On this page, you will find more information about our OTUs’ placement on the phylogenetic tree we made and the ciliates we found in our data.
Phylogenetic Tree
This is our complete tree with rhizaria in red, stramenopiles in green, alveolates in blue, and ciliates within the alveolates in teal. The ciliates take up a large portion of the tree.
Where are the ciliates we found located?
We selected the clade of ciliates from our tree. The dark blue letters are the ciliate reference sequences, teal letters are our OTUs that BLASTed to ciliates, and purple are our OTUs with no BLAST ID but are nested within the ciliate reference sequences. There are two sequences in orange that we took a deeper look into.
Close-up image
This is a closer look at the ciliate tree, where you can see more clearly the two greenhouse-specific ciliates we found.
Description of Possible Ciliates Found
Within our top 10 OTUs, the second and third most abundant OTUs by readnumber (OTU1 and OTU2) did not have a BLAST ID. When we manually BLASTed these two OTUs with blastn, there was very low coverage and/or ID, indicating that either these were contaminants or were species new to GenBank/perhaps specific to the greenhouse. Both BLASTed with closest similarity to ciliates, closest to Trochiliopsis australis (OTU1) and Pseudomicrothorax (OTU2) on our tree but with longer branches and nested within other OTUs. We concluded that these are likely not contaminants but are greenhouse ciliates that are new to molecular data.
Extra Observations
Long branches of Phylogenetic Tree
In an attempt to look for contamination within our OTUs, we manually BLASTed long branch OTUs from our tree (branch lengths above 0.3). For the most part, it was unclear whether the OTU was a contaminant because it had low coverage BLAST hits both within and outside of SAR, so we did not end up removing any OTUs.
All figures and tables presented on this website were made by Jailene and Hannah using R/RStudio, Google Sheets, Procreate, and Microsoft Excel.
Works Cited