In the Bely lab, my first experience with phylogenetic research was generating trees to support the position of sequenced genes in Pristina leidyi‍. I searched NCBI BLAST to find the same genes in representative organisms across the tree of animals. I trimmed, translated, and aligned these sequences then used Geneious Prime to generate trees.

In relation to my undergraduate honors thesis, after local field sampling and extraction from a sediment sample, each Pristina specimen's posterior fragments were used to extract DNA using a Qiagen DNeasy Blood and Tissue Kit. I used PCR to amplify a fragment of cytochrome c oxidase subunit I (COI).

Using the same methods, I extracted the DNA from and amplified the same gene in the specimens from the Potomac River Basin. In those specimens I additionally amplified histone 3 (H3). Lastly, from our collaborator Christer Erséus, I received additional COI and H3 sequences from international Pristina specimens.

I used various bioinformatic pipelines (including Geneious and IQTREE) to align and concatenate all the sequences from H3 and COI before analyzing possible phylogenetic relationships to find the one with the best maximum likelihood. In all trees, I included outgroups comprised of annelids from the genus Rhyacodrilus as well as Chaetogaster. Lastly, I visualized the trees using FigTree and annotated them in Adobe Illustrator.