Genome-wide detection and characterization of positive selection in human populations

With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2). We used 'long-range haplotype' methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population:LARGE and DMD, both related to infection by the Lassa virus, in West Africa;SLC24A5 and SLC45A2, both involved in skin pigmentation, in Europe; and EDAR and EDA2R, both involved in development of hair follicles, in Asia.     

Habitat use of leatherside chub ( Gila copei ) in the presence of predatory brown trout ( Salmo trutta )

The objectives of this study were to (1) examine distribution and habitat use of leatherside chub ( Gila copei ) in a creek with high densities of predatory brown trout ( Salmo trutta ), and (2) compare study results with published accounts of leatherside chub habitat use in streams with few or no brown trout. A 14-km section of Diamond Fork Creek, Utah, was point-shocked to determine macrohabitat (main channel and lateral habitat) and microhabitat (current, depth, substrate, and cover) use of leatherside chug. At the macrohabitat level, leatherside chub were most common in lower reaches of Diamond Fork Creek where the channel was braided and lateral habitats (cutoff pools and backwaters) were abundant. Only a single leatherside chub was found in the main channel of Diamond Fork. Investigations in other systems lacking brown trout indicated that leatherside chub occupy main channel habitats. At the microhabitat level, we found significant positive associations between presence of leatherside chub and both habitat depth and silt. In addition, we found a significant negative association between presence of leatherside chub and number of brown trout. Our results suggest predation by brown trout may limit leatherside chub to lateral habitats that could provide refugia against predation. The introduction of brown trout to systems with little lateral habitat could have serious effects on persistence of resident leatherside chub populations.     

Winter food habits of cougars from northeastern Oregon

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Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey

Although jawless vertebrates are apparently capable of adaptive immune responses, they have not been found to possess the recombinatorial antigen receptors shared by all jawed vertebrates. Our search for the phylogenetic roots of adaptive immunity in the lamprey has instead identified a new type of variable lymphocyte receptors (VLRs) composed of highly diverse leucine-rich repeats (LRR) sandwiched between amino- and carboxy-terminal LRRs. An invariant stalk region tethers the VLRs to the cell surface by means of a glycosyl-phosphatidyl-inositol anchor. To generate rearranged VLR genes of the diversity necessary for an anticipatory immune system, the single lamprey VLR locus contains a large bank of diverse LRR cassettes, available for insertion into an incomplete germline VLR gene. Individual lymphocytes express a uniquely rearranged VLR gene in monoallelic fashion. Different evolutionary strategies were thus used to generate highly diverse lymphocyte receptors through rearrangement of LRR modules in agnathans (jawless fish) and of immunoglobulin gene segments in gnathostomes (jawed vertebrates).