On the limits of fitting complex models of population history to f-statistics:

These results show that at least with regard to the AG analysis, a key historical conclusion of the study (that the predominant genetic component in the Indus Periphery lineage diverged from the Iranian clade prior to the date of the Ganj Dareh Neolithic group at ca. 10 kya and thus prior to the arrival of West Asian crops and Anatolian genetics in Iran) depends on the parsimony assumption, but the
preference for three admixture events instead of four is hard to justify based on archaeological or other arguments.

Why did the Shinde et al. 2019 AG analysis find support for the IP Iranian-related lineage being the first to split, while our findGraphs analysis did not? The Shinde et al. 2019 study sought to carry out a systematic exploration of the AG space in the same spirit as findGraphs—one of only a few papers in the literature where there has been an attempt to do so—and thus this qualitative difference in findings is notable. We hypothesize that the inconsistency reflects the fact that the deeply-diverging WSHG-related ancestry (Narasimhan et al. 2019) present in the IP genetic grouping at a level of ca. 10% was not taken into account explicitly neither in the AG analysis nor in the admixture-corrected f4-symmetry tests also reported in Shinde et al. (2019).

This piece arguing for the end to cousin marriage in the UK in The Times (driven by Pakistanis) took me to a paper in PLOS One, Genetic and reproductive consequences of consanguineous marriage in Bangladesh:

The mean prevalence of CM in our studied population was 6.64%. Gross fertility was higher among CM families, as compared to the non-CM families (p < 0.05). The rate of under-5 child (U5) mortality was significantly higher among CM families (16.6%) in comparison with the non-CM families (5.8%) (p < 0.01). We observed a persuasive rise of abortion/miscarriage and U5 mortality rates with the increasing level of inbreeding. The value of lethal equivalents per gamete found elevated for autosomal inheritances as compared to sex-linked inheritance. CM was associated with the incidence of several single-gene and multifactorial diseases, and congenital malformations, including bronchial asthma, hearing defect, heart diseases, sickle cell anemia (p < 0.05). The general attitude and perception toward CM were rather indifferent, and very few people were concerned about its genetic burden.

A rate around 5% is in line with my intuition and what I’ve seen elsewhere, though there is wide variance by locality. The best thing about the paper is the chart above, the offspring of first cousin marriage have mortality rates 3 times greater than non-cousin marriages. There are other numbers relating to disease, etc. The paper is good because it’s from a developing country without world-class healthcare (though no longer a total basketcase) so you can see disease risk plainly.

More generally in relation to “cousin marriage”

– I have seen “outbred” Pakistani genomes that look like the product of cousin marriage due to the practice’s frequently earlier on in the pedigree

– This is comparable to some Indian caste groups that practice exogamy (North Indian) on the jati level. The jati has been endogamous so long that everyone has become a second cousin…