Lactase persistence in East Africa - Prevalence and genetic variability

[Fez]

The core group studied were Somalilanders as told below

Abstract:

"The subsistence strategies of human populations have left traces in the past that are recognizable today in the genetic structure of their descendants. One example is lactase persistence (LP), which occurs primarily in populations where dairy production and consumption of fresh milk were widespread in the past. LP is also an example of parallel evolution, as it evolved independently in several populations in Africa and Eurasia. Five known single nucleotide polymorphism (SNP) variants are associated with this phenotype. The variant designated -13 910*T is typical for Western Eurasia and pastoralists of the West African Sahel, while the variant -13 915*G dominates in the Arabian Peninsula and among the Arabs of the East Sahel. In addition to these two variants, three more occur in East African populations, namely -14 010*C, -14 009*G and -13 907*G.

The aim of this thesis is to expand knowledge about LP in the East African region by analyzing a previously unexplored population from Somaliland. Almost 100 DNA samples from this region were analyzed, in which a section including all pro-LP variants was sequenced. The obtained data were subjected to basic population-genetic tests and put into context with already published data from East Africa. On their basis, a statistical interpretation of LP frequency data of 107 populations, grouped according to subsistence strategy, linguistic affiliation and geographical location, was also performed, with the aim of revealing the internal diversity of the region. The results of the work showed that the total frequency of LP in the Somaliland population is relatively low (13%), represented primarily by the East African variant -13 907*G and the Arabic variant -13 915*G. Genetic proximity to Ethiopian pastoralists and farming groups from Sudan reflects historical migration links in the region. The obtained data further indicate that the most significant factor influencing the genetic variability of LP is not, as expected, selected subsistence (only 6.36%), but linguistic affiliation (10.97%), which probably reflects deeper historical and genetic links. This work thus expands the knowledge about the genetic diversity of LP from the Somaliland region and contributes to a better understanding of the complex biological, cultural and historical factors that participated in the formation of this trait in East Africa"

PCA graphs of where the Somaliland samples plot for LP

Wider map of North east Africa comparing rates of LP and the types of mutations most frequent

13 915*G and 13 910*T are Arabian and European respectively. The other 2 LP variants are native East African

 

[Fez]

Translated statement made on the SL samples


"Genetic analysis of variants associated with LP in the Somaliland population confirmed the original hypotheses (see hypotheses 1 and 2 in chapter 3.2), while the representation and share of individual LP variants in the overall LP phenotype partially serves as support for the second hypothesis. The highest share was held by 2 variants: the East African variant -13 907*G, contributing to a total frequency of 6% and the so-called Arab variant -13 915*G, at a frequency of 5%. The presence of these variants is logical in the context of the geographical location of Somaliland, i.e. on the border of East Africa and the Arabian Peninsula, and it is assumed that -13 915*G was introduced into the population as a result of the spread of Arab pastoralists (Priehodová 2017; Priehodová et al. 2017). -13 907*G, with its presumed origin in Cushitic-speaking populations of eastern Ethiopia, represents East African heritage (Tishkoff et al. 2009). In addition to the -13 907*G variant, the -14 010*C and -14 009*G variants also contribute to East African heritage, with a frequency of 1%, and their origin is also located in East Africa. This representation of variants correlates with the results of the study by Ali et al. (2020) showing that approximately 60% of Somali genetic heritage is of East African origin and the remaining approximately 40% is West Asian."

Link: http://hdl.handle.net/20.500.11956/199364

 

[balanbalis]

I’m reading this even though my stomach tried kill me since I chose to eat icecream 3 days in a row

 

[giire12]

On the Map there are four Somali location, SO1, SO2, SO3 and SML. The SO3 is maybe Harta Sheekh. SO2 is likely Mogadishu and SO3 maybe Jigjiga? SML Somaliland

 

[Fez]

On the Map there are four Somali location, SO1, SO2, SO3 and SML. The SO3 is maybe Harta Sheekh. SO2 is likely Mogadishu and SO3 maybe Jigjiga? SML Somaliland

SML does represent Somaliland. SO1 and SO3 are from Somali region but we cannot be sure of tribal origins. SO2 represents Agricultural Somalis from the south

 

[Fez]

I’m reading this even though my stomach tried kill me since I chose to eat icecream 3 days in a row

13% Is a small Number. Many people in my own fam have a hard time with dairy products

 

[Midas]

Is that really possible considering somalis were mainly nomads and the single largest thing in their diet was milk ? Are camel milk and cows milk that different?

 

[Fez]

Is that really possible considering somalis were mainly nomads and the single largest thing in their diet was milk ? Are camel milk and cows milk that different?

@Shimbiris Gave a good explanation on this. Adaptation was the Key for us and many other Nomadic groups

The vast majority of Mongols are not lactase persistent genetically like Northern Europeans. They're even less lactase persistent than us by a wide margin, last I checked. Yet a fair number of Mongols and even Han Chinese report being able to consume a significant amount of milk without issues. There is evidence in the literature I've seen over the years that populations overtime develop the proper gut microbiome for digesting certain things like the Japanese with seaweed and our ancestors and Mongols with raw milk. If I'm not mistaken, I don't genetically carry many of the markers for lactase persistence yet I can chug a gallon of milk, raw or pasteurized, and feel absolutely normal throughout the day after with no diarrhea or anything like that.

It's the gut microbiome. Somalis who have trouble with dairy are most likely damaged in some way in that respect. Most people are, to be honest. I remember reading how there were so many strains of things like lactobacillus that are heavily depleted in modern people compared to before due to things like SAD type diets, microbiotically compromised mothers and birthing through methods like c-sections. Sad stuff.

Also, another thing to keep in mind is that a lot of pastoralist populations didn't historically just chug raw milk. Our ancestors, including the ancestors of groups like the Mongols, the Maasai and even the Bedouin very often fermented milk into things like yogurt and sourmilks which heavily depleted the lactose and left you with the protein, fat, vitamins, mineral and probiotics.

A lot of the milk was also used to make butter, ghee and in the case of some of these cultural groups cheeses as well. Camel milk was historically pretty much impossible to make cheese from so cheese wasn't much of a thing across the Sahara and for Somali nomads but the rest like sourmilks, yogurts, butter, cream and ghee were very, very common. And one thing all of those things have in common is little to no lactose. If you've left raw milk to ferment for 2-3 days then there's probably only trace amounts of lactose left and almost nobody is THAT sensitive. Same goes for butter, cream and even more so with ghee.

 

[Garaad Awal]

I carry the NE African one. True son of the Eastern Desert. What’s even better I carry two copies of it which means my kids have it as well

 

[NidarNidar]

Feed ChatGPT SNP for lactose tolerance.

You do not carry the major European (rs4988235), Middle Eastern (rs41380347), East African, or West African lactase persistence alleles.

Your genotype suggests lactase non-persistence.

rs41525747 = CG: This SNP is very rare and weakly studied (some minor effect in Central Asian groups). But the A allele is the persistence variant — you don't carry it.

rs182549 is missing — not critical, as it’s just a proxy for rs4988235.

Meanwhile, I drink milk without any issues.

 

[Top J]

I drink half a litre of milk a day + yoghurt no probs

 

[Garaad Awal]

Feed ChatGPT SNP for lactose tolerance.

You do not carry the major European (rs4988235), Middle Eastern (rs41380347), East African, or West African lactase persistence alleles.

Your genotype suggests lactase non-persistence.

rs41525747 = CG: This SNP is very rare and weakly studied (some minor effect in Central Asian groups). But the A allele is the persistence variant — you don't carry it.

rs182549 is missing — not critical, as it’s just a proxy for rs4988235.

Meanwhile, I drink milk without any issues.

Farmer ass nigga

 

[Garaad Awal]

rs41525747 = CG: This SNP is very rare and weakly studied (some minor effect in Central Asian groups). But the A allele is the persistence variant — you don't carry it.

That’s the NE African variant. You are not a farmer ass nigga after all

 

[Garaad Awal]

Apparently for those of you who tested with 23&me. If you get AA on the Middle Eastern rs41380347, this means you are positive. Correct me if I’m wrong

 

[Fez]

Apparently for those of you who tested with 23&me. If you get AA on the Middle Eastern rs41380347, this means you are positive. Correct me if I’m wrong

I'm already Positive for 2 Variants how could 3 be possible

 

[Garaad Awal]

I'm already Positive for 2 Variants how could 3 be possible

View attachment 366275

My bad it is indeed negative for the Bedouin Arab one . I get CC for rs145946881 on FTDNA but so does my wife which means something is off. I assume it’s on a different direction so I’m probably negative for the South Cushitic & Bedouin one. Seems I only carry the NE African one (GG).

 

[Fez]

My bad it is indeed negative for the Bedouin Arab one . I get CC for rs145946881 on FTDNA but so does my wife which means something is off. I assume it’s on a different direction so I’m probably negative for the South Cushitic & Bedouin one. Seems I only carry the NE African one (GG).

If you've tested on AncestryDNA can you check for that same SNP rs145946881. It's mildly surprising for me as it looks rare outside Kenya/Tanzania

 

[Riftvalley]

Somalis who are lactose intolerant are more peaceful.

 

[NidarNidar]

My bad it is indeed negative for the Bedouin Arab one . I get CC for rs145946881 on FTDNA but so does my wife which means something is off. I assume it’s on a different direction so I’m probably negative for the South Cushitic & Bedouin one. Seems I only carry the NE African one (GG).

I've never had an issue drinking milk, though I have gluten sensitivity.

 

[giire12]

rs4988235 2 136608646 GG, rs182549 2 136616754 CC, rs41380347 2 136608651 AC

ChatGPT said:​

Thanks for sharing your data! Let’s go through your results one by one:

---

Interpretation of Your Genotypes for Lactase Persistence​

SNP	Genotype	Interpretation
rs4988235	GG	Lactase non-persistent (associated with lactose intolerance in Europeans)
rs182549	CC	Also associated with lactose intolerance (correlates with GG at rs4988235)
rs41380347	AC	One copy of a variant associated with lactase persistence in Middle Eastern and East African populations

---

What This Means:​

• The GG at rs4988235 and CC at rs182549 are the ancestral genotypes, typically indicating lactose intolerance in European populations.
• However, your AC at rs41380347 is interesting — the A allele at this SNP has been associated with lactase persistence in some Middle Eastern and East African populations.

---

Conclusion:​

• Based on rs4988235 and rs182549, you would likely be lactose intolerant if you're of European ancestry.
• However, your AC at rs41380347 may partially compensate, depending on your ancestry. This could indicate some lactase persistence especially if you have Middle Eastern or East African ancestry.

---

So, Can You Digest Lactose?​

• If you're of European ancestry: You're likely lactose intolerant, genetically.
• If you're of mixed ancestry or have Middle Eastern/East African roots: You might still tolerate lactose better than expected due to rs41380347.
• Your actual tolerance can vary — some people produce lactase despite "intolerant" genotypes, and others may lose tolerance with age.

Chatgpt is confused