The Evolution of Evolvability: Gene Regulation Networks

[swamidass (S. Joshua Swamidass)]

Continuing the discussion from Evolution of the Genetic Code:

An interesting conversation on evolving evolvability arose in one thread.

@swamidass

I would agree that the much of this process might be neutral initially. However, it causes the beneficial mutations that contribute its selection. So we can’t quite call it neutral draft. There is a causative relationship between evolvability and selection.

On another thread, @art points out that RNA expression evolution only requires small amounts of “information.”

@Art

Because, once one digs into the mechanisms by which small RNAs work, one realizes that this system is actually a low-information (by ID parlance) way to dramatically alter gene expression networks, and thus of growth and development. The implications vis-a-vis evolution are obvious, and not at all kind to the standard ID party line.

Which brings me to this really interesting paper on the evolution of evolvability.

An individual-oriented evolutionary model is used to shed light on this matter. Each individual has a genome from which its gene regulatory network is derived. Mutations, such as gene duplications and deletions, alter the genome, while the resulting network determines the gene expression pattern and hence fitness. With this protocol we let a population of individuals evolve under Darwinian selection in an environment that changes through time.

Our work demonstrates that long-term evolution of complex gene regulatory networks in a changing environment can lead to a striking increase in the efficiency of generating beneficial mutations.

Evolution of Evolvability in Gene Regulatory Networks

[swamidass (S. Joshua Swamidass)]

Also, @John_Harshman, look at this, which seems to be a restatement of what I was saying earlier…

Why evolvability appears to have increased over evolutionary time is an important unresolved biological question. Unlike most candidate explanations, this paper proposes that increasing evolvability can result without any pressure to adapt. The insight is that if evolvability is heritable, then an unbiased drifting process across genotypes can still create a distribution of phenotypes biased towards evolvability, because evolvable organisms diffuse more quickly through the space of possible phenotypes. Furthermore, because phenotypic divergence often correlates with founding niches, niche founders may on average be more evolvable, which through population growth provides a genotypic bias towards evolvability. Interestingly, the combination of these two mechanisms can lead to increasing evolvability without any pressure to out-compete other organisms, as demonstrated through experiments with a series of simulated models. Thus rather than from pressure to adapt, evolvability may inevitably result from any drift through genotypic space combined with evolution’s passive tendency to accumulate niches.

Evolvability Is Inevitable: Increasing Evolvability without the Pressure to...

That makes sense to me.

[John_Harshman]

@swamidass

That makes sense to me.

As I said, species selection.

[gbrooks9 (George)]

@swamidass

@swamidass quoted this:
“…complex gene regulatory networks in a changing environment can lead to a striking increase in the efficiency of generating beneficial mutations.”

Hence we have the two least discussed parameters!

One:
A lab population of fruit flies will not change much over time if its environment does little changing and if its survival is rarely tested by changed in climate, predation or food supply.

Two:
Populations equipped with better than average genetic replication systems will probably be slower than average to adapt to changes, and will probably become extinct more quickly than pooulations equipped with more sloppy genetic replicatiin systems… but only to a point commensurate with the volatility of the average change the population experiences!