Felix Chandrakumar has prepared and added three additional ancient DNA kits to GedMatch. Thanks Felix! This is a wonderful service you’re performing for the genetic genealogy community!
- The Linearbandkeramik (LBK) sample, also referenced as “Stuttgart,” reflecting where it was discovered in Germany. This individual was an early farmer dating from about 7,500 years ago and was one of the samples analyzed for the paper, Ancient genomes suggest three ancestral populations for present-day Europeans. Kit F999916
- The La Brana-Arintero sample from Leon, Spain, about 7000 years old, represents a pre-agricultural European human genome – in other words, before the agriculturists from the Near East arrived. In an article at Science Daily, they have reconstructed his face. Original academic article available here. Kit F999915
- The Mal’ta sample, from Siberia, about 24,000 years of age. The results were discussed in article, Native American Gene Flow – Europe?, Asia and the Americas, and the original article is available here. Kit F999914
These kits, along with the ones listed earlier, give us the opportunity to compare our own DNA with that of ancient people in specific populations. It’s like taking a step back in time and seeing if we carry any of the same small segments as these people did – suggesting of course that we descend from the same population.
This Ancient European DNA map by Richard Stevens shows the European locations where ancient DNA has been retrieved.
Recent discussion has focused on determining what matches to these specimens actually mean to genetic genealogists today. We obviously don’t have that answer at this point. We know that, due to their age, these samples are not close relatives in terms of genealogy generations, but in some cases, we find that we have matches far larger than one would expect to be found utilizing the 50% washout per generation math.
Endogamy, especially in a closed population such as Native Americans is certainly one explanation. That doesn’t explain the European matches however – either to Anzick, the Native American specimen, nor Europeans to the European samples. The higher no-call rate in the autosomal files can contribute as well, but wouldn’t account for all matches. In some cases, maybe everyone carries the same DNA because the population carries that DNA in very high rates – but the population carries the DNA in very high rates because the ancient ancestors did as well…so this is a bit of circular logic. All that said, we’re still left wondering what is real and what is Memorex, so to speak?
Ancient DNA is changing our understanding of the human past, and that of our ancestors. It allows us a connection to the ancient people that is tangible, parts of them found in us today, as unbelievable as it seems.
When Svante Paabo discovered that modern Europeans all carry pieces of Neanderthal DNA, he too was struck by what I’ll call “the disbelief factor,” thinking, of course, that it can’t possibly be true. He discussed this at length in his book, Neanderthal Man, In Search of Lost Genomes, and the steps taken by his team to prove that the matches weren’t in error or due to some problem with the ancient genome reconstruction process. Indeed, all Europeans and Asians carry both Neanderthal and Denisovan DNA, and by the same process of the DNA being carried by the entire population at one point, which must be the avenue for contemporary humans to carry other ancient DNA as well. As we find individual matches to small pieces of DNA with these matches, how much of that is “real” versus convergence or a result of no-calls in the ancient files?
Reducing pervasive false positive identical-by-descent segments detected by large-scale pedigree analysis. E. Y. Durand, N. Eriksson, C. Y. McLean.
“Analysis of genomic segments shared identical-by-descent (IBD) between individuals is fundamental to many genetic applications, from demographic inference to estimating the heritability of diseases. A large number of methods to detect IBD segments have been developed recently. However, IBD detection accuracy in non-simulated data is largely unknown. In principle, it can be evaluated using known pedigrees, as IBD segments are by definition inherited without recombination down a family tree. We extracted 25,432 genotyped European individuals containing 2,952 father-mother-child trios from the 23andMe, Inc. dataset. We then used GERMLINE, a widely used IBD detection method, to detect IBD segments within this cohort. Exploiting known familial relationships, we identified a false positive rate over 67% for 2-4 centiMorgan (cM) segments, in sharp contrast with accuracies reported in simulated data at these sizes. We show that nearly all false positives arise due to allowing switch errors between haplotypes when detecting IBD, a necessity for retrieving long (> 6 cM) segments in the presence of imperfect phasing. We introduce HaploScore, a novel, computationally efficient metric that enables detection and filtering of false positive IBD segments on population-scale datasets. HaploScore scores IBD segments proportional to the number of switch errors they contain. Thus, it enables filtering of spurious segments reported due to GERMLINE being overly permissive to imperfect phasing. We replicate the false IBD findings and demonstrate the generalizability of HaploScore to alternative genotyping arrays using an independent cohort of 555 European individuals from the 1000 Genomes project. HaploScore can be readily adapted to improve the accuracy of segments reported by any IBD detection method, provided that estimates of the genotyping error rate and switch error rate are available.”
I’m pleased to see that they are addressing smaller segments, in the 2cM-4cM range, because those are the ranges some are finding in matches to these ancient genomes. A few matches are even larger.
Of course, all of this ancient matching has caused an upsurge in interest in the cultures and populations of these ancient people whose DNA we carry.
I find this graphic very interesting from the paper, Toward a new history and geography of human genes informed by ancient DNA, just published this month, by Joseph Pickrell and David Reich. This map, which shows the population movement into and out of geographic regions of the world in the past, is especially interesting in that several back migrations are shown into Africa. I’ve never seen the “history of the world in population migration” summed up quite so succinctly before, but it helps us understand why certain DNA is found in specific locations.
As we find and fully sequence additional ancient DNA specimens, we’ll be able to better understand how the ancient populations were related to each other, and then, how we descend from each of them.
This is a fascinating age of personal discovery!