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Tag: Human Genetics
Reflections on the evolution at ASHG 2012
As most readers know I was at ASHG 2012. I’m going to divide this post in half. First, the generalities of the meeting. And second, specific posters, etc.
Generalities:
- Life Technologies/Ion Torrent apparently hires d-bag bros to represent them at conferences. The poster people were fine, but the guys manning the Ion Torrent Bus were total jackasses if they thought it would be funny/amusing/etc. Human resources acumen is not always a reflection of technological chops, but I sure don’t expect organizational competence if they (HR) thought it was smart to hire guys who thought (the d-bags) it would be amusing to alienate a selection of conference goers at ASHG. Go Affy & Illumina!
- Speaking of sequencing, there were some young companies trying to pitch technologies which will solve the problem of lack of long reads. I’m hopeful, but after the Pacific Biosciences fiasco of the late 2000s, I don’t think there’s a point in putting hopes on any given firm.
- I walked the poster hall, read the titles, and at least skimmed all 3,000+ posters’ abstracts. No surprise that genomics was all over the place. But perhaps a moderate surprise was how big exomes are getting for medically oriented people.
- Speaking of medical/clinical people, I noticed that in their presentations they used the word ‘Caucasian‘ a lot. This was not evident in the pop-gen folks. It shows the influence of bureaucratic nomenclature in modern medicine, as they have taken to using somewhat nonsensical US Census Bureau categories.
- Twitter was a pretty big deal. There were so many interesting sessions that I found myself checking my feed constantly for the #ASHG2012 hashtag. It was also an easy way to figure out who else was at the same session (e.g., in my case, very often Luke Jostins).
- If you could track the patterns of movements of smartphones at the conference it would be interesting to see a network of clustering of individuals. For example, the evolutionary and population genomics posters were bounded by more straight-up informatics (e.g., software to clean your raw sequence data), from which there was bleed over. But right next to the evolution and population genomics sections (and I say genomics rather than genetics, because the latter has been totally subsumed by the former) you had some type of pediatric disease genetics aisles. I wasn’t the only one to have a freak out when I mistakenly kept on moving (i.e., you go from abstruse discussions of the population structure of Ethiopia, to concrete ones about the likely probability of death of a newborn with an autosomal dominant disorder, with photos of said newborn!).
The arcane art of ancient admixture
I have mentioned the PLoS Genetics paper, The Date of Interbreeding between Neandertals and Modern Humans, before because a version of it was put up on arXiv. The final paper has a few additions. For example, it mentions the generally panned (at least in the circles I run in) PNAS paper which suggested that ancient population structure could produce the same patterns which were earlier used to infer admixture with Neandertals (the authors also point to Yang et al. as a support for the proposition of admixture rather than structure). The primary result, dating the admixture between Neandertals and anatomically modern humans ~40-80,000 years before the present, is reiterated.
An interesting aspect is that their method is to utilize linkage disequilibrium (LD) decay. It’s interesting because tens of thousands of years is a hell of a long time to be able to detect an admixture event via LD! In particular because there’s likely a palimpsest effect where there are intervening admixtures and other assorted demographic events (e.g., bottlenecks and selective sweeps can also generate LD). So how’d they do it? Basically the authors figured out a way to ascertain which pairs of SNPs may have introgressed from Neandertals by comparing the frequency in modern humans to Neandertals at those given SNPs (in particular, by looking at variants at low frequency in Africans and derived in Neandertals). A major technical problem here is the “genetic map” which allows one to assess what the nature of recombination over time is going to be which breaks apart the associations which are the hallmark of LD is not particular precise enough to robustly allow them to make the inferences that they want.
Most mtDNA lineages expanded before the Neolithic?
A new short communication in Scientific Reports suggests that most demographic expansion as ascertained using mtDNA occurred before the Neolithic. MtDNA analysis of global populations support that major population expansions began before Neolithic Time:
Agriculture resulted in extensive population growths and human activities. However, whether major human expansions started after Neolithic Time still remained controversial. With the benefit of 1000 Genome Project, we were able to analyze a total of 910 samples from 11 populations in Africa, Europe and Americas. From these random samples, we identified the expansion lineages and reconstructed the historical demographic variations. In all the three continents, we found that most major lineage expansions (11 out of 15 star lineages in Africa, all autochthonous lineages in Europe and America) coalesced before the first appearance of agriculture. Furthermore, major population expansions were estimated after Last Glacial Maximum but before Neolithic Time, also corresponding to the result of major lineage expansions. Considering results in current and previous study, global mtDNA evidence showed that rising temperature after Last Glacial Maximum offered amiable environments and might be the most important factor for prehistorical human expansions.
You don’t need “genes” for genetics
After yesterday’s post I feel it is important again to reiterate that there is an unfortunate tyranny of the gene-as-physical-entity when it comes to our understanding of human heredity. To clarify what I mean, I think it is useful to borrow a framework from Andrew Brown. On the one hand you have a conventional modern mainstream understanding of the gene as a molecular biological entity, fundamentally derived from DNA and its role as envisaged by Francis Crick and James Watson, but with roots deeper back into the physiological genetic tradition which Sewall Wright was embedded within. In contrast to this concrete and biophysical conception of the gene there are those who conceive of the gene as an abstract unity of analysis. Richard Dawkins is the primary proponent of this viewpoint on the public intellectual scene, though men such as William D. Hamilton self-consciously understood the difference between their own genetics, and that which arose out of the insights of Crick and Watson.
The Bushmen tell us a lot about human evolution because they are humans who have evolved
When it comes to the human genetics of the Khoe-San there’s a little that’s stale and unoriginal for me in terms of presentation. The elements are always composed the same. The Bushmen are the “most ancient” humans, who can tell us something about “our past,” about “our evolution.” Tried & tested banalities just bubble forth unbidden. I have no idea why. There’s a new paper in Science on the genetics of the Khoe-San, which includes Bushmen, which brought to mind this issue for me because of the outrageous nature of the press releases.
The title of the paper itself is a testament to vanilla, Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History. This is absolutely not surprising. Are you shocked that the Khoe-San have adaptations? Or that African history is complex? The wonder of it all! This paper actually revisits much of the same ground as Pickrell et al.’s originally titled The genetic prehistory of southern Africa. Before Dr. Pickrell executes throw-down on me on Twitter let me concede that I have no creative ideas to offer in terms of an alternative title. Rather, I have an idea: perhaps in the future scientists could explore the evolutionary genetic basis for steatopygia? The trait is not limited just to Khoe-San, my distant cousins the Andaman Islanders also exhibit it. Perhaps this is the ancestral state of the human lineage? This is a situation where the titles just write themselves!
The brambly bush of humanity
Over at Haldane’s Sieve there are more than preprints posted, there are commentaries from the authors as well. For example, for The genetic prehistory of southern Africa, the first author, Dr. Joseph K. Pickrell, has a extended comment up.
But occasionally you get contributions & perspectives from non-authors which are very interesting. And it is to one of these I want to draw your attention, Thoughts on: The date of interbreeding between Neandertals and modern humans. It’s a comment on The date of interbreeding between Neandertals and modern humans. In the post Dr. Graham Coop contends:
At this point you are likely saying: well we know that Neandertals existed as a [somewhat] separate population/species who are these population X you keep talking about and where are their remains? Population X could easily be a subset of what we call Neandertals, in which case you’ve been reading this all for no reason [if you only want to know if we interbred with Neandertals]. However, my view is that in the next decade of ancient human population history things are going to get really interesting. We have already seen this from the Denisovian papers [1,2], and the work of ancient admixture in Africa (e.g. Hammer et al. 2011, Lachance et al. 2012). We will likely discover a bunch of cryptic somewhat distinct ancient populations, that we’ve previously [rightly] grouped into a relatively small number of labels based on their morphology and timing in the fossil record. We are not going to have names for many of these groups, but with large amounts of genomic data [ancient and modern] we are going to find all sorts of population structure. The question then becomes not an issue of naming these populations, but understanding the divergence and population genetic relationship among them.
This is a bold contention, and I suspect some physical anthropologists will take issue with it. But it’s a testable prediction. We’ll know if it’s panned out in 2020. I may still be blogging between now and then, and so I will now self-importantly label this “Coop’s Conjecture.” Is there anyone who wants to wager some money on Coop’s Conjecture? Any side of the bet you think is a sure thing?
Not all genes are created the same
The map to the right shows the frequencies of HGDP populations on SLC45A2, which is a locus that has been implicated in skin color variation in humans. It’s for the SNP rs16891982, and I yanked the figure from IrisPlex: A sensitive DNA tool for accurate prediction of blue and brown eye colour in the absence of ancestry information. Brown represents the genotype CC, green CG, and blue, GG. Europeans who have olive skin often carry the minor allele, C. While SLC24A5 is really bad at distinguishing West Eurasians from each other, SLC45A2 is better. Though both are fixed in Northern Europe, the former stays operationally fixed in frequency outside of Europe, in the Near East. As I stated earlier the proportions of the ancestral SNP in the Middle Eastern populations in the HGDP seem to be easily explained by the Sub-Saharan admixture you can find in these groups.
In contrast major SNPs in SLC45A2 are closer to disjoint between Europeans and South Asians. For example I’m a homozygote for the C allele. And yet even here we need to be careful. I want in particular to draw your attention to the frequencies in the Middle Eastern populations, the Sardinians, and the Kalash of Pakistan.
The Kalash, and their Nuristani cousins, have often been observed to have “European” physical features. These populations even trade in legends of descent from the Macedonians of Alexander. And the genetics here shows why. Though the Kalash far are more closely related to other Northwest South Asians than to Europeans, on the subset of genes which are implicated in pigmentation many of them could actually “pass” for Europeans. In fact, it is interesting to me that by these measures the Sardinians are no more European than groups like the Kalash and the Druze (in contrast to the total genome, where Sardinians may be the best reference for Western Europeans). They have a lower frequency of the SNP strongly associated with blue eyes than either of these groups, for example.
In the above paper they also produced a chart which illustrated the relationships of HGDP populations as a measure only of the six SNPs they used in their prediction method. These are markers which distinguish blue and brown eye color in Europeans efficiently.
Genes & geography – the great correlation
A paper is out in PLoS Genetics which attempts to formalize the relationship between genes and geography, A Quantitative Comparison of the Similarity between Genes and Geography in Worldwide Human Populations. They found a reasonable correlation, but there are two issues. First, African hunter-gatherers tend to reduce the correlation. This makes sense. If you think of African genetic variation to a great extent being shaped by the wave front of Bantu expansion, then isolation by distance works well enough. But the Pygmies, Hadza, etc., are isolated shoals which disrupt the smoothness of the sea of Bantu genetic variation. Second, they found a really good correlation in Asia. But one should be cautious about this:
However, although the concordance of a PCA plot with geography is perhaps best known for Europe — which does not have a barrier of comparable importance to the Himalayas — we obtained the unexpected result that in spite of the Himalaya barrier, the Procrustes similarity score was actually highest in Asia. When further examining the population structure on separate sides of the Himalayas, we found lower similarity scores between genes and geography in our East Asian and Central/South Asian samples. Especially for the East Asian sample, our results indicate weaker correlation between genes and geography in the east-west direction.
Humanity 2.0
Dienekes points to a David Reich video where he shows his hand as to future possible results to come out of his lab. The short of it is that it seems likely that most agricultural populations exhibit the same dynamic outlined in Reconstructing Indian History. At the least you have an intrusive group admixing with indigenes. At the extreme you have total replacement. The pattern is confirmed for India, Ethiopia, and Southeast Asia. It seems highly likely in Europe. There are other rumored results in East Asia which might shake things up.
On a minor note, I do want to add that I think many archaeologists aren’t going to be totally surprised that modern Europeans don’t derive by and large from Aurignacians. But, the relatively recent nature of the map of genetic variation which we take for granted probably will shock, and result in a high degree of skepticism. Yet if I had to bet I would bet on the model being sketched out by David Reich. These admixtures and replacements are likely to resolve some confusions of our understanding of the settlement of the world using simple tree models with branching points tens of thousands of years in the past (e.g., you already know that Oceanians will have a longer branch because of archaic admixture).
The first, second, and third nations
By now you’ve probably read about the paper which reports that there seem to have been three waves of humans migrating into the New World prior to the arrival of Europeans. A major aspect of this result is that it does not emerge out of a vacuum, but rather comes close to settling an old question in linguistics. The late Joseph Greenberg generated a series of audacious phylogenies of languages of the world. Greenberg’s attempts received mixed reviews. It seems that there is little controversy about some of his classifications of African languages, but linguists of American native dialects rejected his division of the languages of the New World into three broad families, Eskimo-Aleut, Na-Dene, and Amerind. Eskimo-Aleut is rather self-evident. Na-Dene encompasses a group of languages in northwest North America, along with some significant outliers such as Navajo. Amerind seems to roughly be a grab-bag of everything else. The linguistic trichotomy also lent itself to a narrative of three migrations. L. L. Cavalli-Sforza gave his support to Greenberg’s framework in The History and Geography of Human Genes, and it seems most non-linguists are particularly congenial toward his tendency of ‘lumping.’ In contrast, linguists remain more skeptical ‘splitters,’ at lease those who have a more ethnographic disciplinary bent. Geneticists have not always supported Greenberg’s suppositions. For example, many of the members of the same group which authored this paper implicitly put the kibosh on the attempt to construct a unified linguistic family which spanned the Andaman Islanders and the Papuans.
The method of the paper was relatively straightforward, assuming you are already somewhat familiar with the statistical genetic esoterica which was unveiled a few years ago by this group and others. Basically you take genetic data in the form of hundreds of thousands of SNPs, and you test the patterns of variation in that data across populations against explicit models of demographic history, represented visually by phylogenetic trees. You can see here that the sampling was relatively thick, except for the United States. Chalk this up to politics. I’ve been hearing about this particular problem in relation to this paper for over a year now. Not having asked any of the members of the group directly I obviously am going off hearsay, but the lack of American samples is most definitely not a feature. It’s a bug. In the supplement they also note that they couldn’t get Na-Dene data from another research group. Almost certainly that’s because of bioethical issues and legal contractual constraints.
Despite all this drama, the scientific isn’t too hard to understand. Aside from the nifty statistics one problem is that many of these native groups have European and African admixture, but there are workarounds to that (e.g., just pull out genomic segments which are indigenous, and use those). The outcome is neatly visualized in the figure below:
SMBE 2012
Dienekes has summaries up of human-related abstracts of Society for Molecular Biology & Evolution 2012.
1) Remember these are not papers, and some of the abstracts may never become papers, at least in recognizable form
2) Speaking of which, Estimating a date of mixture of ancestral South Asian populations:
Abraham's genetic threads
Every few days my Google Alerts have been dropping in my inbox reviews of Harry Osters’ Legacy: A Genetic History of the Jewish People. The latest is in the The Tablet, A Case for Genetic Jewishness:
For a Jewish genetics researcher, being told in print that ‘Hitler would certainly have been very pleased’ by your work can’t be pleasant. But that’s what happened in 2010 to Harry Ostrer, a geneticist at the Albert Einstein College of Medicine, when he and his colleagues published a study showing that Jews in three different geographical areas had certain collections of genes that made them more biologically similar to one another than they were to non-Jews in the same regions. The work also showed that Jews around the world could trace their ancestry to a group of people who lived in the Middle East 2,000 years ago; that meant, however, that certain genetic signatures could be used to identify Jews, indicating that Jews share a common biological identity beyond their religious affiliation—which is what inspired the Hitler crack.
I don’t plan on reading Legacy because I already read the paper which it is based on, Abraham’s Children in the Genome Era: Major Jewish Diaspora Populations Comprise Distinct Genetic Clusters with Shared Middle Eastern Ancestry. It is now open access, so you can read it too. As implied in the article in The Tablet the biggest finding in this paper is that most of the world’s Jewry seem to share tracts of the genome which are ‘identical by descent’ (IBD). You don’t have to be a geneticist to intuit that being IBD implies relatively recent and elevated shared descent from a common set of ancestors. In particular the authors were looking for segments of the genome where individuals shared the same sequence of genetic markers. Very long sequences indicate a relatively recent common ancestor, while many short ones suggest more distant but numerous common ancestors.
The real secret history of the Mongols?
Thank god for steppe hyper-patriarchy; it’s a model which we can test. Dienekes points me to a paper, The Y-chromosome C3* star-cluster attributed to Genghis Khan’s descendants is present at high frequency in the Kerey clan from Kazakhstan, which is notable for increasing sample coverage of the distribution of “Genghis Khan haplotype.” As you might recall in 2003 a paper reported that a particular Y-chromosomal phylogeny was extremely common in Central Eurasia, and, that it had expanded rather rapidly starting approximately ~1,000 years ago. The natural supposition was that this was connected to the rise of Genghis Khan, from whom male-line descent in particular has become a matter of pride and prestige across the former domains under his rule. Subsequent researchers have supported this finding insofar as the distribution of the haplotype does tend to drop off among the “Western Mongols,” who were for various reasons marginal during the time of Genghis Khan, and whose ruling class were subsequently diminished in part due to their lack of a Genghiside pedigree.
The evolution of the human face
The face is an important aspect of our phenotype. So important that facial recognition is one of many innate reflexive cognitive competencies. By this, I mean that you can recognize a face in a gestalt manner, just like you can recognize a set of three marbles. You don’t have to think about it in a step-by-step fashion. Particular types of brain injuries can actually result in disablement of this faculty, and a minority of humans seem to lack it altogether at birth (prosopagnosia). That’s why I’ve long been interested in the genetic architecture and evolution of craniofacial traits. I long ago knew the potential range of pigmentation phenotypes for my daughter because both her parents have been genotyped, but when it comes to facial features we’re stuck with the old ‘blending inheritance’ heuristic. The most obvious importance of teasing apart the genetic architecture of craniofacial traits is forensics. It might not put the sketch artist out of a job, but it would be an excellent supplement to problematic eye witness reports.
But it isn’t just forensics. The issue has evolutionary relevance. It looks like that in terms of morphology our own lineage has had a lot of diversity up until recently. I’m thinking in particular of the ‘archaic’ looking humans recently discovered in China and Nigeria, who seem to have persisted down into the Holocene. More generally, humans as a whole have become more gracile over the last 10,000 years. Why? There are two extreme answers we can look to. First, gracile humans have replaced robust humans. Second, natural selection for gracility has resulted in the in situ evolution of many populations over the last ~10,000 years. An interesting aspect of this is that it looks as if many salient traits have been targets of selection, and therefore evolution and population differentiation.
Here the top 10 SNPs which deviate from the overall phylogenetic tree of population relationships in the HGDP data set:
Neanderthals came in all colors
There’s a report in Science about a new short paper about Neandertal pigmentation genetics. The context is this. First, in 2007 an ingenuous paper was published which inferred that it may be that Neandertals had red hair, at least based on an N = 2 from two divergent locations. The new study looks at three Croation samples, and reports genotypes which are correlated with a swarthier phenotype in modern populations. But the results are neither here nor there: everyone interviewed in the paper assumes that like modern Europeans Neandertals were a polymorphic set of populations when it comes to pigmentation. There are lots of reasons for this agreement, despite issues one might take with this paper.
The report on the paper in Science has two sections which I want to zoom in on. First, “Nearly 60% of the formula’s predictions matched the subjects’ actual physical appearance, the authors say. The team considers that accuracy rate satisfactory, given the complexity of the genetics behind skin color and other physical traits.” Do you consider 60 percent satisfactory? What curve are you grading on? I’m willing to bet that the reporter didn’t consider 60 percent satisfactory, and neither do I. If you look in the paper you’ll see that their method predicts that a Yoruba in the HGDP sample has blue eyes and red hair. Several of the Papuans are predicted to have blue eyes.
Beyond trees and European trees
Submitted for your approval, a very important post and preprint from Dr. Joseph Pickrell, Identifying targets of natural selection in human and dog evolution. If you read the preprint there’s a lot of good stuff. Dienekes highlighted the most relevant aspect: representation of genetic relationships with phylogenetic trees mask the likely reality of gene flow and admixture. In the guts of the paper though Pickrell et al. use their framework to identify some novel patterns. For example, that Cambodians may be descended in small part from some basal Eurasian lineage (~15 percent), perhaps their equivalent of “Ancient South Indians”? Using ADMIXTURE and such it has long been evident that there’s something funny there. My own working assumption was that the relatives of “Ancient South Indians” could be found in Southeast Asia, though these results (preliminary as they are) might imply something even more interesting. Second, there is a tidbit which might lend support to the fans of the Solutrean model, or can be interpreted in that way (I suspect that it does not, but it could be spun in such a fashion).
Men on the move and women in place?
After posting on Basque mtDNA I wanted to make something more explicit that I alluded to below, that uniparental lineages are highly informative, but they may not be representative of total genome content. This is plainly true in the case of mestizos from Latin America, but we don’t need genetics to point us in the right direction on this score, we have plenty of textual evidence for asymmetry in sexes when it came to admixture events in the post-Columbian era. Rather, I want to note again the issue of South Asia. When it comes to mtDNA the good majority of South Asian lineages are closer to those of East Asia than Western Eurasia. By this, I do not mean to say that that they’re particular close to East Asian lineages, only that if you go back in the phylogeny the South Asian lineages (I’m thinking here of haplogroup M) they tend to coalesce first with East Asian lineages before they do so with West Eurasian lineages.
Here is a quote from one of the definitive papers on this topic:
The race question: are bonobos human?
Recently Jason Antrosio began a dialogue with readers of this weblog on the “race question.” More specifically, he asked that we peruse a 2009 review of the race question in the American Journal of Physical Anthropology. Additionally, he also pointed me to another 2009 paper in Genome Research, Non-Darwinian estimation: My ancestors, my genes’ ancestors. Normally I don’t react well to interactions anthropologists who are not Henry Harpending or John Hawks. But Dr. Antrosio engaged civilly, so I shall return the favor.
I did read all the papers in the American Journal of Physical Anthropology special issue, as well the Genome Research paper. My real interest here are specific questions of science, not history or social science. But I will address the latter areas rather quickly. I am not someone who comes to this totally naked of the history or social science of the race question. I’ve read many books on the topic. And as a colored person who has moderate experience with racism I get rather bored and irritated with excessively patronizing explanations of how racism afflicts us coloreds from white academics (non-white academics who focus on this subject are usually careerists or activists who don’t have to make much pretense toward scholarly substance and can be duly ignored, at least in my experience). The main point which I think we can all agree upon is that colloquial understanding of race has only a partial correlation with any genetic understanding of race. I myself have ranted against the confusions which have ensued because of the conflation of the two classes, and it is certainly a legitimate area of study, but it is not my primary concern. And importantly, I have no great primary interest in battling racism.
Population structure using haplotype data
The Pith: New software which gives you a more fine-grained understanding of relationships between populations and individuals.
According to the reader survey >50 percent of you don’t know how to interpret PCA or model-based (e.g., ADMIXTURE) genetic plots, so I am a little hesitant to point to this new paper in PLoS Genetics, Inference of Population Structure using Dense Haplotype Data, as it extends the results of those earlier methods. But it’s an important paper, and at some point I’ll starting using their software. The “big picture” is that earlier methods left “some information on the table.” That’s partly due to the fact that they were developed (or in the case of PCA leveraged, as it’s a very general technique) in an era where very dense marker data sets were not available (today we’re shifting to full genome sequences in many cases!). The information left on the table would be haplotype structure. Genetic variation in a concrete form manifests as sequences along a line, many of them physically connected. These correlations of nearby variant markers represent haplotypes of great interest, because they are excellent clues to admixture or divergence events across populations. In contrast the older methods, were looking at variation from marker to marker, each in turn independently, which collapses some of the important genomic structure that we can now inspect (in fact, linkage disequilibrium due to these correlations can distort some of the results in the older methods, so you want to “thin” your marker set).
Let me make this concrete for you. On 23andMe you can see where your friends shake out on a PCA plot using the HGDP data set as a reference. What this means is that the HGDP data set is used to generate independent dimensions of genetic variation. As is the usual case in these analyses the largest dimension separates Africans from everyone else, and the second largest dimension separates Asians from Europeans and Africans. 23andMe customers are then projected upon this variation, so you can get a sense where you are positioned in the clusters. To the left is a zoom in on the section for Central/South Asians. You can see that one of my friends, highlighted with a green color, falls almost perfectly in the Uygur cluster. According to ancestry estimates my friend is 50 percent Asian and 50 percent European. The “representative” Uygur in the 23andMe chromosome painting gives about the same results. But these are total genome estimates. The historical nature of my friend’s admixture and that of the Uygur woman is very different, as one can see in the below figure.
Out of Africa and out of Siberia
The latest edition of The American Journal of Human Genetics has two papers using “old fashioned” uniparental markers to trace human migration out of Africa and Siberia respectively. I say old fashioned because the peak novelty of these techniques was around 10 years ago, before dense autosomal SNP marker analyses, let alone whole genome sequencing. But mtDNA, passed down the maternal line, and Y chromosomes, passed from father to son, are still useful. Prosaically they’re useful because the data sets are now so large for these sets of markers after nearly 20 years of surveying populations. More technically because these two regions of the genome do not recombine they lend themselves to excellent representation as a tree phylogeny. Finally, mtDNA in particular is particularly amenable to estimates via molecular clock methodologies (it has a region with a higher mutational rate, so you can sample a larger range of variation over a given number of base pairs; you can use STRs, which mutate rapidly, for Y chromosomes, but there seems to be a lot of controversy in dating).
The papers are The Arabian Cradle: Mitochondrial Relicts of the First Steps along the Southern Route out of Africa and Mitochondrial DNA and Y Chromosome Variation Provides Evidence for a Recent Common Ancestry between Native Americans and Indigenous Altaians. Dienekes has already commented on the first paper. I am not going to take a detailed position on either, but I have to add that we need to be very careful of extrapolating from maternal or paternal lineages, and, assuming that population turn over is low enough that we can make phylogeographic inferences about the past from the present. For example, if you look at mtDNA South Asians as a whole strongly cluster with East Asians and not Europeans, while if you look at Y chromosomes you see the reverse. The whole genome gives a more mixed picture. Additionally, ancient DNA analyses in Northern Eurasia are showing strong discontinuities between past and present populations. So coalescence back to last common ancestor between two different lineages in two different regions may actually be due to diversity in a common source population more recently, which entered into demographic expansion and replaced other groups.
If you need the papers, email me. Some of you know the alphabet soup of haplogroups better than I do. Below are two figures which I think give the top line results.
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