Ancient DNA from Nubian and Somali wild ass provides insights into donkey ancestry and domestication

Birgitta Kimura et al.

Genetic data from extant donkeys (Equus asinus) have revealed two distinct mitochondrial DNA haplogroups, suggestive of two separate domestication events in northeast Africa about 5000 years ago. Without distinct phylogeographic structure in domestic donkey haplogroups and with little information on the genetic makeup of the ancestral African wild ass, however, it has been difficult to identify wild ancestors and geographical origins for the domestic mitochondrial clades. Our analysis of ancient archaeological and historic museum samples provides the first genetic information on the historic Nubian wild ass (Equus africanus africanus), Somali wild ass (Equus africanus somaliensis) and ancient donkey. The results demonstrate that the Nubian wild ass was an ancestor of the first donkey haplogroup. In contrast, the Somali wild ass has considerable mitochondrial divergence from the Nubian wild ass and domestic donkeys. These findings resolve the long-standing issue of the role of the Nubian wild ass in the domestication of the donkey, but raise new questions regarding the second ancestor for the donkey. Our results illustrate the complexity of animal domestication, and have conservation implications for critically endangered Nubian and Somali wild ass.

Link

UPDATE

From the paper:

Malana, a remote plateau in the upper reaches (Altitude 2,633 meters) of Parvati valley in Kullu district of Himachal Pradesh, India is an abode to mysterious group of people commonly known as Malanis. Rosser (1955) describes Malana as a hermit village with an aspect of cohesiveness and intense group loyalty that sustains a virulent and suspicious community attitude towards outsiders. Formidable mountain barriers namely Chandrakhani (3,677m); Deo-Tibba (3,732 m) and Rashol Jot (3,238 m) on three sides coupled with the curious efforts of the people to retain their cultural and social uniqueness have ensured virtual biological isolation of the village from the surrounding societies.

and:

We predicted Y chromosome haplogroups from Y-STR data by the use of the Haplogroup Predictor program. The observed haplotypes, predicted haplogroups of the Malana population and the Bayesian probability are reported in Table 4. We found only four haplogroups in the Malana population. Haplogroup J2a1h accounted for 60% of all Y chromosomes. Other haplogroups were R1a (~27%), H (10%) and L (3%). The Bayesian probability was greater than 62% in all the samples.

Hum Biol. 2010 Apr;82(2):123-41.

New World populations (Totonac and Bolivian) are placed between Nepalese and Kyrgyzstanis, indicating higher affinity of these American samples to central Asians than to eastern Asians.

This is more likely an artifact of the mixed (Caucasoid-Amerindian) ancestry of these American samples, rather than an indication of their Central Asian origin, as the authors seem to believe. This is an important caveat, as American Indians and Central Asians are “pulled together” by their shared West Eurasian ancestry of post-Columbus and Neolithic/Chalcolithic Age origin respectively, and correspondingly “pulled away” by Mongoloids proper from East Asia who lack that admixture.

Polynesians also deviate from East Asians towards Europeans, less strongly than Central Asians, and this reflects low-level admixture between ancestral Polynesians and colonial-era Europeans.

The Eurasian PCA is interesting:

At the sub-continental level, we focus first on Eurasia, where most of our samples have been selected (Figure 4A). Overall, PC1 and PC2 mainly reflect the geographic distribution of the populations, with the majority of genetic variation accounted for by their locations. PC1 (accounting for 62.7% of the variance) reflects an east-west gradient, while PC2 (3.3% of the variance) reflects a north-south gradient.

There is absolutely no reason (based on geographical distance) for PC1 to account for twenty times more variance than PC2. PC1 reflects the racial contrast between Caucasoids and Mongoloids, while PC2 reflects the much weaker latitudinal adaptation and south-to-north spread of humans into the higher latitudes.

Another thing to notice is how tightly clustered Caucasoids are, from the Atlantic to Iraq (a distance of about 4,000km), which is -conservatively- about half the distance between Pakistan and South India. This is due to the fact that South Asians were formed by admixture of two elements: an extraneous Caucasoid one and an indigenous Paleo-Indian one. Notice also that this variable admixture (highest Caucasoid component in Brahmins) is not really compatible with an indigenous origin of the caste system, as has been proposed on non-scientific grounds.

More spread (given geographical distance) is also observed in Central Asia and Southeast Asia, and this is explained by relatively recent admixture between Caucasoids and Mongoloids (in the former) and Paleo-Indian-like morphological “Australoids” and Mongoloids (in the latter).

The results of ADMIXTURE analysis (for Eurasian individuals) are presented in graphical format in the paper itself, for (K=7).

Not much to comment on this that hasn’t been seen before:

One observation is the existence of some “red” West Asian component in the N. European sample, which is not found in Slovenians. This may parallel the peculiarity of the Caucasoid components observed for Russians and Lithuanians recently, although the several Caucasoid components detected in that study are folded into 2 in the current one.

Notice also, how “red” is the main extraneous component in Indian Brahmins. As expected, even Brahmins are predominantly of “indigenous” origin, as these Brahmins are from Tamil Nadu and Andhya Pradesh, and not from North India. The West Asian affiliations of the main Caucasoid component are evident, and agree with Behar et al. (2010) where South Asians had a major overlap with West Asians (light green) and a minor one with Europeans (dark blue). In this paper, with a lower K the different European and West Asian subclusters are not visible.

The most interesting part of the study -for me- was the inclusion of three novel African samples, the Luhya, Alur, and Hema. Notice the blue component in these people, which resolves partially to orange at K=12. This is an indication of Eurasian affinities that are mostly lacking in other black Africans.

All in all, a very interesting paper which adds important new populations to the discussion of human origins. Also of note, the free availability of the paper’s genotype data and supplementary material at the Jorde Lab.

Genomics doi:10.1016/j.ygeno.2010.07.004

Toward a more uniform sampling of human genetic diversity: A survey of worldwide populations by high-density genotyping

Jinchuan Xing et al.

High-throughput genotyping data are useful for making inferences about human evolutionary history. However, the populations sampled to date are unevenly distributed, and some areas (e.g., South and Central Asia) have rarely been sampled in large-scale studies. To assess human genetic variation more evenly, we sampled 296 individuals from 13 worldwide populations that are not covered by previous studies. By combining these samples with a data set from our laboratory and the HapMap II samples, we assembled a final dataset of ~ 250,000 SNPs in 850 individuals from 40 populations. With more uniform sampling, the estimate of global genetic differentiation (FST) substantially decreases from ~ 16% with the HapMap II samples to ~ 11%. A panel of copy number variations typed in the same populations shows patterns of diversity similar to the SNP data, with highest diversity in African populations. This unique sample collection also permits new inferences about human evolutionary history. The comparison of haplotype variation among populations supports a single out-of-Africa migration event and suggests that the founding population of Eurasia may have been relatively large but isolated from Africans for a period of time. We also found a substantial affinity between populations from central Asia (Kyrgyzstani and Mongolian Buryat) and America, suggesting a central Asian contribution to New World founder populations.

Link

In addition, we have a new participant, Allen Ray Berry, #195, expected, it appears, to be a Barry/Berry.    His kit hasn’t yet been returned to FTDNA.

Internal diversification of mitochondrial haplogroup R0a reveals post-Last Glacial Maximum demographic expansions in South Arabia