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One Gene to Banish One Concept
Carrion Crow

Carrion Crow

Haeckel's "tree of life"

Haeckel’s “tree of life”

Being the way we are we humans attempt to comprehend the world in a manner which is intuitively graspable. Obviously some ideas are derived from environmental inputs. If you learn a little math and start talking about a multi-dimensional universe beyond the three spatial ones which we can grasp, then obviously you’re seeing the power of higher order abstraction detached from lived experience. But science is usually not so rarefied in relation to our lived reality. Our intuitions about the world often interface with our broader theories, many of which clearly shape scientific models, even if in the end these models extend far beyond the limits of our Gestalt cognition. How we grasp the whole of the universe has an effect on how we break nature apart at its joints.

The evolutionary ideas which were ascendant in the Victorian age, crowned by Charles Darwin’s theory of the origin of species via natural selection, illustrate both of these realities. On the one hand evolutionary ideas are as old as the Greeks, and likely older in that the Ionians made formal and abstract many folk theories which were likely floating about in the world of antiquity. But there were those then, and now, who had difficulty comprehending the evolutionary nature of speciation, and the morphological change which results in phyletic gradualism (e.g., for Creationists “macroevolution” is always the problem). The likely psychological root of skepticism of speciation is that humans seem to have innate ideas as to the nature of kinds and categories. Plato’s speculations about eternal forms leverage deep intuitions that we have about the world around us which can be discerned even in infants that there are essences, an order and plan. What evolutionary biologists term “population thinking” is not natural, and continuity is often rendered in a discrete fashion when it comes to everyday terminology. A concept such as species has the dual benefit of both being intuitive and aligning with our natural prejudices about the world, and also being useful in the everyday practice of science. But the fact is species are not a real phenomenon, such as the acceleration of a ball in space, but a useful shorthand which brackets a range of concepts.

speciation My attitude toward the term “species” is strongly informed by the instrumental views which are interleaved throughout H. Allen Orr and Jerry Coyne’s book from the mid-aughts, Speciation. That is not to say that the book is perfect, at least from the perspective of some plant biologists. But that’s why I emphasize an instrumental view of species, what might be a useful classification for a plant biologist may not be a useful one for a zoologist, let alone a bacterial geneticist. Species as a concept only exists to delineate and clarify our thinking unless you have a religious model which presupposes ideal kinds brought about by the hand of a designer. Scientific taxonomy is only a rough and approximate mapping of the reality of natural history and evolutionary genetics, which it purports to collapse informatively. And with all the problems with the species concept, recall that it is the “most real” of taxonomic categories which we use (e.g., the biological species concept is moderately coherent).

Naturally this does not mean that there are no differences between the populations we term species, simply that we shouldn’t lose sight of the fact that the way we describe nature is often shorthand which obscures as well as illuminates. The debate about species concepts can be informative and interesting, but it has its limits. I do not hold to the position that there is “one definition to rule them all.” Which brings me to a new paper in Science on crows, The genomic landscape underlying phenotypic integrity in the face of gene flow in crows:

The importance, extent, and mode of interspecific gene flow for the evolution of species has long been debated. Characterization of genomic differentiation in a classic example of hybridization between all-black carrion crows and gray-coated hooded crows identified genome-wide introgression extending far beyond the morphological hybrid zone. Gene expression divergence was concentrated in pigmentation genes expressed in gray versus black feather follicles. Only a small number of narrow genomic islands exhibited resistance to gene flow. One prominent genomic region (<2 megabases) harbored 81 of all 82 fixed differences (of 8.4 million single-nucleotide polymorphisms in total) linking genes involved in pigmentation and in visual perception—a genomic signal reflecting color-mediated prezygotic isolation. Thus, localized genomic selection can cause marked heterogeneity in introgression landscapes while maintaining phenotypic divergence.

Citation: Poelstra, J. W., et al. "The genomic landscape underlying phenotypic integrity in the face of gene flow in crows." Science 344.6190 (2014): 1410-1414.

Citation: Poelstra, J. W., et al. “The genomic landscape underlying phenotypic integrity in the face of gene flow in crows.” Science 344.6190 (2014): 1410-1414.

You may wonder how a paper on the population genomics of crows relates to the broader philosophical issues I was alluding to earlier. Simple, as science advances it sheds light on the true and fine-grained shape of the world around us, rather than our coarse preconceptions. We look through the glass darkly to infer our innate ideas. Modern taxonomy has its origins in Carl Linnaeus’ system, and the status of carrion vs. hooded crow in terms of whether they are species or subspecies has a history which goes back at least to this period. This paper in Science seems to have “solved” the issue in substance, if not style. By substance I mean that the authors have extracted enough genetic information that all the blank spots in our discussion are filled in to my satisfaction. On the whole genome level one can’t differentiate the two crow species/subspecies as clear and distinct entities. German carrion crows are genetically closer to Polish hooded crows in terms of total genome content. But, when it comes to a few specific regions of the genome which affect diagnostic physical characteristics, the pigment of pelage, as well as variation in behaviour, the two groups in fact are quite distinct. To obtain these sorts of results the science had to be top notch. Or at least 2014, not 1814. They sequenced a male hooded crow to greater that 100x coverage to generate a reference sequence, which is very high. Then they sequenced a 60 carrion and hooded crows to greater than 10x coverage, which is reasonable for population genomic work, especially if you can align it to the reference.

Citation: Poelstra, J. W., et al. "The genomic landscape underlying phenotypic integrity in the face of gene flow in crows." Science 344.6190 (2014): 1410-1414.

Citation: Poelstra, J. W., et al. “The genomic landscape underlying phenotypic integrity in the face of gene flow in crows.” Science 344.6190 (2014): 1410-1414.

The basic major result is illustrated in the figure to the right. What you see is that overall the genetic divergence between German carrion crows and Spanish carrion crows, the latter being the putative source population, is rather large comparatively (Spanish vs. Germany vs. Swedish vs. Polish). In contrast there is minimal genetic divergence between German carrion crows and Polish hooded crows, as one might predict by geographic. But, there are exceptional regions of the genome, as is clear when you look at the emphasized spikes in F ST. In other words, continuous gene flow has homogenized between population differences, as you’d except from basic theory (across two demes N >= 1 sufficient to prevent divergence), but selection pressures along very salient traits have resulted in a shaper distinction along a few genomic regions. The interesting point here is though that this isn’t due to any ecological distinction. For example, when it comes to pigmentation some human populations (e.g., Africans and Melanesians) resemble each other despite huge whole genome differences (Melanesians are just another branch of “Out of Africa” humanity). But one can posit a clear ecological rational for why this might be. Not so for carrion and hooded crows. Intuitively it seems obvious that Germany shares more ecologically with Poland than it does with Spain. So what’s going on? The authors provide a likely answer: “A key feature that distinguishes the crow system is the apparent lack of ecological selection on the maintenance of separate phenotypes. Instead, the data presented here are consistent with the idea that assortative mating and sexual selection can exclusively cause phenotypic and genotypic differentiation.” Instead of a speciation gene, these may be “speciation genomic regions” (yes, it has less of a ring to it, I admit).

So where does this leave us in terms of species concept? Well, your mileage may vary. In the accompanying commentary by Peter de Knijff there is some bashing the bar code of life idea of systematically identifying species differences using DNA. I don’t think there’s a problem with the bar code of life as long as one understands that one shouldn’t confuse the measure with what one is measuring. The concept species is not like the speed of light, it is freighted with assumptions, and means different things to different people. If one understands that ahead of time then a consistent language or measuring stick can still be highly useful, if not ultimately informative in a deep ontological sense (i.e., atoms/quarks are fundamental to material objects in a way that species are not in regards to variation among living organisms).

This specific result is also not entirely surprising, though it is nice to see it worked out in a specific case. The connection between physical appearance and species distinctions is an old and intuitive one, despite the importance of genealogical concepts when it comes to our intuitive essentialism. And this applies to taxonomic levels which are lower, as far back as Charles Darwin sexual selection was posited as the reason for racial differences in appearance for humans (Jared Diamond promoted this view in The Third Chimpanzee). Back in 2003 Henry Harpending brought to my mind the idea that human differences in phenotypes can persist across populations despite overall genomic similarities. To me this reinforces that genomics has come not to bring peace to old truths, but a sword of empirical reality to old preconceptions. Rather than dithering as to the “best” term to describe genetic variation and evolutionary process, we can actually go about describing it in close to its entirety, and let the chips fall where they may. Compute and quantify. The rest is commentary.

• Category: Science • Tags: Genomics, Population Genetics, Speciation 
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  1. Great post. This is a truly important paper and links well with the currently hot topic of ‘supergenes’ recently reviewed by Thomson and Jiggins in Heredity:

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  2. “Intuitively it seems obvious that Germany shares more ecologically with Poland than it does with Spain.”

    It may not be relevant to this but generally I wonder if there’s an eco-border somewhere around Poland and Germany related to the effect of the Gulf stream i.e. a line where the effect tapers off and it becomes full continental.

  3. Razib-

    This is a very good piece. Probably the best this month.

    Just thought I’d say ‘kudos.’ You’re quality posts on genetics often don’t get the comments and circulation of the lighter stiff.

  4. #3, the genetics posts are the ones which have the ‘long tail’ in terms of driving search traffic 5 years after being posted.

    #2, if the change is clinal you would see the genetic change like that too. but it’s not. at least for the salient trait.

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