One thousand plant transcriptomes and the phylogenomics of green plants

Abstract: Green plants (Viridiplantae) include around 450,000–500,000 species1, 2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life

Organizational Factors in Commercial Aviation Accidents 1990-2000

Recently several major transportation accidents have brought significant attention to the role of organizational factors in supporting safety within high-risk critical systems. However, little is essentially known about the types of organizational factors that contribute to these accidents, as there has yet to be a comprehensive analysis of these factors. This paper elaborates on the types of organizational factors that have contributed to pilot-error related aviation accidents in U.S. commercial aviation. Specifically, we analyzed 60 accidents with organizational cause factors from 1990-2000. Results from this analysis indicate that the type and frequency of organizational factors that contribute to accidents varies across type and size of aviation operations. However, the data also argue for a more thorough analysis of organizational factors during an investigation so that a clearer understanding of the actual contributing factors to an accident involving pilot error can be discerned

Development and Validation of a Survey to Assess Safety Culture in Airline Maintenance Operations

This paper describes the development and validation of a survey to assess safety culture in airline maintenance operations according to the five-factor model of safety culture proposed by Wiegmann et al. (2002). Maintenance technicians at two FAR Part 121 scheduled passenger airlines (N = 109 and 76) completed the original version of the survey. The results yielded useful diagnostic information about the safety culture of each airline, but factor analyses indicated that the five-factor model may not be adequate to describe the data. A more complex model is proposed and modifications to the survey are suggested

Assessing SNP genotyping of noninvasively collected wildlife samples using microfluidic arrays

Noninvasively collected samples are a common source of DNA in wildlife genetic studies. Currently, single nucleotide polymorphism (SNP) genotyping using microfluidic arrays is emerging as an easy-to-use and cost-effective methodology. Here we assessed the performance of microfluidic SNP arrays in genotyping noninvasive samples from grey wolves, European wildcats and brown bears, and we compared results with traditional microsatellite genotyping. We successfully SNP-genotyped 87%, 80% and 97% of the wolf, cat and bear samples, respectively. Genotype recovery was higher based on SNPs, while both marker types identified the same individuals and provided almost identical estimates of pairwise differentiation. We found that samples for which all SNP loci were scored had no disagreements across the three replicates (except one locus in a wolf sample). Thus, we argue that call rate (amplification success) can be used as a proxy for genotype quality, allowing the reduction of replication effort when call rate is high. Furthermore, we used cycle threshold values of real-time PCR to guide the choice of protocols for SNP amplification. Finally, we provide general guidelines for successful SNP genotyping of degraded DNA using microfluidic technology