Phenotype does not imply ancestry (always)

One of the questions I often get relate to whether “trait X comes from population Y and does that mean if one has trait X that one has more ancestry from population Y.” To give an illustration, I have had people ask “I have blue eyes, does that mean I am more ‘Western Hunter-Gather’ than other people?”

One issue is that though the WHG tended toward high frequency of the derived OCA2-HERC2 haplotype, other populations clearly carried it, the other is that admixture is so far in the past that having blue or brown eyes is not informative to any degree of ancestry. There were probably relict populations of WHG less than 4,000 years ago (David has mentioned of a sample less than 3,000 years ago in Scandinavia), but the admixture of WHG into other groups was very long ago. More than 1,500 generations ago. To a great extent, it seems plausible that even within populations variation in ancestral fractions should be marginal to non-existent.

But this is a verbal model. A new preprint on bioRxiv has posted a formal model that outlines the different parameters that shape the trajectory of this decoupling between phenotype and ancestry. Assortative mating and the dynamical decoupling of genetic admixture levels from phenotypes that differ between source populations:

Source populations for an admixed population can possess distinct patterns of genotype and phenotype at the beginning of the admixture process. Such differences are sometimes taken to serve as markers of ancestry—that is, phenotypes that are initially associated with the ancestral background in one source population are taken to reflect ancestry in that population. Examples exist, however, in which genotypes or phenotypes initially associated with ancestry in one source population have decoupled from overall admixture levels, so that they no longer serve as proxies for genetic ancestry. We develop a mechanistic model for describing the joint dynamics of admixture levels and phenotype distributions in an admixed population. The approach includes a quantitative-genetic model that relates a phenotype to underlying loci that affect its trait value. We consider three forms of mating. First, individuals might assort in a manner that is independent of the overall genetic admixture level. Second, individuals might assort by a quantitative phenotype that is initially correlated with the genetic admixture level. Third, individuals might assort by the genetic admixture level itself. Under the model, we explore the relationship between genetic admixture level and phenotype over time, studying the effect on this relationship of the genetic architecture of the phenotype. We find that the decoupling of genetic ancestry and phenotype can occur surprisingly quickly, especially if the phenotype is driven by a small number of loci. We also find that positive assortative mating attenuates the process of dissociation in relation to a scenario in which mating is random with respect to genetic admixture and with respect to phenotype. The mechanistic framework suggests that in an admixed population, a trait that initially differed between source populations might be a reliable proxy for ancestry for only a short time, especially if the trait is determined by relatively few loci. The results are potentially relevant in admixed human populations, in which phenotypes that have a perceived correlation with ancestry might have social significance as ancestry markers, despite declining correlations with ancestry over time.

There are a lot of words and math. It’s quite gnarly. But the figure at the top of the post shows the major effect.


– loci in a trait (e.g., height) means that association between ancestry and trait decays more slowly
– stronger assortative mating of phenotype means that the association between ancestry and trait decays more slowly
– stronger assortative mating on ancestry means that the association between ancestry and trait decays more slowly

Since historically people did not have individualized genome-wide ancestry results “assortative mating on ancestry” means by physical appearance in the generality. To me panel E above is really what you should focus on. About 10 genes impact the phenotype, and assortative mating is at 0.5 (between 0 and 1.0). You see the correlation is already only ~0.50 between genome-wide ancestry and the trait in about 10 generations.

Anyway, dig into the math. I read the whole thing but didn’t go over the math in detail. The model and simulations make intuitive sense. I’d be curious how they fit empirical results (which are cited in the paper).


3 thoughts on “Phenotype does not imply ancestry (always)

  1. In my opinion, phenotype does almost always correlate to genotype BUT at the population level.

    For example, some Maghrebi Berber *individuals* look indistinguishable from Iberians but if you have *groups* of both it is fairly easy to distinguish who is who.

  2. @Some Guy: The point is it doesn’t have to be. Selection could create from a mixed Northern European – Subsaharan African population a Northern European phenotype again, a Subsaharan, an intermediate or something completely new based on the variants available. Its selection which makes the difference. You could create 4 vastly different phenotypes with very different adaptive qualities from the same mixed ancestral population. In fact, mixed populations with their wider variation might be able to move into a new and more extreme adaption even faster. The only decisive factor is the amount and direction of the selective pressures.
    In about 10 generations you could create, from the example mentioned, very different daughter populations which have phenotypically little to nothing with each other to do in comparison to the world wide variation of the human species, but would share still the same neutral ancestry.

    In theory one new daughter population could be even darker or lighter than both ancestral groups, because that a population is mixed doesn’t have to mean that anything of one side must survive in the phenotype. Its just in the mix as long as selection “allows it”.

    For your example: You could create from a Berber source population, which is fairly mixed, a more Northern European shifted daughter population than actual Iberians. Fact is, it didn’t happen, but its possible.

    All the phenotypes we see today came up from very different ancestral forms, so the only limitations are available variation and selective pressures. In a mixed population all elements of the ancestral phenotypes will be present, so they can resurge very fast.

  3. “In a mixed population, all elements of the ancestral phenotypes will be present so that they can resurge very fast.”

    @Obs How about Bengalis? If the most significant chunk of Bengalis genetic component is Iranian HG related IVC followed by AASI, Steppe, NE Asian and SE Asian, how do the selective pressures work on them?
    Iranian HG/IVC itself is Basal eurasian+ANE, so those folks had various phenotypes themselves, then when they got mixed with AASI more variation came out. The same circumstance when Indo Aryan came and to end up with NE Asian related tribes. Bengalis skin complexion varies, but the majority have light/medium brown tone, I guess the selection pressure was due to the subtropical environment of Bengal. I wonder if Bengal had Temperate climate, would Bengalis have ended up having white or olive skin tone like their Iranian related IVC, Steppe and NE Asian ancestors?


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