New paper on afghan population

[Karachi]

This paper is just published recently:

Afghanistan has held a strategic position throughout history. It has been inhabited since the Paleolithic and later became a crossroad for expanding civilizations and empires. Afghanistan's location, history, and diverse ethnic groups present a unique opportunity to explore how nations and ethnic groups emerged, and how major cultural evolutions and technological developments in human history have influenced modern population structures. In this study we have analyzed, for the first time, the four major ethnic groups in present-day Afghanistan: Hazara, Pashtun, Tajik, and Uzbek, using 52 binary markers and 19 short tandem repeats on the non-recombinant segment of the Y-chromosome. A total of 204 Afghan samples were investigated along with more than 8,500 samples from surrounding populations important to Afghanistan's history through migrations and conquests, including Iranians, Greeks, Indians, Middle Easterners, East Europeans, and East Asians. Our results suggest that all current Afghans largely share a heritage derived from a common unstructured ancestral population that could have emerged during the Neolithic revolution and the formation of the first farming communities. Our results also indicate that inter-Afghan differentiation started during the Bronze Age, probably driven by the formation of the first civilizations in the region. Later migrations and invasions into the region have been assimilated differentially among the ethnic groups, increasing inter-population genetic differences, and giving the Afghans a unique genetic diversity in Central Asia.

http://www.plosone.org/article/info%...l.pone.0034288

[Karachi]

A total of 8,706 samples were used in the analyses including 204 newly genotyped samples from Afghanistan. The genotyping results and the subjects' paternal province and their city or village of origin when available are listed in Table S2. The dataset used include Middle Easterns (2,720 samples) [10], [11], [12], [13], [14], Central/South Asians (1,335 samples) [15], [16], [17], [18], East Asians (1,029 samples) [15], [19], Caucasians (1,525 samples) [20], West Russians (545 samples) [21], Europeans (1,123 samples) [21], [22], [23], [24], [25], and Africans (222 samples) [26], [27]. More details on the analyzed samples are listed in Table S3.

Results Top

Genotyping revealed 32 halpogroups present in Afghanistan's ethnic groups among our samples. Haplogroups R1a1a-M17, C3-M217, J2-M172, and L-M20 were the most frequent when Afghan ethnic groups were pooled, together comprising >66% of the chromosomes. Absolute and relative haplogroup frequencies are tabulated in Table S4.
Haplogroup frequencies across the major ethnic groups revealed large differences. In particular, frequencies of haplogroup C3-M217, which is mainly found in East Asia, and haplogroup R1a1a-M17, which is found in Eurasia, varied substantially among the Afghan groups. C3-M217 was significantly more frequent (p = 4.55×10−9) in Uzbeks (41.18%) and Hazaras (33.33%) than it was in Tajiks (3.57%) and Pashtuns (2.04%). On the other hand, R1a1a-M17 was significantly more frequent (p = 3.00×10−6) in Pashtuns (51.02%) and Tajiks (30.36%) than in Uzbeks (17.65%) and Hazaras (6.67%). RM networks of C3-M217 (Figure S1A) and R1a1a-M17 (Figure S1B) show that when a haplogroup was infrequent in an ethnic group, its haplotypes existed on branches not shared with other Afghans, suggesting that the underrepresented haplogroups are not the result of a gene flow between the ethnic groups, but probably a direct assimilation from source populations.
Haplogroups autochthonous to India [15]; L-M20, H-M69, and R2a-M124 were found more (p = 0.004) in Pashtuns (20.41%) and Tajiks (19.64%) than in Uzbeks (5.88%) and Hazaras (5%). E1b1b1-M35 was found in Hazaras (5%) and Uzbeks (5.88%) but not in Pashtuns and Tajiks. RM network of E1b1b1-M35 (Figure S1C) shows that Afghanistan's lineages are correlated with Middle Easterners and Iranians. We also note the presence of the African B-M60 only in Hazara, with a relatively recent common founder ancestor from East Africa as shown in the RM network (Figure S1D).
PCA of the haplogroups frequency (Figure 1) also shows differences among Afghans. Although the worldwide populations are mostly clustered according to geography, Afghan groups appear to show more affinity to non-Afghans than to each others. Pashtun and Hazara in Afghanistan and Pakistan show affinity to their ethnic groups across borders. The Afghan Tajiks show equal distance to Central Asia and to Iran/Caucasus/West Russia. The Afghan Hazara, Afghan Uzbek, and Pakistan Hazara sit between East Asia and the Middle East/Europe-Caucasus/West Russia cluster.


ore details about the structure of the Afghan population appear in the MDS of the 's (Figure 2B) which shows that the Afghan Pashtun and Tajik are closer to North and West Indians than to the other Afghans; Hazara and Uzbek. This cluster also sits between East Europeans and Iranians more close to the Iranians especially to East Azerbaijan. Furthermore, Barrier (Figure 2A) shows that Barrier IV splits the Afghan populations separating the Hazara and Uzbek from the Pashtun, Tajik and the Indian populations, creating groups of populations that have less variation within the groups (2.30%, p<0.001) and more variation among groups (10.48%, p<0.001) compared to populations grouped by region or country (within groups = 4.95%, p<0.001, among groups = 7.16%, p<0.001) (Table S5).

A previous study on Pakistan [39], that included ethnic groups also present in Afghanistan (Baluch, Hazara, Pashtun), showed that Y-chromosome variation was structured by geography and not by ethnic affiliation. With the exception of Hazara, all ethnic groups in Pakistan were shown to have similar Y-chromosome diversity, they clustered with South Asians, and they are close to Middle Eastern males. A Y-chromosome study [40] on populations from Turkmenistan, Uzbekistan, Kazakhstan, Kyrgyzstan, and Tajikstan, found that there is greater diversity among populations that share the same ethnic group than among the ethnic groups themselves. These observations support a common genetic ancestry hypothesis for these populations irrespective of ethnicity. We have also found substantial differences among the various groups of Afghanistan. The inter-ethnic comparisons however could not be tested in this study since information on tribe and clan affiliation was not available. The high genetic diversity observed among Afghanistan's groups has also been observed in other populations of Central Asia [41], [42], [43], [44], [45]. It is possibly due to the strategic location of this region and its unique harsh geography of mountains, deserts and steppes, which could have facilitated the establishment of social organizations within expanding populations, and helped maintaining genetic boundaries among groups that have developed over time into distinct ethnicities.
The RM networks of the major common haplogroups show that the flow of paternal lineages among the various ethnic groups is very limited, and it is consistent with high level of endogamy practiced by these groups. Similar Y-chromosome results have been previously reported among the Central Asian ethnic groups [40], but with less pronounced genetic differentiation in maternal lineages [40], most likely the results of endogamous practices that were tolerant to assimilation of foreign females.
The prevailing Y-chromosome lineage in Pashtun and Tajik (R1a1a-M17), has the highest observed diversity among populations of the Indus Valley [46]. R1a1a-M17 diversity declines toward the Pontic-Caspian steppe where the mid-Holocene R1a1a7-M458 sublineage is dominant [46]. R1a1a7-M458 was absent in Afghanistan, suggesting that R1a1a-M17 does not support, as previously thought [47], expansions from the Pontic Steppe [3], bringing the Indo-European languages to Central Asia and India.
MDS and Barrier analysis have identified a significant affinity between Pashtun, Tajik, North Indian, and West Indian populations, creating an Afghan-Indian population structure that excludes the Hazaras, Uzbeks, and the South Indian Dravidian speakers. In addition, gene flow to Afghanistan from India marked by Indian lineages, L-M20, H-M69, and R2a-M124, also seems to mostly involve Pashtuns and Tajiks. This genetic affinity and gene flow suggests interactions that could have existed since at least the establishment of the region's first civilizations at the Indus Valley and the Bactria-Margiana Archaeological Complex.
Furthermore, BATWING results indicate that the Afghan populations split from Iranians, Indians and East Europeans at about 10.6 kya (95% CI 7,100–15,825), which marks the start of the Neolithic revolution and the establishment of the farming communities. In addition, Pashtun split first from the rest of the Afghans around 4.7 kya (95% CI 2,775–7,725), which is a date marked by the rise of the Bronze Age civilizations of the region. These dates suggest that the differentiation of the social systems in Afghanistan could have been driven by the emergence of the first urban civilizations. However, the dates suggested by BATWING should be treated with care, since BATWING does not model gene flow and differential assimilation of incoming migrations. These events could alter the time of split. However, it was previously shown that topologies and times of splits in the modal trees generated by BATWING are insensitive to in-migration [13], which leaves BATWING timing results insusceptible to in-migrations and invasions that might be expected to reduce the times of split [13]. On the other hand, the times of population splits for BATWING's modal trees are very susceptible to subsequent migration between those populations. This means that the 2 major waves of splitting could have occurred earlier, but since RM networks of the major haplogroups show limited gene flow between the ethnic groups and since the population structure suggested by MDS and Barrier correlate populations from the historically connected [2] Bronze Age sites to Pashtun and Tajik, BATWING suggested splits in Afghan populations at 4.7 kya (95% CI 2,775–7,725) are very probable. A previous study by Heyer et al conducted in Central Asia [40] have also estimated significantly older dates for the emergence of ethnic groups from what has been historically known. These older dates may be explained by the fact that This suggests that the ethnic groups could have resulted from a encompass fusion of different populations [40] or that ethnicities developed were established from anin already structured population(s).

[Karachi]

The Islamic invasion in the 7th century CE left an immense cultural impact on the region, with reports of Arabs settling in Afghanistan and mixing with the local population [49]. However the genetic signal of this expansion is not clearly evident: some Middle Eastern lineages such as E1b1b1-M35 are present in Afghanistan, but the most prevalent lineage among Arabs (J1-M267) was only found in one Afghan subject. In addition, the three Afghans that identified their ethnicity as Arab, had lineages autochthonous to India.

[Karachi]

^ reading all the above it seems to me that the most ancient population of afghanistan was actually tied to India, Pashtuns even in afghanistan are showing 20% haplogroups native to India and even Tajik (afghans) are showing 19%. afghanistan may have been linked to the indus valley civilization in it's history, maybe that's the reason. Of course later in history many outsiders came and mixed with the native populations. Today's afghans are very diverse

[Amir al Ghaznavi]

very interesting article

[haviZsultan]

Nice...

[evilbunny]

The Islamic invasion in the 7th century CE left an immense cultural impact on the region, with reports of Arabs settling in Afghanistan and mixing with the local population [49]. However the genetic signal of this expansion is not clearly evident: some Middle Eastern lineages such as E1b1b1-M35 are present in Afghanistan, but the most prevalent lineage among Arabs (J1-M267) was only found in one Afghan subject. In addition, the three Afghans that identified their ethnicity as Arab, had lineages autochthonous to India.

E1b1b1, J2 and T need not be Arab and it could also be Greek as they are quite similar.

[DMXX]

My analysis of the results. I retract my earlier post as some of my criticism has been reciprocated there.