Multiple-scale roost habitat comparisons of female Merriam’s Wild Turkeys in the southern Black Hills, South Dakota

Because quantity and quality of roosting habitat can affect Merriam’s Wild Turkey ( Meleagris gallopavo merriami ) distribution, we described habitat characteristics of Merriam’s turkey roost sites in the southern Black Hills of South Dakota. Varying proportions of Merriam’s turkeys in the southern Black Hills depended on supplemental feed from livestock operations during the 2 winters of our study, whereas the remainder wintered in forested habitat away from supplemental feed. We compared characteristics of roost habitat occupied by female turkeys from both groups. We located turkeys with radio-transmitters in the early morning and late evening to find roost sites. Female Merriam’s turkeys in the southern Black Hills roosted exclusively in ponderosa pine trees, primarily on the upper portions of ridges on easterly aspects. Generally, trees >30 cm diameter at breast height (dbh) were chosen for roosting, but turkeys also roosted in trees with smaller dbh. During winter months, turkeys that relied on supplemental feeding roosted adjacent to the ranch-farmstead where the supplemental food was located. Generally, these turkeys used the same roost site(s) throughout the winter, whereas turkeys that remained in the forest during winter used multiple roost sites. We suggest maintaining stands of trees >30 cm dbh on the upper portions of easterly aspects to provide suitable roosting habitat for female Merriam’s Wild Turkeys in the southern Black Hills.     

Comparative tolerance of four stocks of cuttthroat trout to extremes in temperature, salinity, and hypoxia

Four stocks of cutthroat trout ( Oncorhynchus clarki ) were exposed to high temperature, high salinity, and low dissolved oxygen to determine inherent differences. The fish tested included 2 stocks of Bonneville cutthroat trout ( O. c. utah ), a lacustrine stock derived from Bear Lake and a fluvial-origin stock from southern Utah (Manning Meadow Reservoir). The other 2 stocks tested were from Electric Lake (largely Yellowstone cutthroat trout, O. c. bouvieri ) and Jackson Hole, Wyoming (fine-spotted Snake River cutthroat trout, O. c. subsp.). Temperature tests were either critical thermal maximum (CTM) or 96-hour trials using juveniles acclimated between 12.5° C and 18.0° C. Two CTM end points were temperature at first loss of equilibrium (CTM eq ) and onset of spasms (CTM s ). There were no significant differences in CTM eq among test fish acclimated to 18.0° C, but CTM s was significantly higher for Bear Lake Bonneville (30.0°C) than for Snake River (29.6° C) or southern Bonneville (29.7° C) stocks. With fish acclimated at 13.0° C, there were no significant differences among the stocks in CTM eq or CTM s . Differences among stocks varied significantly among nine 96-hour tests. Overall, it appeared that the southern Bonneville stock had slightly better survival at warmer temperatures than other stocks. In 24-hour survival tests at high salinities, the Snake River stock had the lowest tolerance, with significant mortality occuring at 18% (29.5 mS · cm -1 conductivity). The southern Bonneville stock had the highest tolerance, with no mortality until 22% (38 mS · cm -1 ). Bear Lake Bonneville and Electric Lake stocks had 60% and 30% mortality, respectively, at 21% (36 mS · cm -1 ). Hypoxia tolerance measured by resistance time, 24-hour mortality, or probit analysis (LEC 50 ) did not differ among stocks. The 24-hour LEC 50 was 2.34 mg O 2 · L -1 for all stocks combined.     

A framework for variation discovery and genotyping using next-generation DNA sequencing data

Recent advances in sequencing technology make it possible to comprehensively catalog genetic variation in population samples, creating a foundation for understanding human disease, ancestry and evolution. The amounts of raw data produced are prodigious, and many computational steps are required to translate this output into high-quality variant calls. We present a unified analytic framework to discover and genotype variation among multiple samples simultaneously that achieves sensitive and specific results across five sequencing technologies and three distinct, canonical experimental designs. Our process includes (i) initial read mapping; (ii) local realignment around indels; (iii) base quality score recalibration; (iv) SNP discovery and genotyping to find all potential variants; and (v) machine learning to separate true segregating variation from machine artifacts common to next-generation sequencing technologies. We here discuss the application of these tools, instantiated in the Genome Analysis Toolkit, to deep whole-genome, whole-exome capture and multi-sample low-pass (～4×) 1000 Genomes Project datasets.     

The genome of Theobroma cacao

We sequenced and assembled the draft genome of Theobroma cacao, an economically important tropical-fruit tree crop that is the source of chocolate. This assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of these genes anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example, flavonoid-related genes. It also provides a major source of candidate genes for T. cacao improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions.     

Positional cloning of Sorcs1, a type 2 diabetes quantitative trait locus

We previously mapped the type 2 diabetes mellitus-2 locus (T2dm2), which affects fasting insulin levels, to distal chromosome 19 in a leptin-deficient obese F2 intercross derived from C57BL/6 (B6) and BTBR T+ tf/J (BTBR) mice. Introgression of a 7-Mb segment of the B6 chromosome 19 into the BTBR background (strain 1339A) replicated the reduced insulin linked to T2dm2. The 1339A mice have markedly impaired insulin secretion in vivo and disrupted islet morphology. We used subcongenic strains derived from 1339A to localize the T2dm2 quantitative trait locus (QTL) to a 242-kb segment comprising the promoter, first exon and most of the first intron of the Sorcs1 gene. This was the only gene in the 1339A strain for which we detected amino acid substitutions and expression level differences between mice carrying B6 and BTBR alleles of this insert, thereby identifying variation within the Sorcs1 gene as underlying the phenotype associated with the T2dm2 locus. SorCS1 binds platelet-derived growth factor, a growth factor crucial for pericyte recruitment to the microvasculature, and may thus have a role in expanding or maintaining the islet vasculature. Our identification of the Sorcs1 gene provides insight into the pathway underlying the pathophysiology of obesity-induced type 2 diabetes mellitus.     

A QTL influencing F cell production maps to a gene encoding a zinc-finger protein on chromosome 2p15

F cells measure the presence of fetal hemoglobin, a heritable quantitative trait in adults that accounts for substantial phenotypic diversity of sickle cell disease and beta thalassemia. We applied a genome-wide association mapping strategy to individuals with contrasting extreme trait values and mapped a new F cell quantitative trait locus to BCL11A, which encodes a zinc-finger protein, on chromosome 2p15. The 2p15 BCL11A quantitative trait locus accounts for 15.1% of the trait variance.