Effects of Management Practices on Grassland Birds: Field Sparrow

Field Sparrow (Spizella pusilla): Breeding range Suitable habitat Area requirements Brown-headed Cowbird brood parasitism Breeding-season phenology and site fidelity Species’ response to management Management Recommendations Habitat Characteristic

Effects of Management Practices on Grassland Birds: Grasshopper Sparrow

Grasshopper Sparrow (Ammodramus savannarum): Breeding range Suitable habitat Area requirements Brown-headed Cowbird brood parasitism Breeding-season phenology and site fidelity Species’ response to management Management Recommendations Habitat Characteristic

Effects of Management Practices on Grassland Birds: Sprague’s Pipit

Sprague’s Pipit (Anthus spragueii): Breeding range Suitable habitat Area requirements Brown-headed Cowbird brood parasitism Breeding-season phenology and site fidelity Species’ response to management Management Recommendations Habitat Characteristic

Effects of Management Practices on Grassland Birds: Sprague’s Pipit

Sprague’s Pipit (Anthus spragueii): Breeding range Suitable habitat Area requirements Brown-headed Cowbird brood parasitism Breeding-season phenology and site fidelity Species’ response to management Management Recommendations Habitat Characteristic

Effects of Management Practices on Grassland Birds: Grasshopper Sparrow

Grasshopper Sparrow (Ammodramus savannarum): Breeding range Suitable habitat Area requirements Brown-headed Cowbird brood parasitism Breeding-season phenology and site fidelity Species’ response to management Management Recommendations Habitat Characteristic

EFFECTS OF MANAGEMENT PRACTICES ON GRASSLAND BIRDS: HORNED LARK

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 4,000 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species’ nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species’ response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species’ breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management is posted at the Web site mentioned below

Effects of Management Practices on Grassland Birds: Burrowing Owl

Burrowing Owl ( Speotyto cunicularia hypugaea): Breeding range Suitable habitat Prey habitat Area requirements Brown-headed Cowbird brood parasitism Breeding-season phenology and site fidelity Species’ response to management Management Recommendations Characteristic

Hundreds of variants clustered in genomic loci and biological pathways affect human height

Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P < 0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.

Modeling of Environmental Effects in Genome-Wide Association Studies Identifies SLC2A2 and HP as Novel Loci Influencing Serum Cholesterol Levels

Genome-wide association studies (GWAS) have identified 38 larger genetic regions affecting classical blood lipid levels without adjusting for important environmental influences. We modeled diet and physical activity in a GWAS in order to identify novel loci affecting total cholesterol, LDL cholesterol, HDL cholesterol, and triglyceride levels. The Swedish (SE) EUROSPAN cohort (NSE = 656) was screened for candidate genes and the non-Swedish (NS) EUROSPAN cohorts (NNS = 3,282) were used for replication. In total, 3 SNPs were associated in the Swedish sample and were replicated in the non-Swedish cohorts. While SNP rs1532624 was a replication of the previously published association between CETP and HDL cholesterol, the other two were novel findings. For the latter SNPs, the p-value for association was substantially improved by inclusion of environmental covariates: SNP rs5400 (pSE,unadjusted = 3.6×10−5, pSE,adjusted = 2.2×10−6, pNS,unadjusted = 0.047) in the SLC2A2 (Glucose transporter type 2) and rs2000999 (pSE,unadjusted = 1.1×10−3, pSE,adjusted = 3.8×10−4, pNS,unadjusted = 0.035) in the HP gene (Haptoglobin-related protein precursor). Both showed evidence of association with total cholesterol. These results demonstrate that inclusion of important environmental factors in the analysis model can reveal new genetic susceptibility loci

Effect of HLA-DRB1 alleles and genetic variants on the development of neutralizing antibodies to interferon beta in the BEYOND and BENEFIT trials

BACKGROUND: Treatment of multiple sclerosis (MS) with interferon β can lead to the development of antibodies directed against interferon β that interfere with treatment efficacy. Several observational studies have proposed different HLA alleles and genetic variants associated with the development of antibodies against interferon β. OBJECTIVE: To validate the proposed genetic markers and to identify new markers. METHODS: Associations of genetic candidate markers with antibody presence and development were examined in a post hoc analysis in 941 patients treated with interferon β-1b in the Betaferon® Efficacy Yielding Outcomes of a New Dose (BEYOND) and BEtaseron®/BEtaferon® in Newly Emerging multiple sclerosis For Initial Treatment (BENEFIT) prospective phase III trials. All patients were treated with interferon β-1b for at least 6 months. In addition, a genome-wide association study was conducted to identify new genetic variants. RESULTS: We confirmed an increased risk for carriers of HLA-DRB1*04:01 (odds ratio (OR) = 3.3, p = 6.9 × 10-4) and HLA-DRB1*07:01 (OR = 1.8, p = 3.5 × 10-3) for developing neutralizing antibodies (NAbs). Several additional, previously proposed HLA alleles and genetic variants showed nominally significant associations. In the exploratory analysis, variants in the HLA region were associated with NAb development at genome-wide significance (OR = 2.6, p = 2.30 × 10-15). CONCLUSION: The contribution of HLA alleles and HLA-associated single-nucleotide polymorphisms (SNPs) to the development and titer of antibodies against interferon β was confirmed in the combined analysis of two multi-national, multi-center studies