PumaPlex 1.0: Data generated during the development of the SNP markers and SNP genotypes of pumas

Pumas are one of the most studied terrestrial mammals because of their widespread distribution, substantial ecological impacts, and conflicts with humans. Extensive efforts, often employing genetic methods, are undertaken to manage this species. However, the comparison of population genetic data is difficult because few of the microsatellite loci chosen are shared across research programs. Here, we describe the development of PumaPlex, a high-throughput assay to genotype 25 single nucleotide polymorphisms in pumas. We validated PumaPlex in more than 700 North American pumas (Puma concolor couguar), and demonstrated its ability to generate reproducible genotypes and accurately identify individuals. Furthermore, we compared PumaPlex with traditional genotyping of 12 microsatellite loci in fecal DNA samples and found that PumaPlex produced significantly more genotypes with fewer false alleles. PumaPlex promotes the cross-laboratory comparison of genotypes, is easily expandable in the future, and is a valuable tool for the genetic monitoring and management of North American puma populations.

Sedimentology, foraminiferal assemblage, and isotope record of the Agulhas Bank region

The Agulhas Bank region, south of Africa, is an oceanographically important and complex area. The leakage of warm saline Indian Ocean water into the South Atlantic around the southern tip of Africa is a crucial factor in the global thermohaline circulation. Foraminiferal assemblage, stable isotope and sedimentological data from the top 10 m of core MD962080, recovered from the western Agulhas Bank Slope, are used to indicate changes in water mass circulation in the southeastern South Atlantic for the last 450 kyr. Sedimentological and planktonic foraminiferal data give clear signals of cold water intrusions. The benthic stable isotope record provides the stratigraphic framework and indicates that the last four climatic cycles are represented (i.e. down to marine isotope stage (MIS) 12). The planktonic foraminiferal assemblages bear a clear transitional to subantarctic character with Globorotalia inflata and Neogloboquadrina pachyderma (dextral) being the dominant taxa. Input of cold, subantarctic waters into the region by means of leakage through the Subtropical Convergence, as part of Agulhas ring shedding, and a general cooling of surface waters is suggested by increased occurrence of the subantarctic assemblage during glacial periods. Variable input of Indian Ocean waters via the Agulhas Current is indicated by the presence of tropical/subtropical planktonic foraminiferal species Globoquadrina dutertrei, Globigerinoides ruber (alba) and Globorotalia menardii with maximum leakage occurring at glacial terminations. The continuous presence of G. menardii throughout the core suggests that the exchange of water from the South Indian Ocean to the South Atlantic Ocean was never entirely obstructed in the last 450 kyr. The benthic carbon isotope record and sediment textural data reflect a change in bottom water masses over the core location from North Atlantic Deep Water to Upper Southern Component Water. Planktonic foraminiferal assemblages and sediment composition indicate a profound change in surface water conditions over the core site approximately 200-250 kyr BP, during MIS 7, from mixed subantarctic and transitional water masses to overall warmer surface water conditions.

Investigation of cell fate decision in Schizosaccharomyces pombe by ncRNA annotation and statistical analyses

Studies in the fission yeast Schizosaccharomyces pombe (S. pombe) have done much to inform the view of heterochromatin and its control by the RNA interference (RNAi) machinery. Using cDNA synthesised from poly(A)-enriched RNA samples, numerous novel ncRNA loci were discovered, and the 50 and 30 ends of many other genes were refined in previous studies. Although some of these transcripts may encode novel proteins the function of the majority is yet to be determined. The authors have used strand-specific deep sequencing of RNA, irrespective of poly(A) status, to reveal a highly structured antisense programme that modulates gene expression to dictate cell fate decisions during sexual differentiation. They show that an extensive and elaborate array of ncRNA production accompanies sexual differentiation in the fission yeast S. pombe. Experimental manipulation suggests that these transcripts specifically regulate the function of the target genes.