Autoregressive gamma processes

We introduce a class of autoregressive gamma processes with conditional distributions from the family of noncentred gamma (up to a scale factor). The paper provides the stationarity and ergodicity conditions for ARG processes of any autoregressive order p, including long memory, and closed‐form expressions of conditional moments. The nonlinear state space representation of an ARG process is used to derive the filtering, smoothing and forecasting algorithms. The paper also presents estimation and inference methods, illustrated by an application to interquote durations data on an infrequently traded stock listed on the Toronto Stock Exchange (TSX). Copyright © 2006 John Wiley & Sons, Ltd.     

The complete genome sequence of Francisella tularensis, the causative agent of tularemia

Francisella tularensis is one of the most infectious human pathogens known. In the past, both the former Soviet Union and the US had programs to develop weapons containing the bacterium. We report the complete genome sequence of a highly virulent isolate of F. tularensis (1,892,819 bp). The sequence uncovers previously uncharacterized genes encoding type IV pili, a surface polysaccharide and iron-acquisition systems. Several virulence-associated genes were located in a putative pathogenicity island, which was duplicated in the genome. More than 10% of the putative coding sequences contained insertion-deletion or substitution mutations and seemed to be deteriorating. The genome is rich in IS elements, including IS630 Tc-1 mariner family transposons, which are not expected in a prokaryote. We used a computational method for predicting metabolic pathways and found an unexpectedly high proportion of disrupted pathways, explaining the fastidious nutritional requirements of the bacterium. The loss of biosynthetic pathways indicates that F. tularensis is an obligate host-dependent bacterium in its natural life cycle. Our results have implications for our understanding of how highly virulent human pathogens evolve and will expedite strategies to combat them.     

Randomly amplified polymorphic DNA analysis (RAPD) of Artemisia subgenus Tridentatae species and hybrids

Species of Artemisia (subgenus Tridentatae ) dominate much of western North America. The genetic variation that allows this broad ecological adaptation is facilitated by hybridization and polyploidization. Three separate studies were performed in this group using randomly amplified polymorphic DNA (RAPD). Fifty-seven 10-mer primers generated nearly 400 markers from genomic DNA obtained from leaf tissue. These studies were (1) a measure of the variability of plants within and between populations and between subspecies using 5 A. tridentata ssp. wyomingensis populations, 2 A. cana ssp. cana populations, and 1 A. cana ssp. viscidula population; (2) an examination of the hypothesis that tetraploid (4 x ) Artemisia tridentata spp. vaseyana derives de novo from diploid (2 x ) populations via antopolyploidy; and (3) an examination of the validity of the status of putative hybrids that have been produced by controlled pollination. These later hybrid combinations- A. tridentata ssp. tridentata × A. t. ssp. vaseyana , A. t. ssp. wyomingensis × A. tripartita , and A. cana ssp. cana A. tridentata ssp. wyomingensis - were made to combine traits of parental taxa in unique combinations with possible management application. RAPD marker data were subjected to similarity and UPGMA clustering analyses. RAPD markers were effective in measuring genetic diversity at different systematic levels. Individual plants within a population were approximately 55% to > 80% similar to one another; populations within subspecies gave corresponding values of similarity, probably a result of the combined effects of large population sizes and wind pollination. The 2 subspecies of A. cana were approximately 45% similar. At least some 4 x populations of A. tridentata ssp. vaseyana apparently derive de novo from 2 x plants based on their being embedded in 2 x phenogram groups, thus reinforcing evidence that autopolyploidy plays an important role in Tridentatae population biology. Two ( A. tridentata ssp. tridentata × A. t. ssp. vaseyana and A. cana ssp. cana × A. tridentata ssp. wyomingensis ) of the 3 putative hybrid combinations were confirmed to include hybrids. These hybrids may have potential in management applications. Additional use of RAPD technology combined with other techniques may be useful in delimiting genetic characteristics and in guiding artificial selection in Tridentatae .     

The Medicago genome provides insight into the evolution of rhizobial symbioses

Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing ～94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa's genomic toolbox.