The trait of lactase persistence (lactose tolerance) is probably one of the better schoolbook examples of natural selection in human populations. The reasons for this are probably two-fold. There is a very strong signature of selection within a specific gene known to associate with the trait in question in many populations. And, there is a very compelling historical narrative which explains rather neatly how this particular functional change could have undergone such strong selection within the past ~5,000 years across these populations. But the elucidation of the origin and spread of this genetic adaptation is also interesting because it looks as if it was not a singular event. Populations as disparate as Arabians, Danes, and Masai seem to carry different alleles around the locus of interest which confer the ability to digest milk. This illustrates the fact when selection pressures have a viable target, there is a rapid response on the genomic level. At some point during the maturation of a mammal the regulatory pathway which produces lactase enzyme shuts down. Yet within numerous human populations this gradual shutdown process has been short-circuited.
The variety of response in relation to this adaptation was brought home to me as I read Diversity of Lactase Persistence Alleles in Ethiopia – Signature of a Soft Selective Sweep, in the latest issue of The American Journal of Human Genetics:
One of the primary concerns/questions I had about Luca Pagani’s paper on the genetic origin of Ethiopians is that he found that their West Eurasian ancestor was closer to Levantine than Arabian. I was confused by this because on model-based clustering (e.g., Admixture) when you push down to a fine level of granularity you always see that the Ethiopians cluster with the Yemenis for their non-African ancestry. More precisely, Yemeni Jews are often ~100% component X, which ~50% of the ancestry of Ethiopians.
From what I recall Pagani et al. used haplotype windows which they assigned to Eurasian or African ancestral components, and they compared these to the populations related to the putative ancestral groups. Because Pagani et al. used blocks of the genome, rather than just on specific genotypes, I weight their finding more strongly. But I wanted to double check with TreeMix if the finding in Admixture was peculiar.
So again, I took a ~150,000 SNP set ran it on TreeMix with migration = 5.
Again, you see that the gene flow to the Ethiopians is coming from a position on the tree rather close to Yemenite Jews. One model which may explain this, and still align with Pagani’s findings, is that Arabians themselves are a synthetic population. A “pure” Yemenite Jew may have ancient admixture of African affinity beneath an intrusive element from the north. The parallelism between Ethiopia and Arabia in this model is clear, with the major difference being magnitude of the source population admixture (greater in Arabia), as well as some differences of the target population.
This again reiterates us to be careful of trust first-blush summaries.
Liya Kebede, Credit
There is a new paper, Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool, which is being sensationalized in the media. For example, the BBC headline: ‘DNA clues to Queen of Sheba tale’. I assumed that this was just the media, but to my surprise the authors themselves mention the ‘Sheba tale’ in their discussion for various reasons. This is unfortunate. Though it is true Ethiopians have a legend of descent from the queen of Sheba (and through her relationship to king Solomon the ancient Hebrews), if there is a scholarly consensus about the location of Sheba, it is probably in southwest Arabia (i.e., modern Yemen). But the reality is that it is probably just as likely that the story in the Hebrew Bible is an interleaved synthesis of legend and reality, and that disentangling the nuggets of truth so as to establish the location of the real Sheba is going to be impossible (it is just as likely that the real queen of Sheba, if she existed, was a Levantine notable who was given a more exotic provenance by the redactors of the Hebrew Bible).
As for the paper itself, it is of some interest. I’ve blogged and analyzed Ethiopian data myself, but the sample coverage here is awesome. Additionally, the authors attempted to ascertain time since admixture in relation to the Ethiopian population for their West Eurasia and African ancestral components, as well as sniffing around for signatures of selection in the genome. The highlights:
In the post yesterday I reported what was generally known about the Horn of Africa, that its populations seem to lie between those of Sub-Saharan African and Eurasia genetically. This is totally reasonable as a function of geography, but there are also suggestions that this is not simply a function of isolation by distance (i.e., populations at position 0.5 on the interval 0.0 to 1.0 would presumably exhibit equal affinities in both directions due to gene flow). For example, you observe the almost total lack of “Bantu” genetic influence on the Semitic and Cushitic populations of the Horn of Africa, and the lack of Eurasian influence in groups to the south and west of the Horn except to some extent the Masai.
Tacking horizontally in terms of discipline, over the past few generations there has been a veritable cottage industry making the case for the recent origin of many ethno-linguistic populations through a process of cultural self-creation. Clearly there are many cases of this, some of them studied in depth by anthropologists (e.g., the shift from Dinka to Nuer identity). But there has been an unfortunate tendency to over-generalize in this direction. In some ways this is peculiar insofar as these models presuppose the infinite plasticity of culture without observing the sharp and strong norms which those very same phenomenon can enforce. The genetic isolation of non-Muslims in the Middle East after the rise of Islam seems rather well validated by the evidence from genomics. The norms of both Muslims and non-Muslims strongly biased them toward endogamy, and nature of Islamic hegemony and domination was such that Muslims were the ones who were likely to have cosmopolitan affinities with the “Islamic international.” In contrast, non-Muslim minorities began a long process of involution after the Islamic Arab conquests, only disrupted in the past century by emigration and to a lesser extent emancipation.
So back to the Horn of Africa. The vast majority of the people of the Horn of Africa speak an Afro-Asiatic language. Arabic and Hebrew are the most famous members of this group, but it is a very broad classification, ranging from the dialects of the Berbers in the Maghreb all the way to ancient Akkaddian. There are two large subfamilies of particular note and interest here: Semitic and Cushitic. The map above shows the distribution within the Horn of Africa. One can “quick & dirty” summarize the pattern here by observing that Semitic languages in Ethiopia tend to be concentrated in the north-central Christian highlands, while Cushitic is found everywhere else. Additionally, there is the confluence between religion and ethnicity, as there are Cushitic Muslims (Somalis, Afar, etc.) and Cushitic Christians (many Oromo, etc.). From what I can gather many Cushitic social and political elites have had a tendency toward assimilating into an Amhara Semitic identity (Haile Selassie’s mother was a Muslim Oromo). We could therefore generate a possible model where Semitic langauges arrived late to Ethiopia and spread through elite emulation, so the difference between Semitic and Cushitic peoples should be marginal in the genomic dimension (such as the marginal differences between Hausa and Yoruba in Nigeria). Or, we could posit that the Semitic element is distinctive from a pre-existent Cushitic substratum.
To make a long story short by running more ADMIXTURE with a Horn of Africa centered data set I have discerned that one can actually differentiate Cushitic and Semitic elements in the Horn and tentatively identify them with different ancestral components. First, the technical details….
In light of my last post I had to take note when Dienekes today pointed to this new paper in the American Journal of Physical Anthropology, Population history of the Red Sea—genetic exchanges between the Arabian Peninsula and East Africa signaled in the mitochondrial DNA HV1 haplogroup. The authors looked at the relationship of mitochondrial genomes, with a particular emphasis upon Yemen and the Horn of Africa. This sort of genetic data is useful because these mtDNA lineages are passed from mother to daughter to daughter to daughter, and so forth, and are not subject to the confounding effects of recombination. They present the opportunity to generate nice clear trees based on distinct mutational “steps” which define ancestral to descendant relationships. Additionally, using neutral assumptions mtDNA allows one to utilize molecular clock methods to infer the time until the last common ancestor of any two given lineages relatively easily. This is useful when you want to know when a mtDNA haplgroup underwent an expansion at some point in the past (and therefore presumably can serve as a maker for the people who carried those lineages and their past demographic dynamics).
What did they find? Here’s the abstract:
Archaeological studies have revealed cultural connections between the two sides of the Red Sea dating to prehistory. The issue has still not been properly addressed, however, by archaeogenetics. We focus our attention here on the mitochondrial haplogroup HV1 that is present in both the Arabian Peninsula and East Africa. The internal variation of 38 complete mitochondrial DNA sequences (20 of them presented here for the first time) affiliated into this haplogroup testify to its emergence during the late glacial maximum, most probably in the Near East, with subsequent dispersion via population expansions when climatic conditions improved. Detailed phylogeography of HV1 sequences shows that more recent demographic upheavals likely contributed to their spread from West Arabia to East Africa, a finding concordant with archaeological records suggesting intensive maritime trade in the Red Sea from the sixth millennium BC onwards. Closer genetic exchanges are apparent between the Horn of Africa and Yemen, while Egyptian HV1 haplotypes seem to be more similar to the Near Eastern ones.
Much of this is totally concordant with the results we’ve generated from the autosomal genome. Though the autosomal genome is much more difficult when it comes to implementing many of the tricks & techniques of phylogeography outlined above, it does offer up a much more robust and thorough picture of genetic relationships between contemporary populations. Instead of a a distinct and unique line of paternal or maternal ancestry, thousands of autosomal SNPs can allow one t o get a better picture of the nature of the total genome, and the full distribution of ancestors.
The map to the left shows the spatial gradients of the broader haplogroup under consideration, HV1. But what about the branches? Below is an illustration of the phylogenetic network of branches of HV1, with pie-charts denoting the regional weights of a given lineage:
In the open thread someone asked: “Any recent stuff on the genetics of Ethiopians.” That prompted me to look around, because I’m curious too. Poking around Wikipedia I couldn’t find anything recent. A lot of the studies are older uniparental lineage based works (NRY and mtDNA). Ethiopia is interesting because unlike almost all other Sub-Saharan African nations it has a long written history. Culturally and linguistically it has both Sub-Saharan African, and non-Sub-Saharan African, affinities. The languages of highland Ethiopia are clearly Semitic. Those of lowland Ethiopia are Cushitic, a branch of the broader Afro-Asiatic language family concentrated around the Horn of Africa (Somali is a Cushitic language, though most Ethiopian nationals who speak a Cushitic dialect are of the Oromo group).
From a human evolutionary genetic perspective, Ethiopia also has specific interest. It is likely that the main recent pulse of humans Out of Africa traversed this region. Additionally, there is some evidence of deep time connections between the groups ancestral to Ethiopians and the Khoisan of southern Africa. It may be that Ethiopians and Khoisan are reservoirs of ancient genetic variation in Sub-Saharan Africa which as been overlain by Bantu in most other regions outside of West Africa. Finally, Ethiopians are known to have high altitude adaptations. This could be due to long term residence in the region, or, assimilation of favorable alleles from the long term residents by later populations.
Fortunately we can get a sense of the genetic affinities of Ethiopians thanks to a paper published last spring, The genome-wide structure of the Jewish people. The focus was clearly on Jews, but they surveyed Amhara & Tigray (Semitic speaking highlanders), Ethiopian Jews (similar ethnically to the Amhara & Tigray, but religiously non-Christian), and Oromo. In the PCA the Oromo and Semitic speaking populations are pretty obviously distinct clusters.