Sunday, May 19, 2013

Holly Bik
I really enjoyed the presentation by Holly Bik from UC Davis. I was really excited that her studies involved nematodes because that is what I study in the Phillips lab. She stated that they estimate there to be between 1 to 100 million species of nematode, although only 28 thousand have been described to date. It was interesting to learn that scientists believe the majority of benthic metazoans to be nematodes (80%) and this percentage may be even higher at greater depths. She suggested that there might be up to 100,000 to 84 million nematodes per meter squared at these depths.

Acrobeles complexus
The next part of her talk involved discussion of eukaryotic organisms. She spoke a little bit about different environmental impacts and biodiversity. Essentially, she mentioned two subjects that we have been readily talking about in class.

She then mentioned the topic of phylogeography. Phylogeography is the study of the historical processes that may be responsible for the geographic distribution of individual organisms. This is a field that I don’t hear a lot about but I feel that it is one that has a lot of connection to biological diversity and may help make sense of evolutionary relatedness in cases where phylogenetic estimations are insufficient.

GenGIS example
She also discussed many of the different programs people use to identify and illustrate different species richness/abundance measurements. She mentioned the GenGIS software that might be usable to create some cool maps that include biodiversity measurements.

Then she dove into current problems with the sequencing of Eukaryotes. Due to genome wide duplication events, the gene encoding the ribosomal RNA is found multiple times in Eukaryotes. In fact, the number of duplications is also very stochastic and thus some organisms have significantly more copies than others. This poses a problem if one is attempting to quantify the number of organisms of a given species in an area, as is often done with microbes.

The next topic was OTUs (operational taxonomic units), something we covered briefly in class. A common difficulty is correlating OTUs with biological species. She noted that currently it is difficult to align Eukaryotic sequences to known organisms because the current databases are “…patchy and sparsely sampled.” A good resource for many known sequences, both eukaryotic and prokaryotic, is Silva.

She also tried to reinforce the necessity of teamwork in order to make the achievement of these goals more feasible. Currently, her research group is working on an open-source platform called PhyloSift which is to be used to analyze the phylogeny and taxonomy of genomes/metagenomes.

Another phylogenic approach that is apparently very efficient is Arb. Unfortunately, there is a steep learning curve and apparently not many people know how to use it well. 

I looked into some of Dr. Bik’s research and found that she posts frequently on the website Deep Sea News. Many of her articles can be found there.

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