View Full Version : Lack of lactase persistence alleles amongst South Sudanese Nilotic peoples

05-29-2021, 07:16 PM
A while back I read the pre-print The genetic variation of lactase persistence alleles in northeast Africa (https://www.biorxiv.org/content/10.1101/2020.04.23.057356v1.full) on Biorxiv, and I was quite surprised to read about the situation regarding lactase persistence alleles amongst South Sudanese people:

No LP-associated alleles were found in the Nilotic populations of South Sudan. Due to the close proximity of SASS populations to East Africa it is surprising that there is no evidence of the derived −14010:C allele in the SASS populations. This absence in Nilotic South Sudanese populations, despite the occurrence in Nilotic Tanzanians and Kenyans, where it is significantly associated with LP, has previously been noted (Tishkoff et al., 2007), and is in agreement with a previous study, that found the South Sudanese Nilotes to have remained largely isolated (Hollfelder et al., 2017).

Various reasons are there for my confusion. The biggest one is that they are surrounded by ethnic groups who do carry various lactase persistence alleles and that their lifestyle would be a very strong driver for the spread of LP. Another point is that those people are just gargantuan and a mainstaple of their diet is raw milk. Being lactose intolerant does not mean that you cannot consume lactose products but it certainly affects the amount of nutritition you can derive from it. Another point being previous research articles (not based on genetics) actually indicating that they did have lactose tolerant people amongst them.

The authors of this study did provide an interesting possibility:

The lack of LP-associated alleles in the agro-pastoralist Nilotic populations has been observed before (Hassan et al., 2016; Tishkoff et al., 2007) despite the intermediate prevalence of lactose-digesters (>20%) in tested Nilotic populations (Bayoumi et al., 1981, 1982; Tishkoff et al., 2007).This might be indicative of unknown LP associated variants in the Nilotic populations. LP associated alleles are also absent in the Hausa of Sudan, although a Hausa population of Cameroon had previously shown 0.139 allele frequency of −13910:T (Mulcare et al., 2004). In an early study of lactose digesters in Sudan (Bayoumi et al., 1981) the Nuba and the Messiria also showed higher LP-phenotypes than predicted in this study.

Even though this study investigated a range of Nilotic populations, no LP-associated SNPs were detected in these agropastoralist populations, that have been shown to be able to digest milk in hydrogen breath tests (Bayoumi et al., 1981, 1982; Tishkoff et al., 2007). Further studies on Nilotic populations will reveal more about the substructure in northeast Africa (Hollfelder et al., 2017) and can be informative about the underlying biology of LP in Nilotic populations.

I am wondering what you guys think. is it likely the Nilotic peoples of South Sudan have as of yet undiscovered alleles that cause lactase persistence? Or did their body just adopt "the hard way" to their lifestyles?

05-29-2021, 10:28 PM
Speaking of LP do you know what dairy products were consumed by Neolithic farmers and Indo-Europeans? When did yogurt pop up?

05-30-2021, 06:35 AM
Do we know when they adopted pastoralism? I believe they took it up later and this explains for low frequency of the alleles.

What's more interesting is the Hadza who happen to carry the14010:C allele at low frequency but have the ability to digest milk at a very high freq.

05-30-2021, 09:00 AM
Do we know when they adopted pastoralism? I believe they took it up later and this explains for low frequency of the alleles.

What's more interesting is the Hadza who happen to carry the14010:C allele at low frequency but have the ability to digest milk at a very high freq.

AFAIK the common proto-stage of Nilotic languages indicate that its people were already practising pastoralism, which fits with the archaeological data of their supposed homeland. This basically means they have been pastoral for thousands of years, rather than only a few centuries.

The Shilluk enter the historical records with their kingdom halfway through the second millenium AD and prior to that there were tons of migration of pastoral Nilotic peoples going southwards. I dont think we have any historical evidence of them still being forager peoples during these periods.

Given what we see in the west, LP can spread pretty rapidly amongst a population if their population numbers aren't huge. This rapid spread is also seen amongst the Maasai for example.

So how come there was no positive selection for LP amongst Nilotic peoples in their original homeland?

The simple answer would be that the various LP alleles were not part of their genepool, and only became part of the Nilotic peoples as they expanded southwards acquiring Cushitic-related ancestry, who were very much did have such alleles.

Were they really so genetically isolated that in the many centuries of them interacting with neighbouring peooles who did have LP there was no sufficient geneflow from these populations that could lead to an entry of LP associated alleles in their genepool?

Kind of odd considering the cultural and linguistic influences both Cushitic and Nubian peoples had amongst the Nilotes.

06-03-2021, 05:04 PM
Its crazy how far this allele that originated in the Caucasus has spread so far.

06-07-2021, 03:24 PM
I have been watching this closely i believe they may have undiscovered alleles.
I think the LP version they do have when found could also be found in Sahelians and perhaps Senegambians.

06-07-2021, 05:12 PM
Bayoumi et al (1982) tested for lactase persistence phenotype in 282 south Sudanese (almost all Nilotes) and found that 74% of them did not produce lactase according to a hydrogen breath test (gut bacteria fermenting lactose produce hydrogen, and much less is produced when human lactase is taking away the lactose). So in fact they seem to have a fairly low frequency of lactase persistence, not just of known LP alleles, and must have adapted to the diet some other way. Though as noted a quarter of them *did* digest the lactose, so they may *also* have an presently unknown LP variant!

06-07-2021, 07:48 PM
Just to add....i am never going to do this work but:

I think there could be some surprises (https://www.researchgate.net/publication/230796967_Stronger_signal_of_recent_selection_for_ lactase_persistence_in_Maasai_than_in_Europeans)wh en we map the distribution of LP variants onto the distribution of of Major African/Non African cattle breeds.
Some of them like -13915*G are even thought to not even be associated with cattle but rather Camels. This means we also need to include the variable of milk from sheep and goats.
Considering the differences between Ovicaprid and Cattle milk, I have flirted with the idea that maybe some of these mutations (like -13915*G) arose in relation to non cattle milk consumption.

I dont know the history of non Cattle milk consumption in the Middle East and North Africa to investigate this further.
I DO know that the Fertile Crescent possible only has one indigenous LP variant despite 3 domesticates (Ovid,Cattle,Camel). Africa has like 4 to 6, so there was something different about milk consumption on the Africa side of the Red Sea that let to so much LPP diveristy.