Wednesday, November 19, 2014

Two New Baryons Predicted By The Standard Model Discovered At LHC

The large hadron collider (LHC) has discovered two never before detected baryons (three quark composite structures in the same category as protons and neutrons), the Xi_b'- and Xi_b* 

The discovery is reported in a preprint here. The baryons have a bottom quark, a down quark and a strange quark each.  One has spin 1/2 and the other has spin 3/2.  The masses are essentially at the Standard Model predicted values.

A summary of the possible mesons and baryons in the Standard Model can be found at a previous post at this blog.  In the pertinent part that post noted that:
3. A chi baryon (isospin 1/2) (three horizontal lines) (J=1/2 or 3/2) have[sic] one light quark and two heavy quarks.

All four chi baryons without charm and bottom quarks, and all four chi baryons with one strange quark and one charm quark have been observed experimentally. Both of the J=1/2 bottom chi baryons and one of the two J=3/2 bottom chi baryons have been observed experimentally. One of the two J=1/2 double charmed chi baryon has also been observed.

Scientists have not yet observed one of the J=3/2 bottom chi baryons, one of the J=1/2 double charmed chi baryons, both of the J=3/2 double charmed baryons, any of the four of the charmed bottom chi baryons, or any of the four of the double bottom chi baryons.

Thus, exactly half of the twenty-four kinds of chi baryon ground states have been observed so far. In general, the baryons not yet observed are the heaviest ones.
This discovery involves the J=3/2 bottom chi baryon, and a first excited state of the J=1/2 bottom chi baryon above the ground state (the ground state of which has been observed already).  The double charmed chi baryons and the double bottom chi baryons remain to be observed, as do a variety of excited states.

Was mtDNA haplogroup H present in Mesolithic Iberia?

Today, the predominant mtDNA haplogroup in Europe is H.  It is absent from numerous ancient DNA samples everywhere to the north of the Olive Oil-Butter line in Europe before the advent of farming in Europe, and remains rare until the Copper Age that coincides with the advent of the Corded Ware culture in Central and Eastern Europe, and with the Bell Beaker culture of Western Europe.

There are a couple of studies, however, that claim to have found mtDNA haplogroup H in Iberia in the archaeological period immediately prior to the arrival of farming and herding there, sometimes called the Mesolithic era or Epipaleolithic era, that corresponds to the pre-Neolithic Holocene era.  There are quite early, but not as definitively Mesolithic, examples of mtDNA H in Italy and Southeastern Europe.  There is also mtDNA H in the early Neolithic Fertile Crescent (which is earlier in absolute dating than the Neolithic elsewhere).

The Iberian studies are the strongest evidence far mtDNA H having an origin in the Franco-Cantabrian refugia, as opposed to arising with the first farmers (and herders) or subsequent migrations that had run their course by the end of the Bronze Age in Europe (i.e. prior to 1200 BCE), or earlier.

Bell Beaker blogger challenges the validity of these studies in a pair of recent posts here and here.  He focuses on two points:

1.  The context of the ancient mtDNA H samples called Mesolithic is dubious, coming from old excavations of shell middens where samples were interspersed with Neolithic era pottery as well as older materials, and is also subject to other concerns related to its provenance.

2.  C14 dating of bone from people who had a shellfish heavy diet as the people buried in the shell middens that were a source for key ancient DNA samples are not reliable in the way that they are for terrestrial individuals.  Basically, their diet altered the baseline C14 levels upon which C14 data is premised from the standard assumptions concerning that baseline that are used to date the bones.

These criticisms, at a minimum, are not frivolous.  And, if these troublesome data points are excluded, in part on the intuition that extraordinary claims should require extraordinary evidence, then the rest of the ancient DNA data from Europe falls together into a much simpler picture.  In that picture, a much larger share of modern Europe's maternal genetic heritage arrived with the first farmers (or second wave of farmers), rather than dating back to integration of the continent's indigenous hunter-gatherer population into frontier farming communities (a more plausible possibility in the case of women than in men).  Bell Beaker blogger, in particular, doubts that mtDNA H could really have been so geographically confined for so long if it was really indigenous.

On the other hand, new autosomal DNA evidence seems to indicate that modern Europeans have fairly substantial genetic European hunter-gatherer ancestry.

I'm interested in hearing the opinions of others on these methodological critiques of this key evidence, upon which key conclusions about European prehistory and population genetics rests.

Tuesday, October 28, 2014

More Evidence Of Pre-Columbian Contact With Asia

In a recent post at this blog I recapped the evidence for pre-Columbian contact with the Americas after the Beringian land bridge was inundated. There were three main waves of subsequent migration:

* Saqqaq and Dorest Paleo-Eskimo populations are traceable to a wave of migration ca. 3500 BCE. These two archaeological cultures represent a single wave of demic migration and have genetic identity with each other (but admixed very little with other Native Americans before their demise).

* Early Na-Dene people arrive in Alaska ca. 1500 BCE.

* The 6th to 7th century CE Berginian Birnirk culture (in turn derived from Siberian populations) is the source of the proto-Inuit Thule people, who were the last substantial and sustained wave of pre-Columbian peoples to migrate to the Americas.

There were also several instances of less substantial and sustained migration, many of which have just become widely known:

* Around 1000 CE, Lief Erickson led a small population of Vikings to a short lived agricultural settlement called Vinland in maritime Canada. Recent discoveries announced in National Geographic in November of 2012 established that there were trade relations between the Vikings and indigeneous Arctic people at around the same time at the Northern tip of Canada's Baffin Island.

* From around 900 CE to 1100 CE, the "people who lived . . . in what today is the Lambayeque region, about 800 kilometers (500 miles) north of Lima, [Peru] had genetic links to the contemporaneous populations of Ecuador, Colombia, Siberia, Taiwan and to the Ainu people of northern Japan." These people were practitioners of the Middle Sican culture. It is not clear to what extent this contact was Austronesian in origin.

* I said then that:
Late in the period of Austronesian expansion (probably not earlier than 700 CE, with radiocarbon dated examples found in the Cook Islands by 1000 CE), perhaps from a final launching point at Easter Island, the kumara, a yam-like plant native to South America and possibly native to Peru, entered Austronesian territory and became a staple food. But, no genetic traces of the New World are found in Austronesian populations. It is possible that the kumara's arrival in Oceania and the Asian genetic influences found in Middle Sican graves involved the same instance of cultural Old World-New World contact.
The evidence now contradicts that contention insofar as it claims that there is no genetic evidence of Precolumbian contact in Polynesia. Razib Khan notes a new paper demonstrating that Easter Islanders have approximately 8% Native American admixture in their autosomal DNA arising from a Precolumbian admixture event. He notes that: "The rough dates for Amerindian ancestry admixture are in the range of 1300 to 1400 A.D., which match reasonably well with when Easter Island was settled."

* Razib also notes in the same post a new paper whose abstract states:
[W]e present 14C dates, and morphological, isotopic and genomic sequence data from two human skulls from the state of Minas Gerais, Brazil, part of one of the indigenous groups known as ‘Botocudos’. We find that their genomic ancestry is Polynesian, with no detectable Native American component. Radiocarbon analysis of the skulls shows that the individuals had died prior to the beginning of the 19th century. Our findings could either represent genomic evidence of Polynesians reaching South America during their Pacific expansion, or European-mediated transport.
As Razib sums up the finding of the paper in that post:
[H]eretofore the reasonable assumption about these Polynesian remains in interior Brazil were the product of escaped slaves, but there is an 80-90% probability that they died before any such enslavement of Polynesians could have occurred. In fact both remains may be pre-Columbian!
Both of the new papers appear in the most recent issue of the Journal Current Biology.

* Wikipedia summarizes many, but not all of these contacts, and adds others that I have not listed above.  Few are credible, but there is plausible evidence to support a few additional minor Old World-New World contacts.

* The Austronesians, the culture behind both of the latest two finds, are the same seafaring people who transplanted a community of their people from Indonesia, language intact, all of the way to Madagascar, with a small amount of South Asian admixture picked up along the way.

Of course, while these contacts did occur, none of them had the epic consequences that the era of European contact with the Americas begun by expedition of Christopher Columbus did.

New Insights From 45,000 Year Old Siberian Ancient DNA

A new study has the oldest modern human ancient DNA sequence every analyzed, from 45,000 in Siberia, assigned the name Ust’-Ishim.

Some key points:
The Y chromosome sequence of the Ust’-Ishim individual is . . . inferred to be ancestral to a group of related Y chromosomes (haplogroup K(xLT)) that occurs across Eurasia today. . . . The Ust’-Ishim mtDNA sequence falls at the root of a large group of related mtDNAs (the ‘R haplogroup’), which occurs today across Eurasia. . . . 
Based on genotyping data for 87 African and 108 non-African individuals, the Ust’-Ishim genome shares more alleles with non-Africans than with sub-Saharan Africans (|Z| = 41–89), consistent with the principal component analysis, mtDNA and Y chromosome results. . . . Among the non-Africans, the Ust’-Ishim genome shares more derived alleles with present-day people from East Asia than with present-day Europeans (|Z| = 2.1–6.4). . . . However, when an ~8,000-year-old genome from western Europe (La BraƱa) or a 24,000-year-old genome from Siberia (Mal’ta 1) were analysed, there is no evidence that the Ust’-Ishim genome shares more derived alleles with present-day East Asians than with these prehistoric individuals (|Z| < 2). This suggests that the population to which the Ust’-Ishim individual belonged diverged from the ancestors of present-day West Eurasian and East Eurasian populations before—or simultaneously with—their divergence from each other. The finding that the Ust’-Ishim individual is equally closely related to present-day Asians and to 8,000- to 24,000-year-old individuals from western Eurasia, but not to present-day Europeans, is compatible with the hypothesis that present-day Europeans derive some of their ancestry from a population that did not participate in the initial dispersals of modern humans into Europe and Asia.

Assuming that this corresponds to the number of mutations that have accumulated over around 45,000 years, we estimate a mutation rate of 0.43 × 10−9 per site per year (95% CI 0.38 × 10−9 to 0.49 × 10−9) that is consistent across all non-African genomes regardless of their coverage. This overall rate, as well as the relative rates inferred for different mutational classes (transversions, non-CpG transitions, and CpG transitions), is similar to the rate observed for de novo estimates from human pedigrees (~0.5 × 10−9 per site per year14, 15) and to the direct estimate of branch shortening. As discussed elsewhere, these rates are slower than those estimated using calibrations based on the fossil record and thus suggest older dates for the splits of modern human and archaic populations. [Ed. by Dienekes This is a very direct confirmation of the "slow" autosomal rate of ~1.2x10-8 mutations/generation/bp using a technology much different than those used before to estimate this. The slower mutation rate implies that major splits in human history (such as the Out-of-Africa event) took place much earlier than the Upper Paleolithic revolution and the spread of humans across Eurasia.] . . .

[W]e estimate that the admixture between the ancestors of the Ust’-Ishim individual and Neanderthals occurred approximately 50,000 to 60,000 years BP, which is close to the time of the major expansion of modern humans out of Africa and the Middle East.
In other words, this person lived just 5,000-15,000 years after Neanderthal admixture, a time which is on the recent end of other estimates of the timing of this event.

As a minor point, the discovery of 45,000 modern human remains in Siberia at all, provides a strong direct calibration point from which modern humans were known to be present at a specific out of Africa location.