Monday, October 3, 2011

New World Prehistory Headlines

Dienkes, and the sources he links, have a wealth of interesting new developments in the study of prehistoric linguistics and genetics. I describe the discoveries pertinent to the New World in this post, leaving the Old World results for another post (if I find time to write one).

Many come from the abstracts announced in the final program the International Conference in Porto, Portgual on "Comparing Ancient and Modern DNA Variability
in Human Populations" set for November 23-25 of this year.

There are six papers that address New World prehistory, with presenter and title shown below:

* Michael H. Crawford, "Current developments in molecular and population genetics of contemporary and ancient Aleut and Eskimo populations"
* Maanasa Raghavan, "Prehistoric migrations into the New World High-Arctic: A genetic perspective"
* Justin Tackney, "Ancient and modern genetic diversity of IƱupiat populations from the Alaskan North Slope: insights into Paleo- and Neo-Eskimo origins"
* Paula Campos, "The First Americans, DNA from Pre-Clovis Coprolites in Oregon, U.S.A."
* Francesc Calafell, "Can the Y chromosome in current men carrying the Colon or Colombo surnames be used to reveal the origin of Christopher Columbus"
* Monica Sans, "Extermination or continuity? Mitochondrial DNA Native lineages in Uruguay"

Who Were The Pre-Clovis People?

The crown jewel of these sessions is the Campos paper (his co-authors are Dennis L. Jenkins, Thomas W. Stafford, Jr., and Eske Willerslev):

The timing, route and origin of the first human migration into the Americas are still heavily debated. The most widely accepted dates of occupation relate to the Clovis complex, ~11,000 to 10,800 14C years before the present (yr B.P.) (13.2-13.1 to 12.9-12.8 ka), a distinct technology that appears to have originated and spread throughout North America in as little as 200 to 300 years.

However, human mitochondrial DNA recovered from coprolites found at the Paisley 5 Mile Point Caves, in south-central Oregon, suggest human presence as early as 12,300 14C years B.P (coprolites were directly dated by accelerator mass spectrometry). These coprolites are >1000 14C years older than the accepted dates for the Clovis complex.

Here we present new genetic, archaeological and stratigraphical data that further confirm these results. Nothing is known about the genetic relationship between these Pre-Clovis human remains and the Clovis culture or other modern humans. Our current work is looking at using PEC (primer extension capture) coupled with state-of-the-art next generation sequencing (Illumina, Hi Seq) to target the complete mitochondrial genome of Clovis and Pre-Clovis people in order to help resolve the phylogenetic placement of these first Americans and possibly disentangle issues surrounding the origin of the first Americans and the timing and route of these migrations.

Anthropologists have suggested that the physical anthropology from skeletal remains suggests that there was population replacement between a brief Paleo-Indian wave and the Clovis people of North America. But, it is hard to distinguish differences in physique that arise due to factors like better diet as hunting techniques are perfected and the climate improves, from differences associated with the presence of separate genetic lineages. With the exception of the Arctic area of North America, the modern DNA patterns in Native Americans and most other evidence has pointed to a single human colonization event in the narrow window when the land bridge across Berginia was open.

This ancient DNA comparison could seal the deal one way or the other, given the direct nature of the genetic evidence involved and link between the dating evidence and the ancient DNA that prevents a confounding of dates due to a shift of ancient DNA materials into an older strata. If the Clovis sample shows continuity with modern Native American DNA, while the pre-Clovis sample is from an mtDNA haplogroup not found in later DNA samples from the Americas, a replacement scenario is strongly supported (although disappearance of mtDNA lines due to genetic drift is another possible scenario). The abstract is coy when it comes to announcing what they actually found as a result of their examination, so we'll have to wait a couple of months to see what they announce.

In any case, the paper is quite an impressessive feat for a scientific analysis of a pile of shit in Oregon.

The Genetics of Arctic North America's Prehistory

The three papers on prehistoric population layers in the Arctic all support the current three layer paradigm in which first the Saqqaq (Arctic Paleo-Eskimos) which was present 2000 BCE, then the Dorset (second wave Arctic Paleo-Eskimos), and finally the Thule (proto-Inuits) from ca. 1000 CE, successively sweep Arctic North America while having little genetic impact on Native American populations further South, that presumably have origins that date back to the initial colonization of the Americas by modern humans from Asia (who are the first hominins to live there). Ancient DNA shows genetic continuity from the Thule to modern Inuits (whose genetics are remarkably homogeneous), dominated by the A2a, A2b, and D3 mtDNA haplotypes, while "Haplotype D2 (3%), found among modern Aleut and Siberian Eskimos, was identified at a low frequency in the modern samples but not the ancient. This haplotype was recently identified in an ancient Paleo-Eskimo Saqqaq individual from western Greenland."

Based on the sampling of 11 Aleut populations of the Archipelago, contemporary Aleuts exhibit only A (primarily A2a1) and D (D2a1) mt-DNA haplogroups. Mantel tests of genetic and geographic distances have produced a highly significant correlation of r=0.717 (p < 0.0001) indicating that the genetic structure reflects the settlement patterns that are preserved in the maternal DNA. In contrast, there is no significant relationship between geography and genetics based on Y-chromosome haplotypes-since the gene flow from Europeans into the Aleut gene pool was unidirectional. Genetic barrier analysis of contemporary mt-DNA sequence distributions indicate genetic discontinuity, reflecting the expansion of the Aleuts from the eastern to the central islands stimulated by climatic changes 6,000 years ago. Ancient DNA analyses of skeletal remains from three Aleutian regions (Mink Island, Port Moller and Brooks River) by Dennis O'Rourke (University of Utah) and his colleagues, reveals the presence of haplogroups A and D in two regions but B2 in one region. The presence of B is suggestive of prehistoric gene flow from Alaska and Kodiak Island populations. Whole genomic sequencing of the 4,000 year old PaleoEskimo, "Inuk," indicated that the Saqqaq sequences clustered with the Chukchi and Koryaks of Siberia-suggesting an earlier migration from Siberia along the northern slope of Alaska to Greenland. The mt-DNA sequences from the PaleoEskimo is D2a1, found primarily in Aleut populations. These data indicate that ancient DNA data provide significant insights into the evolution and migration of contemporary populations and vice versa.

Was Columbus a Catalan or a Northern Italian?

The results from the Columbus paper, which investigates whether it would be possible to determine his DNA type from the DNA of New World individuals bearing his surname who might be his patriline descendants looks at Spanish and Italian people with his surname today. In Spain, a few lineages match most men of that surname, but in Italy, "Colombo is actually the most frequent surname in Lombardy, where foundlings and orphans used to be given the surname Colombo.", so it would be harder to show a link between Columbus and modern men whose surnames indicate that they might be descended from him.

The New World comparison is merely proposed and not conducted, so the study offers nothing in the way of answers to the question it poses.

Assimilation v. Elimination

A core issue in the study of transitions from indigenous hunter-gatherer societies to food producing ones is the extent to which native populations are replaced, or simply incorporated into the new dominant society. A study from Uruguay support the assimilation theory in that context.

The study from Uruguay uses ancient DNA and modern population genetics to argue that the Native American genetic component of current populations in Uruguay show about a 30% mtDNA and 10% autosomal DNA contribution from Native Americans and that the contribution observed appears to derive almost entirely from the several now non-existent tribes that were present in Uruguay at the time of European colonization, with the distributions of modern Native American DNA components largely tracking their pre-colonial regional ranges within Uruguay, rather than imported Native American contributions from elsewhere in the New World.

Is Hunter-Gatherer Language Evolution Different?

Apart from this upcoming conference, another important study disproves the contention that hunter-gatherer languages may borrow from each other at such a high rate that they cannot be effectively modeled into linguistic family relationships in a tree-like manner. If true, this would explain why it has proven so hard to classify the language of the Americas into large linguistic families.

Instead, hunter-gather languages are shown to have linguistic borrowings that don't differ materially from the linguistic borrowing of agriculturalists. Most hunter-gatherer languages had very low levels of linguistic borrowing from nearby languages, while a handful of outliers in a 41 language set that including Native American languages of the Amazon and California and Northern Australia, had higher rates of borrowing for language specific reasons largely unrelated to their status as hunter-gatherer languages. This result could be very helpful in efforts to make mathematical models of linguistic evolution more accurate.

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