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

December 4, 2013

How genetics are rewriting the history of the Caribbean

Filed under: Christopher Columbus,Genetics,Native Americans,science — Razib Khan @ 2:47 am
Over the past century history has been approached from many different angles, despite the stereotype of scholars haunting dusty archives. Adventurers once called antiquarians became archaeologists, and inspired the fictional Indiana Jones. Today it is the turn of the geneticists to put their stamp upon history. By tracing patterns of variation they gain insights as to the [...]

December 1, 2012

Northern Europeans and Native Americans are not more closely related than previously thought

A new press release is circulating on the paper which I blogged a few months ago, Ancient Admixture in Human History. Unlike the paper, the title of the press release is misleading, and unfortunately I notice that people are circulating it, and probably misunderstanding what is going on. Here’s the title and first paragraph:

Native Americans and Northern Europeans More Closely Related Than Previously Thought

Released: 11/30/2012 2:00 PM EST
Source: Genetics Society of America

Newswise — BETHESDA, MD – November 30, 2012 — Using genetic analyses, scientists have discovered that Northern European populations—including British, Scandinavians, French, and some Eastern Europeans—descend from a mixture of two very different ancestral populations, and one of these populations is related to Native Americans. This discovery helps fill gaps in scientific understanding of both Native American and Northern European ancestry, while providing an explanation for some genetic similarities among what would otherwise seem to be very divergent groups. This research was published in the November 2012 issue of the Genetics Society of America’s journal GENETICS

 

The reality is ta Native Americans and Northern Europeans are not more “closely related” genetically than they were before this paper. There has been no great change to standard genetic distance measures or phylogeographic understanding of human genetic variation. A measure of relatedness is to a great extent a summary of historical and genealogical processes, and as such it collapses a great deal of disparate elements together into one description. What the paper in Genetics outlined was the excavation of specific historically contingent processes which result in the summaries of relatedness which we are presented with, whether they be principal component analysis, Fst, or model-based clustering.

What I’m getting at can be easily illustrated by a concrete example. To the left is a 23andMe chromosome 1 “ancestry painting” of two individuals. On the left is me, and the right is a friend. The orange represents “Asian ancestry,” and the blue represents “European” ancestry. We are both ~50% of both ancestral components. This is a correct summary of our ancestry, as far as it goes. But you need some more information. My friend has a Chinese father and a European mother. In contrast, I am South Asian, and the end product of an ancient admixture event. You can’t tell that from a simple recitation of ancestral quanta. But it is clear when you look at the distribution of ancestry on the chromosomes. My components have been mixed and matched by recombination, because there have been many generations between the original admixture and myself. In contrast, my friend has not had any recombination events between his ancestral components, because he is the first generation of that combination.

So what the paper publicized in the press release does is present methods to reconstruct exactly how patterns of relatedness came to be, rather than reiterating well understood patterns of relatedness. With the rise of whole-genome sequencing and more powerful computational resources to reconstruct genealogies we’ll be seeing much more of this to come in the future, so it is important that people are not misled as to the details of the implications.

Northern Europeans and Native Americans are not more closely related than previously thought

A new press release is circulating on the paper which I blogged a few months ago, Ancient Admixture in Human History. Unlike the paper, the title of the press release is misleading, and unfortunately I notice that people are circulating it, and probably misunderstanding what is going on. Here’s the title and first paragraph:

Native Americans and Northern Europeans More Closely Related Than Previously Thought

Released: 11/30/2012 2:00 PM EST
Source: Genetics Society of America

Newswise — BETHESDA, MD – November 30, 2012 — Using genetic analyses, scientists have discovered that Northern European populations—including British, Scandinavians, French, and some Eastern Europeans—descend from a mixture of two very different ancestral populations, and one of these populations is related to Native Americans. This discovery helps fill gaps in scientific understanding of both Native American and Northern European ancestry, while providing an explanation for some genetic similarities among what would otherwise seem to be very divergent groups. This research was published in the November 2012 issue of the Genetics Society of America’s journal GENETICS

 

The reality is ta Native Americans and Northern Europeans are not more “closely related” genetically than they were before this paper. There has been no great change to standard genetic distance measures or phylogeographic understanding of human genetic variation. A measure of relatedness is to a great extent a summary of historical and genealogical processes, and as such it collapses a great deal of disparate elements together into one description. What the paper in Genetics outlined was the excavation of specific historically contingent processes which result in the summaries of relatedness which we are presented with, whether they be principal component analysis, Fst, or model-based clustering.

What I’m getting at can be easily illustrated by a concrete example. To the left is a 23andMe chromosome 1 “ancestry painting” of two individuals. On the left is me, and the right is a friend. The orange represents “Asian ancestry,” and the blue represents “European” ancestry. We are both ~50% of both ancestral components. This is a correct summary of our ancestry, as far as it goes. But you need some more information. My friend has a Chinese father and a European mother. In contrast, I am South Asian, and the end product of an ancient admixture event. You can’t tell that from a simple recitation of ancestral quanta. But it is clear when you look at the distribution of ancestry on the chromosomes. My components have been mixed and matched by recombination, because there have been many generations between the original admixture and myself. In contrast, my friend has not had any recombination events between his ancestral components, because he is the first generation of that combination.

So what the paper publicized in the press release does is present methods to reconstruct exactly how patterns of relatedness came to be, rather than reiterating well understood patterns of relatedness. With the rise of whole-genome sequencing and more powerful computational resources to reconstruct genealogies we’ll be seeing much more of this to come in the future, so it is important that people are not misled as to the details of the implications.

July 12, 2012

Native Americans are not special snowflakes

Filed under: Anthroplogy,Native Americans — Razib Khan @ 10:45 pm

Dienekes, in response to Living Anthropologically, Petty identity politics indeed, or, holding a grudge is no excuse for anti-science:

I won’t argue about the veracity or details of this version of history, but surely native Americans from the US were not especially mistreated compared to other people colonized by Europeans?

I mean, there are now samples from Native Australians, East Indians, Sub-Saharan Africans, Native Americans from all over the Americas except the US. Why don’t all these people not “hold a grudge” for their bad treatment at the hands of Europeans, but, apparently, are perfectly willing to participate in genetic research if it’s explained to them how they might learn more about their ancestors from it?

And, why limit ourselves to people colonized by Europeans? Surely, Slavs, for example, have a lot of things to say about German Rassenkunde scientists belittling them, studying their skulls to “prove” they are an inferior race, and hatching up and executing plans for their annihilation. So, why do the Russians give the Denisova fingerbone to ze Max Planckfolks to study, or allow them to study ancient DNA from all over their territory?

Scour the literature for a while, and you’ll find plenty of (modern) Germans studying Jews, and Jews studying pretty much everybody, ...

The past as a cultural landscape

Filed under: Anthroplogy,Archaeology,Native Americans — Razib Khan @ 9:03 pm

By now you have read that the Clovis people may have had contemporaries. In case you didn’t know, until about ~10 years the “standard model” of the peopling of the Americas was that around ~13,000 years ago one single population crossed into the New World via Beringia, and rapidly swept north to south in ~1,000 years. These were the Clovis people, associated with a particular toolkit, and perhaps implicated in megafaunal extinctions. Today this model is no longer held to be sacrosanct, though no clear successor has emerged. It does seem likely that some sort of pre-Clovis population is presumed to exist. These data are interesting because they indicate that there may have been geographical structure in cultural forms even at this early stage in North America, implying that the original peopling of America was not homogeneous. That is, there may have been several founding groups.

I find this entirely plausible. It strikes me that a fear years ago a tendency toward rhetorical extremism occasionally found purchase when it came to the settlement of the peripheries of the human range, Oceania and the New World. Jared Diamond famously proposed that ...

November 17, 2010

Icelanders descended from Native Americans?

ResearchBlogging.orgThat is the question, and tentatively answered in the affirmative according to a new paper in The American Journal of Physical Anthropology. A new subclade of mtDNA haplogroup C1 found in icelanders: Evidence of pre-columbian contact?:

Although most mtDNA lineages observed in contemporary Icelanders can be traced to neighboring populations in the British Isles and Scandinavia, one may have a more distant origin. This lineage belongs to haplogroup C1, one of a handful that was involved in the settlement of the Americas around 14,000 years ago. Contrary to an initial assumption that this lineage was a recent arrival, preliminary genealogical analyses revealed that the C1 lineage was present in the Icelandic mtDNA pool at least 300 years ago. This raised the intriguing possibility that the Icelandic C1 lineage could be traced to Viking voyages to the Americas that commenced in the 10th century. In an attempt to shed further light on the entry date of the C1 lineage into the Icelandic mtDNA pool and its geographical origin, we used the deCODE Genetics genealogical database to identify additional matrilineal ancestors that carry the C1 lineage and then sequenced the complete mtDNA genome of 11 contemporary C1 carriers from four different matrilines. Our results indicate a latest possible arrival date in Iceland of just prior to 1700 and a likely arrival date centuries earlier. Most surprisingly, we demonstrate that the Icelandic C1 lineage does not belong to any of the four known Native American (C1b, C1c, and C1d) or Asian (C1a) subclades of haplogroup C1. Rather, it is presently the only known member of a new subclade, C1e. While a Native American origin seems most likely for C1e, an Asian or European origin cannot be ruled out.

The core of the article treads the confusing gray zone between rock-hard precise science and the more vague and intuitive truths of history. One the rock-hard part, there is a huge literature on maternal genetic lineages, the mtDNA. Because this genetic material is copious it was some of the first to be analyzed using molecular clock models. A molecular clock is a feasible with mtDNA because it is haploid; it is only inherited through females and so is not subject to recombination which might break apart associations of distinctive genetic markers. Instead of being a reticulated mesh the genealogy of mtDNA is a clean and inverted elegant tree leading back to a common ancestress. You are finding the line of your mother’s mother’s mother’s mother’s….


But synthesizing this clarity with human history is more difficult, because we are dependent on the bias of text, and even more tendentious clues from oral history and archaeology. Because of Iceland’s Lutheran Christian heritage the maternal lineage here could be traced back to 1700. This does not mean that the first woman in the line that we know of was born like Athena from the head of her father; rather, the records were not kept well enough to continue unbroken back to the medieval era. We do know that the first permanent Norse settler in Iceland arrived in 874, and, that very few immigrants from Scandinavia added diversity to the gene pool after ~1000. Iceland is a small and poor island, so quickly reached its Malthusian maximum. How else to explain that Icelanders made a secondary migration to Greenland?

The most obvious explanation for the existence of the subclade of the C1 lineage is that it arrived recently. Without knowing anything else that is what you’d have assumed. But as noted above the individuals who carry it have been traced back to a common ancestor in the early 18th century; these are native Icelanders, at least if native means anything substantive. An second point which rejects recent injection of this lineage into the gene pool: the Icelanders are their own special branch of C1, C1e. The phylogenetic tree of C1 below illustrates the  relationship of the branches to each other. Since the font is so small, I added in clarifying labels (from top to bottom it’s C1a to C1e, with further clades such as C1d1):

icetree1

As you can see, this is mostly an Amerindian clade, with some some Asians. But, by surveying the public data they did find two individuals who were European who carried possible C1e. I’ll quote:

…, using the criteria of one mutational difference from C1e when sequences were avail- able for only hypervariable segment 1 (HVS1) or 2 (HVS2) and two mutational differences when both HVS1 and HVS2 sequences were available. The result was a shortlist of 276 sequences that we suggest be checked first for C1e coding region mutations (Supp. Info. Table S3). We note that for the sequences for which geographical information is available, all but two were sampled from individuals with Native American ancestry—i.e. from the Canary Islands and Germany.

The German sequence…represents a perfect match to the Icelandic C1e for the short HVS1 fragment spanning sites 16024–16365. This raises the intriguing, but perhaps unlikely, hypothesis that C1e is a European-specific subclade of C1, following the precedent of the European and Native American subclades of mtDNA haplogroup X2…However, given the dense sampling of mtDNA variation in European populations, it is clear that C1e is exceedingly rare, a fact that weighs against a hypothesis of antiquity in Europe.

They believe that the Canary Islander is probably the result of admixture during the Spanish colonial era with someone who returned from the New World colonies.  The German is the one to focus on. A plausible alternative model is that C1e is a very low frequency European lineage, which increased in frequency in Iceland simply through genetic drift because of that island’s small population. Remember that though C1e is rare in Iceland, its frequency is much higher than in Northern Europe as a whole. Though here we must be cautious because the typing was preliminary in the Germany case, the authors note that “This is because there are no other known human mtDNA sequences belong to C1e out of the 6747 complete sequences available in the literature.” Also, the authors observe that there is variation among the Iceland C1e lineages, mutations which differentiate them. This further tilts the playing field toward an early entrance of the lineage into Iceland, probably before Columbus, because a late arrival would not have had time to build up mutational variation in the region of Iceland where C1e is found.

572px-Bjork_and_the_Swan_DressAs this subclade is absent among Native Americans, you may wonder as to a relationship to Greelanders or Inuit. The larger C1 haplogroup as a whole is not evident in these populations. You can inspect the geographical distribution closer yourself. If this woman was a non-European, she was not maternally related to the peoples who replaced the Norse in Greenland. Though we should also be careful about assuming that the present genetic variation in the American Arctic is representative of pre-modern variation.

If the Greenland and ancient European hypotheses are rejected, what we have is a woman who entered the Icelandic society from an extinct lineage of Native Americans, probably from the northeast (or perhaps her Greenland Norse mother was of this line). What the Norse would have termed Markland. It is tempting to point to the Norse settlement at L’Anse aux Meadows in Newfoundland. Perhaps the Europeans had enslaved a native woman, and taken her back to their homeland when they decamped? But more likely to me is the probability that the Norse brought back more than lumber from Markland, since their voyages spanned centuries.

Finally, does this explain Bjork? I doubt it. A minority of Scandinavians, especially ones of Sami background, exhibit an “Asiatic” cast to their features. The autosomal genomic content of the Icelanders is what you’d expect, Scandinavian leavened with British, and twisted with their own particular history of population bottlenecks. Only the precision of mtDNA typing brought the reality of the woman who carried C1e into the light. In terms of total genome content she is one of tens of thousands of ancestors to any given descendant, and she may be one of the less common ones in the family trees because of her likely lower status. Though the flip side of the nature of mtDNA, and the inbred aspect of the Iceland pedigree, is that probably all native Icelanders can draw many lines of descent to this woman.

Citation: Ebenesersdóttir SS, Sigurðsson A, Sánchez-Quinto F, Lalueza-Fox C, Stefánsson K, & Helgason A (2010). A new subclade of mtDNA haplogroup C1 found in icelanders: Evidence of pre-columbian contact? American journal of physical anthropology PMID: 21069749

Image Credit: Cristiano Del Riccio

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