Armstrong, D. G., Hurwitz, B. L., & Lipsky, B. A. (2015). Set Phages to Stun: Reducing the Virulence of Staphylococcus aureus in Diabetic Foot Ulcers. Diabetes, 64(8), 2701-3.
Cranston, K. A., Hurwitz, B., Ware, D., Stein, L., & Wing, R. A. (2009). Species trees from highly incongruent gene trees in rice. Systematic biology, 58(5), 489-500.
Several methods have recently been developed to infer multilocus phylogenies by incorporating information from topological incongruence of the individual genes. In this study, we investigate 2 such methods, Bayesian concordance analysis and Bayesian estimation of species trees. Our test data are a collection of genes from cultivated rice (genus Oryza) and the most closely related wild species, generated using a high-throughput sequencing protocol and bioinformatics pipeline. Trees inferred from independent genes display levels of topological incongruence that far exceed that seen in previous data sets analyzed with these species tree methods. We identify differences in phylogenetic results between inference methods that incorporate gene tree incongruence. Finally, we discuss the challenges of scaling these analyses for data sets with thousands of gene trees and extensive levels of missing data.
Bomhoff, M., Youens-Clark, K., Ponsero, A. J., Hurwitz, B. L., Choi, I., & Hartman, J. H. (2018). Libra: Using Hadoop for Comparative Metagenomics. HPDC.
Degnan, P. H., Leonardo, T. E., Cass, B. N., Hurwitz, B., Stern, D., Gibbs, R. A., Richards, S., & Moran, N. A. (2010). Dynamics of genome evolution in facultative symbionts of aphids. Environmental microbiology, 12(8), 2060-9.
Aphids are sap-feeding insects that host a range of bacterial endosymbionts including the obligate, nutritional mutualist Buchnera plus several bacteria that are not required for host survival. Among the latter, 'Candidatus Regiella insecticola' and 'Candidatus Hamiltonella defensa' are found in pea aphids and other hosts and have been shown to protect aphids from natural enemies. We have sequenced almost the entire genome of R. insecticola (2.07 Mbp) and compared it with the recently published genome of H. defensa (2.11 Mbp). Despite being sister species the two genomes are highly rearranged and the genomes only have ∼55% of genes in common. The functions encoded by the shared genes imply that the bacteria have similar metabolic capabilities, including only two essential amino acid biosynthetic pathways and active uptake mechanisms for the remaining eight, and similar capacities for host cell toxicity and invasion (type 3 secretion systems and RTX toxins). These observations, combined with high sequence divergence of orthologues, strongly suggest an ancient divergence after establishment of a symbiotic lifestyle. The divergence in gene sets and in genome architecture implies a history of rampant recombination and gene inactivation and the ongoing integration of mobile DNA (insertion sequence elements, prophage and plasmids).
Hurwitz, B. L., Hallam, S. J., & Sullivan, M. B. (2013). Metabolic reprogramming by viruses in the sunlit and dark ocean. Genome biology, 14(11), R123.
Marine ecosystem function is largely determined by matter and energy transformations mediated by microbial community interaction networks. Viral infection modulates network properties through mortality, gene transfer and metabolic reprogramming.
