Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference.

Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single-nucleotide polymorphisms. As an empirical example, we use a double-digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high-altitude mountains in Mexico.

The challenges of building theory by combining lenses

The article presents a discussion of foundational issues in the field of management science, focusing on advances in management theory and research. The metaphor of explanatory lenses is used as a rubric to illustrate the theoretical challenges involved in elucidating the interrelationships of various factors in organizational behavior. The importance of clarifying such interrelationships is emphasized, from the standpoint of editing scholarly papers on such topics for publication. Topics discussed include communication and psychology in management, economics, and behavioral finance.