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Genetics of Lactose Intolerance: An Updated Review and Online Interactive World Maps of Phenotype and Genotype Frequencies - Augusto Anguita-Ruiz
This is an interesting study. Interesting parts are highlighted. Points
1. This is the latest study including datasets from the popular studies. This current dataset is dated to July2020 2. According to the paper. Report by population is available 3. So some West Africans carry the highest frequency of LP 4. Italians and some southern Europeans carry as little as 30% LP 5. Bedoiuns, Sudanese and West African Fulani carry as much as 80% LP genes. Keep in mind the Fulani carry typical SSA lineage such as E1b1a. 6. LP is found all over the globe, including Native Americans – North, Central and South 7. Very low levels in East Asia. Why would the Americans carry LP and not East Asia if the supposed migration route was via East Asia and Beringia 8. At least 18 additional genes have been discovered related to LP 9. The LP genes all seems to have arisen at the same time. I repeat. “ALL LP GENES SEEMS TO HAVE ARISEN AT THE SAME TIME”. This is a very important point. 10. The least diverse genes are found ……you guessed it….Northern Europeans. 11. 13910(supposed European origin although it is the least diverse in Europe – sic) can be found in Algeria, Mozab and other Berbers, Fulani, Cameroon, South Sudan, Coquimbo Chile, rural Mexico, North America 12. 13495 is a new variant discovered in Europe but also found worldwide It is in LD with 13910. 13495 is older than 13910!!!! 13. Almost all variants exist within East Africa/Arabia, that span 100-base pair…guess what? “European” 13910 is WITHIN that region. Lol! SMH. Meaning??!! 14. Nigeria and Cameroon is not West Africa anymore…lol!
I agree all have risen at the same time in the Great Lakes region of Africa. That would mean that Africans somehow contacted the American mainland in late Neolithic or pre-historic times. The Great Lakes region carry ALL genotype of LP including 13910. European carry the least diverse haplotype of 12910 yet the author conclude the LP genotype originated in Africa. How blind or obtuse can you be?
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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-------------------- Genetics of Lactose Intolerance: An Updated Review and Online Interactive World Maps of Phenotype and Genotype Frequencies - Augusto Anguita-Ruiz
3.4. Lactase Phenotypes and Their Genetics Origin Our interactive map constitutes the most comprehensive and updated resource for exploring LP frequencies worldwide. Besides including all available literature reports on LP frequencies till 20 July 2020, our map further -- a detailed description for each included study (incorporating information related to geographical location, ethnicity, number of individuals analyzed, reported frequency, and literature references). One of the greatest virtues of our interactive map is its ability to organize large amounts of data in a single shot, which otherwise would be hosted in unpleasantly big tables. As a fully extendable and interactive graphic, our tool further constitutes an upgrade over previously published static world maps, allowing users a personalized data exploration at the same time as accessing complete reports by population. ). As can be observed, the frequency of LP varies greatly among populations, ranging from 0% to almost 100%, with the highest rates found in people of northern European descent and some populations from West Africa, East Africa, and the Middle East (http://bionit.ugr.es/pages/invest igacion/software/bioinformatics-methods-software). The frequency decreases as one moves to the south and east of the map (with 30% of LP reported in Italy). This descending gradient is disrupted in some European countries with a strong cultural admixture tradition, such is the case of Spain (with reported frequencies ranging from 47% to 91%). Interestingly, LP is particularly frequent in some milk consuming nomads and pastoralist communities of the Afro-Arabian area in comparison to their neighboring populations (e.g., 86% in Beduin Saudi, 88% in Ben-Amir, 80% in Haddendoa, and 70% in Fulani). There is a very low level of LP in the Asiatic countries (15% in China, and 0% in South Korea, Vietnam, and Cambodia).
Regarding the USA and Mexico, although they present a relatively
3.5 Current status of Genetics… In addition to these five genetic markers, up till now, eighteen new SNPs mapping the MCM6 have also been associated with LP in specific populations, thereby making a total of twenty-three known SNPs that currently underlie the genetic etiology of LP (Table 1). Interestingly, these variants seem to have arisen during the same time period, but independently in different human populations, and this is the reason why LP has become a textbook example of convergent regulatory evolution, and gene-culture co-evolution. In the presented Table 1, we display the known identifiers for mentioned variants as well as any evidence of functional control on LCT expression according to the literature. Analysis of an 80 kb haplotype covering the region of LCT and the upstream MCM6 enhancer has further confirmed a tight association of these LP variants with particular haplotypes [10,12,14], and shows that haplotype diversity also differs between populations, with the least diversity observed in Northern Europeans [9].
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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For the remaining twelve frequent and widely studied SNPs, we have created a database including all available information for minor allele worldwide frequencies reported till July 2020 in the literature (Supplementary Table S2). For the most genotyped variants among these twelve markers (those SNPs that have been studied in more than ten different populations around the world), we have further created an interactive map following the same format as the one previously presented for LP phenotype data. The six genetic variants represented in the interactive map comprise13910:C>T (rs4988235), 3495:C>T (rs4954490), 4009:T>G (rs869051967), 13907:C>G (rs41525747), 13915:T>G (rs41380347), and 14010:G>C (rs145946881)), for which we further include information related to ethnicity, number of genotyped individuals, reported minor allele frequencies, and literature references. This interactive map is hosted at (http://bionit.ugr.es/pages/investigacion/software/bioinformatics-methods-software) and a static capture is presented in Figure 4. For the construction of such a database and interactive map,
As can be observed in our map, 13.910:C>T is not only a European mutation but also underlies the LP phenotype all over Asia, including in various populations from Russia, Pakistan, and Iran; Central Asia (prevalence of 30% in herders); and Nepal (prevalence of up to 34% in herders from the north) [77,78]. It is also the primary LP-associated mutation in Algerians (17–33%), Mozabites (22%), and other Berber populations (14–23%) from North Africa, as well as in Fulani (23–48%) from both Central Africa (Cameroon) and East Africa (South Sudan). Interestingly
the 13.910:C>T has also been found at a moderate frequency in South America (22% in communities from the Coquimbo region in Chile) [25,79], Central America (20% in rural areas from Mexico), and in North America (21–82%). Although it was thought that in all of Eurasia the LP phenotype was monogenic, a second variant, the 13495:C>T, was described and found to be widely spread worldwide (87% prevalence in Norway, 96% in Ireland, 78% in UK, 50% in Spain, Italy, and Portugal, as well as a frequency higher than 15% in other Eurasians regions such as Azerbaijan, Georgia, Uzbekistan, Russia, Mongolia, Pakistan, and India). In all the populations where the 13495:C>T has been found, the variant exhibits very similar frequencies to the 13.910:C>T, with a practically complete LD described for both markers (D’ = 0.99 according to the 1000 Genomes Project Phase 3). Located just outside the enhancer MCM6 region, the 13495:C>T has been shown to occur as a derived allele on an ancestral haplotype and to be older than the 13.910:C>T [9].
The situation is different in the Arabian peninsula and East Africa, where four different mutations have been found to be associated with LP: 13.907:C>G (rs41525747), 13.915:T>G (rs41380347), 14.009:T>G (ss820486563), and 14.010:G>C (rs145946881), all of which cluster in the intron 13 of the MCM6, within a 100-base-pair interval of each other that includes the 13.910:C>T [12,14,16,65,66,74]. All of these mutations result in an increase of lactase activity in vitro [10,12,13,16,39,65,66,70–74], and two of them, 13.907:C>G and 13915:T>G, seem to affect binding of Oct-1 [10,73]. While 14.010:G>C is most prevalent as one goes to East Africa (32–46%) [12] and South Africa (13–20%) [80,81], 13.907:C>G and 14.009:T>G are most prevalent among the Beja people of Sudan and in Ethiopia. On the other hand, 13915:T>G is the most common variant in camel herders from the Middle East (72–88%) [10,82], and is also extended among almost all Central-East African populations (Kenya, Sudan, Cameroon, Nigeria, Chad).
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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Thanks for the further confirmation that all genes are African genes.
Population genetics, was once assumed to be the 'Great white Hope' to prove White Supremacy extended to ancient times has not met the expectations of the Academe. Prior to population genetics both the social and natural sciences failed to support the superiority of Caucasian and mongoloid people over the Black/Negro race. This confirmation resulted from the study of craniometrics, ancient skeletons, anthroplogy, archaeology , history and linguistics, that the first people to explore the earth and build civilizations were the Africans who expanded across the world through several migrations.
White supremacist recognizing this reality and had hoped population genetics would disprove the abundance of evidence that except for couple hundred years of whites dominating history during the Greco-Roman period and since 1492. Population genetics are based on to assumptions. The first assumption, is that the populations existing on the continents of Africa, Eurasia and the America have always been occupied by four major populations (races); Africa: Negroes or Sub-Saharan Black Africans; Eurasia: Caucasians in Western Europe, the Middle East, South Asia and Asia Minor; Mongoloids in East and Southeast Asia, and Oceanic (Black) people of the pacific Islands; and finally semi-mongoloid people in the Americas called native Americans. The population geneticists supported this division of mankind based on a unique package of genes which they claimed were unique to the populations living in these geographical regions.
The second population genetics assumption is that these populations existed in isolation. This isolation they claimed lasted for thousands of years until the advent of the Atlantic slave trade, when Africans were introduced into the Americas and Eurasia.
These assumptions lacked any foundation. A simple examination of history would have falsified these theories. they were falsified by the fact that the archaeological evidence indicated that the first inhabitants of every continent were Negroes. This along with the fact that Black Moors from Africa ruled much of Western Eurasia for almost 1000 years made the two assumptions population genetics was founded on invalid.
The more population geneticists study the ancient DNA, the more discoveries that Africans--Black people were the first carriers of genes that supposedly made Europeans unique such as Lactose Intolerance, the genes for light skin, Y-chromosome R, and mtDNA L (M,N), is predominately found among Africans and originated in Africa--confirm the reality that much of ancient history was, and is the history of Black people. The race that represents the indigenous--aboriginal people of every continent on earth. Thusly, population genetics in the final nail in the coffin of the idea that population genetics would validate white supremacist ideas about the absence of Black Africans in World History.
-------------------- C. A. Winters Posts: 13012 | From: Chicago | Registered: Jan 2006
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Low Prevalence of Lactase Persistence in Bronze Age Europe Indicates Ongoing Strong Selection over the Last 3,000 Years – Joachim Burge
Summary Lactase persistence (LP), the continued expression of lactase into adulthood, is the most strongly selected single gene trait over the last 10,000 years in multiple human populations. It has been posited that the primary allele causing LP among Eurasians, rs4988235-A [1], only rose to appreciable frequencies during the Bronze and Iron Ages [2, 3], long after humans started consuming milk from domesticated animals. This rapid rise has been attributed to an influx of people from the Pontic-Caspian steppe that began around 5,000 years ago [4, 5]. We investigate the spatiotemporal spread of LP through an analysis of 14 warriors from the Tollense Bronze Age battlefield in northern Germany (∼3,200 before present, BP), the oldest large-scale conflict site north of the Alps. Genetic data indicate that these individuals represent a single unstructured Central/Northern European population. We complemented these data with genotypes of 18 individuals from the Bronze Age site Mokrin in Serbia (∼4,100 to ∼3,700 BP) and 37 individuals from Eastern Europe and the Pontic-Caspian Steppe region, predating both Bronze Age sites (∼5,980 to ∼3,980 BP). We infer low LP in all three regions, i.e., in northern Germany and South-eastern and Eastern Europe, suggesting that the surge of rs4988235 in Central and Northern Europe was unlikely caused by Steppe expansions. We estimate a selection coefficient of 0.06 and conclude that the selection was ongoing in various parts of Europe over the last 3,000 years.
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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