Abe

Microcosm

abe — Tue, 06 May 2008 18:18:43 +0000

Carl Zimmer’s new book:

http://darkside.newsvine.com/_news/2008/05/06/1470427-book-review-carl-zimmers-microcosm

Nine lives of Myxococcus

abe — Tue, 15 Apr 2008 13:24:28 +0000

Fiegna and Velicer (2005) decribe a series of experiments with nine natural isolates of Myxococcus xanthus in the PLOS Biology paper “Exploitative and Hierarchical Antagonism in a Cooperative Bacterium” (PLoS Biology. 3. 11. e370. 2005). Using sporolation efficiency (D) as a measure of social productivity, the authors describe pairwise competition experiments (n=9;n(n-1)/2=36) to reveal 1) a dominance hierarchy and 2) a propensity for some strains to “exploit” other strains. The depression of sporolation efficency in most mixed cultures leads the authors to suggest that each strain may be socially limited, or even outright antagonistic toward other strains possibly through divergence and isolation via local adaptation.

NYT-Judson blog

abe — Wed, 26 Mar 2008 13:37:55 +0000

Olivia Judson gives a layman’s summary of the significance of studying beneficial mutations.

http://judson.blogs.nytimes.com/

Going vinyl: Replaying life’s record

abe — Wed, 27 Feb 2008 17:46:23 +0000

Travisano et al. (1995) is an elegant, tidy and and helpful study. But I’m hesitant to take away larger lessons from such an experiment. As they note in the last paragraph, it is over deep time that the cumulative effect of adaptation, chance and history ultimately shape the evolutionary trajectory of a taxon. The “Replaying of life’s tape” question is a macroevolutionary one and, as they state in the second paragraph, the experiment simply can’t be done. While their bacterial experiment is instructive and demonstrates a method of teasing apart fundamental forces of evolution on a nano-evolutionary scale, the relative contribution of chance, adaptation and historical contingency during the course of evolution cannot ever be extrapolated from their findings. For example, over long periods of time, cell size, for which they demonstrate “chance” evolution, might be under heavy adaptive selection. Maybe this is an obvious point that they themselves make, and i’m sorry I will miss the discussion, but here’s a modified analogy:

A vinyl record consists of tens of thousands (maybe more?) of bumps imprinted along a single spiraled groove. In the lab we can’t even replay a whole bump.

Their final comment that “Over much longer periods, the footprint of history might eventually become too deep to be obscured even by intense selection”, is interesting, but I think possibly backwards. Intense, prolonged and gradual selection, over deeper time, will more likely obscure history and circumvent local contingencies of genetic happenstance.

A Borg Theory of Bacterial Systematics

abe — Tue, 12 Feb 2008 22:17:24 +0000

From Aristotle, Linneaus, Darwin, Mayr to Hennig to…….Cohan? Ideas on the fundamental “units” of the biological organization of individuals.

Let’s forget the word “species or “populations” for a second and just consider that all individual organisms have a definable relationship to one and other. We all share common ancestry; you, me, the tuna fish you ate for lunch, the bacteria that was in the mayonaisse and one of those Sulfolobus cells from Kamchatka (thanks Darwin). But we can group each other according to similarity (thanks Linneaus), which turns out to be an indirect, but generally good measure of relatedness (Darwin again). When individuals over time are trading, sharing, swapping DNA, we see that those individuals are inescapably part of a collective meta-individual, a kind of amorphous borg (http://en.wikipedia.org/wiki/Borg_(Star_Trek)). We can call these meta-individuals species, populations, sub-populations, meta-populations, whatever depending on the magnitude and frequency of exchange and relatedness. But, cohesion within these meta-individuals depends purely and simply on DNA exchange, without which individuals will diverge and eventually be cutoff from the borg. With microbes especially, this DNA trading can occur at vastly different rates and between a large continuum of individual relatedness. Over time, space and local ecology can conspire to diminish or enhance DNA trading between individuals. But whatever the forces that ultimately partition groups of individuals, natural groupings of individuals, representing the result of evolutionary history, need to be defined according to one’s view and interests.

Cohan emphasizes the importance of an ecology-based theory of systematics, no small task. While the ecotype concept has to part of the equation for uncovering the natural groupings of microbes, it seems that, as a starting point we can take a purer and simpler approach, one that ultimately informs the ecotype, the borders of which seem as elusive as ’species’ and depends on too many variables and nuances. It seems inevitable that whatever we decide to do, artificial demarcations are neccesary. So, for starters, in order to describe the natural groupings of individual organisms, why do we need to know anything about the ecology at all?

Here’s wiki’s definition of systematics:

“Biological systematics is the study of the diversity of life on the planet Earth, both past and present, and the relationships among living things through time.”

Our theory of bacterial systematics can be….. evolution. Look at as much genetic data as you can and do your best to explain patterns of relatedness. Where natural groupings exist, develop a hypothesis about evolutionary forces and test it. Ecotypes will become part of the explanation, but every bacterial meta-individual will have its own unique story.

Some things are everywhere, and with time the environment selects

abe — Wed, 30 Jan 2008 19:56:25 +0000

I would like to suggest a factor that may be important in the “everything is everywhere” discussion: Time

Whitaker et al (2003) clearly demonstrate that, at least for niche-deprived extremophiles like Sulfolobus, populations diverge genetically according to geographical isolation and are not partitioned according to intrinsic niche characteristics (fig 1). So on a microevolutionary scale, there appear to be barriers to dispersal that prevent (or delay, to think temporally) random mating (panmixia) among Sulfolobus populations, leading to detectable differentiation between geographical locales. But, Sulfolobus is a globally distributed taxon and even if global dispersal is limited, it may not be impossible, but just require more time. This in no way diminishes the claim of endemism, but over deep time panmixia may rule, even among extremophiles. This view would predict that taxa with fewer barriers to dispersal, would have lower levels of population structure due to the shorter length of time required to outcross.

Bacterial latitudes

abe — Sun, 27 Jan 2008 23:55:33 +0000

On the latitudinal gradient question, Fierer and Jackson 2006 answer “no” to the correlation of diversity with latitude:

http://www.pnas.org/cgi/reprint/103/3/626

This article, “The diversity and biogeography of soil bacterial communities”, neatly summarizes some general trends in the distribution of bacterial diversity using an RFLP approach on 16S. They set their study in the context of the omnipresent quote, attributed by them (incorrectly, apparently) to Beijerinck (1913): “Everything is everywhere, the environment selects”, or as Becking (1934) actually put it, “alles is overal; maar het milieu selecteert”, more accurately translated to “Everything is everywhere, but the environment selects”. (Rutger de Wit and Thierry Bouvier argue the “but” is an important part of the meaning (Envron.Microb. 2006. 8(4), 755).) Anyhow, Fierer and Jackson show that the best predictor of bacterial diversity is soil pH and that microbial biogeography is “controlled primarily by edaphic variables”.

I’ll read the assigned paper now and see what they say…..

Why I am taking this class

abe — Thu, 24 Jan 2008 00:39:47 +0000

I am looking forward to reviewing and discussing the current literature on microbial genome evolution. Generally, I am interested in the evolution of genomic variation, and the origin of major genomic features (e.g. genes, introns) and processes (e.g. recombination, mutation). Specifically, I am interested in how principles and predictions of population genetics can be tested using prokaryotic systems, a group whose ecology and genetics I am largely ignorant. This class will fill a void in my training as a genomicist, as my time at UNH has been spent studying eukaryotic genomes, primarily the genome of Daphnia pulex, an important ecological model organism. This class, with its emphasis on ecology and experiment, may help me better relate genomic observations with natural history and ecology.