On smurfs – playing around with genetic drift in a spatially structured population

A lot of people seem to struggle with the idea that stochastic processes can produce deterministic outcomes on grand scales. A prime example is genetic drift and how its results (and it’s interactions with silent mutations) can be used to assess past population structures and sizes.

As I’m increasingly finding that a good way to better understand a concept is to build it into a little model where you can tweak the parameters at your will (and also as an exercise in try-except-constructions and classes), I’ve written some Python code that simulates neutral evolution(0). It doesn’t show anything new, but it may be didactical. The bottom line is the following graph, which shows how the diversity of a population (the number of different alleles present) starts to oscillate around a point of equilibrium between mutations introducing new variants and existent once drifting out of the population after a while, the level where that equilibrium is reached being function of the population size and irrespective of initial diversity.

The total diversity (number of different genotypes) of a population over time under 3×2 conditions – different initial diversity and three different population sizes; log-scale on y-axis.

What this little toy of mine can not measure is different types of diversity: In my model, all variants are created equal, and don’t stand in any special relation to each other, so when I assume a possibility space of 100000, if and when a carrier of variant #73489 undergoes a mutation, the result can be any of the remaining 99999 possible variants. In reality, variants form a network of possible transformations, with variants that are closer or more distant from each other. So my model (even if it allowed to change the size of a population over time, which would currently require some ugly hacks) is insufficient to distinguish a large population that is the result of a recent expansion from a medium-sized population from a large population that is the result of a not-so-recent expansion from a small population – both will show less diversity than is expected for their size, from which fact, absent a way to tell different types of diversity apart, we could only conclude (assuming we know the mutation rate and reproduction patterns) is that either of these things must have happened. In reality, one would have (say) hundred different variants most of which are close to each other (converging at just a few right before the expansion started), while the other might have the same number of variants, but those would be more distinct from each other. Another feature of real genomes absent in this simple model is that you can track the variants of multiple genetic loci individually. This allows to diagnose subdivisions of the population when the limits of the ranges of individual variants correlate, which they shouldn’t if sheer distance in an otherwise uniform population is all that’s at work.

These shortcomings notwithstanding, the model is sufficient to see the effect of population size on gross diversity.

The baseline

Let’s start with a very small population, i.e. 50 smurfs.(1)

Link

A must read by the always superb Kate Clancey:

“I had no power to say ‘that’s not okay:’” Reports of harassment and abuse in the field

The transition from quantity to quality, in multicolor pictures

In many natural systems, we observe phase transitions, or sudden emergence of qualitatively different behaviour once a certain threshold is reached through gradual, quantitative changes. This insight opens some interesting doors for conceptualising (the evolutionary roots of) human language, but this isn’t the post to elaborate on these. Here, I just want to offer a graphical illustration, using a rather more simple model, of how small, barely perceptible changes of the local properties of a system can drastically change its global properties.

Below, you see black and white pictures of a 2-dimensional random matrix of 0s and 1s, 1s black. The three pictures represent the results for three different probabilities `P` for a dot to become a 1 during the stage in which the matrix is generated, 57%, 59%, and 61%. I dare you to guess which is which without enlarging the images in order to be able to read what it says in the title bar! I know I couldn’t for my life, they all look the same to me.

But exactly within this range of values of `P`, the global property of connectivity or permeability of the system changes in dramatic ways. If, instead of blackening all 1s, we sort them into clusters of mutually connected spots (through paths only using the four main directions), and code those clusters with color, we’ll see that with P-values as high as 0.585, we still get a haphazard assemblage of clusters of various size (in this and the following picture, the single largest cluster is coded black, the second largest red, and for the rest, the other colors are recycled as often as may be necessary, so when you see a large patch of, say, orange, it doesn’t necessarily mean that they’re indeed one and the same cluster, but for black and red you can be sure they are):

Alas, once we move up to 0.595, the global structure has changed: We’re no longer looking at a multitude of independent clusters of roughly comparable size, but rather at a supercluster that alone alone covers a clear majority of the 1s, with all other essentially just islands within the sea of points that are connected to the the supercluster:

Not a lot changes when we go further up to 0.6 – the islands just become smaller:

 

By just increasing the ratio of ones so slightly that you won’t even notice the difference in a black-and-white representation, we’ve come to the point where you can walk almost anywhere from any starting point without ever stepping on the zeros.

(Code below fold)

Creationist linguistics: It exists

For many years, my only contact with Creationist linguistics was through a parody – a parody of intelligent design in general more than of Creationist linguistics at that. I’m pretty sure that q_pheevr, the author of “The Wrathful Dispersion controversy: A Canadian perspective“, meant to ridicule Intelligent Design proponents by translating their arguments into a realm where they are even more blatantly absurd than otherwise.

Apparently, that’s still not absurd enough for some real folks out there. I particularly love the knots this guy (Wieland, 1999) has to get into within one and the same paragraph:

I think it is misleading to talk about any ‘evolution of language.’ Changes in language come about mostly from humanity’s inventiveness, innate creativity, and flexibility, not from random genetic mutations filtered by selection. And languages studied today in the process of change appear mostly to be getting simpler, not more complex. [...] Perhaps ‘devolution’ of language would be a better term.

His factual errors are only icing:

[...] the Sino-Asiatic language family, which includes Chinese, Japanese and Korean [...]

Duursma (2002) is if anything even funnier. 

(With a nod to Anatol Stefanowitsch at Sprachlog (German))

Bred to die

Once every while, some creationist will come along who seems to believe that the fact that animals and humans die represents evidence against evolution. The “logic” is that natural selection should inevitably favour longevity/potential immortality since an infinite lifetime means infinite possibilities for reproduction. I’ve always considered this “proof” a proof of the person’s mathematical illiteracy and little else – after all, with any non-zero death rate, the chance to actually survive that long converges to zero with longish finite lifespans, and so does the benefit from potential immortality.

The last time this argument came up, I used the opportunity to practice my new programming skills, so here’s a little script that simulates mortals and “immortals” evolving within the same population. You can play with the parameters, such as extrinsic death rate and rate of reproduction, and decide whether there is a trade-off to (potentially) living longer in terms of slower maturation (there should be, because that’s what we observe in real animals), and whether there’s a bias in life-shortening vs. life-prolonging mutations (there should be, again). We’re pretending that (potential) immortality is actually physically possible for complex organisms, and in fact that once you’re able to survive 160 years, you might as well be immortal.

Here’s what you get when you run the model with biased mutation rates (.003 for life shortening mutations vs. .001 for life-prolonging ones), and no trade-off, and a rate of reproduction of 0.25 per adult per year. We see that there’s a lot of noise, but on the long run the type which lives up to 57 or so years carries the day. Beyond that age, being hypothetically able to live longer doesn’t carry enough of a benefit for selection to overcome the direction of drift when you aren’t going to live that long anyway:

And here’s what you get when you include a very moderate trade-off: The most-short-lived individuals reach maturity at 4 (1 year before they’re bound to die), while the immortals reach it at six, and intermediate degrees of longevity have varying chances of joining the club when they’re in between. In effect, this represents about 10% later maturation per doubling of lifespan, which looks like a very fair deal, but alas this is enough to clearly favour the shorter lived variants over immortals:

Code below fold. Don’t tell me it’s slow, but feel free to tell me how to make it faster:

Hierarchical structures, and linguistic wars

Via Norbert Hornstein’s blog, I came across a recent paper in Royal Society Proceedings B (Frank, Bod, and Christiansen, 2012). In this post, I will present my own two cents on the new “language wars”, focussing on Frank et al.’s arguments against overestimating the roles played by hierarchical structure in language use, and on Hornstein’s treatment or lack thereof as exemplifying the defensive reactions generative linguists often display towards any and all challenges from outside.

Peripheral anatomy and cognitive traits in crows, with a word on humans

An new paper in Nature Communications (Troscianko et al, 2012; see also the discussion at Not Exactly Rocket Science) suggests that the extraordinory extent of tool use by the New Caledonian crow (NCC) is accompanied by a morphology that differentiates them from other corvids. Specifically, a straight bill and a ever so slightly different position of their eyes enlarging their binocular sector, i.e. the part of the visual field where they have increase depth perception, allows them to follow what they’re doing with their tools much better than other crows, even when operating in narrow openings.