Monitoring with a modified Robel pole on meadows in the central Black Hills of South Dakota

This study using a modified Robel pole was conducted in the central Black Hills, South Dakota. The objectives were to test the relationship between visual obstruction readings and standing herbage, develop guidelines for monitoring, and estimate sample size. The relationship between visual obstruction and standing herbage was linear with 2 segments in a piecewise model. Regression coefficients were highly significant ( P ≤ 0.001). Standard error of the estimate for a single mean was 373 kg ? ha –1 . Herbage ranged from 89 to 3821 kg ? ha –1 with a mean of 1416 kg ? ha –1 . The average number of visually obstructed bands was 6.4 and ranged from 0.21 to 20.4. Cluster analyses grouped the visual obstruction readings into 3 management categories: short, medium, and tall. A minimum of 3 transects (20 stations per transect) is recommended for monitoring areas ≤259 ha (1 section) to be within 20% of the mean at 80% confidence. The protocol developed to monitor standing herbage is accurate, precise, and easy to apply. This tool provides pertinent information for managers to develop guidelines based on the bands and/or standing herbage for monitoring livestock and wildlife use.     

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.     

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.     

Daily and yearly movement of the Devil's Hole pupfish Cyprinodon diabolis Wales in Devil's Hole, Nevada

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Genome-wide association and linkage identify modifier loci of lung disease severity in cystic fibrosis at 11p13 and 20q13.2

A combined genome-wide association and linkage study was used to identify loci causing variation in cystic fibrosis lung disease severity. We identified a significant association (P = 3.34 × 10(-8)) near EHF and APIP (chr11p13) in p.Phe508del homozygotes (n = 1,978). The association replicated in p.Phe508del homozygotes (P = 0.006) from a separate family based study (n = 557), with P = 1.49 × 10(-9) for the three-study joint meta-analysis. Linkage analysis of 486 sibling pairs from the family based study identified a significant quantitative trait locus on chromosome 20q13.2 (log(10) odds = 5.03). Our findings provide insight into the causes of variation in lung disease severity in cystic fibrosis and suggest new therapeutic targets for this life-limiting disorder.     

Identification of low-frequency variants associated with gout and serum uric acid levels

We tested 16 million SNPs, identified through whole-genome sequencing of 457 Icelanders, for association with gout and serum uric acid levels. Genotypes were imputed into 41,675 chip-genotyped Icelanders and their relatives, for effective sample sizes of 968 individuals with gout and 15,506 individuals for whom serum uric acid measurements were available. We identified a low-frequency missense variant (c.1580C>G) in ALDH16A1 associated with gout (OR = 3.12, P = 1.5 × 10(-16), at-risk allele frequency = 0.019) and serum uric acid levels (effect = 0.36 s.d., P = 4.5 × 10(-21)). We confirmed the association with gout by performing Sanger sequencing on 6,017 Icelanders. The association with gout was stronger in males relative to females. We also found a second variant on chromosome 1 associated with gout (OR = 1.92, P = 0.046, at-risk allele frequency = 0.986) and serum uric acid levels (effect = 0.48 s.d., P = 4.5 × 10(-16)). This variant is close to a common variant previously associated with serum uric acid levels. This work illustrates how whole-genome sequencing data allow the detection of associations between low-frequency variants and complex traits.     

Genome-wide association study identifies a new melanoma susceptibility locus at 1q21.3

We performed a genome-wide association study of melanoma in a discovery cohort of 2,168 Australian individuals with melanoma and 4,387 control individuals. In this discovery phase, we confirm several previously characterized melanoma-associated loci at MC1R, ASIP and MTAP-CDKN2A. We selected variants at nine loci for replication in three independent case-control studies (Europe: 2,804 subjects with melanoma, 7,618 control subjects; United States 1: 1,804 subjects with melanoma, 1,026 control subjects; United States 2: 585 subjects with melanoma, 6,500 control subjects). The combined meta-analysis of all case-control studies identified a new susceptibility locus at 1q21.3 (rs7412746, P = 9.0 × 10(-11), OR in combined replication cohorts of 0.89 (95% CI 0.85-0.95)). We also show evidence suggesting that melanoma associates with 1q42.12 (rs3219090, P = 9.3 × 10(-8)). The associated variants at the 1q21.3 locus span a region with ten genes, and plausible candidate genes for melanoma susceptibility include ARNT and SETDB1. Variants at the 1q21.3 locus do not seem to be associated with human pigmentation or measures of nevus density.     

A transition zone complex regulates mammalian ciliogenesis and ciliary membrane composition

Mutations affecting ciliary components cause ciliopathies. As described here, we investigated Tectonic1 (Tctn1), a regulator of mouse Hedgehog signaling, and found that it is essential for ciliogenesis in some, but not all, tissues. Cell types that do not require Tctn1 for ciliogenesis require it to localize select membrane-associated proteins to the cilium, including Arl13b, AC3, Smoothened and Pkd2. Tctn1 forms a complex with multiple ciliopathy proteins associated with Meckel and Joubert syndromes, including Mks1, Tmem216, Tmem67, Cep290, B9d1, Tctn2 and Cc2d2a. Components of this complex co-localize at the transition zone, a region between the basal body and ciliary axoneme. Like Tctn1, loss of Tctn2, Tmem67 or Cc2d2a causes tissue-specific defects in ciliogenesis and ciliary membrane composition. Consistent with a shared function for complex components, we identified a mutation in TCTN1 that causes Joubert syndrome. Thus, a transition zone complex of Meckel and Joubert syndrome proteins regulates ciliary assembly and trafficking, suggesting that transition zone dysfunction is the cause of these ciliopathies.     

The genome of the extremophile crucifer Thellungiella parvula

Thellungiella parvula is related to Arabidopsis thaliana and is endemic to saline, resource-poor habitats, making it a model for the evolution of plant adaptation to extreme environments. Here we present the draft genome for this extremophile species. Exclusively by next generation sequencing, we obtained the de novo assembled genome in 1,496 gap-free contigs, closely approximating the estimated genome size of 140 Mb. We anchored these contigs to seven pseudo chromosomes without the use of maps. We show that short reads can be assembled to a near-complete chromosome level for a eukaryotic species lacking prior genetic information. The sequence identifies a number of tandem duplications that, by the nature of the duplicated genes, suggest a possible basis for T. parvula's extremophile lifestyle. Our results provide essential background for developing genomically influenced testable hypotheses for the evolution of environmental stress tolerance.