Tuesday, June 25, 2013

Dogs, crows and garbage: phenogenetic drift

Scavenger hunts
Monday's the day trash gets picked up in our neighborhood. When I was out running early this Monday morning, I passed a scene I see not infrequently -- a group of crows congregated around a plastic trash bag, its contents spilling into the street and the birds tugging at anything in it that looked appetizing.  As I ran by, two of the birds flew but one brazen bird stayed right where he was, guessing that I was no threat to him.

Crows are very smart, and not just because they've figured out how easily plastic garbage bags are breached.  I've also seen them congregated around trash barrels with the lids knocked off.  I've never seen them actually take the lids off, but it must be they do.  When I was a child it was dogs who got into the trash.  This was before leash laws, when it really was a dog's life.  Dogs we keep as pets now have only ancestral memory to recollect the halcyon days of wandering the streets untethered on trash day.  Now it's a crow's life.

But sometimes it's bears, too.  A mother bear and her three cubs were making the rounds of our neighborhood a few weeks ago, knocking down bird feeders and compost bins, and this isn't an unusual occurrence.  The wilding of America?

This morning's sighting reminded me of a piece in the February 21 New York Review of Books by Russell Baker in which he reviews a book by Jim Sterba, Nature Wars: The Incredible Story of How Wildlife Comebacks Turned Backyards into Battlegrounds. I have not read the book, though now that I'm remembering this, I just might have to. Unhappily for the author, Baker's is one of those pieces that makes you think can skip the book, even as he gives it a fine review.

In any case, Baker describes seeing a pair of foxes mating in his garden situated, he says, just two blocks from the county courthouse in the bustling center of town. The encroachment into human-populated areas of animals who were once sighted only at a distance is becoming increasingly more common.
Sterba ... argues persuasively that events like this foxes-in-the-garden sighting are evidence that humans are losing some kind of property rights struggle with creatures of the wild. He cites an extensive history of resolute and sometimes blatantly hostile real-estate invasion by beavers, Canada geese, wild turkeys, and white-tailed deer, all of which were once assumed to be picturesque and even lovable denizens of the dark and safely remote forest. In-town appearances by coyotes and bears are now commonplace in communities across the country, and trespassers in my own garden, aside from the foxes, have included groundhogs, possums, skunks, feral cats, and one blue heron that ate all the koi with which we thought to beautify the fish pond.
Lucky heron.  As Baker points out, in the last fifty years these animals have discovered that life can be a lot easier closer to town, and food a lot more abundant.
The woods have no garbage cans and dumpsters filled with discarded food, no lovingly tended tomato plants, no ready-to-pluck dahlias and nasturtiums, no tasty, newly planted shrubs. 
Best of all from the animal viewpoint, humans are no longer the same dangerous predators who once pushed the beaver close to extinction and reduced the entire North American white-tailed deer population to a trifling 500,000 scarcely a century ago [there are now 25-40 million]. Sterba believes that this human withdrawal from combative relations with woodland animals is one of the major causes of their proliferation: man as killer has undergone a softening change.
Indeed, the crow standing in the middle of the road waiting for me to run by its food source is evidence of exactly that.

It doesn't matter who does it
But here's the thing -- whoever's doing the scavenging, there's still garbage spread all over the street.  And this is an apt metaphor for an important way that evolution works.  Yes, gene function is often conserved, so that the same gene (Pax6) is involved in photoreception in the eye of fruit flies and frogs and humans, and the human form of the gene can be transplanted into even distantly related species and the eye will still be made.  But it's also true that often a trait is conserved but the genetic scaffolding is very different.  Natural selection might preserve the phenotype, the trait, but it can't see the genotype, leaving it free to vary.

Ken and his then post-doc, Malia Fullerton, published a paper in Theoretical Population Biology in 2000 describing just this, though others have described it as well (reviewed by Brian Hall in his 2003 book, Keywords And Concepts In Evolutionary Developmental Biology.) The effect is called 'phenogenetic drift' to indicate that the trait's genetic basis can change. This is not the same as genetic drift, which is when genetic variation that has no effect on a trait, or at least on reproductive success ('fitness'), changes over the generations, and it's not the same as phenotypic drift, when traits vary over generations but that variation doesn't affect fitness.  This happens, therefore, regardless of whether there is selection, even strong selection, or not.  A prerequisite, or partial one at least, is that many genes contribute to the trait, so that different combinations of variants in these genes can lead to similar traits.

Hall uses the example of proteins that make up the lens of the eye. They can be unrelated among taxa, as long as they let light pass through. Kazu Kawasaki, a very skilled research scientist in our lab, has written a number of papers describing the evolution of mineralization in vertebrates. One of his early papers is on the changing genetic basis of vertebrate teeth. He has found a gene family, that he calls SCPP genes, that varies widely among species, and yet contributes to the formation of mineralized tissues -- teeth and bone -- in all of them.

As Hall concludes his section on this subject, "Phenogenetic relationships are less determinative for more complex traits."  There are many genetic pathways to being tall, or to developing heart disease, or to being a fast runner  And that's before we even throw environmental factors into the mix.  Genetic determinism, which we've blogged about often, is simply too easy to assume, often incorrectly so.  When you look out the window on trash day and see garbage strewn all over the street, don't leap to judgment about who did.  It's only when you find the bear scat or a crow feather that you'll know.  But even then, do allow for the possibility that the neighbor's dog got loose.


Holly Dunsworth said...

Do you consider phenogenetic drift to be a synonym for relatively weak selection? (I say "relatively weak" because selection appears to sometimes prevent any genetic variation.)

Anne Buchanan said...

Phenogenetic drift is an outcome, so no. Also, selection can be strong but because it's on the trait and not the genetic architecture of the trait, phenogenetic drift can still occur.

But, given that anything that can happen does, sometimes phenogenetic drift happens when selection is apparently strong and sometimes it does not.

As you say, sometimes selection appears to prevent any genetic variation, but sometimes not. So, as with all of evolution, there are no rules!

Holly Dunsworth said...

Selection is also an outcome isn't it?

Ken Weiss said...

No. The idea is that many genes contribute to a phenotype. Many different genotypes can contribute to a similar phenotype, so without selection, each allele just drifts. Say gene 1 with allele A and a, and gene 2 with alleles B and b, and stature is how many capital-letter alleles you have. Very short is genotype aabb. Sort of short is aAbb, aaBb, aabB, or Aabb. Same stature, different genotypes. Each allele just drifts.

Now think of this under selection (and extend to many contributing genes, not just two). Still many genotypes can give same phenotype, and hence same selective value. But because the selection is distributed over many alleles and genes, say tens or hundreds as we see for so many traits (like stature), and because in this circumstance the same alleles, in different combinations can be associated with different phenotypes (some favored, others not), even under selection each allele's frequency will basically evolve by drift.

Anne Buchanan said...

I think of it as a force more than an outcome. Help me out with this!

Ken Weiss said...

In my usage and I think general usage, selection is the process (or 'force'), and the 'response' to selection (or the resulting adapted trait) is the outcome.

This is semantics only, I think, unless you have something else in mind.

Holly Dunsworth said...

For both comments.... Thanks.

Holly Dunsworth said...

I'm not having trouble with phenogenetic drift (was trained well by some folks I know back in grad school!) ... just couldn't help but wonder about what I asked in my initial question. And then my question about "outcome" reflects my search to find real meaningful differences among these processes. I can't find any yet.

Holly Dunsworth said...

That's not true. I can't find *many* yet is what I should have written.

Ken Weiss said...

Difference between what processes?
The idea is that, whether under selective pressure or not, the reproductive effect on individual alleles contributing to a trait, when many genes are contributing, can be that their frequency changes mainly by chance (when no selection, totally by chance; when selection, for most alleles, nearly just by chance).

Selection can be strong, weak, or absent (well, s=0 exactly is rather mystic, as we say in our MT book). Purifying selection that allows little or no variation, can be strong, actually.

The point is that selection operates on individuals and its effect can be so spread among individual alleles that they change frequency largely as if just by chance.

Does this clarify?

Holly Dunsworth said...

Thanks Ken. I don't need any clarification. I was just chatting away. Sorry to beg the effort!

Holly Dunsworth said...

I didn't realize that you and Malia were among the first to describe this. Were you *the* first?

Ken Weiss said...

I believe so. I think someone, whose name I can't recall (Waddington? Penrose?) may have used the term long ago, but not in the sense Malia and I did.