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.

3-T direct MR arthrography of the wrist: value of finger trap distraction to assess intrinsic ligament and triangular fibrocartilage complex tears.

PURPOSE: To determine the value of applying finger trap distraction during direct MR arthrography of the wrist to assess intrinsic ligament and triangular fibrocartilage complex (TFCC) tears. MATERIALS AND METHODS: Twenty consecutive patients were prospectively investigated by three-compartment wrist MR arthrography. Imaging was performed with 3-T scanners using a three-dimensional isotropic (0.4 mm) T1-weighted gradient-recalled echo sequence, with and without finger trap distraction (4 kg). In a blind and independent fashion, two musculoskeletal radiologists measured the width of the scapholunate (SL), lunotriquetral (LT) and ulna-TFC (UTFC) joint spaces. They evaluated the amount of contrast medium within these spaces using a four-point scale, and assessed SL, LT and TFCC tears, as well as the disruption of Gilula's carpal arcs. RESULTS: With finger trap distraction, both readers found a significant increase in width of the SL space (mean Δ = +0.1mm, p ≤ 0.040), and noticed more contrast medium therein (p ≤ 0.035). In contrast, the differences in width of the LT (mean Δ = +0.1 mm, p ≥ 0.057) and UTFC (mean Δ = 0mm, p ≥ 0.728) spaces, as well as the amount of contrast material within these spaces were not statistically significant (p = 0.607 and ≥ 0.157, respectively). Both readers detected more SL (Δ = +1, p = 0.157) and LT (Δ = +2, p = 0.223) tears, although statistical significance was not reached, and Gilula's carpal arcs were more frequently disrupted during finger trap distraction (Δ = +5, p = 0.025). CONCLUSION: The application of finger trap distraction during direct wrist MR arthrography may enhance both detection and characterisation of SL and LT ligament tears by widening the SL space and increasing the amount of contrast within the SL and LT joint spaces.