Phylogeny of Parasitic Parabasalia and Free-Living Relatives Inferred from Conventional Markers vs. Rpb1, a Single-Copy Gene

Parabasalia are single-celled eukaryotes (protists) that are mainly comprised of endosymbionts of termites and wood roaches, intestinal commensals, human or veterinary parasites, and free-living species. Phylogenetic comparisons of parabasalids are typically based upon morphological characters and 18S ribosomal RNA gene sequence data (rDNA), while biochemical or molecular studies of parabasalids are limited to a few axenically cultivable parasites. These previous analyses and other studies based on PCR amplification of duplicated protein-coding genes are unable to fully resolve the evolutionary relationships of parabasalids. As a result, genetic studies of Parabasalia lag behind other organisms.Comparing parabasalid EF1α, α-tubulin, enolase and MDH protein-coding genes with information from the Trichomonas vaginalis genome reveals difficulty in resolving the history of species or isolates apart from duplicated genes. A conserved single-copy gene encodes the largest subunit of RNA polymerase II (Rpb1) in T. vaginalis and other eukaryotes. Here we directly sequenced Rpb1 degenerate PCR products from 10 parabasalid genera, including several T. vaginalis isolates and avian isolates, and compared these data by phylogenetic analyses. Rpb1 genes from parabasalids, diplomonads, Parabodo, Diplonema and Percolomonas were all intronless, unlike intron-rich homologs in Naegleria, Jakoba and Malawimonas.The phylogeny of Rpb1 from parasitic and free-living parabasalids, and conserved Rpb1 insertions, support Trichomonadea, Tritrichomonadea, and Hypotrichomonadea as monophyletic groups. These results are consistent with prior analyses of rDNA and GAPDH sequences and ultrastructural data. The Rpb1 phylogenetic tree also resolves species- and isolate-level relationships. These findings, together with the relative ease of Rpb1 isolation, make it an attractive tool for evaluating more extensive relationships within Parabasalia

Hashing and Indexing: Succinct DataStructures and Smoothed Analysis

2noreservedWe consider the problem of indexing a text T (of length n) with a light data structure that supports efficient search of patterns P (of length m) allowing errors under the Hamming distance. We propose a hash-based strategy that employs two classes of hash functions—dubbed Hamming-aware and de Bruijn—to drastically reduce search space and memory footprint of the index, respectively. We use our succinct hash data structure to solve the k-mismatch search problem in 2n log σ + o(n log σ) bits of space with a random- ized algorithm having smoothed complexity O((2σ)k(log n)k(log m+ξ)+ (occ + 1) · m), where σ is the alphabet size, occ is the number of occur- rences, and ξ is a term depending on m, n, and on the amplitude ε of the noise perturbing text and pattern. Significantly, we obtain that for any ε > 0, for m large enough, ξ ∈ O(log m): our results improve upon previous linear-space solutions of the k-mismatch problem.mixedAccademicoPOLICRITI, Alberto; PREZZA, NicolaPolicriti, Alberto; Prezza, Nicol

Litter quality indirectly influences community composition, reproductive mode and trophic structure of oribatid mite communities: a microcosm experiment

Abstract Our knowledge of the assembly processes of species-rich oribatid mite communities is fairly limited. Also, very little information is available on the effects of habitat factors on these processes. In this paper, the role of litter quality in pattern formation was investigated in a microcosm experiment using the ‘‘home-field advantage’’ approach. Native (home) and foreign (away) types of microarthropod assemblages were extracted from three types of litter samples (Turkey oak, Scots pine and black locust tree), and transferred alive into ‘home’ and ‘away’ samples, which have been defaunated and reinoculated with microorganisms to form microcosms. Microarthropods were extracted from the microcosms after incubation for 3–12 months. In addition to species identification and abundance records, some chemical properties of thelitter were measured. We hypothesized that oribatid mite communities deteriorate, the proportion of parthenogenetic individuals decreases and the proportion of omnivorous individuals increases in ‘away’ microcosms in contrast to ‘home’ systems. Pine and oak litter were favourable for all the three types of oribatid communities since their community traits in these types of litter were found to be similar to ‘home’ litter. Black locust litter was favourable only for its native oribatid community in the long run. The proportion of parthenogenetic individuals partly supported our hypothesis, mainly in black locust litter. The relative abundance of omnivorous individuals did not differ significantly between treatments. Litter quality is likely to influence oribatid mite assemblages only indirectly