Monday, March 7, 2011

Everything's just the same, unless it isn't

Holly's latest poem, and her typically thoughtful comments about it, raise many fundamental problems in evolutionary biology.

She pointed out that while none of us is descended from today's monkeys, humans and monkeys alike are descended from some common ancestor.  She noted that we typically refer to that ancestor as a 'monkey', and drawings of how it probably looked, look like, well, like monkeys!  So how is it that we've changed but they haven't?

The usual image of Darwinian evolution is of continual change driven by relentless competition, often likened to the Red Queen in Through the Looking Glass, who had to run as fast as she could to stay in the same place.  But if that is so, and the environment (which includes competing species) is always changing, then how can a species not always be changing?

Fly in amber; Wikimedia Commons
There are countless instances of fossils so remarkably similar to today's descendants that one couldn't tell the difference.  A squid, complete with ink and looking as tasty as today's calamari; flies in amber caught cleaning their legs the way flies do today.  Beetles and barnacles, ferns, and fish all that look just like what we can see on a walk or dip, but tens or hundreds of millions of years old.  This is nothing compared to the appearance of the some of the very earliest fossils that are known, call 'stromatolites' that look exactly like bacterial microfilms today, but are 3.8 billion years old!

This is stasis on a grand scale and it's compatibility with adaptive change that is also clearly occurring  is what Gould and Eldridge were addressing with their idea of 'punctuated equilibrium'.  Their idea was that very stable environments lead to stable ecosystems that can last a long time but that at some point and in some local area too small to be found in the fossil record, local conditions favor major adaptive change and the lucky descendants are competitively advanced enough to expand into the larger area from which we then find them in the fossil record.

(Fossilized fern, 350 million yrs old; public domain)
Take beetles, horseshoe crabs, or bacteria, in which this stasis has been seen, and compare the DNA sequences of the present-day species and what we  find is that their sequences have diverged by an amount roughly corresponding to their ancestry in the fossil record.  That is, genome-wide, they have diverged as you'd expect--even if their morphology and behavior seem to have stayed unchanged.

I was at a meeting in Brazil and discussing this with the population ecologist Doug Futuyma.  We posted on this subject last April.  Doug's idea, which he has expressed in papers, is roughly that chromosomal incompatibility prevents too much mixing among contemporary species, maintaining them as isolates even if they live in the same area. 

One explanation is that the visible traits are controlled by functional parts of the genome, that might be highly conserved over time, but comprise a minority of the overall genome sequence, so that the rest of the genome is free to accumulate functionless variation in a clock-like way.

We certainly know that the more functional parts of genomes are much slower to change, and sometimes go a long time without changing, than the less functional parts.  Presumably the same is true of traits, too.

But this is at least a bit strange, because there are in all cases, after all, lots of diverged, clearly different descendant species alive today.  Many kinds of beetles, crabs, and flies.  How did they escape from the prison of stasis?  One possibility is an observer bias: of all the countless ways to vary from a common starting point, given the chance aspects of genomic change, a species here and there might--just by chance--not experience much change, while other species under the same circumstances did change.  Afterward, our attention is drawn to the static exception, which we misperceive as having stayed put for some important functional reason.  That would be a perception bias on our part, and say nothing about Nature.

Doug dismissed that idea, saying that ecologists making these observations wouldn't make such a mistake.  His idea of hybrid sterility could explain how a number of species could stay isolated, even though living in the same place, but why wouldn't there be evolution within each?

Maybe Darwin's ideas about the steady if very gradual nature of evolution were wrong, even adaptive evolution.  Maybe it is less steady and more herky-jerky than he thought.  Maybe the environment isn't changing very fast (say, the composition of a given ocean region), and through Darwinian selection it maintains traits rather constantly, but in a somewhat different way than is usually thought.

We usually think of a gene for this and a gene for that. But if the traits we're seeing conserved are affected by many genes, and all selection does is trim off the extreme (too green of a shell, or too pale), then the central tendency of the trait, how most individuals look, can stay the same, while the underlying genes are, in fact, changing.  This is known as phenogenetic drift.

So, it is possible that our and our monkey friends' common ancestor was monkey-like in terms of its fossilized skeleton, while its genome, on average, diverged appropriately.  In some lineages, such as that which led to apes and then to us, something changed in some local population, that led to an initial species divergence.  This set up a group of animals today whose common ancestor with monkeys was a 'monkey', but whose common ancestor with each other was an 'ape'--one that may have looked like today's apes.  Each resemblance group maintains several descendant members, but there are split-off groups that diverge but themselves maintain similarities.

In any event, Holly raised the right questions, regardless of how she feels about her ancestors!


James Goetz said...

I suppose a lot of natural history involved adaptive radiation followed by more adaptive radiation, and so on. In many of these cases, the adaptive radiations allowed populations of ancestral morphologies to remain mostly intact due to purifying selection while other populations developed new morphologies while exploiting new niche, while this cycle kept repeating itself.

I also suppose that in many cases populations diverged in distance and evolved new chromosomes but little morphological change, and then the divergent populations came back to the same geographical area while interbreeding was hindered, as presumed by Futuyma.

I also noticed that most discoveries of adaptation at the DNA level had nothing to do with morphological change, so we cannot judge adaptive history merely at the morphological level.

Perhaps I'm merely describing things without answering the question why, but I'm unsurprised by the outcome, not that I've always been unsurprised by the outcome.:)

James Goetz said...

I thought of an example of what I consider and unsurprising example. Is anybody surprised that amphibians continued to thrive while amniotes exploited many habitats?

Hmm, I also need to consider if the history of this was unlikely or is my lack of surprise about it because of my familiarity with the evidence? For example, are we merely extraordinarily lucky that we have such evidence of extant "ancestral" morphologies that made it possible for Darwin to make his discovery?

Ken Weiss said...

The nested bursts of divergence would be the standard answer for the pattern of overall genetic diversity, and for reconstructing phylogenies 'cladistically' (into nested branches). That's shown, more or less for the first time, in Darwin's single figure in Origin of Species.

But why would any member stay the same? 'Purifying selection' is the standard answer, and may be right, but it says that while some species (say, beetles) diverged in all sorts of ways, some stayed absolutely changeless (at least, in terms of the traits we can see in fossils, and by extension much besides).

It is a challenge to understand how such selection would work, though various stories can be suggested.

Ken Weiss said...

Bacteria et al. are still here, but as the post and Holly's Monkey poem point out, we are descended from their ancestors and they 'just happen' to look like what's here today.

Darwin was clear about that, more so than Lamarck, and Michael Ruse wrote Monad to Man, to show the pervasive but erroneous view that evolution is 'progressive' or means progress.

So the conservation-with-divergence raises lots of questions, and I think we're largely still guessing about the answers. Clearly it's not a rarity in some senses, but just saying 'natural selection' is a form of hand-waving, given what we know about the complexity of things at the gene level. Curious to me, at least!