommodate fully this complex picture.

Beluga whales use calls to convey various information to group members. Is this communication similar to humans? We addressed this question by using the framework of stimulus equivalence. Stimulus equivalence consists of three phases: if the animal is trained to match A to B and B to C, symmetry is demonstrated by matching BA and CB, transitivity by matching AC, and equivalence by matching CA. We tested the spontaneous establishment of cross-modal stimulus equivalence between visual and auditory symbols in a beluga whale nicknamed Nack. Nack could make symmetrical choices in novel objects untrained. Moreover, visual/auditory cross-modal transitivity was formed spontaneously. Nack succeeded in six tasks, including an untrained task concerning stimulus equivalence. We conclude that Nack spontaneously formed cross-modal stimulus equivalence between visual and auditory symbols. Cross-modal stimulus equivalence was considered to exist only in humans because of linguistic faculty; however, Nack exhibited the same understanding as humans.