Dienekes and Maju have both commented on a new paper which looked at the likelihood of lactase persistence in Neolithic remains from Spain, but I thought I would comment on it as well. The paper is: Low prevalence of lactase persistence in Neolithic South-West Europe. The location is on the fringes of the modern Basque country, while the time frame is ~3000 BC. Table 3 shows the major result:
Lactase persistence is a dominant trait. That means any individual with at least one copy of the T allele is persistent. As Maju noted a peculiarity here is that the genotypes are not in Hardy-Weinberg Equilibrium. Specifically, there are an excess of homozygotes. Using the SJAPL location as a potentially random mating scenario you should expect ~7 T/C genotypes, not 2. Interestingly the persistent individual in the Longar location also a homozygote.
HWE makes a few assumptions. For example, no selection, migration, mutation, or assortative mating. Deviation from HWE is suggestive of one of these dynamics. The sample size here is small, but the deviation is not to be dismissed. Recall that lactase persistence has dominant inheritance patterns. If the trait was being positively selected for you would only need one copy. The enrichment of homozygotes is unexpected if selection in situ is occurring here. It can not be ruled out that one is observing the admixture of two distinct populations. One generation of random mating would generate HWE, but when populations hybridize in realistic scenarios this is not always a plausible assumption. Rather, assortative mating often persists over the generations, slowing down the diminishing of population substructure.
Stepping back from speculation in this case what can we say? First, the LCT locus has a large mutational target. The trait of lactase persistence has arisen multiple times via different mutational events across the Old World. But, there does seem to be one particular variant which is found from Spain to Northern India. There is some circumstantial evidence that the allele had its origin somewhere in Central Eurasia, but currently its modal frequency is in Northern Europe, Scandinavia and Germany. The region in the genome around this mutation is characterized by a very long haplotype. It is one of the most definitive loci as a candidate for natural selection in the human genome. There is now a fair amount of ancient DNA evidence that lactase persistence in Europe is a feature of the last ~5,000 years or so. Among the modern Basques the frequency of the allele is 66 percent.
For me the key issue is teasing apart the role of migration and selection in each specific case. It does not seem to be correct that the frequency of the -13910T LCT allele in Basques and Punjabis is reflective of the frequency of recent common ancestry. That implies that natural selection is at work at this locus. On the other hand, the haplotype which is present in both the Basque and Punjabis is likely to be descended from a common set of individuals, implying that there is a genealogical chain connecting these two very distinct and distant Eurasian populations. Therefore, we can potentially make some inferences about the power of migration in spreading distinctive alleles. Often we partition selection from genealogical information, because selection so often serves to distort the signal. But the genealogical patterns may lay at the heart of the distribution of different natural selective events at the LCT locus.
Overall, I would say that the results from ancient DNA are disordering and clouding simple elegant models. One hopes and presumes that as sample sizes increase in this domain we’ll start to see more clarity as new paradigms crystallize.
Citation: European Journal of Human Genetics, 10.1038/ejhg.2011.254
Razib Khan’s degrees are in biochemistry and biology. He has blogged about genetics since 2002, previously worked in software development, is an Unz Foundation Junior Fellow and lives in the western US. He loves habaneros.
January 16th, 2012 at 12:03 pm
Makes me wonder about the Hindu thing. An actual taboo might hint at a moment in time with a group of people hungry enough to want to eat their cattle who could only survive if they didn’t.
January 16th, 2012 at 7:21 pm
The case for the T allele having selective advantage in situ for the Basque seems pretty weak, because it is no so nearly powerfully enriched in neighboring populations and a nearby older Neolithic site find it to be lacking.
I think a more plausible theory is that there was migration into the region from someplace where this allele would have had selective advantage, and that something else, like RH blood types, allowed the Basque to maintain higher levels of endogamy that better preserved the source population frequency than other neighboring populations where a lack of an RH blood type barrier allowed for greater dilution of the T allele brought by other groups of migrants to Iberia.
My personal suspicion is that the Basque ethnogenesis took place right around the time of these ancient DNA samples with substantial contributions from a Bell Beaker population and that the TT homozygotes are probably Bell Beaker migrants, while the CC homozygotes are probably indigeneous peoples relative to the Bell Beaker migrants. But, I’d love to see a richer description of the cultural and physical anthropology corrolates of the individuals and sites from which these samples are drawn.
January 18th, 2012 at 5:41 pm
“I’d love to see a richer description of the cultural and physical anthropology corrolates of the individuals and sites from which these samples are drawn”.
Fair enough, Andrew. I also itched of some curiosity when I read that… so I made a search and found:
http://digital.csic.es/bitstream/10261/10203/1/Verona2.pdf
Both necropolis indicate a warrying (archer) people or military burials, becaus used arrowpoints are the main grave good and arrow-caused injuries are generalized (we can assume many died from such injuries). Adult males are unnaturally dominant in both sites.
Neither burial is megalithic (they are just south of the Megalithic area) but a dolmen from Catalonia discussed in the same paper (Can Martorell) also indicates some sort of militarization (70 arrow points, many used, and just a few pottery fragments). While there is no clear direct relation among them and the corpses, these display trauma injuries of some sort.
January 19th, 2012 at 12:55 am
“The case for the T allele having selective advantage in situ for the Basque seems pretty weak, because it is no so nearly powerfully enriched in neighboring populations and a nearby older Neolithic site find it to be lacking.”
It’s the Atlantic coast and mountainous areas i.e. very rainy areas where crops are relatively poor but cows produced exceptional amounts of milk compared to what they produce elsewhere. So the relevant neighboring populations are only along the coast not inland (except heavy rainfall inland mountainous areas like the Alps).
European rainfall: http://imageshack.us/f/527/eurprcyfz7.jpg/
Lactase persistence:
http://3.bp.blogspot.com/_Ish7688voT0/S3peNPiquTI/AAAAAAAACTA/C_Sa0T2dfrQ/s1600/lpg.png
The slipper seems to fit.
Also
Rainfall map of India: http://www.twitsnaps.com/share/fullphoto/41666_indiamapannualrainfall.jpg
Knowing nothing more than there’s a lot of LP in northern India and the assumption that there’s an optimal amount of rainfall for the grass to milk production system aka cow, i’m going to guess the highest frequency of LP in northern India will be found in the pale orangy shaded parts of Gujarat, Rajasthan, Haryana and Punjab with maybe an extension in the Kashmir and a few blobs along the west coast.
Predictive ability ftw.
I’d also predict those areas will have higher levels of things like wheat allergies than their neighboring less rainy, crop-dominated populations
The other interesting thing is camels i.e. Arabia, because apparently they can produce even more milk than cows – under the right conditions for camels.
January 19th, 2012 at 7:03 pm
Grey: the region you pointed to in India is actually the driest one, bordering the Thar Desert. Pastoralism is actually often an activity of marginal areas not too good for crops: some are lush but too humid, as you say of Atlantic Europe but others are mostly dry. However even in South Asia, the focus of the real phenotype persistence is in Sindh (which is bound by deserts and semi-deserts but centered along a historically and prehistorically important alluvial plain, much like Egypt or Mesopotamia, which may be more familiar to you).
You are putting the cart before the horses: you have embraced too vehemently the belief in the adaptive origin of lactose tolerance and that keeps you from looking at the facts for what they are: neither cow primacy nor lush fields are requirements for lactose tolerance in real life. There is probably some association with some populations in which pastoralism has been historically important (not necessarily bovine, not at all) but then other pastoralist populations do not display the phenotype, including some (Central Asians) exposed to very different genetic inputs, but at residual levels.
So I think it’s worth considering that the evolutionary (adaptive) aspect of this phenotype’s distribution (and related alleles) may only be enhanced and not fundamentally determined everywhere by pastoralism or arguable dietetic advantages (never mind cows and lush fields).
January 20th, 2012 at 2:06 am
“”Grey: the region you pointed to in India is actually the driest one, bordering the Thar Desert…However even in South Asia, the focus of the real phenotype persistence is in Sindh (which is bound by deserts and semi-deserts but centered along a historically and prehistorically important alluvial plain, much like Egypt or Mesopotamia, which may be more familiar to you).”
Yes, that was a wild guess to see if someone knew because my googling failed
Sindh ty.
///
“Pastoralism is actually often an activity of marginal areas not too good for crops: some are lush but too humid, as you say of Atlantic Europe but others are mostly dry.”
Yes, it’s about differential calorie production rather than milk per se.
///
“You are putting the cart before the horses: you have embraced too vehemently the belief in the adaptive origin of lactose tolerance and that keeps you from looking at the facts for what they are: neither cow primacy nor lush fields are requirements for lactose tolerance in real life.”
I thought it was an established theory so originally i was more surprised than embracing – though since finding the map of euro rainfall i think the onus is on alternative theories. (I’m not saying it proves anything – just a very strong correlation.)
I’m not really saying cows and lush fields are requirements i’m saying differential calorie production / consumption is what created the selective pressure (if there was one) and the highest differential is more likely to be in areas where the maximum amount of milk calories can be produced. Cows and lush fields (or camels in some environments) fit one half of that equation.
However it’s the differential that matters. There’s no selective pressure in those areas now even though they are still the best for milk production because anyone can go into a shop and buy bread. So LP, if it was selected, also likely requires an environment where there was limited production of other sources of calories at the same time.
///
“There is probably some association with some populations in which pastoralism has been historically important (not necessarily bovine, not at all) but then other pastoralist populations do not display the phenotype, including some (Central Asians) exposed to very different genetic inputs, but at residual levels…So I think it’s worth considering that the evolutionary (adaptive) aspect of this phenotype’s distribution (and related alleles) may only be enhanced and not fundamentally determined everywhere by pastoralism or arguable dietetic advantages (never mind cows and lush fields).”
Sure if i had to guess i’d guess the basic allele could randomly pop up anywhere through not switching off infant lactase leading to residual levels of LP everywhere. (If so i’d imagine more east Asians have it than is assumed but maybe not the same alleles that have already been identified elsewhere). Only under very specific conditions where there was an extreme calorie differential for a period of time or over bursts of time i.e. starvation events does it expand from those residual levels.
Simple experiment, take 1000 people who have 10% LP, put them on an island with no food and airdrop 400 calories per person per day in bread and 400 calories per person per day in cheese and 400 in milk and check LP frequency after three generations. Differential starvation = selective pressure.