Publications

The first Anchored Phylogenomics project in birds resolves one of the greatest challenges in dinosaur systematics: resolving the deep branches of the avian phylogeny. The combination of high taxon sampling and high levels of phylogenetic information in anchored loci facilitated identification of several novel clades and successfully placed enigmatic species.

Anchored Phylogenomic data provide support for a monophyletic radiation of Pseudoxyrhophiine snakes in Madagascar. Feeding specialization associated with tooth venom delivery is thought to have played a major role in the early diversification of this radiation.

Anchored Phylogenomics provided resolution at both phylogeographic and phylogenetic levels in skinks. In a comparison to transcriptome data, Anchored Phylogenomic data sets were found to perform as well or better and to be more cost effective, thus allowing greater taxon sampling. This study collected data using the original Vertebrate v1 capture probe design. We have since developed a much improved amniote-specific design.

Improved modeling and Anchored Phylogenomic data facilitate resolution of deep relationships in the fish clade Ovalentaria. This study collected data using the original Vertebrate v1 capture probe design. We have since developed a much improved fish-specific design that have been used in several projects currently underway.

Narrow mouth frog (Microhylidae) relationships are studied using the original Vertebrate 1 design.

Anchored hybrid enrichment (v1 Vertebrate design) is used to sequence 333 nuclear loci for estimating the phylogeny of Caenodhidian snakes.

Science reviews emerging hybrid enrichment approaches, including Anchored Hybrid Enrichment.

We review current methods for phylogenomic data collection and analysis, highlighting hybrid enrichment as an efficient method for collecting high quality data.

We present the Anchored Phylogenomics approach. Using a small number of reference genomes in vertebrates, we develop an enrichment kit that can be used to obtain hundreds of loci for any vertebrate species. This new approach removes the primary bottleneck in phylogenetics - locus development, and reduces the cost of data collection by several orders of magnitude.

We present a restriction-enzyme-based method for developing nuclear loci for shallow scale phylogenetics.

The promises and pitfalls of next-generation sequencing data in phylogeography