Tree-Structured Stick Breaking Processes for Hierarchical Data

Many data are naturally modeled by an unobserved hierarchical structure. In this paper we propose a flexible nonparametric prior over unknown data hierarchies. The approach uses nested stick-breaking processes to allow for trees of unbounded width and depth, where data can live at any node and are infinitely exchangeable. One can view our model as providing infinite mixtures where the components have a dependency structure corresponding to an evolutionary diffusion down a tree. By using a stick-breaking approach, we can apply Markov chain Monte Carlo methods based on slice sampling to perform Bayesian inference and simulate from the posterior distribution on trees. We apply our method to hierarchical clustering of images and topic modeling of text data.

The freshwater zooplankton of Sri Lanka, with a discussion of tropical freshwater zooplankton composition

Based on the study of over 500 zooplankton samples collected in Sri Lanka during 1965-1974, the species composition from different habitats is analysed. The zooplankton assemblage is typically tropical with relatively few species of Cladocera and Copepoda. The Rotifera include a large number of species of the genus Brachionus. The limnetic zooplankton resembles the pond zooplankton closely in that all the eurytopic species found in the different types of habitats, including ponds; also occur in the limnetic zooplankton. The large Cladocera belonging to the genus Daphnia are very rare. In general, large zooplankters are absent. The size composition of the zooplankton has a smaller range than in temperate regions. This is due to the absence of large-sized zooplankton species. The reasons for the differences in species variety and size composition between zooplankton of temperate and tropical regions is perhaps due to a number of factors. These include the effects of high and uniform temperatures, food availability and predation by fish and invertebrates.

Comparative molecular cytogenetic studies in the order Carnivora: mapping chromosomal rearrangements onto the phylogenetic tree

We have made a set of chromosome-specific painting probes for the American mink by degenerate oligonucleotide primed-PCR (DOP-PCR) amplification of flow-sorted chromosomes. The painting probes were used to delimit homologous chromosomal segments among human, red fox, dog, cat and eight species of the family Mustelidae, including the European mink, steppe and forest polecats, least weasel, mountain weasel, Japanese sable, striped polecat, and badger. Based on the results of chromosome painting and G-banding, comparative maps between these species have been established. The integrated map demonstrates a high level of karyotype conservation among mustelid species. Comparative analysis of the conserved chromosomal segments among mustelids and outgroup species revealed 18 putative ancestral autosomal segments that probably represent the ancestral chromosomes, or chromosome arms, in the karyotype of the most recent ancestor of the family Mustelidae. The proposed 2n = 38 ancestral Mustelidae karyotype appears to have been retained in some modern mustelids, e.g., Martes, Lutra, ktonyx, and Vormela. The derivation of the mustelid karyotypes from the putative ancestral state resulted from centric fusions, fissions, the addition of heterochromatic arms, and occasional pericentric inversions. Our results confirm many of the evolutionary conclusions suggested by other data and strengthen the topology of the carnivore phylogenetic tree through the inclusion of genome-wide chromosome rearrangements. Copyright (C) 2002 S. KargerAG, Basel.