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View Full Version : What other LP mutations exist besides 13910T and 22018A?



newtoboard
02-09-2014, 04:42 PM
It is clear that the two mutations mentioned above can't explain LP rates founds in some part of the Asia. The Southern Indus Valley has LP frequencies approaching 100% for example and places like Arabia likely have little to none of the two mutations above. Yet they still have regions where LP approaches 100% so what other mutations are at work? How are they distributed? And how did they spread?

Jean M
02-09-2014, 05:02 PM
Lactase-persistence genes of East African origin are 13907G and 14010C.
Another found in Ethiopia −14009T>G. (Jones 2013.)
A compound allele (13915G and 3712C) found in Saudis and East Africans probably originated in the Middle East. (Enattah 2008; Ingram 2009.)
A rarer lactase-persistence allele (13913C) was discovered in two cases in Italy, and subsequently reported in Cameroon, Sudan, Ethiopia, and the Bedouin population in Saudi Arabia. (Järvelä 2009; Piepoli 2007.)



Jones, B.L. et al. 2013, Diversity of Lactase Persistence Alleles in Ethiopia: Signature of a Soft Selective Sweep, AJHG, Volume 93, Issue 3, 5 September 2013, 538–544. http://www.sciencedirect.com/science/article/pii/S0002929713003261
Enattah, N. S. et al. 2007. Evidence of still-ongoing convergence evolution of the lactase persistence T-13910 alleles in humans, The American Society of Human Genetics, 81 (3), 615-625.
Enattah, N. S. et al. 2008. Independent introduction of two lactase-persistence alleles into human populations reflects different history of adaptation to milk culture, American Journal of Human Genetics, 82 (1), 57-72.
Ingram, C. J. E. et al. 2009. Lactose digestion and the evolutionary genetics of lactase persistence, Human Genetics, 124 (6), 579-591.
Järvelä, I. et al. 2009. Molecular genetics of human lactase deficiencies, Annals of Medicine, 41 (8), 568-575.
Piepoli, A. et al. 2007. Genotyping of the lactase-phlorizinhydrolase C/T-13910 polymorphism by means of a new rapid denaturing high-performance liquid chromatography-based assay in healthy subjects and colorectal cancer patients, Journal of Biomolecular Screening, 12 (5), 733-739.
Tishkoff, S. et al. 2006. Convergent adaptation of human lactase persistence in Africa and Europe, Nature Genetics 39, 31 - 40. http://www.nature.com/ng/journal/v39/n1/full/ng1946.html

Jean M
02-09-2014, 08:05 PM
Found another study of interest.

Sarah Catherine Hill, Talal Ramadan Mohammad, Toomas Kivisild, Effect of nomadic subsistence practices on lactase persistence associated genetic variation in Kuwait, American Journal of Physical Anthropology, Volume 152, Issue 1, pages 140–144, September 2013
http://onlinelibrary.wiley.com/doi/10.1002/ajpa.22313/abstract


Lactase persistence (LP)—the ability to digest lactose in adulthood—is paradigmatic of Holocenic dietary change affecting the evolutionary trajectory of specific populations. Kuwait represents one location of high LP where the variation in associated genomic regions has not been examined. Here, we present new sequence data from a 427 bp amplicon 14 kb upstream of the LCT (lactase) gene for two Bedouin tribal populations, the Ajman and Mutran. We estimate the frequency of known LP associated alleles and discuss the impact of nomadic-pastoralism on the associated genetic variation. We observe high frequency (56% on average) of the −13,915*G allele in both tribes, which is consistent with the high prevalence of LP in Kuwait. Whilst LP associated alleles occur in Kuwait at a similar frequency to other regional populations, we suggest that the −13,915*G allele frequency among the Kuwaiti Bedouin may be higher than among non-Bedouin Kuwaitis, possibly due to greater historical reliance on milk consumption or genetic drift.

Jean M
03-14-2014, 03:28 PM
New paper just out: http://www.cell.com/AJHG/abstract/S0002-9297%2814%2900067-6, as mentioned on the new DNA papers thread (http://www.anthrogenica.com/showthread.php?709-New-DNA-Papers&p=33854#post33854).

Alessia Ranciaro et al., Genetic Origins of Lactase Persistence and the Spread of Pastoralism in Africa, The American Journal of Human Genetics, 13 March 2014


In humans, the ability to digest lactose, the sugar in milk, declines after weaning because of decreasing levels of the enzyme lactase-phlorizin hydrolase, encoded by LCT. However, some individuals maintain high enzyme amounts and are able to digest lactose into adulthood (i.e., they have the lactase-persistence [LP] trait). It is thought that selection has played a major role in maintaining this genetically determined phenotypic trait in different human populations that practice pastoralism. To identify variants associated with the LP trait and to study its evolutionary history in Africa, we sequenced MCM6 introns 9 and 13 and ∼2 kb of the LCT promoter region in 819 individuals from 63 African populations and in 154 non-Africans from nine populations. We also genotyped four microsatellites in an ∼198 kb region in a subset of 252 individuals to reconstruct the origin and spread of LP-associated variants in Africa. Additionally, we examined the association between LP and genetic variability at candidate regulatory regions in 513 individuals from eastern Africa. Our analyses confirmed the association between the LP trait and three common variants in intron 13 (C-14010, G-13907, and G-13915). Furthermore, we identified two additional LP-associated SNPs in intron 13 and the promoter region (G-12962 and T-956, respectively). Using neutrality tests based on the allele frequency spectrum and long-range linkage disequilibrium, we detected strong signatures of recent positive selection in eastern African populations and the Fulani from central Africa. In addition, haplotype analysis supported an eastern African origin of the C-14010 LP-associated mutation in southern Africa.

Razin Khan has a post on this, jokingly titled http://www.unz.com/gnxp/lost-blonde-tribes-in-africa/

He highlights one interesting paragraph from the text.


In fact, the T-13910 variant in the Mozabite from Algeria occurred on the same haplotype background as observed in Middle Eastern populations, whereas the Fulani from Cameroon and the Bulala from Chad shared the same haplotype background with Europeans. The Fulani also shared a distinct T-13910 haplotype background with the Arabic Baggara. These patterns suggest that the distribution of observed haplotype variation might be due to gene flow that occurred over time from outside and within Africa possibly during key historical events, such as the settlement of the Roman Empire in parts of northern Africa and the expansion of the Arabs prior to and during the Ottoman empire within the last 2,000 years. These inferred migration events are also consistent with studies based on mtDNA, Y chromosome, and autosomal genetic variation.

He suggests that the European haplotype arrived with the Vandals.

Rathna
03-14-2014, 03:37 PM
Genetic Origins of Lactase Persistence and the Spread of Pastoralism in Africa
Ranciaro et al



http://www.cell.com/AJHG/abstract/S0002-9297(14)00067-6

It seems that the paper isn't for free, but, through the Supplements, I got the paper and the supplements. For free. Very interesting.

vettor
03-14-2014, 09:21 PM
New paper just out: http://www.cell.com/AJHG/abstract/S0002-9297%2814%2900067-6, as mentioned on the new DNA papers thread (http://www.anthrogenica.com/showthread.php?709-New-DNA-Papers&p=33854#post33854).

Alessia Ranciaro et al., Genetic Origins of Lactase Persistence and the Spread of Pastoralism in Africa, The American Journal of Human Genetics, 13 March 2014



Razin Khan has a post on this, jokingly titled http://www.unz.com/gnxp/lost-blonde-tribes-in-africa/

He highlights one interesting paragraph from the text.



He suggests that the European haplotype arrived with the Vandals.

You need to read mozabite history........it states they came from the persian gulf and where chased out to arrive in modern algeria

Jean M
03-15-2014, 10:16 AM
it states they came from the persian gulf and where chased out to arrive in modern algeria

Who were? if you are talking about the Vandals, we know they settled in North Africa. Razib heads his post with a jokey title "Lost blond tribes", but he is completely serious in his suggestion that the European LP came from them.

vettor
03-15-2014, 07:22 PM
Who were? if you are talking about the Vandals, we know they settled in North Africa. Razib heads his post with a jokey title "Lost blond tribes", but he is completely serious in his suggestion that the European LP came from them.

mozabite people


The vandals are just a confederation of small germanic tribes from modern northern Poland ( pomeranian area). The Vandili confederation.

ADW_1981
03-16-2014, 01:54 AM
Would it not also be plausible that R1b, at least in the western world was responsible for the spread of the European 13910 allele variant into Central Africa with pastoralism? One of the earliest branches, R1b1c is rather substantial among the groups mentioned who ironically also have this same mutation. The Vandal link is a little far fetched if you ask me.