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
Sunday, May 19, 2013
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.
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.
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
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