Large temperature drop across the Eocene-Oligocene transition in central North America

The Eocene-Oligocene transition towards a cool climate (approximately 33.5 million years ago) was one of the most pronounced climate events during the Cenozoic era. The marine record of this transition has been extensively studied. However, significantly less research has focused on continental climate change at the time, yielding partly inconsistent results on the magnitude and timing of the changes. Here we use a combination of in vivo stable isotope compositions of fossil tooth enamel with diagenetic stable isotope compositions of fossil bone to derive a high-resolution (about 40,000 years) continental temperature record for the Eocene-Oligocene transition. We find a large drop in mean annual temperature of 8.2 +/- 3.1 degrees C over about 400,000 years, the possibility of a small increase in temperature seasonality, and no resolvable change in aridity across the transition. The large change in mean annual temperature, exceeding changes in sea surface temperatures at comparable latitudes and possibly delayed in time with respect to marine changes by up to 400,000 years, explains the faunal turnover for gastropods, amphibians and reptiles, whereas most mammals in the region were unaffected. Our results are in agreement with modelling studies that attribute the climate cooling at the Eocene-Oligocene transition to a significant drop in atmospheric carbon dioxide concentrations.     

Influence of soil water availability on competition among leafy spurge ( Euphorbia Esula ) and grasses

Some perturbations differentially influence invasive plant and grass production. For example, growth regulator herbicides and biological control agents can dramatically reduce leafy spurge production while having little or no influence on grass production, and overgrazing can reduce grass production while not substantially influencing leafy spurge production because cattle typically ingest little or no leafy spurge. To predict how grass production will respond to a perturbation that influences only leafy spurge and to predict how leafy spurge production will respond to a perturbation that affects only grasses, competitive relationships must be understood. Seeding mixtures of leafy spurge and 2 grasses were planted in experiments and grown for 127 days to determine whether different water application regimes influenced competition among these 3 species. Competition became less intense as the number of water applications increased. If this finding holds true under field conditions, then it indicates that competition is less intense in years and locations with numerous precipitation events. Competitive interactions (i.e., competition coefficients) were less variable when water was applied more frequently, but the ability of models to account for variation in plant weight (i.e., r 2 ) was not influenced by the frequency of water application. This suggests that models will predict invasive plant and grass biomass with equal accuracy in years with few or many precipitation events. Competitive effects were similar regardless of grass species, which suggests that grasses might be considered collectively in predicting response to perturbations in the field.     

Disturbance of lekking Lesser Prairie-Chickens ( Tympanuchus pallidicinctus ) by Ring-necked Pheasants ( Phasianus colchicus )

Lesser Prairie-Chicken ( Tympanuchus pallidicinctus ) populations have experienced dramatic rangewide declines (up to 92%) since settlement of the Great Plains. This decline has been attributed to changes in land-use practices, such as conversion of native rangelands to intensive agriculture and increased grazing pressure. These changes may increase the impact of interspecific competition on populations. We documented disturbance of lekking Lesser Prairie-Chickens by Ring-necked Pheasants ( Phasianus colchicus ). Future management and research should take into account possible impacts to Lesser Prairie-Chickens during the breeding season.     

Diets of sympatric Lahontan cutthroat trout and nonnative brook trout: implications for species interactions

Nonnative brook trout ( Salvelinus fontinalis ) have been implicated in declines of stream-living Lahontan cutthroat trout ( Oncorhynchus clarki henshawi ), a threatened trout endemic to the Lahontan Basin of northeastern California, southeastern Oregon, and northern Nevada. Brook trout may displace Lahontan cutthroat trout through 2 mechanisms: interspecific predation and competition for food. To evaluate the evidence for these alternatives, we examined stomach contents of 30 trout of each species captured in the North Fork Humboldt River, northeastern Nevada, to compare number, size, and taxonomic composition of prey. Taxonomic dietary overlap was high (81.4%) between brook and Lahontan cutthroat trout. Both species were nonselective in their feeding habits. Lahontan cutthroat trout consumed over 2.5 times as many prey on average, but brook trout consumed significantly larger prey. No trout of either species occurred in fish diets. Only a single fish, a Paiute sculpin ( Cottus beldingi ), was found in stomachs, and the majority (>90%) of prey consisted of insect taxa. Size and number of prey consumed were positively related to fish size for Lahontan cutthroat trout, but not for brook trout. These results do not provide compelling evidence to suggest feeding by Lahontan cutthroat trout is limited by presence of large numbers of brook trout in the North Fork Humboldt River. However, fundamental differences in each species utilization of food in this system indicate that a better understanding of observed differences may help to explain the variable success of brook trout invasions across stream habitats in the Lahontan Basin and their potential effects on Lahontan cutthroat trout.     

Characteristics of swift fox dens in northwest Texas

The swift fox ( Vulpes velox ) was classified in 1995 as a candidate for listing under the Endangered Species Act. Since then, several studies have addressed survey methods for monitoring swift fox populations. The purpose of this paper is to assist field researchers in documenting the presence of swift foxes by identification of recently active den sites. We propose that swift foxes have unique external den characteristics that can be distinguished during aerial surveys. We collected data from 30 swift fox den complexes on both continuous rangeland and landscapes fragmented by cropland in northwest Texas. There were no differences in den characteristics between landscape types ( P > 0.10). The number of openings per den ranged from 1 to 8 and had an average opening height of 20 cm. As number of openings increased, the maximum distance between openings also increased ( r = 0.88, P Canis latrans ) and red foxes ( Vulpes vulpes ), 2 species that can be sympatric with swift foxes. We suggest that aerial den searching followed by ground verification may be an effective technique for determining presence of swift foxes in areas of short-grass prairies and fragmented habitats.     

A high-resolution survey of deletion polymorphism in the human genome

Recent work has shown that copy number polymorphism is an important class of genetic variation in human genomes. Here we report a new method that uses SNP genotype data from parent-offspring trios to identify polymorphic deletions. We applied this method to data from the International HapMap Project to produce the first high-resolution population surveys of deletion polymorphism. Approximately 100 of these deletions have been experimentally validated using comparative genome hybridization on tiling-resolution oligonucleotide microarrays. Our analysis identifies a total of 586 distinct regions that harbor deletion polymorphisms in one or more of the families. Notably, we estimate that typical individuals are hemizygous for roughly 30-50 deletions larger than 5 kb, totaling around 550-750 kb of euchromatic sequence across their genomes. The detected deletions span a total of 267 known and predicted genes. Overall, however, the deleted regions are relatively gene-poor, consistent with the action of purifying selection against deletions. Deletion polymorphisms may well have an important role in the genetics of complex traits; however, they are not directly observed in most current gene mapping studies. Our new method will permit the identification of deletion polymorphisms in high-density SNP surveys of trio or other family data.     

Genome assembly comparison identifies structural variants in the human genome

Numerous types of DNA variation exist, ranging from SNPs to larger structural alterations such as copy number variants (CNVs) and inversions. Alignment of DNA sequence from different sources has been used to identify SNPs and intermediate-sized variants (ISVs). However, only a small proportion of total heterogeneity is characterized, and little is known of the characteristics of most smaller-sized (<50 kb) variants. Here we show that genome assembly comparison is a robust approach for identification of all classes of genetic variation. Through comparison of two human assemblies (Celera's R27c compilation and the Build 35 reference sequence), we identified megabases of sequence (in the form of 13,534 putative non-SNP events) that were absent, inverted or polymorphic in one assembly. Database comparison and laboratory experimentation further demonstrated overlap or validation for 240 variable regions and confirmed >1.5 million SNPs. Some differences were simple insertions and deletions, but in regions containing CNVs, segmental duplication and repetitive DNA, they were more complex. Our results uncover substantial undescribed variation in humans, highlighting the need for comprehensive annotation strategies to fully interpret genome scanning and personalized sequencing projects.     

Population genomics of human gene expression

Genetic variation influences gene expression, and this variation in gene expression can be efficiently mapped to specific genomic regions and variants. Here we have used gene expression profiling of Epstein-Barr virus-transformed lymphoblastoid cell lines of all 270 individuals genotyped in the HapMap Consortium to elucidate the detailed features of genetic variation underlying gene expression variation. We find that gene expression is heritable and that differentiation between populations is in agreement with earlier small-scale studies. A detailed association analysis of over 2.2 million common SNPs per population (5% frequency in HapMap) with gene expression identified at least 1,348 genes with association signals in cis and at least 180 in trans. Replication in at least one independent population was achieved for 37% of cis signals and 15% of trans signals, respectively. Our results strongly support an abundance of cis-regulatory variation in the human genome. Detection of trans effects is limited but suggests that regulatory variation may be the key primary effect contributing to phenotypic variation in humans. We also explore several methodologies that improve the current state of analysis of gene expression variation.     

The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome

We determined the complete genome sequence of Clostridium difficile strain 630, a virulent and multidrug-resistant strain. Our analysis indicates that a large proportion (11%) of the genome consists of mobile genetic elements, mainly in the form of conjugative transposons. These mobile elements are putatively responsible for the acquisition by C. difficile of an extensive array of genes involved in antimicrobial resistance, virulence, host interaction and the production of surface structures. The metabolic capabilities encoded in the genome show multiple adaptations for survival and growth within the gut environment. The extreme genome variability was confirmed by whole-genome microarray analysis; it may reflect the organism's niche in the gut and should provide information on the evolution of virulence in this organism.