Species-specific responses of Late Quaternary megafauna to climate and humans

Despite decades of research, the roles of climate and humans in driving the dramatic extinctions of large-bodied mammals during the Late Quaternary period remain contentious. Here we use ancient DNA, species distribution models and the human fossil record to elucidate how climate and humans shaped the demographic history of woolly rhinoceros, woolly mammoth, wild horse, reindeer, bison and musk ox. We show that climate has been a major driver of population change over the past 50,000 years. However, each species responds differently to the effects of climatic shifts, habitat redistribution and human encroachment. Although climate change alone can explain the extinction of some species, such as Eurasian musk ox and woolly rhinoceros, a combination of climatic and anthropogenic effects appears to be responsible for the extinction of others, including Eurasian steppe bison and wild horse. We find no genetic signature or any distinctive range dynamics distinguishing extinct from surviving species, emphasizing the challenges associated with predicting future responses of extant mammals to climate and human-mediated habitat change.     

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.     

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

The systematic translation of cancer genomic data into knowledge of tumour biology and therapeutic possibilities remains challenging. Such efforts should be greatly aided by robust preclinical model systems that reflect the genomic diversity of human cancers and for which detailed genetic and pharmacological annotation is available. Here we describe the Cancer Cell Line Encyclopedia (CCLE): a compilation of gene expression, chromosomal copy number and massively parallel sequencing data from 947 human cancer cell lines. When coupled with pharmacological profiles for 24 anticancer drugs across 479 of the cell lines, this collection allowed identification of genetic, lineage, and gene-expression-based predictors of drug sensitivity. In addition to known predictors, we found that plasma cell lineage correlated with sensitivity to IGF1 receptor inhibitors; AHR expression was associated with MEK inhibitor efficacy in NRAS-mutant lines; and SLFN11 expression predicted sensitivity to topoisomerase inhibitors. Together, our results indicate that large, annotated cell-line collections may help to enable preclinical stratification schemata for anticancer agents. The generation of genetic predictions of drug response in the preclinical setting and their incorporation into cancer clinical trial design could speed the emergence of 'personalized' therapeutic regimens.     

Recruitment of entomopathogenic nematodes by insect-damaged maize roots

Plants under attack by arthropod herbivores often emit volatile compounds from their leaves that attract natural enemies of the herbivores. Here we report the first identification of an insect-induced belowground plant signal, (E)-beta-caryophyllene, which strongly attracts an entomopathogenic nematode. Maize roots release this sesquiterpene in response to feeding by larvae of the beetle Diabrotica virgifera virgifera, a maize pest that is currently invading Europe. Most North American maize lines do not release (E)-beta-caryophyllene, whereas European lines and the wild maize ancestor, teosinte, readily do so in response to D. v. virgifera attack. This difference was consistent with striking differences in the attractiveness of representative lines in the laboratory. Field experiments showed a fivefold higher nematode infection rate of D. v. virgifera larvae on a maize variety that produces the signal than on a variety that does not, whereas spiking the soil near the latter variety with authentic (E)-beta-caryophyllene decreased the emergence of adult D. v. virgifera to less than half. North American maize lines must have lost the signal during the breeding process. Development of new varieties that release the attractant in adequate amounts should help enhance the efficacy of nematodes as biological control agents against root pests like D. v. virgifera.     

Ecology of flannelmouth sucker in the Lee's Ferry tailwater, Colorado River, Arizona

We investigated ecology of flannelmouth sucker ( Catostomus latipinnis ) from 1992 to 1997 in the 26-km Lee's Ferry reach of the Colorado River immediately below Glen Canyon Dam, Arizona. We captured by electrofishing a total of 212 fish and recaptured 52 previously tagged by others. Flannelmouth sucker were captured throughout the tailwater but tended to aggregate about 5 km of the dam, possibly reflecting blockage of historic migration routes. Catch per hour of electrofishing did not differ among years but was greater from November to February than other periods, suggesting seasonal movements of flannelmouth sucker into the tailwater: Mean lengths and weights of fish did not differ among years or seasons. Length frequency analyses also indicated there were no significantly yearly trends in proportion of catch within size classes of fish. Mean condition differed only among seasons and was greatest in February, lowest in August, coinciding respectively with pre- and post-spawning periods of flannelmouth sucker in tributary just down from Lee's Ferry. Recaptured fish migrated from initial tagging locations 1.4-23.1 km downstream from Lee's Ferry. Fifty-nine percent of recaptured fish with known initial tagging locations increased in length, and fish tagged initially as subadults or adults, respectively, grew an average of 45.9 mm and 5.5 mm per year.     

Magneto-thermal convection in solar prominences

Coronal cavities are large low-density regions formed by hemispheric-scale magnetic flux ropes suspended in the Sun's outer atmosphere. They evolve over time, eventually erupting as the dark cores of coronal mass ejections. Although coronal mass ejections are common and can significantly affect planetary magnetospheres, the mechanisms by which cavities evolve to an eruptive state remain poorly understood. Recent optical observations of high-latitude 'polar crown' prominences within coronal cavities reveal dark, low-density 'bubbles' that undergo Rayleigh-Taylor instabilities to form dark plumes rising into overlying coronal cavities. These observations offered a possible mechanism for coronal cavity evolution, although the nature of the bubbles, particularly their buoyancy, was hitherto unclear. Here we report simultaneous optical and extreme-ultraviolet observations of polar crown prominences that show that these bubbles contain plasma at temperatures in the range (2.5-12)?×?10(5) kelvin, which is 25-120 times hotter than the overlying prominence. This identifies a source of the buoyancy, and suggests that the coronal cavity-prominence system supports a novel form of magneto-thermal convection in the solar atmosphere, challenging current hydromagnetic concepts of prominences and their relation to coronal cavities.     

Diets of sympatric bobcats and coyotes during years of varying rainfall in central Arizona

We collected fecal samples (scats) of sympatric bobcats ( Lynx rufus ) and coyotes ( Canis latrans ) between 2000 and 2003 in a 53,600-ha area of the Upper Sonoran Desert in central Arizona. Our objective was to investigate composition, diversity, and overlap of diets of bobcats and coyotes in relation to varying rainfall in the Sonoran Desert of central Arizona. In general, bobcats ate more rodents than did coyotes, and coyotes ate more lagomorphs, large prey, and fruit/seeds than did bobcats. Composition of bobcat diets was independent of differences among years in annual rainfall and seasonal rainfall during summer–autumn (May–October) and winter–spring (November–April). Composition of coyote diets also was independent of drought conditions among years during summer–autumn, but coyotes ate more large prey and fewer rodents during years with winter–spring drought. Seasonally, bobcats ate more rodents than did coyotes in summer–autumn and winter–spring, whereas coyotes ate more lagomorphs than did bobcats during winter– spring, and more large prey and fruit/seeds in both seasons. Coyotes ate more large prey and lagomorphs during winter–spring, when seasonal rainfall was higher, and more fruit/seeds in summer–autumn, when seasonal rainfall was lower. Diversity of diets was consistently higher for coyotes than for bobcats, and increased for bobcats but not for coyotes during winter–spring drought and during higher seasonal rainfall in winter–spring. Overlap of diets between predators was independent of rainfall levels. We suggest that bobcats in the Sonoran Desert are more selective, specialized predators and that coyotes are more generalist, opportunistic predators. We hypothesize that, although diversity of bobcat food items and composition of coyote diets differ with varying rainfall in the Sonoran Desert, patterns of feeding strategy are independent of seasonal differences in precipitation and effects of drought, and bobcats and coyotes partition food resources independently of varying rainfall.