Corrections, corrections

In my post about microsatellites and mitochondria there were a few errors. Fortunately, the author of the paper that formed the basis for a large portion of what I wrote also happens to be my professor. I petitioned him for review:

I stated that mtDNA is powerful as a tool for determining relations within a species. It should have read that mtDNA is useful for determining certain evolutionary patterns. There’s little excuse for this mistake.

I said genetic variation as determined by microsatellites is an indicator for population health. This may be true, but it isn’t possible to really be sure. If natural selection is acting upon these points, then populations with more variation may have better fitness.

I stated that populations are managed via arbitrary geographical lines. I actually meant political lines, but it’s unclear if that is true. This depends upon the level of coordination in management and conservation between the U.S. and Canada, and precisely where the borders fall. More on this later. Update: The political lines largely follow the geographical divides. There is some overlap, but it is minor.

I’ve also corrected some minor language here and there, as well as a citation (the paper I used was from 2004, not 2003). All the updates can be reviewed on the original post.

Thanks to Chris for his help.

Microsatellites and mitochondria

Mitochondrial DNA (mtDNA) is useful for determining the phylogeny, or relationships, between closely related species. It is inherited, generally, only from mother to offspring, so it doesn’t face problems such as recombination since it isn’t recombining with other DNA before being passed on (except through horizontal transfer, or “genetic swapping” between bacteria).

One recent discovery using mitochondrial DNA has found that a sort of “pre-human” was walking around while humans and Neanderthals were still rocking out.

The sequence indicates the hominin’s line diverged about a million years ago from the line that gave rise to both humans and Neanderthals and that split about 500,000 years ago.

That makes it younger than Homo erectus, the pre-human that spread out of Africa to much of the world about 1.9 million years ago.

“It is some new creature that has not been on our radar screen so far,” said Svaante Paabo, a colleague of Krause’s who specializes in analyzing ancient DNA.

And it would have lived near to both modern humans and Neanderthals. “There were at least three … different forms of humans in this area 40,000 years ago,” Paabo said.

The article goes on to state that more research is needed to determine just where it qualitatively sits on the evolutionary tree. My point, however, is that mtDNA has proved useful in this analysis, giving a tentative quantitative determination and a tentative qualitative indication.

This is all in stark contrast to microsatellites. These are short tandem repeats, or units of repeating DNA sequences. For example, CACACACACACACACACACA is commonly seen throughout eukaryotes and the chloroplastic genomes of plants (usually every few thousand base pairs). They are generally neutral.

Microsatellites have relatively high mutational rates for a variety of reasons. Whereas in mitochondria the mutational rate can partially be chalked up to the fact that mitochondria is bacterial in origin, microsatellites have polymerase slippage to thank, or bad DNA replication, let’s say. Other studies suggest unequal crossing-over. At any rate, this mutation rate lends itself to population studies using microsatellites.

By using microsatellites as genetic markers, it is possible to determine genetic variation within a population. This works for investigating both temporal and spatial population structure, two important factors in management and conservation of species. For instance, Lage et al. 2004 looked at Atlantic cod populations ranging across Browns Bank, Georges Bank, and Nantucket Shoals. At the time of the research, the Gulf of Maine cod were treated as a separate stock from the Nantucket Shoals and Georges Bank Atlantic cod. Browns Bank cod were even more separate as a stock since they are in Canadian waters. Using microsatellites, the researchers found Nantucket Shoals cod to have a distinct population structure from those on Georges Bank and Browns Bank, which were genetically similar. One likely reason is due to currents which keep Georges Bank cod on Georges Bank as well as somewhat rare currents which likely transport larvae from Browns Bank over the Fundian Channel (which adult cod are unlikely to traverse since they are ground-huggers and the channel is deep and cold). The conclusion is that the health of Atlantic cod populations might be better served by treating them as separate stocks based upon the discovered genetic variation, instead of the current method of utilizing particular geographical lines which may not reflect all population ‘barriers’.

The shortcoming, however, with microsatellites is that they are not useful for deep phylogenetic analysis. Their high mutation rate makes them virtually useless after a few thousand generations; they are good for pedigrees and population structure analysis, but they do not offer insights into distant relationships. Occasionally they may remain the same or nearly the same over long periods of time, but the rhyme and reason probably has nothing to do with the microsatellites themselves. Instead, they likely are located near a site of selection on a locus, thus conserving them for longer than just those few thousand generations.

Lage CR, Kuhn K, Kornfield I. (2004) Genetic differentiation among Atlantic cod (Gadus morhua) from Browns Bank, Georges Bank, and Nantucket Shoals. Fishery Bulletin, 102:289-297.

Update: Thanks to Chris Lage for offering his advice and corrections on this.