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.

Advertisements

8 Responses

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

    Just a point of clarification – it was not a sort of ‘pre-human’ – it was a hominin of a different lineage, but it apprently wan’t ‘pre’ anyone that is a live today.

  2. “God might have created, and doubtless did create, the world with all the marks of antiquity and completeness which it now exhibits.”

  3. I was quoting the article when I said “pre-human”, but I used scare quotes instead of quotation marks since the statement is a little misleading.

  4. Also, the Fundian Channel is referenced as the Northeast Channel in the picture.

  5. So, here’s a question from someone considering embarking on a phylogeographic study of one widely dispersed bug species: Which would you use?

    First assume the microsatellites and their primers are already known from previous studies. Then assume they’re not. Affect your decision?

  6. I’m not going to pretend to be qualified to answer this with more than a basic, exploratory guess. Here is an answer from one of the authors (Chris) cited in this post.

    One might start by looking at mitochondrial D-loop (ie. control region) sequence which may have intraspecific variation at different geographical locations. One might then look at any microsatellite variation from previous published studies. If there are no published microsatellite primers one could develop them but this is both time-consuming and expensive. Both types of markers should be first examined across widely separated geographic regions first to see if there is any signal. If there is variation at widely dispersed areas then there may or may not be signal at smaller geographic locations. If there is too much variation at these markers to see any strong signal, then one might investigate variation at more conserved regions of the mitochondrial genome (i.e. Cytochrome-B, etc.).

  7. […] My favorite post from this month was the one on mitochondria and microsatellites. I wrote about the difference between how the two are utilized in studies on populations and […]

  8. […] The reason is clear: there is nothing but chance that can maintain a neutral mutation. (This is why microsatellites are great for studying short-term generational changes, but not deep evolutionary […]

Leave a comment

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

%d bloggers like this: