Welcome! This blog is being created by students in the courses Population Ecology and Biological Diversity at the University of Oregon. It is one component of their work, and for each course will unfold throughout the term. +Jessica Green & Ann Womack
Monday, May 13, 2013
Simple and effective visualization of data is key in biology.
Dr. Bik’s lecture called, “Eukaryotes are microbes, too” raised questions about biodiversity, phylogeography and methods for visualizing data. Dr. Bik presented data on nematode diversity and abundance in deep-sea marine environments. She claims that there are between 1-100 million species worldwide with around 4,000 marine species. Of these 4,000 species >80% are benthic metazoan. Nematodes are highly abundant in the sample she took ranging from 100,000 -84 million per meter squared. Her data collection methods were pretty standard, taking samples from the environment, extracting environmental DNA, amplifying rRNA, high throughput sequencing, and then creating a community analysis. Dr. Bik focused most of her lecture on the idea of creating a system for a simple yet effective way to visual and analyze the genetic community present. Dr. Bik is interested in viewing the OTUs (operational taxonomic units) as “clouds” and correlating OTUs with biological species diversity. Taxonomic units are currently assigned to OTUs but many inaccuracies are present. Blast/RDP approaches have accuracies critically dependent on reference databases and Eukaryote sequence databases are often patchy and sparsely sampled. The majority of the deep-sea microbiome is hardly researched making it extremely difficult and ambiguous to the assigned taxonomy. Dr. Bik suggested a best-fit method for metagenomic data. Marker genes for bacteria, archaea, eukaryotes and viruses would make taxonomy assignments based on probability much more accurate. Interactive html5 that is now available allows for probability distributions and creation of better visualizations. Visual tools will need to be developed for novel discoveries. Dr. Bik’s analogy to kayak.com models an example for future metagenomic data sites where results can be filtered and advanced real time settings can explore data. I really enjoyed Dr.Bik’s talk and am thrilled to see a bridge between social media, biology and new visualization methods.