Jason A. Turner

Tigers and their close relatives (Panthera) are some of the world’s most endangered species. Here we report the de novo assembly of an Amur tiger whole-genome sequence as well as the genomic sequences of a white Bengal tiger, African lion, white African lion and snow leopard. Through comparative genetic analyses of these genomes, we find genetic signatures that may reflect molecular adaptations consistent with the big cats’ hypercarnivorous diet and muscle strength. We report a snow leopard-specific genetic determinant in EGLN1 (Met39>Lys39), which is likely to be associated with adaptation to high altitude. We also detect a TYR260G>A mutation likely responsible for the white lion coat colour. Tiger and cat genomes show similar repeat composition and an appreciably conserved synteny. Genomic data from the five big cats provide an invaluable resource for resolving easily identifiable phenotypes evident in very close, but distinct, species. Tigers are an endangered species and therefore understanding their genetic architecture could aid conservation efforts. Here, the authors report the first genome sequence of the Amur tiger and, through close species comparative genomic analysis, provide insight into the genome organization, evolutionary divergence and diversity of big cats.

High selenium (Se) in watersheds can cause detrimental effects to many vertebrate species, but less is known regarding its effects on invertebrates comprising the basis of the food chain. This study addressed the response of a natural community of chironomid (midge) species to Se in 2 high-gradient streams that join to form a sandy-bottom front-range stream known to contain increasing downstream concentrations of Se. We identified a total of 151 species of adult male midges (n = 714) collected in 2007 and 2008 from 14 sites in the Fountain Creek Watershed, Colorado, USA. In the initial analysis, the midge community was assessed for possible effects of Se and pH by using binary sets of 25 variables by means of canonical correspondence analysis (CCA) procedures. Further computations revealed significant relationships between the presence of midges and spring total Se (P = 0.0006, unfiltered water), dissolved Se (P = 0.0006, filtered water), and pore water Se (P = 0.0034, interstitial water in coarse and fine gravels) in the spring season. In the fall, the community showed a significant response to total Se (P = 0.0500), a strong association with dissolved Se (P = 0.0044), and a weaker yet significant association with pore water Se (P = 0.1266). We have not found reports indicating either positive or negative responses of midges to increasing Se in field studies. Although there were no significant associations of midges with lower pH during the spring in any fraction of the water (P = 0.7367, 0.7367, and 0.7469, respectively), there were significant associations to higher pH during the fall in all fractions (P ≤ 0.0100). Mean concentrations of dissolved Se in lower-elevation sites ranged from 2.05 to 9.69 µg/L in the spring and from 2.67 to 18.59 µg/L in the fall; mean pH ranged from 7.5 to 7.8 in the spring and from 8.0 to 8.1 in the fall (2007). The association of silt/clay particles with the occurrence of midges was not significant in any of the waters in the spring or fall. Since some chironomid midges have a tendency to be found in areas exhibiting increasing Se in a downstream gradient in Fountain Creek, would they be found in similar water quality profiles in other watersheds? This possibility warrants serious study in other streams, particularly in the western United States where Se has been entering aquatic food chains of fish, birds, and mammals.

Fountain Creek in Colorado USA is a major tributary that confluences with the Arkansas River at Pueblo, Colorado, the result being the tributary's influence on Arkansas River water quality affecting down-stream users. In a previous study, we found that bryophytes (aquatic plants) accumulated selenium in Fountain Creek watershed and this finding prompted us to investigate the extent of the metalloid in the whole-body tissues of fish. One hundred 11 fish (six species) were collected and analyzed for Se by inductively-coupled plasma emission mass spectrometry. Analysis of all analytical data also showed mercury in all of the fish whole bodies and selected tissues. There was a general increase in selenium but a decrease in mercury in fish with downstream travel-distance. The highest whole-body selenium was in Pueblo, Colorado (3393 µg/kg, dry weight; 906 µg/kg, wet weight); the highest mercury in fish was in the Monument Creek tributary north of Colorado Springs, Colorado (71 µg/kg, dry weight; 19 µg/kg, wet weight). In four tissues of 11 female fish captured, selenium was highest in the livers at eight sites but highest in the ovaries at three sites. Mercury was highest in the epaxial muscle at all sites. Selenium availability could be due to the watershed lithology and land uses; however, mercury could be carried by atmospheric deposition from coal-fired power plants and historic mining activities. Selenium in fish tissues and water samples were compared to U.S. national water quality criteria.