Instantaneous vs. continuous admixture dynamics (Jin et al. 2012)

A new paper in AJHG discusses the distribution of chromosomal segments of distinct ancestry (CSDAs) under three different models of admixture dynamics (left). In the hybrid isolation (HI) model, admixture is instantaneous and results in a hybrid population that evolves with drift and recombination only. In the gradual admixture (GA) model, the hybrid population continues to receive admixture from the unadmixed parental populations. Finally, in the continuous gene flow model (CGF), one of the populations becomes admixed while the other continues to exist unadmixed and to contribute to the admixed one.

In practical terms, the HI model results in the diminution of CSDA length due to recombination over time, and at "present" there is a paucity of long CSDAs. In the GA model there are more long CSDAs for both populations, while in the CGF model there is an asymmetry in the CSDAs donated by Pop1 and Pop2, with those from the "donor" population being longer (because fresh "long" segments are added in every generation).

The conclusions of the paper regarding some particular admixture cases are also interesting. For African Americans:

Although the actual population admixture of African Americans might be more complex than what our simulation suggested, the CGF1 model setting at 14 generations was found to be reasonably  epresentative, capturing the main pattern of the population admixture dynamics.

The CGF1 model has Africans as recipients and Europeans as donors. This makes sense, since African Americans are descended from slaves who were transported to the New World, with the slave trade ending centuries ago, hence there was mostly no replenishment of the AA population with fresh African-origin individuals. On the other hand, European Americans, both due to social dynamics and their numerical majority continued to exist as a distinct population that contributed to the AA population.

I should mention that according to HAPMIX, the admixture time was 7 generations, with is close to the 6 +/- 1 generations inferred by rolloff analysis by Moorjani et al. So, in this case this admixture time appears to be an "average" of a continuing process of admixture that began 14 generations ago.

Onto Mexicans:

In short, the GA model at 24 generations fit the empirical data best among all these simulated scenarios, as indicated by the distribution of EMDs.

Again, this makes sense, because in Mexico there continued to exist unadmixed populations of Europeans and Amerindians that contributed to the Mestizo population of the country.

On the African admixture in Mozabites:

Comparing the empirical distribution of CSDAs with that simulated, we found that the Mozabite admixture process essentially fit the HI model with 100 generations since admixture. There was an almost complete absence of recent gene flow from European populations to the Mozabite gene pool (Figure 6A). For the Sub-Saharan African ancestral component, there were more long CSDAs at the tail of empirical distribution than those in the HI model, which confirmed that recent gene flow from African populations had contributed to the Mozabite gene pool (Figure 6B). 

Again, this makes sense: Berber groups were not replenished from other Caucasoid sources, so their original admixture with native Africans resulted in a blend that persisted largely unaffected by "Europeans", but did find occasion of admixture with Sub-Saharans. Hence, the asymmetry in the presence of long "European" vs. "Sub-Saharan" segments.

A similar pattern was evident for Bedouin, Palestinians, and Druze:

Analyses of European ancestral component in Bedouin and Palestinian populations also showed that the empirical distributions essentially fit the HI model for both populations (Figures 6C and 6E). Although the empirical CSDA distribution of Sub-Saharan African ancestral component also fit the HI model  best, both distributions showed a long tail at the right compared with those under the HI model, indicating that recent gene flow from Sub-Saharan Africans also contributed to the two admixed populations (Figures 6D and 6F). ... For Druze, their European component of ancestry fit the HI model very well. However, their African ancestral component contained much shorter CSDAs than those of simulated (Figure S14), which might indicate that previous studies had underestimated the admixture time of Druze. In addition, populations receiving recent gene flow from their parental populations showed higher variation of individual ancestral proportions than those who did not (Figure S13).

The Druze have well-known Egyptian connections, and they may have largely avoided Sub-Saharan African admixture during the Islamic period, principally because of its avoidance of proselytism. Hence, their African admixture may stem from Egyptian adherents who were themselves a product of much earlier Caucasoid/Sub-Saharan admixture during the course of pre-Islamic Egypt.


The American Journal of Human Genetics, 25 October 2012 doi:10.1016/j.ajhg.2012.09.008

Exploring Population Admixture Dynamics via Empirical and Simulated Genome-Wide Distribution of Ancestral Chromosomal Segments

Wenfei Jin et al

Abstract

The processes of genetic admixture determine the haplotype structure and linkage disequilibrium patterns of the admixed population, which is important for medical and evolutionary studies. However, most previous studies do not consider the inherent complexity of admixture processes. Here we proposed two approaches to explore population admixture dynamics, and we demonstrated, by analyzing genome-wide empirical and simulated data, that the approach based on the distribution of chromosomal segments of distinct ancestry (CSDAs) was more powerful than that based on the distribution of individual ancestry proportions. Analysis of 1,890 African Americans showed that a continuous gene flow model, in which the African American population continuously received gene flow from European populations over about 14 generations, best explained the admixture dynamics of African Americans among several putative models. Interestingly, we observed that some African Americans had much more European ancestry than the simulated samples, indicating substructures of local ancestries in African Americans that could have been caused by individuals from some particular lineages having repeatedly admixed with people of European ancestry. In contrast, the admixture dynamics of Mexicans could be explained by a gradual admixture model in which the Mexican population continuously received gene flow from both European and Amerindian populations over about 24 generations. Our results also indicated that recent gene flows from Sub-Saharan Africans have contributed to the gene pool of Middle Eastern populations such as Mozabite, Bedouin, and Palestinian. In summary, this study not only provides approaches to explore population admixture dynamics, but also advances our understanding on population history of African Americans, Mexicans, and Middle Eastern populations.

Link

Refinement of ancestry informative markers in Europeans (Tian et al. 2009)

From the paper:

In general, Fst values corresponded to geographical relationships with smaller values between population groups with origins in neighboring countries/regions (e.g. Tuscan/Greek, Fst = 0.001) compared with those from very different regions in Europe (e.g. Russian/Palestinian, Fst = 0.020) similar to previous studies [10].

...

The current study extends the analysis of European population genetic structure to include additional southern European groups and Arab populations. Even within Italy, the relative position of northern Italians compared with subjects from Tuscany is consistent with the general geographic correspondence of PCA results. Interestingly, the majority of Italian Americans (NYCP 4 grandparent defined) appear to derive from southern Italy and overlap with subjects of Greek heritage. Both of these observations are consistent with previous historical information [30,31].

The paired Fst table confirms that the closest population to Greeks are Italians (negative Fst=-0.0001) and Tuscans (Fst=0.0005). Much further apart are Spaniards (Fst=0.0035) and Germans (Fst=0.0039), who are still much closer than the most distant Russians (Fst=0.0108) and Orcadians (Fst=0.103).

The low genetic distance between Greeks and Italians (the lowest in the table), suggests, once again, that southern Italians are little more than Latin-speaking Greeks as their history suggests, without discounting the possibility that they have experienced some non-Greek admixture.

Also of interest is the proximity of Ashkenazi Jews to Greeks and Italians which are about twice closer to them than Bedouins, Palestinians, or Druze from the Near East. As I have argued before, a major component in the ancestry of Jews was picked up in Hellenistic-Roman times; most published models of Ashkenazi Jewish origins have only considered admixture between a Near Eastern component with a northern European (German-Slavic) component. Indeed, Ashkenazi Jews are closer to several European populations than they are to Middle Eastern ones

However, as the PCA analysis shows, Ashkenazi Jews are distinct from both Europeans and non-Jewish Middle Eastern populations and cannot be viewed as a simple mix of the two; their distinctiveness must be -in part- due to the specific features of the small founder population of that community after it became effectively reproductively semi-isolated from gentiles after Roman times. It would be interesting to see different Jewish communities studied in the context of a broad variety of European and Middle Eastern populations, to determine whether Ashkenazi distinctiveness is specifically Ashkenazi or more generally Jewish distinctiveness; I would bet on a combination of the two.

Also of interest is the analysis of European populations in comparison to South Asian Burusho and Balochi, which shows on the one hand, substantial homogeneity of West Eurasians compared to South Asians, but also, to some extent, the transitional nature of some populations such as Bedouins or Adygei.

Related: A previous article by Tian et al.

UPDATE (Aug 29)

The PCA analysis is also quite interesting:

Some observations:

• In Α we see a west-east differentiation in northern Europe, with Irish and Russians in the two ends of PC1.
• In Β we see differentiation of non-Jewish southern European populations from Ashkenazi Jews along PC1 and from Druze, Palestinians, and Bedouins, along PC2. Greeks are concentrated near the center at the lower left quadrant.
• In C we see all the populations using only ancestry-informative markers and in D with all 270k markers. The two plots are similar, although use of the full set results in clearer results. We observe a cline of populations from the Near East to Northern Europe at the bottom. A little discontinuity between Greeks and Arabs would probably disappear if geographically intermediate populations had been included. Ashkenazi Jews are differentiated from the entire sample, suggesting that due to genetic drift, selection, or cryptic other ancestry (?) they cannot be reckoned as a simple European-Near Eastern mix genetically.

UPDATE (Aug 30):

Here is a dendrogram I created based on the paired Fst table from the paper. It is of course better to refer to the original table, but the plot, nonetheless shows in a different form "southern" (divided into European and Arab clusters) and "northern" (divided into "western" and "eastern" clusters).

Also a dendrogram after removing the island populations of Orkney and Sardinia, and the non-IE Basques.

Mol Med. 2009 Aug 24. [Epub ahead of print]

European Population Genetic Substructure: Further Definition of Ancestry Informative Markers for Distinguishing Among Diverse European Ethnic Groups.

Tian C, Kosoy R, Nassir R, Lee A, Villoslada P, Klareskog L, Hammarström L, Garchon HJ, Pulver AE, Ransom M, Gregersen PK, Seldin MF.

The definition of European population genetic substructure and its application to understanding complex phenotypes is becoming increasingly important. In the current study using over 4000 subjects genotyped for 300 thousand SNPs we provide further insight into relationships among European population groups and identify sets of SNP ancestry informative markers (AIMs) for application in genetic studies. In general, the graphical description of these principal components analyses (PCA) of diverse European subjects showed a strong correspondence to the geographical relationships of specific countries or regions of origin. Clearer separation of different ethnic and regional populations was observed when northern and southern European groups were considered separately and the PCA results were influenced by the inclusion or exclusion of different self-identified population groups including Ashkenazi Jewish, Sardinian and Orcadian ethnic groups. SNP AIM sets were identified that could distinguish the regional and ethnic population groups. Moreover, the studies demonstrated that most allele frequency differences between different European groups could be effectively controlled in analyses using these AIM sets. The European substructure AIMs should be widely applicable to ongoing studies to confirm and delineate specific disease susceptibility candidate regions without the necessity to perform additional genome-wide SNP studies in additional subject sets.

Link

Coastal-inland differences in Y chromosomes of the Levant

More on this after I get a hold of and digest the information in the paper.

Just a quick comment, based only on the abstract, that the Levantine populations should be studied in a European context as well, as they have been influenced by prehistoric populations from the Aegean, Greeks, Romans, medieval Crusaders, or Ottomans of various origins.

UPDATE: The paper has several supplementary figures and tables.

In Figure S1 we see the biallelic markers used in this study, and their representation in the various populations. It is a chronic problem with studies of this sort to undertype samples; there are phylogeographically informative markers within haplogroups G, L, E1b1b, and J2 for example, which would have added important information about the specific affinities of these haplogroups in the studied populations.


Inspit of these deficiencies, we may still make some useful observations. For example, IE-speaking Iranians have largely the same haplogroups as Arabs, but a much higher representation of haplogroup J2 compared to J1. The converse is true for all Arabs except the Lebanese. But, we do know, that even in Lebanon itself, Muslims have a higher J1/J2 ratio than Christians, and Islam was the main vehicle of Arabization in the region. The Christians are descended from the pre-Arab Byzantine Greco-Aramaic populations (with an addition of Western European Y-chromosomes in some Christian communities, which would not have substantially upset the J1/J2 balance).

It is fairly clear to me that in the Middle East, Greek and Iranian-settled regions have a higher J2/J1 ratio than regions with solid Semitic or NE Caucasian populations where J1 predominates.

UPDATE II (Aug 27):

The paper reports a near zero frequency of haplogroup J1 in Tunisia and Morocco, after an earlier study by the same authors. However, a different study (Onofri et al.) on Moroccan and Tunisian Y chromosomes report 20 and 35% respectively, which is in agreement with an earlier study on North African Y-chromosomes (Arredi et al.) The discrepancy in the J1 frequency seems too large to have arisen by chance given the sample sizes, and it would be interesting to see how it may have arisen.

Annals of Human Genetics doi:10.1111/j.1469-1809.2009.00538.x

Geographical Structure of the Y-chromosomal Genetic Landscape of the Levant: A coastal-inland contrast

Mirvat El-Sibai et al.

Abstract

We have examined the male-specific phylogeography of the Levant and its surroundings by analyzing Y-chromosomal haplogroup distributions using 5874 samples (885 new) from 23 countries. The diversity within some of these haplogroups was also examined. The Levantine populations showed clustering in SNP and STR analyses when considered against a broad Middle-East and North African background. However, we also found a coastal-inland, east-west pattern of diversity and frequency distribution in several haplogroups within the small region of the Levant. Since estimates of effective population size are similar in the two regions, this strong pattern is likely to have arisen mainly from differential migrations, with different lineages introduced from the east and west.

Link