Ant misbehavin'

There's a new paper in PNAS that looks like one that really is interesting and relatively important. It is a story that made the popular science news, and reports paleontological findings with at least some interesting aspects.

This is the discovery of fossils ants and other insects, preserved in amber (tree resin, basically) that is estimated to be about 95 Million years ago, along with other species of plants. The insects are shown here. Apparently (we're no experts!) it has been thought from the available evidence that the ant lineages originated to the north (Asia or North America), rather than Europe. If the dating of this site is accurate, then the old idea is incorrect. At least, by this ancient time clearly recognizable ants were already in Africa.

Now this is not a story to shatter evolutionary theory, though overturning accepted views, no matter how arcane, gets played in the news headlines as being transformative. But it does seem to qualify as new and worth discovering and so on. That is, its appearance in the news doesn't seem to qualify as just more Big Discovery hype.

There may well be ecological, geological, or climatological reasons why this find is interesting. Or it could just be that, while the environments Way Back When were suitable for some of these arthropods, they just hadn't managed to get to all of them by this time, having originated elsewhere with suitable climate. So ant lovers can now start trying to explain this expansion, and EO Wilson can stop writing bad novels about ants and get back to what he does really well.

But there is something that is much more interesting to us. It's another example of a fact that is already well-known but that these specimens give us the occasion to write about. It's the very deep conservation of very modern-looking form, in this case of insects (but other groups of animals and plants show some similar characteristics).

Now, evolution is supposed to be a relentless struggle to keep ahead, to survive in changing environments (that include the ever-changing mix of other species, climate, and so on). If you look at the DNA from a group of critters like, say, ants, their sequence differences correspond to their species differences, and separation times estimated from the amount of sequence difference correspond to fossil evidence. Since Way Back When, there has been a proliferation of related species, with their own morphological differences and adaptations.

But wait! Why, then, do these very ancient fossils look just basically just like the bugs that bother you when you try to eat out on your back deck? Why can morphology stay essentially unchanged for 100 million years? Why hasn't selection or even just genetic drift (chance changes) led to changes in the form of these bugs?

The standard answer is that selection has kept it so. That means that the environments haven't changed. But why then did the species divergence also occur? Long-term stasis is not a new discovery; it was the basis of a famous, but over-hyped 'theory' called punctuated equilibrium, but that has to do with other aspects of evolution and the fossil record. For us here, what is not so clear at all is how selection keeps form so similar for so long in various lineages, yet allows divergence even in local areas as well as genomewide sequence differences to accumulate in the same way it does for less conserved branches of life. Various evolutionary ecologists, like a prominent acquaintance named Doug Futuyma, have advanced ideas about how genetic incompatibility can keep neighboring populations from interbreeding, so they retain their distinct forms and functions. But even without interbreeding as a source of variation, why doesn't form just drift--very slowly perhaps, but after 100 million years why not noticeably?

We don't have an answer, and maybe the rather superficial answer ('selection made it so') is correct. Even then, how that works with traits affected by many genes, as these insects' form certainly is, is a major question for evolutionary biology....if evolutionary biologists would think more seriously about it rather than assuming the answer is known.

We'll post on this subject again.

African diversity

The latest news from the GenoSphere is the paper in Nature reporting the 'whole genome' sequence of several Africans (described here, among many other places). We take a particular interest in this paper because some of the lead investigators are friends of ours here at Penn State, where much of the sequencing and, in particular, annotation (analysis) work on whole genome and ancient DNA genome analysis is being done.

One is Archbishop Desmond Tutu, the others are San ("Bushmen"). The rationale for this choice besides its manifest value as a publicity stunt is the legitimate representation by Bishop Tutu of the culturally Bantu part of southern Africa and the San to represent another language group. This set of sequences thus at least in a crude way spans the two major and most different populations of the African continent. We know very well that there are differences between these populations in terms of genetic variation (see Sarah Tishkoff's recent paper in Science, 2009., PubMed ID: 19407144). So this study fleshes the picture out in much greater detail (to the extent that can be done with many fewer sampled subjects).

What this study shows is, as every other human whole genome sequence has shown, a multitude of new sequence variants--new in 3 ways: some will be sequencing errors, some will be rare variants in the population that simply haven't yet been seen, and some will really be new: unique mutations between the subjects' parents and themselves.

No major 'disease' variants were seen. Of course, as Tutu's case dramatically shows, he doesn't have any major diseases, but we knew that without needing DNA, from the fact that he's elderly (all 5 subjects were around 80 years old) and in good health (he's had some diseases in the past, but apparently nothing diagnosable genetically yet -- his reaction to this was reportedly 'immense relief', in spite of the fact that he's 80 and has had cancer and TB, albeit treatable so far, a reminder to the rest of us that non-genetic diseases are probably more likely to fell us than anything lurking in our genomes).

The San individuals, too, are adults in good health. In their harsh environment, if you have a real genetic disorder you're not around to be sequenced. Variants for adult milk drinking ability, lighter skin color, or malarial resistance were not found, but that shows mainly what's expected. Skin color is genetically complex, they haven't been fighting malaria, and they're not in the northeast African populations that have adapted to life-long milk drinking.

Whether major disease or other simple trait variants are found in any given person (especially an older healthy adult) will depend entirely on the major variants circulating in their population, their frequency and strength of effect, and the luck of their genetic draw in sampling them from their respective population. Some of the first people sequenced do carry such variants, but others don't. Interesting, informative, and expected.

The great sequence differences among the San individuals was also to be expected. For some historical reasons, they have accumulated more divergence than other African populations. Probably, they are today a relict population that survived being shoved into the Kalahari desert by the expanding, more technically powerful Bantu speakers that is known to have occurred not too many centuries past. Prior to that, they may have been living in small, widely scattered bands across much of sub-Saharan Africa, with little gene flow (marriage exchange) between them. Thus, new variation would arise (as it does everywhere) but staying very local. That, plus chance (genetic drift) will allow differences to accumulate between San populations. Why so many variants were found is curious and may or may not be due to sequencing errors (time will tell), but the deep split seems robust.

The one rather loose statement being made about these samples, and one that is potentially dangerous is that the San have the most 'ancient' human DNA lineages. That's patently false. We all have had the same time since our common human ancestors. There has not likely even been more generations in the San than in other humans (this would depend on the average age at which San, and others, have borne half their children).

Instead of the San being in any way more differently human from the rest of us, their lineage is not older but has simply been more isolated from the rest. It does represent an interesting subject of study, and one long known, for which we now have good data.

These new data go into the bookshelf of whole human genome sequences.

Genome sequencing now can or at least should be moved from the Melodrama Dept to real, routine science. The technology is racing ahead, and soon around $1500 or less will buy you such sequence, indeed, one at 40x coverage--that means, each part of the genome will have been sequenced independently 40 times (on average), greatly increasing the accuracy of the billions of basepair 'calls' from the sequencing device.

(There are some technical issues with the current paper that we can just mention. It is at lower coverage level and hence perhaps slightly more error prone that 40x coverage would be. And not all the sequences reported were 'whole genome'; some were just the protein coding 'exome' parts. These are minor points relative to this post)

We're soon to be whelmed, if not overwhelmed by such sequences, most of which will go into growing data bases where geneticists can analyze the pattern of variation in all sorts of ways. Some disease-related information will surely result, but the hype, hype, hype about how each sequence reveals important disease information will stop. Or it should stop, at least. We can get on with our work, without the TV crews and material-hungry journalists.

This paper is interesting and is a first stage in getting better data on variation in Africa. So far it shows what we knew to be the case about Bantus, San, and about admixture between them in southern Africa. The sequence shows much variation between the groups, and especially among the San, but we've known that for more than 20 years (PNAS, 1989, vol 86, pages 9350-54, PubMed ID 2594772). That work was done by old friends of ours Henry Harpending and Linda Vigilant who at the time, like the current genome sequence authors, were also here at Penn State (and in our own Anthropology Department) at the time.

The lack of major new findings is what would be expected, but demonstrates that we really are learning things from the past generation of studies of genetic variation. The details of future sequences will be worth waiting for, but when they come they will not be worth shouting about.