At the broadest level I use a phylogenetic framework to address questions pertaining to the diversity of eukaryotes at the level of taxa, genomes, and within the environment. My work has clarified the structure of the eukaryotic tree and the early diversification of the domain by focusing on incorporating diverse microbial lineages. This tree serves as the framework on which I assemble broader biological knowledge, from morphological characteristics to genome structures to ecological distribution, into an integrated view of eukaryotic diversity. My current research projects include assessing the broad patterns of eukaryotes in the environment by sampling terrestrial, marine, aquatic, and host-associated environments with high-throughput sequencing technologies.

Eukaryotes in the microbiome

In the Knight lab my research focuses on incorporating eukaryotes into microbial community analyses. In recent years, high-throughput analyses of microbial communities have yielded staggering insights into human health, ecosystem function, and biodiversity. However, these studies have generally targeted the Bacteria, and to a lesser extent the Archaea, but largely ignored eukaryotes. Incorporating eukaryotes into microbial community analyses will enable overall community structure to be elucidated and provide insights into trophic dynamics. Placing microbial community data within the phylogenetic context of the eukaryotic tree of life lends increased power to elucidate ecological and evolutionary processes that have shaped communities. A comprehensive, well curated, and informatics compatible database is central to all of these efforts. Thus, in collaboration with Pelin Yilmaz, the curator of the key Silva database for ribosomal DNA sequences, I have established the Eukaryotic Taxonomy Working Group, which brings together taxonomic and computational experts to find solutions to database classification that satisfy both parties and will be implemented in Silva.

Parfrey LW, Grant J, Katz LA. 2012. Ribosomal DNA is differentially amplified across life cycle stages in the foraminifer Allogromia laticollaris strain CSH. J Foram Res. 42(2):162-166.

Katz LA, Grant J, Parfrey LW, Burleigh JG. 2012. Turning the Crown Upside Down: Gene Tree Parsimony Roots the Eukaryotic Tree of Life. Syst Biol. 61: DOI:10.1093/sysbio/sys026

Knights D, Parfrey LW, Zaneveld JRR, Lozupone CA, Knight, R. 2011. Human-associated microbial signatures: examining their predictive value. Cell Host Microbe. 10(4):292-6.

Zaneveld JR, Parfrey LW, Van Treuren W, Lozupone C, Clemente JC, Knights D, Stombaugh J, Kuczynski J, Knight R. 2011. Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation. Trends Microbiol. 19(10):472-82.

Parfrey LW, Walters WA, Knight R. 2011. Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions. Frontiers Cell Infection Microbiol. 2:153.

Parfrey LW, Lahr DJG, Knoll AH, Katz LA. 2011. Elucidating the timing of eukaryotic diversification. Proc Nat Acad Sci USA. 108(33):13624-13629.

Katz LA, Grant J, Parfrey LW, Gant AL, O’Kelly CJ, Anderson OR, Molestina RE, and Nerad T. 2011. Subulatomonas tetraspora nov. gen. nov. sp. is a member of a previously unrecognized major clade of eukaryotes. Protist. 162:762–773.

Lahr DJG, Parfrey LW, Mitchell E, Katz LA, Lara E. 2011. The chastity of amoebae: re-evaluating evidence for sex in amoeboid organisms. Proc Roy Soc B. 278:2081-2090.

Parfrey LW and Katz LA. 2010. Genome dynamics are influenced by food source in Allogromia laticollaris strain CSH (Foraminifera). Genome Bio. Evol. 2:678-685.

Parfrey LW, Grant J, Tekle YI, Lasek-Nesselquist E, Morrison H, Sogin ML, Patterson DJ and Katz LA. 2010. Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life. Syst Biol. 59(5):518-533.

Tekle YI, Parfrey LW, Katz LA. 2009. Molecular data are transforming hypotheses on the origin and diversification of eukaryotes. BioScience 59:471–481.

Parfrey LW, Lahr DJG, Katz LA. 2008. The dynamic nature of eukaryotic genomes. Mol Biol Evol. 25(4): 787-794.

Yarragudi A, Parfrey LW, Morse RH. 2007. Genome-wide analysis of transcriptional dependence and probable target sites for Abf1 and Rap1 in Saccharomyces cerevisiae. Nucleic Acids Res. 35(1):193-202

Parfrey LW, Barbero E, Lasser E, Dunthorn MS, Patterson DJ, Bhattacharya D, Katz LA. 2006. Evaluating support for the current classification of eukaryotic diversity. PLoS Genetics 2: 2062-2073

Habura A, Goldstein ST, Parfrey LW, Bowser SS. 2006. Phylogeny and ultrastructure of Miliammina fusca: Evidence for secondary loss of calcification in a miliolid foraminifer. J. of Euk. Microbiol. 53(3) :204-10.

Habura A, Wegener L, Travis JL, Bowser SS. 2005. Structural and functional implications of an unusual foraminiferal b-tubulin. Mol Biol Evol. 22(10):2000-2009.