New Fst and Kinship Estimators

And a statement on Identity.

In all cases, emphasis added.

The abstract:

Kinship coefficients and FST, which measure genetic relatedness and the overall population structure, respectively, have important biomedical applications. However, existing estimators are only accurate under restrictive conditions that most natural population structures do not satisfy. We recently derived new kinship and FST estimators for arbitrary population structures [1, 2]. Our estimates on human datasets reveal a complex population structure driven by founder effects due to dispersal from Africa and admixture. Notably, our new approach estimates larger FST values of 26% for native worldwide human populations and 23% for admixed Hispanic individuals, whereas the existing approach estimates 9.8% and 2.6%, respectively. While previous work correctly measured FST between subpopulation pairs, our generalized FST measures genetic distances among all individuals and their most recent common ancestor (MRCA) population, revealing that genetic differentiation is greater than previously appreciated. This analysis demonstrates that estimating kinship and FST under more realistic assumptions is important for modern population genetic analysis.

I’m not a fan of Fst for genetic distance estimates for reasons discussed at this blog, and based on peer-reviewed literature, but it is used for that by many, so let’s see what this paper says.

From the main text:

However, the most commonly-used standard kinship estimator [9, 10, 13–19] is accurate only in the absence of population structure [2, 20]. Likewise, current FST estimators assume that individuals are partitioned into statistically-independent subpopulations [4, 5, 21–23], which does not hold for human and other complex population structures.

About Hispanics:

In particular, since differentiation increases from AFR to EUR to AMR (Fig. 3), the greatest kinship is between individuals with higher AMR ancestry, and the lowest kinship is between individuals with higher AFR ancestry (Fig. 4B and C).

So, it would seem that Hispanics like Mexicans and Peruvians have greater kinship among them than do the Caribbean-type Hispanics who stress Negro admixture to a greater extent.  Genetic differentiation (and kinship) seems highest among Amerindians and Pacific Islanders.

Fst between populations may be “substantially larger” than previously determined:

Remarkably, our estimated FST of 0.260 is substantially larger than estimates around 0.098 from existing approaches (Fig. 3) and previous measurements based on FST [30, 45] or related variance component models [31, 46, 47] — except for some AMOVA  ST estimates [48] (pairwise FST estimates [23, 49– 52] are not generally comparable to our estimate). Existing approaches underestimate FST because they assume zero kinship between subpopulations, clearly incorrect as seen in Fig. 1C, whereas our new approach models arbitrary kinship between individuals and leverages kinship to estimate FST.

Consistent with the “genes follow geography” paradigm, with genetic variation being both clinal and discontinuous.

We typically see that each ancestry cluster is concentrated in a certain geographical region, and this ancestry is also present to a lesser extent in neighboring regions and diminishes with geographical distance from its point of greatest concentration. This again argues for a complex population structure where relatedness at the population level falls on a continuum rather than taking on discrete values. The most notable geographic discontinuities in ancestry were observed for cluster 3, which is roughly West Eurasian ancestry.

And within West Eurasians?

Among West Eurasians, kinship is higher within Europe, reflecting another bottleneck.

So much for those that have denied any differences among West Eurasians.

It would be useful to use the new kinship estimator to get quantitative data for groups and transform those into child equivalents as well. That would be important for biopolitical considerations, an important component, but not the only component, of biopolitical identity. Identity – particularly from the general Yockeyian perspective I espouse – has multiple components.

Interestingly, he authors of this paper take a similar perspective; thus:

This partition into subpopulation is based on geography, history, language families, and our kinship estimates.

If “history” includes cultural/civilizational components, which are the major proximate interests, then this tracks well with my idea of Identity, composed both from the key ultimate interest (genetic kinship) and the major proximate interests. These different sets of interests synergize to form sharp discontinuities which are not present when only one interest is considered in isolation.

Now, I do not agree with the authors including the Ashkenazim in the European subpopulation, but that does not mean their approach is wrong – they are simply following the same simplistic mindset reflected by the testing companies that “they are found in Europe so they are European,” ignoring the history of the Ashkenazim as a Diaspora group akin to the Roma.

But, that’s a minor detail. The major approach of synergistic Identity is sound.