Field of Science

Planning my CIfAR talk

OK, the CIHR proposal is presentable and has been sent to the internal reviewers, so now it's time to start thinking seriously about the talk I'll give at the CIfAR Integrated Microbial Diversity meeting on Sunday morning.  The talk's title is "Sporadic Sex? Scary Food?  The biodiversity of bacterial competence", but I'm going to also talk more generally about the genetic diversity of bacteria, especially the diversity within a single species.

I've started making an outline:
  1. Genetic diversity in eukaryote species:  Not a lot.  The members of a species typically have very similar chromosomes, with the same genes arranged in the same order.  Different versions of the genes differ by no more than a few %, and there are very few differences in gene content or arrangement.
  2. We take this for granted, but it's probably one of the many consequences of sexual reproduction.  Individuals with chromosomes whose genes have been rearranged (by, for example, an inversion) are at a big disadvantage in sexually reproducing species, because such chromosomes don't pair properly with normal chromosomes at meiosis and the resulting gametes often have two versions of some genes and none of others.
  3. What about in bacterial species?  I should probably start by considering what we want 'species' to mean in Bacteria.
  4. For most eukaryotes, the 'biological species concept' is the most useful way to group individuals into species.  In its simplest form, it says that all individuals that can reproduce sexually with each other should be considered members of the same species.
  5. But bacteria don't have eukaryote-type (meiotic) sexual reproduction.  They don't have any process that regularly combines the sets of genes from two individuals and then shuffles them into two 'recombined' sets.  Maybe I'll talk here about what bacteria do have that puts genes into new combinations, or maybe I'll leave this till later.
  6. But we can define bacterial species as groups of individuals for which at least 50% (75%?  90%?) of their genes are recently descended from a common ancestor (recent enough that sequence divergence is no more than a few %), and for which most of these genes are syntenic (arranged in the same order).  This definition works for most of the groupings that microbiologists consider for other reasons to deserve being called species.
  7. For this 50% or 75% or 90% of the genome, the members of a bacterial species are a lot like a eukaryotic species.
  8. But these species are far more genetically diverse than are eukaryote species, because of the other 10% or 25% or 50%.  Many of these sequences are stupendously diverse...
That's as far as I've gotten.  I mustn't forget that I only have 25 minutes to talk, plus 5 for questions...


  1. You start by noting that within a eukaryotic species there isn't much genetic diversity, but then upon trying to define what a bacterial species might be you start narrowing the range of genetic diversity. Then you note the greater level of bacterial diversity (relative to eukaryotic) because of the other 10% or 25% or 50%. So you lost me.

    It seems to me there is a fairly wide gap in intra-species diversity between plants and animals. This might be due to the largely different levels of tolerance to polyploidy (animals tolerating ploidy differences far less than plants - esp. angiosperms). If you have several genomes to draw upon you can tolerate an inversion or a major chromosomal translocation because of the redundancy.

    But there may be another reason that genetic diversity - at least in terms of the straight DNA sequence diversity - is so different between prokaryotic and eukaryotic systems. The eukaryotic systems, at least the more sophisticated large critter systems, have to regulate gene expression in many different cell types and have many more regulatory mechanisms that will eventually translate (pun intended) a more limited sequence space into a wider phenotypic space. And at the end of the day - its really all about the phenotype.

  2. It's certainly true that these ideas need a lot more thinking. A quick google search suggests there's not much data out there about intraspecies genome diversity in eukaryotes.

    If we were to define eukaryote species as groupings of individuals who shared >99% of their genes (excluding obvious new genetic parasites) with no more than, say, 1% sequence divergence, which kinds of organisms would be included and which excluded?

  3. Sharing a percentage of genes in order to qualify as a species (or be split into another species) gets complicated in plants for at least a couple reasons I can see.

    First, as genome size gets quite large, a much larger number of genes would be required to reach the 1% threshold. Thus two Arabidopsis-like samples would need far fewer genes to be divided into different species than say two Allium or two Triticum-like samples.

    And secondly, simply defining what a gene is becomes a bit arbitrary for genomes where there is so much redundancy. Do we count all putative ORFs (regardless of whether they are ever transcribed)? Do we count all transcripts (regardless of whether they're ever translated)? How do we deal with different mRNA splicing events?

    I originally took exception to the description of eukaryotic genetic diversity as "Not a lot". But the more I think about it the more I'm more inclined to think its phenotypic diversity that matters more, and there seems to be a sufficient amount of that.

    And as for levels of intraspecific genetic diversity (at least within angiosperms) it might be best to look at genomes where quite a bit of sequence has been determined. Some of our crop species may help in this regard.


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