Close inbreeding and low genetic diversity in Inner Asian human populations despite geographical exogamy

turko-mongol-indo-iranian

Open access Close inbreeding and low genetic diversity in Inner Asian human populations despite geographical exogamy, by Marchi et al. Scientific Reports (2018) 8:9397.

Abstract (emphasis mine):

When closely related individuals mate, they produce inbred offspring, which often have lower fitness than outbred ones. Geographical exogamy, by favouring matings between distant individuals, is thought to be an inbreeding avoidance mechanism; however, no data has clearly tested this prediction. Here, we took advantage of the diversity of matrimonial systems in humans to explore the impact of geographical exogamy on genetic diversity and inbreeding. We collected ethno-demographic data for 1,344 individuals in 16 populations from two Inner Asian cultural groups with contrasting dispersal behaviours (Turko-Mongols and Indo-Iranians) and genotyped genome-wide single nucleotide polymorphisms in 503 individuals. We estimated the population exogamy rate and confirmed the expected dispersal differences: Turko-Mongols are geographically more exogamous than Indo-Iranians. Unexpectedly, across populations, exogamy patterns correlated neither with the proportion of inbred individuals nor with their genetic diversity. Even more surprisingly, among Turko-Mongols, descendants from exogamous couples were significantly more inbred than descendants from endogamous couples, except for large distances (>40 km). Overall, 37% of the descendants from exogamous couples were closely inbred. This suggests that in Inner Asia, geographical exogamy is neither efficient in increasing genetic diversity nor in avoiding inbreeding, which might be due to kinship endogamy despite the occurrence of dispersal.

Interesting excerpts:

Two cultural groups, which matrimonial systems are reported to differ, coexist in Inner Asia: Turko-Mongols are described as mainly exogamous while Indo-Iranians are thought to be mainly endogamous45. However, it is not always clear if exogamy refers to clan (ethnic) or village (geographical) exogamy. Here, we used a dataset of 16 populations representing 11 different ethnic groups from both cultural groups and we quantified geographical exogamy rates and distances in each population. Using an empirical threshold of 4 km, we confirmed that matrimonial behaviours differ as described in the literature, even though we found some exceptions: three Turko-Mongol populations (out of 14) have less than 50% exogamy, whereas one Indo-Iranian population (out of four) has more than 50% exogamy.(…).

geographic-distance-turko-mongols-indo-iranian
Geographical distances between the birth places of couples in Turko-Mongols and Indo-Iranians. The geographical distances are plotted in log scale (km). Their densities are represented by population (dashed lines) or for the Indo-Iranian and Turko-Mongol groups (solid lines). We represented the average distances within couples per population using a Kernel’s density estimate implemented in R with a smoothing bandwidth of 0.2. See Supplementary Table 1B for population codes.

An additional important result of our study is that geographical distances are not negatively correlated with inbreeding, as could have been expected under an isolation-by-distance model65. Interestingly, a recent study based on a large genealogical dataset, collected across Western Europe and North America, and including birth places information, similarly found an absence of correlation between relatedness and the distance between couples, for the cohorts born before 185066. Our analyses within present-day Turko-Mongols reveal more specifically that the structure of the relationship between geographical distance and mating choice inbreeding is not linear, but rather tends to be bell-shaped, and thus cannot be correctly assessed with a single correlation test. Indeed, descendants from parents born 4 to 40 km apart are more inbred than descendants from endogamous couples (≤4 km) or from long-range exogamous ones (>40 km). As a consequence, close inbreeding exists despite geographical exogamy, and about a third of descendants from exogamous couples are inbred.

These results, in addition to those obtained by [Kaplanis et al. 2018]66, highlight the importance of using geographic distances rather than exogamy rates to characterize the impact of exogamy on inbreeding, as already described when studying patrilocality67. Indeed, when we compare mating choice inbreeding patterns for descendants from exogamous and endogamous couples defined for thresholds of 4, 10, 20 and 30 km, we find no significant differences (for number and total length of class C-ROHs and F-Median coefficient: MWU test p-values > 0.1). We only detect significantly lower values in descendants from exogamous couples for larger distances above 40 and 50 km (p-values < 0.03).

genetic-diversity-turko-mongol-indo-iranian
Genetic diversity (A) and inbreeding patterns (B,C) within populations. Grey lines in (B) represent inbreeding values corresponding to second-cousins and first-cousins. The grey line in (C) represents the homozygosity population baseline expected under panmixia. The number of samples per population is indicated between parentheses. See Supplementary Table 1B for population codes.

Our results also challenge the intuition that exogamy necessarily increases the genetic diversity within a population and therefore reduces drift inbreeding. Indeed, we found that Turko-Mongol populations have a lower genetic diversity (as measured by the mean haplotypic heterozygosity) and more intermediate ROHs associated with drift inbreeding than those of Indo-Iranians despite higher exogamous rates. (…)

Overall, this research sheds light on mating choice preferences: we showed that two thirds of partners that have not dispersed did mate with unrelated individuals, and that drift and mating choice inbreeding is variable, even among close-by populations. We also provide new insights into the relationship between dispersal and inbreeding in humans, based on genetic data, and demonstrate that geographical exogamy is not necessarily negatively associated with mating choice inbreeding, but rather can have a more complex non-linear relationship. Contrary to the common situation in many animals, this finding suggests that Inner Asian human populations who practise exogamy at small geographical scales might be focused on alliance strategies that result in kinship endogamy. (…)

Related:

Quantitative analysis of population-scale family trees with millions of relatives

genealogy-demographic-data

The paper Quantitative analysis of population-scale family trees with millions of relatives, by Kaplanis, Gordon, Shor, et al. Science (2018) 359(6379), based on a study of genealogical information at Geni, is today news worldwide.

Abstract:

Family trees have vast applications in multiple fields from genetics to anthropology and economics. However, the collection of extended family trees is tedious and usually relies on resources with limited geographical scope and complex data usage restrictions. Here, we collected 86 million profiles from publicly-available online data shared by genealogy enthusiasts. After extensive cleaning and validation, we obtained population-scale family trees, including a single pedigree of 13 million individuals. We leveraged the data to partition the genetic architecture of longevity by inspecting millions of relative pairs and to provide insights into the geographical dispersion of families. We also report a simple digital procedure to overlay other datasets with our resource in order to empower studies with population-scale genealogical data.

While the article is behind a paywall, you can still read its preprint at bioRxiv.

Excerpts interesting for genetic genealogy(emphasis mine):

Assessment of theories of familial dispersion

Familial dispersion is a major driving force of various genetic, economical, and demographic processes (…)

First, we analyzed sex-specific migration patterns (21) to resolve conflicting results regarding sex bias in human migration (52). Our results indicate that females migrate more than males in Western societies but over shorter distances. The median mother-child distances were significantly larger (Wilcox, one-tailed, p < 10−90) by a factor of 1.6x than father-child distances (Fig. 4A). This trend appeared throughout the 300 years of our analysis window, including in the most recent birth cohort, and was observed both in North American (Wilcox, one-tailed, p < 10−23) and European duos (Wilcox, one-tailed, p < 10−87). On the other hand, we found that the average mother-child distances (fig. S17) were significantly shorter than the father-child distances (t-test, p < 10−90), suggesting that long-range migration events are biased toward males. Consistent with this pattern, fathers displayed a significantly (p < 10−83) higher frequency than mothers to be born in a different country than their offspring (Fig. 4B). Again, this pattern was evident when restricting the data to North American or European duos. Taken together, males and females in Western societies show different migration distributions in which patrilocality occurs only in relatively local migration events and large-scale events that usually involve a change of country are more common in males than females.

genealogical-tree-generations
An example of the genealogical and demographic information available on the website, with a real pedigree of ~6000 individuals. Green: profiles, red: marriages. The family tree spans about 7 generations

Next, we inspected the marital radius (the distance be-tween mates’ places of birth) and its effect on the genetic relatedness of couples (21). The isolation by distance theory of Malécot predicts that increases in the marital radius should exponentially decrease the genetic relatedness of individuals (53). But the magnitude of these forces is also a function of factors such as taboos against cousin marriages (54).

We started by analyzing temporal changes in the birth locations of couples in our cohort. Prior to the Industrial Revolution (<1750), most marriages occurred between peo-ple born only 10km from each other (Fig. 4A [black line]). Similar patterns were found when analyzing European-born individuals (fig. S18) or North American-born individuals (fig. S19). After the beginning of the second Industrial Revolution (1870), the marital radius rapidly increased and reached ~100km for most marriages in the birth cohort in 1950. Next, we analyzed the genetic relatedness (IBD) of couples as measured by tracing their genealogical ties (Fig. 4C). Between 1650 and 1850, the average IBD of couples was relatively stable and on the order of ~4th cousins, whereas IBD exhibited a rapid decrease post-1850. Overall, the medi-an marital radius for each year showed a strong correlation (R2 = 72%) with the expected IBD between couples. Every 70km increase in the marital radius correlated with a decrease in the genetic relatedness of couples by one meiosis event (Fig. 4D). This correlation matches previous isolation by distance forces in continental regions (55). However, this trend was not consistent over time and exhibits three phases. For the pre-1800 birth cohorts, the correlation between marital distance and IBD was insignificant (p > 0.2) and weak (R2 = 0.7%) (fig. S20A). Couples born around 1800-1850 showed a two-fold increase in their marital distance from 8km in 1800 to 19km in 1850. Marriages are usually about 20-25 years after birth and around this time (1820-1875) rapid transportation changes took place, such as the advent of railroad travel in most of Europe and the United States. However, the increase in marital distance was significantly (p < 10−13) coupled with an increase in genetic relat-edness, contrary to the isolation by distance theory (fig. S20B). Only for the cohorts born after 1850, did the data match (R2 = 80%) the theoretical model of isolation by distance (fig. S20C). Taken together, the data shows a 50-year lag between the advent of increased familial dispersion and the decline of genetic relatedness between couples. During this time, individuals continued to marry relatives despite the increased distance. From these results, we hypothesize that changes in 19th century transportation were not the primary cause for decreased consanguinity. Rather, our results suggest that shifting cultural factors played a more important role in the recent reduction of genetic relatedness of couples in Western societies.

EDIT 3/2/2018: Added details of the article.

See also:

We are all special, which also means that none of us is

Europe_around_800_Charlemagne

Adam Rutherford writes You’re Descended from Royalty and So Is Everybody Else – Anybody you can name from ancient history is in your family tree, which I discovered via John Hawks’ new post The surprising connectedness of human genealogies over centuries.

Excerpt:

One way to think of it is to accept that everyone of European descent should have billions of ancestors at a time in the 10th century, but there weren’t billions of people around then, so try to cram them into the number of people that actually were. The math that falls out of that apparent impasse is that all of the billions of lines of ancestry have coalesced into not just a small number of people, but effectively literally everyone who was alive at that time. So, by inference, if Charlemagne was alive in the ninth century, which we know he was, and he left descendants who are alive today, which we also know is true, then he is the ancestor of everyone of European descent alive in Europe today.

Since most of this blog’s posts support academic disciplines looking for answers to the Indo-European question, and gives constantly reasons against modern genetic (and phylogenetic) identification, I think it is worth at least a quick read for anyone interested in the field.

I recently referred to the interesting series of posts by Graham Coop on this matter.

Featured image: Europe around 800 – the map is public domain from from the Historical Atlas (New York, 1911)

Related:

Genetic vs. genealogical ancestors and actual geographical constraints

genetic_pie_2

Interesting post from Graham Coop, Where did your genetic ancestors come from?

An excerpt:

A thousand years back I’m descended from nearly everyone everywhere in Europe. I’m related to these individuals via millions of lines of descent back through my vast family tree. Yet the majority of the lines back through my pedigree trace to people living in the UK and Western Europe. Many lines trace back to more distant locations, but these are relatively few in number compared to those tracing back to closer to home. Ancestors along each of these lines are (roughly) equally likely to contribute to my genome. Therefore, most of my roughly 2600 genetic ancestors from 1000 years ago, who contributed the majority of my genome to me, will be random people living in the UK and western Europe at that time (who happened to leave descendants).

Looking back a few thousand years more, I’m a descendant of nearly everyone who ever lived almost everywhere in the world (at least those who left descendants, and many did). Yet most of the just over ~6000 individuals from that time who contributed the majority of my genome to me will mostly be found all over Western Eurasia. There’s nothing much special about these individuals who happen to be my genetic ancestors a few thousand years back. They’re likely not royalty. My genetic ancestors are just a random subset of all of my genealogical ancestors, they just happen to be my genetic ancestors due to the vagaries of meiosis and recombination.

As always, a humbling example, e.g. for those looking at haplogroups in the distant past to make modern ethnolinguistic identifications.

Genetics in combination with genealogy poses a question akin to the Ship of Theseus paradox.

Featured image (from the article): Simulation of how much of your autosomal genome is present in each genealogical ancestor as we go back up the generations. Image explained in detail in the article How many genetic ancestors do I have?

Related: