Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease

Using variants from the 1000 Genomes Project pilot European CEU dataset and data from additional resequencing studies, we densely genotyped 183 non-HLA risk loci previously associated with immune-mediated diseases in 12,041 individuals with celiac disease (cases) and 12,228 controls. We identified 13 new celiac disease risk loci reaching genome-wide significance, bringing the number of known loci (including the HLA locus) to 40. We found multiple independent association signals at over one-third of these loci, a finding that is attributable to a combination of common, low-frequency and rare genetic variants. Compared to previously available data such as those from HapMap3, our dense genotyping in a large sample collection provided a higher resolution of the pattern of linkage disequilibrium and suggested localization of many signals to finer scale regions. In particular, 29 of the 54 fine-mapped signals seemed to be localized to single genes and, in some instances, to gene regulatory elements. Altogether, we define the complex genetic architecture of the risk regions of and refine the risk signals for celiac disease, providing the next step toward uncovering the causal mechanisms of the disease.     

Comparative ecology of Sarcobatus baileyi and Sarcobatus vermiculatus in estern California

Greasewood ( Sarcobatus ) is a succulent-leaved, halophytic shrub of North American origin. The genus comprises 2 species: Sarcobatus baileyi and Sarcobatus vermiculatus. Sarcobatus vermiculatus is common throughout much of western North America, but S. baileyi is much more limited in distribution and was previously thought to be endemic to Nevada. Here we document and describe a S. baileyi population in eastern California, comparing its morphology and ecology to an adjacent S. vermiculatus population. Morphologically, S. baileyi is smaller in stature but produces larger seeds; however, fewer S. baileyi seeds germinated and survived a 20-day laboratory incubation compared to seeds of S. vermiculatus. Sarcobatus baileyi has higher leaf Na concentrations and operates at much lower plant water potentials than S. vermiculatus under field conditions; however, no significant differences were observed between the 2 species in long-term water-use efficiency as measured by leaf δ13C. Leaf Na concentrations were very low in both species. Overall, these species differ greatly in a number of traits that are consistent with the upland, nonphreatophytic character of S. baileyi, which is in stark contrast to the phreatophytic character of S. vermiculatus. Both species, however, are very salt tolerant and have low leaf N concentrations, indicating the low nutrient availability and the potentially high salinity of their extreme habitats. Further investigation of comparable desert ridge environments should be conducted to determine the extent of S. baileyi in eastern California, and common garden comparisons of the 2 species should be conducted to compare their ecophysiological traits. El ";greasewood” ( Sarcobatus ) es un arbusto halofítico de origen norteamericano con hojas suculentas. El género consta de dos especies: Sarcobatus baileyi y Sarcobatus vermiculatus. Aunque S. vermiculatus es común en gran parte del oeste de Norteamerica, S. baileyi tiene una distribución mucho más limitada. Se pensaba anteriormente que S. baileyi era endémico a Nevada, pero aquí documentamos y describimos una población en el este de California, comparando su morfología y ecología con las de una población adyacente de S. vermiculatus. Morfológicamente, S. baileyi es más pequeña de altura, pero produce semillas más grandes. Sin embargo, menos semillas de S. baileyi germinaron y sobrevivieron a una incubación en laboratorio de 20 días, comparado con S. vermiculatus. Sarcobatus baileyi opera con potenciales de agua mucho más bajos que los de S. vermiculatus en condiciones de campo y tiene mayores concentraciones de Na en sus hojas. No obstante, no se observaron diferencias significativas en la eficiencia del uso de agua a largo plazo, medida en términos de δ13C entre las 2 especies. Las concentraciones de N en las hojas fueron muy bajas en ambas especies. En general, estas especies difieren mucho en varios rasgos que son consistentes con el carácter no freatofítico de S. baileyi de tierras altas, el cual contrasta claramente con el carácter freatofítico de S. vermiculatus. Ambas especies, sin embargo, son bastante tolerantes a la sal y tienen concentraciones bajas de N en hojas, lo cual indica la baja disponibilidad de nutrientes y la potencial alta salinidad en sus hábitats extremos. Investigaciones adicionales en ambientes comparables de bordes desérticos deberán llevarse a cabo para determinar la extensión S. baileyi en el este de California, además de comparaciones de las dos especies en jardín para comparar sus rasgos ecofisiológicos.     

Winter habitats and foods of Blue Grouse in the Sheeprock Mountains, Utah

Winter habitat use and food habits of Blue Grouse ( Dendragapus obscurus ) were studied in an isolated Utah desert mountain range that contained little typical Douglas-fir ( Pseudotsuga menziesii ) winter habitat. Habitat use was concentrated in the Douglas-fir and pinyon ( Pinus edulis )-juniper ( Juniperus spp. ) habitat. Douglas-fir and pinyon pine were the most consumed foods. Other foods that represented >15% of the composition of an individual fecal sample were limber pine ( Pinus flexilis ), mahogany ( Cercocarpus ledifoliu ), juniper, and an Anteunaria-Cirsium type. The breadth in winter diet indicates that Blue Grouse may successfully occupy other habitats when typical winter habitat is scarce.     

Opportunistic feeding in Sceloporus horridus from Jalisco, Mexico

Based on a sample of 17 adult specimens of Sceloporus horridus taken near Autlan, Jalisco, Mexico in May 1974 just before and just after the first rainfall of the year, we present the first published data on the food habits of this lizard. Important prey item taxa were Homoptera, Coleoptera, Hymenoptera, Orthoptera, and Isoptera. The absence of Homoptera and Orthoptera, and the concomitant greater relative importance of Isoptera and Hymenoptera in the diet after the rain than before indicates opportunistic feeding by S. horridus. Our data suggest that reproduction in this lizard is probably initiated soon after the first rains in late spring.     

Plants of Navajo National Monument

The floristic composition of Navajo National Monument is presented. The flora of the monument consists of 293 species of vascular plants, representing 177 genera and 66 families. The species are scattered throughout 12 plant communities found within the monument. The flora is dominated by forbs (60 percent), followed by shrubs (16 percent), grasses (12 percent) and trees (5 percent). Betatakin canyon exhibits the greatest floristic richness with 223 species being represented and 123 species found only in that area. This is due primarily to two factors: (1) the greater variety of habitats available in the area, and (2) the much longer time the area has been protected from grazing and other manmade disturbance.     

Condition models for wintering Northern Pintails in the Southern High Plains

Three condition models for wintering Northern Pintails ( Anas acuta ) were tested for their ability to predict fat mass, logarithm of fat mass, or a condition index (CI) incorporating fat mass. Equations generated to predict fat mass and the logarithm of fat mass accounted for more than 69% of the variation in these dependent variables. Log transformations of body mass, wing length, and total length explained at least 60% of the variation in CI. All models performed better on an independent data set. Mean prediction error was minimal (≤8% of measured variables) and negative for all models. Regression models apply to live and dead pintails and thus represent tools that have utility in a wide variety of studies on pintail condition.     

Seasonal trends and colonization patterns of macroinvertebrate assemblages in two streams with contrasting flow regimes

Patterns of colonization by macroinvertebrates were examined in two streams that differ in flow regime: a snowmelt system and a mesic groundwater system. Experiments were conducted during spring runoff, summer baseflow, and winter baseflow using artificial substrata. Colonization patterns reflected seasonal changes in benthic macroinvertebrate assemblages and life histories in each stream. The density and biomass of benthic organisms were approximately 3X greater in winter than in either spring or summer for both streams. Similarly, colonization was greater in winter than in spring or summer for both streams. In spring, colonization patterns were different between streams, with colonization being imperceptible in the snowmelt stream. Macroinvertebrate abundance fluctuated during the summer colonization experiment at both sites, resulting from a complex interplay among population emergence, recruitment, and/or movement. Assemblages in the snowmelt system primarily comprised mobile or ruderal taxa, such as Beatis tricaudatus and Chironomidae, whereas relatively sessile taxa, such as Glossoma nigrior , were predominant in the mesic groundwater system. Seasonal patterns of colonization differed among stream types primarily because of the profound interplay of flow regime and temperature on benthic community structure and organism life history.     

Bayesian inference of ancient human demography from individual genome sequences

Whole-genome sequences provide a rich source of information about human evolution. Here we describe an effort to estimate key evolutionary parameters based on the whole-genome sequences of six individuals from diverse human populations. We used a Bayesian, coalescent-based approach to obtain information about ancestral population sizes, divergence times and migration rates from inferred genealogies at many neutrally evolving loci across the genome. We introduce new methods for accommodating gene flow between populations and integrating over possible phasings of diploid genotypes. We also describe a custom pipeline for genotype inference to mitigate biases from heterogeneous sequencing technologies and coverage levels. Our analysis indicates that the San population of southern Africa diverged from other human populations approximately 108-157 thousand years ago, that Eurasians diverged from an ancestral African population 38-64 thousand years ago, and that the effective population size of the ancestors of all modern humans was ～9,000.