Razib Khan One-stop-shopping for all of my content

August 15, 2012

Ötzi – more Neandertal than the average bear

Neandertal ancestry “Iced”:

Evaluating recent evolution, migration and Neandertal ancestry in the Tyrolean Iceman

Paleogenetic evidence from Neandertals, the Neolithic and other eras has the potential to transform our knowledge of human population dynamics. Previous work has established the level of contribution of Neandertals to living human populations. Here, I consider data from the Tyrolean Iceman. The genome of this Neolithic-era individual shows a substantially higher degree of Ne- andertal ancestry than living Europeans. This comparison suggests that early Upper Paleolithic Europeans may have mixed with Neandertals to a greater degree than other modern human populations. I also use this genome to evaluate the pattern of selection in post-Neolithic Europeans. In large part, the evidence of selection from living people’s genetic data is confirmed by this specimen, but in some cases selection may be disproved by the Iceman’s genotypes. Neolithic-living human comparisons provide information about migration and diffusion of genes into Europe. I compare these data to the situation within Neandertals, and the transition of Neandertals to Upper Paleolithic populations – three demographic transitions in Europe that generated strong genetic disequi- libria in successive populations.

March 8, 2012

Seeing Ötzi through our eyes

Filed under: Ötzi — Razib Khan @ 11:29 pm

Dienekes got his hands on Otzi’s genome finally, and decided to confirm some suspicions. In general no great surprise, though I think the number of SNPs he used (44,000) is a little on the low side for the questions he was asking. But the details here aren’t too relevant because all the available evidence points to the “Iceman” being affiliated with modern day Sardinians, of whom we know much more with many more markers.

In any case, he points out that if you run ADMIXTURE you tend to see that Sardinians, and to a lesser extent Basques, are lacking in some ancestral components. One phenomenon which is implied by this is that these populations which are less “cosmopolitan” may reflect more ancient patterns, when there was less admixture. I’ve indicated this myself when it comes to non-Muslim minorities in the Middle East. But one caution I would immediately make is that we are judging the variation of smaller populations by the yardstick of larger populations. Distinct and less numerous groups, such as Sardinians, may show less ancestral cosmopolitanism in part because the reference populations which could be used to adduce such a state no longer exist.

To give an extreme example the Onge of the Andaman Islanders often pop up as a very distinctive genetic component. But what if there were many more related populations in the data sets generating patterns of variation? We might see that the Onge themselves are composites! The idea I’m trying to get across is that we imagine the past was demographically pristine. But if it wasn’t, then our attempts to make inferences become all the more difficult.

October 24, 2011

Ötzi, the dead sea scrolls of genomics?

Filed under: Genomics,Human Genomics,Ötzi,Ötzi the Iceman — Razib Khan @ 2:48 pm

Dienekes points me to the fact that Ewen Callaway has the dirt on what’s going on with Ötzi:

To get a better grip on his ancestry and predisposition to disease, Albert Zink, head of the Institute for Mummies and the Iceman in Bolzano, and his team sequenced Ötzi’s 3 billion base pair nuclear genome from a shard of hip bone. Their sequence covers more than 90 percent of the Iceman’s genome. Their team also analysed DNA preserved in Ötzi’s stomach in hopes of revealing the microbes that colonized his gut.

Zink says his team is keeping most of the results of these studies under wraps, pending publication. They had hoped to have the paper out in time for last week’s Mummy Congress and a television special called Iceman Murder Mystery.

His team plans to use the sequence to determine Ötzi’s status for genetic variations linked to diseases in modern humans, particularly arthrosclerosis. A full nuclear genome will also paint a more detailed picture of the Iceman’s ancestry and his relationship to present-day humans. Zink’s team will ask whether Ötzi is an ancestor of people living in Central Europe today, or whether he and his kin died out and were replaced by migrants from elsewhere, such as the Middle East. To buff up this analysis, they are analysing DNA preserved in the skeletons of other ancient inhabitants of central Europe.

~90 percent of a genome is way more than you’d need for some basic analysis and inference of relationships to contemporary populations. So what’s the big deal? No idea, but this tardiness makes me turn the needle up in terms of assuming that they found some interesting stuff. If it’s what you’d expect, why recheck and beef up your analysis with as much support as you can find? Of course, I hope that they found some interesting stuff, so I shouldn’t trust my own judgments in this area. My own suspicion is that they have found extensive genetic turnover over the past 6,000 years in Western Europe, and they are using modern and ancient samples to flesh-out their model. The two dominant paternal haplogroups in Europe today, R1a and R1b, are suspiciously scarce in the ancient DNA samples.

October 23, 2011

The Ötzi embargo

Filed under: Genomics,Human Genetics,Human Genomics,Ötzi — Razib Khan @ 3:57 pm

Dienekes has some harsh words for the way some science is produced, focusing on the genome of Ötzi the Iceman as a case in point:

Yesterday, I twitted in exasperation that Otzi’s genome, which must have been available in at least some sort of draft form since at least the beginning of this year, has been under lock and key, presumably because of the need to make a big splash with the simultaneous Bolzano conference, TV special, likely imminent journal publication, and all the media stories that will follow.

What I don’t understand: how come no one is editing the Wikipedia entry ahead of time? I wonder in hindsight if there’s no there, there, though I hope I’m wrong about this. Going by the lack of media mention of ahead of the NOVA documentary I do suspect we’re seeing the calm before the embargo explosion.

September 14, 2011

Ötzi, first, but not last, farmer?

Filed under: Ancient DNA,Anthroplogy,Human Genetics,Iceman,Ötzi — Razib Khan @ 8:59 pm

Dienekes relays that Ötzi the Iceman carried the G2a4 male haplogroup. He goes on to observe:

We now have G2a3 from Neolithic Linearbandkeramik in Derenburg and G2a in Treilles in addition to Ötzi from the Alps. G2a folk got around. He joins Stalin and Louis XVI as a famous G2a.

It was already clear with the discovery of G2a in France and Central Europe, that this otherwise uncommon present-day haplogroup in Europe was more prominent during the Neolithic, and Ötzi’s data point seals the case.

In a sense, the triple G2a finds in Neolithic Europe confirm the origins of the European Neolithic population in West Asia, but renew the mystery as to how all the rest of the “players” of the European Y-DNA scene appeared on the scene, with everything except G and I first appearing in the ancient DNA record after the end of the Neolithic.

Yes, I believe that the Paleolithic-Neolithic dichotomy is more hindrance than help in understanding the European past (the Paleolithic itself may have exhibited more population turnover than we can appreciate). I suspect that the two most common European Y haplogroups, R1a and R1b, underwent rapid increase in frequency over the past ~5,000 years. I do not believe that this is necessarily representative of the rest of the genome. The spread of male lineages can be rather unrepresentative.

In other news, Ötzi’s genome is going to drop any day now. My prediction that it’s more West Asian than we might have expected seems more plausible, though less surprising and risky, at this point.

Image credit: 23andMe

June 20, 2011

Hints of Ötzi’s genome

Filed under: Ancient DNA,Ancient Genomes,Genetics,Genomics,Ötzi — Razib Khan @ 7:39 pm

John Hawks points to a report in Science on some morsels of information about Ötzi-the-Iceman’s genetics, The Iceman’s Last Meal:

Also at the meeting, researchers led by geneticist Angela Graefen of the Institute for Mummies and the Iceman reported that they have succeeded in sequencing the Iceman’s whole genome, despite the highly fragmented nuclear DNA. The genome has already revealed some surprises. One preliminary finding shows that the Iceman probably had brown eyes rather than the blue eyes found in many facial reconstructions done by artists. Graefen and her colleagues are also examining the DNA to see if Ötzi possessed genetic predispositions to diseases such as arthritis, which other researchers have diagnosed based on radiological and other evidence.

I’m assuming we’ll know a whole lot more before the end of summer. So I’m going to go out on a limb and make a prediction based on what I suspect about the southern European genetic landscape ~5,000 years ago: Ötzi will be more like contemporary West Asian people, Georgians, Armenians, etc., than modern north Italians and south Germans are. Right or wrong, I hope the results will be interesting!

August 26, 2010

Size doesn’t always matter

Filed under: Anthroplogy,Ötzi,Sample Size — Razib Khan @ 10:56 am

The autosomal genome of Ötzi the Austrian “Iceman” is apparently in the pipeline (from what I can tell they’re doing the analysis right now). What can we learn from one sample? Ann Stone, who was a graduate student on the original team which recovered his body, says:

A specialist in anthropological genetics, Stone is excited by the recent news but also cautious. “It is a sample of one. For us to really say something about that period, you need a sample of 25 to 50 individuals,” she explained during an interview with Deutsche Welle, Germany’s international broadcaster.

This is fine as it goes. Worries about sample size are pretty generic and if the practicalities permitted who wouldn’t want a bigger N? But whether you should worry about sample size is partly conditional on how much the findings deviate from what you’d expect. Imagine for example that ~25% of Ötzi’s genome was of Neandertal origin. Obviously it would be great to have 25 to 50 representative individuals from this region to know whether Ötzi was atypical…but the very finding itself would be of such large effect that an N = 1 would tell us quite a bit. Similarly, one genome of a Sub-Saharan African would be very informative if you had several hundred non-African genomes as a point of comparison (because Sub-Saharan Africans have so much genetic variation which is outside of the distribution found among non-Africans).

Powered by WordPress