Angela
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The actual name of the paper is:
"The Effects of Migration and Assortative Mating on Admixture Linkage Disequilibrium, Noah Zaitlen et al"
It’s a pre-print that can be found at:
http://biorxiv.org/content/biorxiv/early/2016/05/31/056168.full.pdf
I was alerted to it by Razib Khan.
http://www.unz.com/gnxp/details-on-...ope&utm_source=twitterfeed&utm_medium=twitter
As he says, "linkage disequilibrium based estimates of time since admixture often seem to give a relatively low figure in terms of generations. When it comes to non-human organisms in the field one doesn’t know always the demographic history, but with humans we have better records, and I too have noticed that the dates seem extremely skewed toward the recent. Part of this is accounted for by the dodge that these estimates are often sensitive only to the last pulse of admixture, but even then...
Exactly right…even then. This is the problem I have noticed in particular with both of the papers on recent admixture in Europe by the Hellenthal group. The dates they give don’t correlate very well with any documented large population movements.
The authors of the paper maintain that the problem is because " Statistical models in medical and population genetics typically assume that individuals assort randomly in a population. While this simplifies model complexity, it contradicts an increasing body of evidence of non-random mating in human populations. In this work we examine the effects of ancestry-assortative mating on the linkage disequilibrium between local ancestry tracks of individuals in an admixed population. To accomplish this, we develop an extension to the Wright-Fisher model that allows for ancestry based assortative mating. We show that ancestry-assortment perturbs the distribution of local ancestry linkage disequilibrium (LAD) and the variance of ancestry in a population as a function of the number of generations since admixture. This assortment effect can induce errors in demographic inference of admixed populations when methods assume random mating...We observe that LAD depends on the correlation of global ancestry of couples in each generation, the migration rate of each of the ancestral populations, the initial proportions of ancestral populations, and the number of generations since admixture. "
Just so we're clear, this is assortative mating:
http://anthro.palomar.edu/synthetic/synth_8.htm
The population the authors use to test their theories is the African American one, and about their results they go on to state that, " Our estimate of 15 generations since admixture in African Americans is larger than previous estimates[8, 9] and it fits considerably better the known history of African Americans[13]. This suggests that taking assortative mating into account may in some cases be critical in order to obtain the correct demographic history or other population parameters.”
A final comment from Razib Khan: “ The intuition isn’t that difficult. Assortative mating in this case often means that within population there are going to be correlations of segments of genomic ancestry which are the patterns you are tracking to infer backward to the initial admixture…If you see more dense local ancestry tracts in individuals because of positive assortative mating, you may confuse it in your model for very recent admixture…Assortative mating within a population may lead to higher heritable transmission of a trait across generations than you might expect. Many of the model based clustering algorithms which generate the bar plots now ubiquitous in admixture analyses assume Hardy-Weinberg Equilibrium in one’s populations.”
It also, as he and the authors make clear, affects IBD analysis.
If I understand this correctly, assortative mating is present where first cousin marriages are the norm, and also where more generally the population is more isolated because of religion, but also because of political divisions, terrain etc. Given those kinds of situations, in certain regions, certain countries even, dense local ancestry might confound admixture type analyses and even IBD analysis.
It’s something to keep in mind as we move forward.
"The Effects of Migration and Assortative Mating on Admixture Linkage Disequilibrium, Noah Zaitlen et al"
It’s a pre-print that can be found at:
http://biorxiv.org/content/biorxiv/early/2016/05/31/056168.full.pdf
I was alerted to it by Razib Khan.
http://www.unz.com/gnxp/details-on-...ope&utm_source=twitterfeed&utm_medium=twitter
As he says, "linkage disequilibrium based estimates of time since admixture often seem to give a relatively low figure in terms of generations. When it comes to non-human organisms in the field one doesn’t know always the demographic history, but with humans we have better records, and I too have noticed that the dates seem extremely skewed toward the recent. Part of this is accounted for by the dodge that these estimates are often sensitive only to the last pulse of admixture, but even then...
Exactly right…even then. This is the problem I have noticed in particular with both of the papers on recent admixture in Europe by the Hellenthal group. The dates they give don’t correlate very well with any documented large population movements.
The authors of the paper maintain that the problem is because " Statistical models in medical and population genetics typically assume that individuals assort randomly in a population. While this simplifies model complexity, it contradicts an increasing body of evidence of non-random mating in human populations. In this work we examine the effects of ancestry-assortative mating on the linkage disequilibrium between local ancestry tracks of individuals in an admixed population. To accomplish this, we develop an extension to the Wright-Fisher model that allows for ancestry based assortative mating. We show that ancestry-assortment perturbs the distribution of local ancestry linkage disequilibrium (LAD) and the variance of ancestry in a population as a function of the number of generations since admixture. This assortment effect can induce errors in demographic inference of admixed populations when methods assume random mating...We observe that LAD depends on the correlation of global ancestry of couples in each generation, the migration rate of each of the ancestral populations, the initial proportions of ancestral populations, and the number of generations since admixture. "
Just so we're clear, this is assortative mating:
http://anthro.palomar.edu/synthetic/synth_8.htm
The population the authors use to test their theories is the African American one, and about their results they go on to state that, " Our estimate of 15 generations since admixture in African Americans is larger than previous estimates[8, 9] and it fits considerably better the known history of African Americans[13]. This suggests that taking assortative mating into account may in some cases be critical in order to obtain the correct demographic history or other population parameters.”
A final comment from Razib Khan: “ The intuition isn’t that difficult. Assortative mating in this case often means that within population there are going to be correlations of segments of genomic ancestry which are the patterns you are tracking to infer backward to the initial admixture…If you see more dense local ancestry tracts in individuals because of positive assortative mating, you may confuse it in your model for very recent admixture…Assortative mating within a population may lead to higher heritable transmission of a trait across generations than you might expect. Many of the model based clustering algorithms which generate the bar plots now ubiquitous in admixture analyses assume Hardy-Weinberg Equilibrium in one’s populations.”
It also, as he and the authors make clear, affects IBD analysis.
If I understand this correctly, assortative mating is present where first cousin marriages are the norm, and also where more generally the population is more isolated because of religion, but also because of political divisions, terrain etc. Given those kinds of situations, in certain regions, certain countries even, dense local ancestry might confound admixture type analyses and even IBD analysis.
It’s something to keep in mind as we move forward.