Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Immune Investment Is Explained by Sexual Selection and Pace-of-Life, but Not Longevity in Parrots (Psittaciformes)

<div><p>Investment in current reproduction should come at the expense of traits promoting future reproduction, such as immunity and longevity. To date, comparative studies of pace-of-life traits have provided some support for this, with slower paced species having greater immune function. Another means of investment in current reproduction is through secondary sexual characters (SSC). Investment in SSC's is considered costly, both in terms of immunity and longevity, with greater costs being borne by species with more elaborate traits. Yet within species, females prefer more ornate males and those males are typically immunologically superior. Because of this, predictions about the relationship between immunity and SSC's across species are not clear. If traits are costly, brighter species should have reduced immune function, but the opposite is true if SSC's arise from selection for more immunocompetent individuals. My approach was to investigate immune investment in relation to SSC's, pace-of-life and longevity while considering potentially confounding ecological factors. To do so I assessed leukocyte counts from in a novel group, the Psittaciformes. Investment in SSC's best explained investment in immunity: species with brighter plumage had higher leukocyte counts and those with a greater degree of sexual dichromatism had fewer. Ecological variables and pace-of-life models tended to be poor predictors of immune investment. However, shorter incubation periods were associated with lower leukocyte counts supporting the notion that species with a fast pace-of-life invest less in immunity. These results suggest that investment in reproduction in terms of fast pace-of-life and sexual dichromatism results in reduced immunity; however, investment in plumage colour per se does not impose a cost on immunity across species.</p> </div

The relationship between aspects of leukocytes and plumage coloration from bivariate analyses.

<p>In general, species with more elaborate, but not more complex, plumage had higher leukocyte counts. λ values were tested against null models (λ = 0, complete phylogenetic independence) or phylogenetic dependence (λ = 1) using likelihood ratio tests. Significant differences from 0 (first position) and 1 (second position) are denoted by *. Eosinophil counts were not available for one species. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053066#s3" target="_blank">Results</a> for sample size explanations otherwise.</p

Eigenvectors for plumage traits from a phylogenetically informed PCA.

<p>Eigenvectors for plumage traits from a phylogenetically informed PCA.</p

Data from: Fat and happy in the city: eastern chipmunks in urban environments

Cities are rapidly expanding, and wildlife may experience different selection pressures in urban environments when compared to natural habitats. Phenotypic differences between urban and natural populations may occur because of the altered urban environment. Behavior, the activity of the hypothalamic-pituitary-adrenal (HPA) axis and body condition can be expected to differ between urban and natural habitats. We used the eastern chipmunk (Tamias striatus) to test for differences in behavior assayed from an open field test, hair and fecal cortisol concentrations, and body condition (size-corrected body mass), predicting that urban chipmunks would exhibit more exploratory behavior, higher cortisol concentrations, and higher body condition, than their counterparts from natural habitats. We sampled eastern chipmunks in 2 urban areas paired with natural habitats and subjected adult chipmunks to an open field test, collected hair and fecal samples for the determination of cortisol concentrations, and measured body size and body mass to estimate body condition. Eastern chipmunks in urban habitats had significantly different behavior, tending toward reduced locomotion and grooming, and greater latency, than their counterparts from natural habitats. Urban chipmunks also had lower fecal cortisol concentrations than those from natural habitats, and female chipmunks were in better body condition when captured in urban habitats. These results suggest that urban habitats may be relatively benign for urban chipmunks, perhaps because of reduced need for exploration and the availability of anthropogenic food subsidies associated with urban environments

Estimating on-farm methane emissions for sheep production on the Northern Tablelands: establishment of demonstration site

A 36-hectare demonstration site at Armidale on the Northern Tablelands of New South Wales has been established to give livestock producers a practical insight into the magnitude of carbon fluxes, especially methane (CH4), associated with crossbred lamb production. The site contains soil and topographical diversity typical of the region (pH 4.8–5.1 (1:5 CaCl₂); soil organic carbon 1.2–3.8%; cation exchange capacity 3–41 meq/100g). The replicated study over two years will compare animal productivity and emissions of low stocking rate enterprises on a low fertility (hill) section of the site (3.7 DSE/ha) with those of high soil fertility enterprises on the more fertile alluvial flats (6.7 DSE/ha). An EM38 soil map and seven soil samples were used to characterise the soil diversity within the two landscapes and to block each landscape into three classes (A, B, C), with three paddocks/class. Monthly pasture (green and dead DM availability) and regular production data (liveweight gain, fat score, fecundity, wool and lamb carcass weights at slaughter) will be collected. These measures will be used in decision support tools to estimate total on-farm CH₄ emissions, emission per unit product, and to conduct a life cycle analysis of the contrasting enterprises. It is intended to use the site as a regional reference point for effective integration of farm carbon, productivity and economic understandings