A genome‐wide linkage map for the house sparrow (Passer domesticus) provides insights into the evolutionary history of the avian genome

The house sparrow is an important model species for studying physiological, ecological and evolutionary processes in wild populations. Here, we present a medium density, genome wide linkage map for house sparrow (Passer domesticus) that has aided the assembly of the house sparrow reference genome, and that will provide an important resource for ongoing mapping of genes controlling important traits in the ecology and evolution of this species. Using a custom house sparrow 10 K iSelect Illumina SNP chip we have assigned 6,498 SNPs to 29 autosomal linkage groups, based on a mean of 430 informative meioses per SNP. The map was constructed by combining the information from linkage with that of the physical position of SNPs within scaffold sequences in an iterative process. Averaged between the sexes; the linkage map had a total length of 2,004 cM, with a longer map for females (2,240 cM) than males (1,801 cM). Additionally, recombination rates also varied along the chromosomes. Comparison of the linkage map to the reference genomes of zebra finch, collared flycatcher and chicken, showed a chromosome fusion of the two avian chromosomes 8 and 4A in house sparrow. Lastly, information from the linkage map was utilized to conduct analysis of linkage disequilibrium (LD) in eight populations with different effective population sizes (N_e) in order to quantify the background level LD. Together, these results aid the design of future association studies, facilitate the development of new genomic tools and support the body of research that describes the evolution of the avian genome.     

The easy road to genome‐wide medium density SNP screening in a non‐model species: development and application of a 10 K SNP‐chip for the house sparrow (Passer domesticus)

With the advent of next generation sequencing, new avenues have opened to study genomics in wild populations of non‐model species. Here, we describe a successful approach to a genome‐wide medium density Single Nucleotide Polymorphism (SNP) panel in a non‐model species, the house sparrow (Passer domesticus), through the development of a 10 K Illumina iSelect HD BeadChip. Genomic DNA and cDNA derived from six individuals were sequenced on a 454 GS FLX system and generated a total of 1.2 million sequences, in which SNPs were detected. As no reference genome exists for the house sparrow, we used the zebra finch (Taeniopygia guttata) reference genome to determine the most likely position of each SNP. The 10 000 SNPs on the SNP‐chip were selected to be distributed evenly across 31 chromosomes, giving on average one SNP per 100 000 bp. The SNP‐chip was screened across 1968 individual house sparrows from four island populations. Of the original 10 000 SNPs, 7413 were found to be variable, and 99% of these SNPs were successfully called in at least 93% of all individuals. We used the SNP‐chip to demonstrate the ability of such genome‐wide marker data to detect population sub‐division, and compared these results to similar analyses using microsatellites. The SNP‐chip will be used to map Quantitative Trait Loci (QTL) for fitness‐related phenotypic traits in natural populations.     

Anatomy,pollen, and chromosomes of <Emphasis Type="Italic">Adenoa</Emphasis> (Turneraceae), a monotypic genus endemic to Cuba

The monotypic genus Adenoa is endemic to Cuba. Its name alludes to the presence of minute glands on the petal margin, identified in the present study as lachrymiform colleters. Here we describe the morphological, anatomical, palynological, and chromosome features that characterize Adenoa cubensis. The indumentum of Adenoa consists only of stellate trichomes. Unlike many species of the new world genera Piriqueta and Turnera, Adenoa lacks glandular hairs and extrafloral nectaries. Adenoa, Piriqueta, and Turnera share the presence of standard, sessile, and lachrymiform colleters. The leaves of Adenoa have xeromorphic features, which include entire, revolute blade margins, an adaxial hypodermis, and stomata restricted to the abaxial surface. The chromosome number is 2n?=?14, which is probably the ancestral number of the family. Adenoa chromosomes are similar in size to those of Turnera, and are larger than those of Piriqueta. Using the available data, we discuss relationships among the new world genera of Turneraceae.     

Reversal of response to artificial selection on body size in a wild passerine

A general assumption in quantitative genetics is the existence of an intermediate phenotype with higher mean individual fitness in the average environment than more extreme phenotypes. Here, we investigate the evolvability and presence of such a phenotype in wild bird populations from an eleven‐year experiment with four years of artificial selection for long and short tarsus length, a proxy for body size. The experiment resulted in strong selection in the imposed directions. However, artificial selection was counteracted by reduced production of recruits in offspring of artificially selected parents. This resulted in weak natural selection against extreme trait values. Significant responses to artificial selection were observed at both the phenotypic and genetic level, followed by a significant return toward preexperimental means. During artificial selection, the annual observed phenotypic response closely followed the predicted response from quantitative genetic theory ( = 0.96, = 0.56). The rapid return to preexperimental means was induced by three interacting mechanisms: selection for an intermediate phenotype, immigration, and recombination between selected and unselected individuals. The results of this study demonstrates the evolvability of phenotypes and that selection may favor an intermediate phenotype in wild populations.     

Human T lymphocyte activation in the presence of acute myelogenous leukaemia blasts: studies of allostimulated interferon-γ secretion

 Normal peripheral blood mononuclear cells (PBMC responders) were cultured together with non-irradiated allogeneic PBMC (more than 95% leukaemia blasts) derived from patients with acute leukaemia (referred to as leukaemic PBMC stimulators). Cytokine secretion was determined as cytokine concentrations in supernatants. Both normal PBMC and enriched CD4⁺ and CD8⁺ T cells responded to allostimulation with interferon (IFNγ) secretion. Interleukin-1 (IL-1) receptor antagonist and IL-2-neutralizing antibodies decreased IFNγ secretion. Exogenous IL-1β, IL-2 and IL-7 increased allostimulated IFNγ secretion, whereas decreased levels were seen in the presence of IL-6, IL-10 and granulocyte-colony-stimulating factor (G-CSF). During allorecognition IFNγ -neutralizing antibodies decreased acute myelogenous leukaemia (AML) blast secretion of G-CSF. We conclude that (i) both CD4⁺ and CD8⁺ T cells show allostimulated cytokine secretion in response to allogeneic stimulator cells containing a dominating population of native, cytokine-secreting leukaemia blasts, and (ii) IFNγ released during this response can modulate the function of allogeneic AML blasts. Received: 4 June 1996 / Accepted: 15 October 1996     

Spatial variation in the evolutionary potential and constraints of basal metabolic rate and body mass in a wild bird

An organism's energy budget is strongly related to resource consumption, performance, and fitness. Hence, understanding the evolution of key energetic traits, such as basal metabolic rate (BMR), in natural populations is central for understanding life-history evolution and ecological processes. Here we used quantitative genetic analyses to study evolutionary potential of BMR in two insular populations of the house sparrow (Passer domesticus). We obtained measurements of BMR and body mass (M_b) from 911 house sparrows on the islands of Leka and Vega along the coast of Norway. These two populations were the source populations for translocations to create an additional third, admixed ‘common garden’ population in 2012. With the use of a novel genetic group animal model concomitant with a genetically determined pedigree, we differentiate genetic and environmental sources of variation, thereby providing insight into the effects of spatial population structure on evolutionary potential. We found that the evolutionary potential of BMR was similar in the two source populations, whereas the Vega population had a somewhat higher evolutionary potential of M_b than the Leka population. BMR was genetically correlated with M_b in both populations, and the conditional evolutionary potential of BMR (independent of body mass) was 41% (Leka) and 53% (Vega) lower than unconditional estimates. Overall, our results show that there is potential for BMR to evolve independently of M_b, but that selection on BMR and/or M_b may have different evolutionary consequences in different populations of the same species.     

Dual-energy X-ray absorptiometry: analysis of pediatric fat estimate errors due to tissue hydration effects.

Dual-energy X-ray absorptiometry (DXA) percent (%) fat estimates may be inaccurate in young children, who typically have high tissue hydration levels. This study was designed to provide a comprehensive analysis of pediatric tissue hydration effects on DXA %fat estimates. Phase 1 was experimental and included three in vitro studies to establish the physical basis of DXA %fat-estimation models. Phase 2 extended phase 1 models and consisted of theoretical calculations to estimate the %fat errors emanating from previously reported pediatric hydration effects. Phase 1 experiments supported the two-compartment DXA soft tissue model and established that pixel ratio of low to high energy (R values) are a predictable function of tissue elemental content. In phase 2, modeling of reference body composition values from birth to age 120 mo revealed that %fat errors will arise if a "constant" adult lean soft tissue R value is applied to the pediatric population; the maximum %fat error, approximately 0.8%, would be present at birth. High tissue hydration, as observed in infants and young children, leads to errors in DXA %fat estimates. The magnitude of these errors based on theoretical calculations is small and may not be of clinical or research significance.