Collaborator Jeff Peters (Wright State University) has submitted a manuscript that develops a conceptual framework for using ddRAD-seq data to define units for conservation, which was applied to two populations of mottled ducks, one of which is of conservation concern. I assisted in data collection, ddRAD-seq genotyping, and data analyses.

For my postdoc research on comparative genomics of Maleae, de novo assemblies of seven species (five Maleae and two outgroups) have been completed! These assemblies were generated with data from short insert and mate-pair libraries and the AllPaths-LG software. These assemblies contain a similar number of eukaryote BUSCOs found in published rosid genomes, and will be used to study gene fate following a whole genome duplication event in the common ancestor of Maleae.

BUSCO results for Maleae genomes. Searches for single-copy plant orthologs (n = 956) were conducted...

This manuscript describes phylogenetic analyses of two avian genera (Lagonosticta finches and Vidua parasitic finches) using thousands of loci derived from ddRAD-seq. We conducted these analyses using a variety of concatenated data sets (i.e., sequence, indel, and presence-absence characters), and also using numerous species tree methods based on gene trees and single nucleotide polymorphisms.

This work is the product of an NSF Doctoral Dissertation Improvement Grant.

We have now successfully generated long read data for two species using Illumina's new Synthetic Long Read kit. This kit size selects 8-10kb fragments, spreads them in low concentrations across 384 (barcoded) wells, and completes a Nextera-like tagmentation of molecules in each well. Short reads are generated with a HiSeq, and long reads are synthesized in BaseSpace.

One lane of sequencing per sample generated ~500Mb of long read data, with an N50 for longer reads (those ≥1500bp) of ~6500. Now on to exploring the best practices for using these data to increase our scaffold...