Only so many ways

In a way, the limitations of evolution are more interesting to me than its possibilities. It’s cool to figure out how exquisite adaptations and fantastically complex molecular machines might have evolved, but I like my evolution the way Brandon Sanderson likes his magic. If it can do anything, then where’s the fun? Deep underlying rules and constraints are what make it really interesting.

Convergent evolution can hint at such rules. Some of them are just physics and seem pretty straightforward. If you’re a creature swimming in the sea, being streamlined is good for you, and there aren’t that many ways of being streamlined. So dolphins, squid and sharks have the same basic shape despite coming from very different ancestors. Other cases involve more subtle and probably more interesting constraints. The baggage of your ancestry, the interactions in your genome, the pool of available mutations, can all restrict the ways in which you can adapt to a particular challenge. A study I found in the huge backlog of random pdfs on my desktop probes tentatively into the importance of such intrinsic limitations.

Conte et al. (2012) asked a seemingly simple question that has apparently never been systematically investigated before: how often does convergent or parallel evolution of the same trait result from modification of the same genes?

Convergent and parallel evolution are sort of two ends of a continuum. We use parallel evolution to refer to traits that evolved in similar directions starting from the same starting point. For example, three-spine sticklebacks repeatedly lost their bony armour when they moved from the sea to rivers and lakes in various places around the world. The ancestor is the same heavily armoured marine fish in each case, and most freshwater populations underwent very similar changes (including their genetic basis) from this common beginning. At the other end of the scale you find clear instances of convergence, such as “milk” in mammals and birds. Their common ancestors not only didn’t ooze custom-made immune-boosting baby food, they likely didn’t even care for their young.

Back to the paper. Conte et al. conducted what we call a meta-analysis: collecting and analysing data from all published studies that fit their pre-determined set of criteria. Altogether, they looked at a carefully selected set of 25 studies about the genetic basis of convergent traits. Not too great, the authors acknowledge, but it’s a start.

The studies were divided into two sets, because the two main methods of looking at the genetic basis of a trait can’t easily be analysed together. The first set contained genetic mapping studies (“which parts of the genome cause X?”), and the second candidate gene studies (“does this gene cause X?”). The convergent traits in these studies were quite diverse. There was pale skin from cave fish to humans, African and European peoples’ ability to digest lactose as adults, resistance to tetrodotoxin in snakes, wing patterns in butterflies, electric organs in fish…

The comparisons span quite a long time scale. On one end, there are populations within a single species, like lactose-tolerant Europeans and Arabs, that diverged mere tens of thousands of years ago. On the other, pale-skinned cave fish and Swedes are separated by something on the order of 400 million years. This is part of what makes this an exciting study, because you can indirectly observe what happens to genetic constraints over time.

The most exciting, though, is the sheer amount of gene re-use the researchers saw. For mapping studies, they found a 32% chance that the same trait will be associated with the same gene(s) in different species. Candidate genes give an even higher estimate (55%), but that might just be the nature of the beast. When a candidate gene is not behaving as expected it’s probably less interesting and publishable, Conte et al. argue, whereas mapping studies will usually throw up something to write about.*

Within a species, the probability of the same gene being used in the same adaptation gets as high as 80% for both methods. This is despite the fact that often the traits in question are controlled by several genes, any of which could be mutated to the same effect. Where you come from clearly has a huge impact on where (and how) you can go. The impact lessens as you look at increasingly distant species; at a hundred million years of divergence, mapping data show only 10% similarity between convergent traits, and even candidate genes drop to around 40%. (Methinks 10% is still a big number considering how many genes we have, but of course we’re talking about relatively simple traits here, so the number of relevant genes isn’t nearly as high.)

There are some logical possible explanations behind both the high level of genetic convergence in close relatives and the big drop with increasing divergence. For example, it could be that populations within a species have very similar pools of genetic variation. If the same genes vary, then natural selection will “naturally” hit on the same genes when adaptation becomes handy. It’s also likely that the rest of the genome plays a part – closely related populations/species have more similar genetic backgrounds, their genes likely interact with one another in more similar ways, ergo the restrictions on what mutations can become beneficial are also similar. As lineages diverge, so do such interactions and restrictions, lowering the probability that two species evolve the same trait in the same way.

Of course, it’s at this point impossible to say which of the potential reasons actually cause the trends observed in this study, but that wasn’t the point. The authors’ stated goals were pretty modest:

“[O]ur aim here has been to stimulate thinking about these issues and to move towards a quantitative understanding of repeated genetic evolution” (p5044)

In that, I hope, they have succeeded. It’d be lovely to see more of this “big picture” discussion of convergent evolution. Big pictures make Mammals happy.

***

*I’m not sure about that, myself. I think if you’ve got a gene that’s been shown to do X in species after species, a negative finding is a lot more newsworthy than yet another confirmation of the same old shit. I suppose it’s gut feeling versus intuition until someone does a study of that, though 🙂

***

Reference:

Conte GL et al. (2012) The probability of genetic parallelism and convergence in natural populations. Proceedings of the Royal Society B 279:5039-5047

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4 thoughts on “Only so many ways

  1. The Ethical Skeptic November 26, 2012 / 19:36

    Outstanding blog article. The premise question is enlightening – and you address it with clarity and adeptness. Not only do morphological convergences occur, but they are often driven by directly associated replicate nucleotide convergences, and the degree of chance of occurrence of the nucleotide convergence is inversely proportional to the genetic distance between two parallel path species. I love it.

    Now we will have to answer the question concerning: if in the cases wherein two species of a significant genetic distance, obtained the replicate nucleotide convergence via dormancy switching, or via re-establishment of the same genetics via conventional accretive evolution.

    Any studies on the latter?
    Thanks!
    TES

    • Naraoia November 26, 2012 / 19:48

      Cheers! I’m not sure what you mean by “dormancy switching”, TBH…

      Also, I should have stated that it isn’t necessarily nucleotide-level convergence they’re talking about in this study. (Gah, I knew there was something I was forgetting!) For example, changes in the protein-coding sequence of a gene and changes in the regulatory switches of that gene count as the same thing by their criteria.

  2. The Ethical Skeptic November 26, 2012 / 20:45

    Yes, I thought they might be counting them (protein coding and regulatory switching (dormancy switching) as the same thing; which would be the logical first step in the hierarchy of testing. For instance, I would suspect that the allele makeup of the shark’s fluid dynamic morphology (and amazing skin!) should not consist of the same expressed nucleotides of a land mammal who returned to an aquatic environment, as in the case of the Cetacea order for example. They have no common ancestor with that morphological grouping to switch to expression that we currently understand. And if they accreted the exact same allele map via separate parallel evolutionary paths, that would be rather groundbreaking in its discovery.

    Or have we discovered such replicative violations of common ancestry? That would be a fascinating read.

    • Naraoia November 26, 2012 / 21:31

      Nothing springs to mind, at least nothing that involves complex adaptations like that. There was a cool paper I gushed about a while back that showed pretty amazing molecular-level convergence in multiple lineages of viruses, but the situation really restricted the possibilities there. The trait under selection involved a specific protein-protein interaction, which didn’t leave evolution all that much “creative freedom”. The mutations that caused adaptation still weren’t identical.

      Incidentally, if convergent evolution interests you, you could always try Limited Forms Most Beautiful by George McGhee. I found it pretty boring despite the fascinating subject and IIRC the phylogenies were sometimes iffy, but it compiles tons of cases of convergence, including on the molecular level.

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