Primers for Castilleja and their Utility Across Orobanchaceae: II. Single‐copy nuclear loci

Premise of the study: We developed primers targeting nuclear loci in Castilleja with the goal of reconstructing the evolutionary history of this challenging clade. These primers were tested across other major clades in Orobanchaceae to assess their broader utility.Methods and Results: We assembled low-coverage genomes for three taxa in Castilleja and developed primer combinations for the single-copy conserved ortholog set (COSII) and the pentatricopeptide repeat (PPR) gene family. These primer combinations were designed to take advantage of the Fluidigm microfluidic PCR platform and are well suited for high-throughput sequencing applications. Eighty-seven primers were designed for Castilleja, and 27 were found to have broader utility in Orobanchaceae.Conclusions: These results demonstrate the utility of these primers, not only across Castilleja, but for other lineages within Orobanchaceae as well. This expanded molecular toolkit will be an asset to future phylogenetic studies in Castilleja and throughout Orobanchaceae

A matter of phylogenetic scale: Distinguishing incomplete lineage sorting from lateral gene transfer as the cause of gene tree discord in recent versus deep diversification histories

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143759/1/ajb21064_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143759/2/ajb21064.pd

Toward standard practices for sharing computer code and programs in neuroscience

Computational techniques are central in many areas of neuroscience and are relatively easy to share. This paper describes why computer programs underlying scientific publications should be shared and lists simple steps for sharing. Together with ongoing efforts in data sharing, this should aid reproducibility of research.This article is based on discussions from a workshop to encourage sharing in neuroscience, held in Cambridge, UK, December 2014. It was financially supported and organized by the International Neuroinformatics Coordinating Facility (http://www.incf.org), with additional support from the Software Sustainability institute (http://www.software.ac.uk). M.H. was supported by funds from the German federal state of Saxony-Anhalt and the European Regional Development Fund (ERDF), Project: Center for Behavioral Brain Sciences

Effects of using aided AAC methods on assessment and instruction outcomes of rhyming accuracy

Preschoolers\u27 skill in rhyming has been shown to be a powerful predictor of later reading and spelling abilities and, as such, holds important implications for assessing prereading skills in children with little or no functional speech. Such children may use aided methods of augmentative and alternative communication (AAC) such as graphic symbols, as an alternative to or to augment natural speech production. Part One of this study involved determining performance differences that may occur when graphic symbols are provided during rhyme assessment. Thirty-three 3- to 5-year-old nondisabled preschool children were assessed on tasks of rhyme detection, rhyme oddity, and rhyme production under two conditions, with and without graphic symbols. Results indicated that for children with high rhyming ability, the presence of graphic symbols did not substantially alter performance on these rhyming tasks. For children with low rhyming ability, graphic symbols appeared to have assisted them in guessing correct responses, particularly in assessment of rhyme oddity and rhyme production. In Part Two of this study, nine preschool and young school-aged children with severe speech impairments received similar rhyme assessment to subjects in Part One. They were then divided into two groups, and received six weeks of individual rhyme instruction utilizing two different AAC methods--graphic symbols and graphic symbols with synthetic speech output. Follow-up post-instruction assessment performance indicated that children who received rhyme instruction with synthetic speech output demonstrated slight increases in rhyme production in comparison to children who received instruction with graphic symbols only. Children who received rhyme instruction with synthetic speech output also demonstrated marked increases in natural speech production during post-instruction assessment. These results have implications in terms of effective rhyme assessment methods for children with severe speech impairments, as well as providing preliminary support for early provision of voice output communication aids (VOCAs) during rhyme instruction