Draft blog post cleanup #2: Metagenomics meets animals

OK – I am cleaning out my draft blog post list.  I start many posts and don’t finish them and then they sit in the draft section of blogger.  Well, I am going to try to clean some of that up by writing some mini posts.  Here is #2:

Saw an interesting story on Genome Web: ‘Denizens’ of the Deep | The Daily Scan | GenomeWeb.  I have not been able to get the original article yet, but it seems that what they have done can basically be considered metagenomics for animals.  They collected sloughed off cells and other material from a lake and surveyed it for animal DNA.  This seems like a very cool derivative of metagenomic approaches and has enormous potential.  But alas, I never got down to getting access to the paper: Monitoring endangered freshwater biodiversity using environmental DNA so this will have to stay as a mini post.  Damn non open access journals …

Further proof of the ascendancy of microbes: 2011 NSF "biodiversity" grants mostly focused on microbes

As if the readers of this blog needing any more proof of the ascendancy of microbes and microbiology. Well, regardless, here is more. The NSF Announced recipients of the 2011 grants on “Dimensions of Biodiversity” – see The National Science Foundation (NSF) News Diversity of Life on Earth: NSF Awards Grants for Study of Dimensions of Biodiversity

And the recipients are strongly biased towards microbes relative to the general past patterns at many funding agencies.
Microbial focused awards:
Title: Pattern and process in marine bacterial, archaeal, and protistan biodiversity, and effects of human impacts
PI (Principal investigator): Jed Fuhrman, University of Southern California
Summary: Very little about marine microbial systems is understood, despite the fact that these diverse groups dominate cycling of elements in the oceans. Fuhrman and colleagues will compare heavily affected harbor regions with relatively pristine ocean habitat in the Los Angeles basin to understand patterns and relationships in marine microbial communities.

Title: Diversity and symbiosis: Examining the taxonomic, genetic, and functional diversity of amphibian skin microbiota
PI: Lisa Belden, Virginia Polytechnic Institute & State University
Summary: All animals host internal and external symbiotic microbes; most cause no harm and many are beneficial. This study seeks to understand the regulation of microbial communities on the skin of amphibian species, and how they may limit infection by a chytrid fungus that has decimated many amphibian populations around the globe.

Title: Lake Baikal responses to global change: The role of genetic, functional and taxonomic diversity in the planktonPI: Elena Litchman, Michigan State University
Summary: Microscopic plant- and animal-like plankton are the first links in aquatic food chains. This project will study the planktonic food web of the world’s largest, oldest, and most biologically diverse lake–Lake Baikal in Siberia–to predict how native vs. non-native plankton in this ecosystem will respond to accelerating environmental change

Title: Functional diversity of microbial trophic guilds defined using stable isotope ratios of proteinsPI: Ann Pearson, Harvard University
Summary: Studying the ecological interactions among microbes is difficult given their immense diversity and the scale of observation. This project will use isotopic ratios of carbon, nitrogen, hydrogen and sulfur produced during microbial metabolism to link microbes to their roles in biogeochemical and ecosystem processes. This novel approach will contribute to an understanding of what maintains diversity in microbes and, by extension, the roles microbes play in ecosystems.

Title: An integrated study of energy metabolism, carbon fixation, and colonization mechanisms in chemosynthetic microbial communities at deep-sea ventsPI: Stefan Sievert, Woods Hole Oceanographic Institution
Summary: The 1977 discovery of deep-sea hydrothermal vent ecosystems that obtain energy not through photosynthesis, but via inorganic chemical reactions greatly expanded the perception of life on Earth. However, there has been limited progress since then in understanding their underlying microbiology and biogeochemistry. This project will establish an international research program to better understand these deep-sea ecosystems and to place them in a global context.

Title: Functional diversity of marine eukaryotic phytoplankton and their contributions to carbon and nitrogen cyclingPI: Bess Ward, Princeton University
Summary: Marine phytoplankton form the base of food webs in the ocean’s surface layers, and thus represent the first incorporation of biologically important chemicals. This project will study two north Atlantic sites in two seasons to link the genetic diversity and species composition of phytoplankton communities to the carbon and nitrogen biogeochemistry of the surface ocean.

Title: IRCN (International Research Coordination Network): A Research Coordination Network for Biodiversity of CiliatesPI: John Clamp, North Carolina Central University
Summary: Ciliates are abundant, widespread protists found in all aquatic systems on Earth. However, it is estimated that science has described only 25 percent of these ubiquitous microorganisms, mainly in western European and eastern North American waters. This cooperative project is partially supported by the Natural Science Foundation of China, and will establish an International Research Coordination Network for Biodiversity of Ciliates (RCN-BC; including researchers from the United States, China, the United Kingdom and Brazil) to broaden exploration of these important protists.

Amazingly, there are only three awards not focused on microbes:

Title: The climate cascade: Functional and evolutionary consequences of climatic change on species, trait, and genetic diversity in a temperate ant communityPI: Nathan Sanders, University of Tennessee, Knoxville
Summary: Sanders and colleagues will help us understand what mechanisms allow some species to adapt to shifts in climate, rather than migrating or going extinct. This project will reconstruct past adaptations to climate change in a foraging ant common in forests throughout the Eastern United States and sample ant nests introduced to outdoor experimental warming chambers to determine the ant’s capacity to adapt to heat stress.

Title: Integrating genetic, taxonomic, and functional diversity of tetrapods across the Americas and through extinction risk
PI: Thomas Brooks, NatureServe
Most large-scale efforts to assess biodiversity have focused on genetic, taxonomic and functional dimensions individually; it is unknown how these dimensions relate to each other. Brooks and colleagues are using a database of the 13,000 land vertebrates in the Americas to determine how changes in one dimension of biodiversity influence changes in others. Understanding how species composition influences the diversity of certain traits, for example, will improve the efficiency and effectiveness of conservation actions.

Title: Integrating dimensions of Solanumbiodiversity: Leveraging comparative and experimental transcriptomics to understand functional responses to environmental change
PI: Leonie Moyle, Indiana University
This research will highlight the role of drought and herbivore defense in driving the remarkable diversity of wild tomato species. With the economic importance of tomatoes and their relatives (such as peppers and potatoes), this study will help prepare society for the future challenges facing global food security.

And if the PIs of these grants have any sense, they will likely include some microbial studies as part of their projects.  Of course, in the end all ecosystems include a diversity of kinds of organisms, and focusing on microbes over other organisms is also a biased approach.  But we (that is, “Science”) have spent so many years ignoring the dark matter of the biological universe (the term I now use to refer to microbial diversity) that we have to focus on microbes because there is a lot of catching up to do there.

BIS002C "Biodiversity & the tree of life" Lecture2&3 more on phylogeny & trees

Well, tomorrow is going to be a bit crazy for me.  I teach four lectures tomorrow for “BIS002C – Biodiversity and the Tree of Life” and UC Davis.  Well, actually, I do each of two lectures twice.  This happens for two reasons.  First, there are two sections for the class and the way we do it, each faculty gives each lecture for which they are responsible twice.  Second, on Mondays, we do two lectures for each section.  In total there are four lectures per week and our schedule is as follows

Section A:  MWF 11-12 M 6-7
Section B: MWF 3-4 M 7-8

So tomorrow at 11 AM I give Lecture 2 for the class to Section A.  Then at 3 PM I give Lecture 2 to Section B.  Then at 6 PM I give Lecture 3 to Section A.  Then at 7 PM I give Lecture 3 to Section B.  Well, enough trying to make it seem like I am working hard.  Especially after PZ Myers gave me a little grief about this on twitter since, well, my teaching load is not actually that big compared to many.

Anyway – back to the class.  I am going to be posting about the class here as much as I can.  To give people an idea of the whole course this is the general highly simplified schema:

Lectures 1-5 Phylogeny (me)
Lectures 6-13 Microbes (Bacteria, Archaea, microbial euks) (me)
Lectures 14-21 Plants and relatives (Jim Doyle)
Lectures 22-24 Fungi  (Jim Doyle)
Lectures 25-36 Metazoa (Susan Keen)
Lectures 37-38 Wrap up, symbioses, etc (Susan Keen)

I do Lectures 1-13 and possibly 37-38.

For the first week or so I am introducing the students to various aspects of phylogeny and phylogenetic trees.  We do this in part because the rest of the class is oriented around using phylogenies and phylogenetic trees so it is important that the students really understand them.

To that end, tomorrow here is the plan:

Lecture 2 will focus on (a) the components of a phylogenetic tree and what they mean plus (b) taxa and groups in trees.  Among the topics we will cover are rooted trees, rotating trees (e.g., vertical vs. horizontal), rotating branches in trees, monophyletic groups/clades, non monophyletic groupings, outgroups vs. ingroups and more.  Oh in addition we will show the awesome Tree of Life movie that we did not get to on Friday. See below

Lecture 3 will then focus on characters and on tracing character evolution on trees.  Among the topics we will cover include traits vs states, homology, ancestral vs. derived, synapomorphies, and the many faces of homoplasy.  Am planning to start posting slides from the class after lecture hopefully starting soon.  But I keep refining them so not going to post before I am close to done ….

Any comments or suggestions welcome …

BIS002C "Biodiversity & the tree of life" Lecture 1 tomorrow: Intro to phylogeny; #UCDavis

Well, tomorrow begins some serious craziness here at UC Davis for me.  School started today for the Fall Quarter here and tomorrow a class I am co-teaching (with Jim Doyle and Susan Keen) has its first lecture.  The course is labelled BIS002 C “Introduction to Biology”.  It is the third class in a three course/three quarter series.  BIS 002A covers molecular and cellular biology, genetics and related topics (just lecture).  BIS 002B covers the principles of ecology and evolution (with a lab).  And BIS 002C covers “Biodiversity and the Tree of Life” (also with a lab).

A few things to note.  First, each of these courses has to get taught each quarter here, since so many students major in or do something related to life sciences here at Davis.  And on top of this, each course has some 6-700 students (or more).  Alas, since we do not have a lecture hall big enough for this number of students, we have to give each lecture twice.  This means that, for BIS 002C which I only teach a little over a third of, I end up giving 24 lectures over three weeks (2 sections x 4 lectures per week per section = 8 lectures / week).  It is a bit crazy shall we say.  But fun too.  In total, some 2500+ students go through the series per year.

So, tomorrow it begins for me for 3+ weeks of intensity.  But I look forward to it I guess each year since the topics I cover I hold near and dear to my heart.  For the first week of the class, I will introduce the students to phylogeny (what is it, what are phylogenetic trees, how do we infer them, how do we use them).  Then I spend two whole weeks discussing microbial diversity – phylogenetic and functional.  I view this as a privilege in many ways as it is somewhat unusual for 8 lectures to be used in an introductory course on microbial diversity.

Anyway, I will be posting here some comments and details about the class and I thought I would give this tiny introduction.  Tomorrow we will spend some time introducing the course and discussing practical details and then I will get 20-30 minutes to introduce students to phylogenetic trees.  The whole series currently uses as a textbook “Life: The Science of Biology, 8th Edition” by Sadava et al (we are switching over to the 9th edition but not for this quarter) and for class I try to use as many figures from the text as possible.  But I also mix in my own here and there.

Here is an outline for tomorrow after the course intro

1. Introduction to biodiversity of life
2. Discussion of phylogeny
   * Definition
   * Show a few trees
3. Discuss how trees are oversimplifications of true evolutionary history but are useful
   * Populations not shown
   * Not all lineages shown
   * Complication of reticulation/gene transfer
4. Describe different components to a tree
5. Walk through the course outline using a tree of life as a guide
6. 3-4 examples of uses of phylogenetic trees
7. If time permits show a little movie (see below)