Detecting ancient admixture and estimating demographic parameters in multiple human populations

Detecting ancient admixture and estimating demographic parameters in multiple human populations (pdf)

A rather odd looking pdf- runs a lot like a mini PowerPoint presentation, by the man who published the recent paper that concluded there probably was archaic admixture in humans. And yet again.. I see the 40k-60k OOA date in print. Grr.

Detecting ancient admixture and estimating demographic parameters in multiple human populations

We analyze patterns of genetic variation in extant human polymorphism data from the NIEHS SNPs project to estimate human demographic parameters. We update our previous work by considering a larger data set (more genes and more populations), and by explicitly estimating the amount of putative admixture between modern humans and archaic human groups (e.g., Neandertals, Homo erectus, H. floresiensis). We find evidence for this ancient admixture in European, East Asian and West African samples, suggesting that admixture between diverged hominin groups may be a general feature of recent human evolution.

Yet another DNA study that finds evidence of archaic contributions in modern human groups. Odd how these don’t make the news but anything that finds in favour of the OOA gets splattered all over the media.

We estimate admixture proportions of 14 % (95% CI: 8 – 20 %) in the European-American sample and 1.5% (95% CI: 0.5 – 2.5 %) in the East Asian sample. In both cases, the relative log-likelihood for a = 0 (i.e., no ancient admixture) is significantly lower than the maximum likelihood (likelihood-ratio test, p < 10-3) , which provides additional evidence (along with the S* results in the previous paragraph) that ancient admixture occurred. The estimates of admixture rates in Europeans are consistent with estimates of Neandertal admixture obtained from analyses of Neandertal DNA (Serre et al. 2004; Noonan et al. 2006), [. . .] Unlike previous studies, we incorporated admixture between archaic and modern humans as an additional demographic parameter to be co-estimated. Interestingly, we could exclude no admixture (i.e., exclude a = 0) in both of the non-African populations studied

 The observation that all (three) populations studied seem to have evidence for ancient admixture suggests that ancient population structure may be a common feature of all contemporary human populations, and this ancient structure may predate the initial expansion of modern humans out of Africa.

Although some of the archaic DNA isn’t found in Africa, which would make the archaic admixture prior to the OOA hard to explain. This paper also finds evidence for archaic admixture in the Yoruba. I remember reading previously that the X chromosome showed signs of archaic ancestry in one pygmy group, so archaic ancestry in West Africa is supported by another paper. More detail… Testing for Archaic Hominin Admixture on the X Chromosome, which concluded the TMRCA was about 2 million years for one locus on the X chromosome and concludes..

For now, this locus represents a genealogical history that is most consistent with recent admixture from an archaic hominin population in Asia

Which is a far cry from Svante Paabo’s ‘no admixture but they were within the range of modern humans’ claim, which I found a bit odd. So you found they had essentially human DNA with us but decided they didn’t mingle …how?

I’d just like to comment that the OOA/RAR theory leaves absolutely NO room for any ancient DNA cropping in non Africans that doesn’t have a root in Africa- but it does, with remarkable frequency. In other words, the OOA doesn’t ‘fit’. That OOA is true of mostof our ancestry means sod all, it has to be true for all of it and it’s rather blatantly NOT the case, as there are a plethora of non-African but ancient in Eurasia mutations that invalidate it. Particularly the non African MC1R mutation ages that have ages of 100k-250k and a TMRCA of a million years.

Both African and non-African data suggest that the time to the most recent common ancestor is ª1 million years and that the age of the global 314 variant is 650,000 years. On this time scale, ages for the Eurasian distributed Val60Leu, Val92Met, and Arg163Gln variants are 250,000–100,000 years;

I’m going to have to make up a proper list of the DNA studies that find against the OOA theory.

I mapped the reconstruction over the crania.

Having a few minutes spare today, so I thought I’d try to fit the skull under the skin.

It’s not perfect because the face is at a slight angle, but it will do.

mt DNA from La Palma Guanche remains

The maternal aborigine colonization of La Palma (Canary Islands)
Teeth from 38 aboriginal remains of La Palma (Canary Islands) were analyzed for external and endogenous mitochondrial DNA control region sequences and for diagnostic coding positions. Informative sequences were obtained from 30 individuals (78.9%). The majority of lineages (93%) were from West Eurasian origin, being the rest (7%) from sub-Saharan African ascription. The bulk of the aboriginal haplotypes had exact matches in North Africa (70%). However, the indigenous Canarian sub-type U6b1, also detected in La Palma, has not yet been found in North Africa, the cradle of the U6 expansion. The most abundant H1 clade in La Palma, defined by transition 16260, is also very rare in North Africa. This means that the exact region from which the ancestors of the Canarian aborigines came has not yet been sampled or that they have been replaced by later human migrations. The high gene diversity found in La Palma (95.22.3), which is one of the farthest islands from the African continent, is of the same level than the previously found in the central island of Tenerife (92.42.8). This is against the supposition that the islands were colonized from the continent by island hopping and posterior isolation. On the other hand, the great similarity found between the aboriginal populations of La Palma and Tenerife is against the idea of an island-by-island independent maritime colonization without secondary contacts. Our data better fit to an island model with frequent migrations between islands.

More ancient DNA from native North Africa, showing a mainly Eurasian origin for the mt DNA.  The standard result for all ancient North African ADNA.

J1-M267 Y lineage marks climate-driven pre-historical human displacements

J1-M267 Y lineage marks climate-driven pre-historical human  displacements

Sergio Tofanelli et al.
The present day distribution of Y chromosomes bearing the haplogroup J1 M267*G variant has been associated with different episodes of human demographic history, the main one being the diffusion of Islam since the Early Middle Ages. To better understand the modes and timing of J1 dispersals, we reconstructed the genealogical relationships among 282 M267*G chromosomes from 29 populations typed at 20 YSTRs and 6 SNPs. Phylogenetic analyses depicted a new genetic background consistent with climate-driven demographic dynamics occurring during two key phases of human pre-history: (1) the spatial expansion of hunter gatherers in response to the end of the late Pleistocene cooling phases and (2) the displacement of groups of foragers/herders following the mid-Holocene rainfall retreats across the Sahara and Arabia. Furthermore, J1 STR motifs previously used to trace Arab or Jewish ancestries were shown unsuitable as diagnostic markers for ethnicity.

One to add to the J page. I ‘ll have to access the paper later- so no deep insights on this one as yet. Take a month of sick and you do get behind with this stuff.

35,000 year old figurine from Germany

From Hohle Fels in south west Germany and I just love it. Okay, so she looks a bit like a spatchcocked chicken with knockers and stretch marks, but it’s still brilliant. Link

Near Eastern Neolithic genetic input in a small oasis of the Egyptian Western Desert

Near Eastern Neolithic genetic input in a small oasis of the Egyptian Western Desert

The Egyptian Western Desert lies on an important geographic intersection between Africa and Asia. Genetic diversity of this region has been shaped, in part, by climatic changes in the Late Pleistocene and Holocene epochs marked by oscillating humid and arid periods. We present here a whole genome analysis of mitochondrial DNA (mtDNA) and high-resolution molecular analysis of nonrecombining Y-chromosomal (NRY) gene pools of a demographically small but autochthonous population from the Egyptian Western Desert oasis el-Hayez. Notwithstanding signs of expected genetic drift, we still found clear genetic evidence of a strong Near Eastern input that can be dated into the Neolithic. This is revealed by high frequencies and high internal variability of several mtDNA lineages from haplogroup T. The whole genome sequencing strategy and molecular dating allowed us to detect the accumulation of local mtDNA diversity to 5,138 ± 3,633 YBP. Similarly, theY-chromosome gene pool reveals high frequencies of the Near Eastern J1 and the North African E1b1b1b lineages, both generally known to have expanded within North Africa during the Neolithic. These results provide another piece of evidence of the relatively young population history of North Africa.

Spotted on Dienekes, I’ll dig up the full text to add to my Egyptian DNA page later. I’d debate that the J1 was all historic though, bearing in mind the Capsian J1 input into the area, but it is pretty far North. It’s a pretty small sample size (35) for the Y chr info.

Single, Rapid Coastal Settlement of Asia Revealed by Analysis of Complete Mitochondrial Genomes

Single, Rapid Coastal Settlement of Asia Revealed by Analysis of Complete Mitochondrial Genomes

A recent dispersal of modern humans out of Africa is now widely accepted, but the routes taken across Eurasia are still disputed. We show that mitochondrial DNA variation in isolated “relict” populations in southeast Asia supports the view that there was only a single dispersal from Africa, most likely via a southern coastal route, through India and onward into southeast Asia and Australasia. There was an early offshoot, leading ultimately to the settlement of the Near East and Europe, but the main dispersal from India to Australia 65,000 years ago was rapid, most likely taking only a few thousand years.

An older paper, but I like to keep everything I find for reference As a minor point, the calculted age for M here is 64k, but last time I saw it in print it was more like 74k ago. The last age for L3 I saw was more in the 100k area.

My main objections to a recent out of Africa date.

Also known as the ‘I’m not typing this out in the comments anymore‘ entry. I keep seeing the 40k for the out of Africa date in print, and it’s starting to get on my nerves just a bit. Some of sites these don’t have bones, but modern human associated industries. This is not including any sites in or South of the Sahara.

I’ll start with the oldest first.

Skhul, Israel.

Dates ranging from 130,000 -100,000 BP on assorted remains.  The crania shown is Skhul V, roughly dated to 105,000 BP. Many archaic traits, but anatomically modern humans. The in theory is that the 130,000  year old colonisation of Asia failed due to climate conditions, although it didn’t seem to bother the Neanderthals in the area. There’s a gap in the record from 92,000 BP to about 45,000 BP, which only has Neanderthal remains (so far).

Qafzeh, Israel

Modern human remains about 92,000 BP. The best known is of a 12 year old boy.

Jebel Irhoud, Morocco.

Estimated dates range from 160,000 to 90,000 BP. More modern humans with archaic traits-so archaic they were mistaken for Neanderthals for years.

Frontal view of cast of adult male Homo sapiens from Jebel Irhoud in Morocco. Link.

 

Taforalt, Morocco.

Aterian shell beads  found dated from 110,000 BP to 82,000 BP. The Aterian was continuous in North Africa until the Dabban and IberoMaurassian industries 40,000 and 20,000 BP.

Henan province, China.

Modern human teeth dated to around 94,000 BP, and the Xuchang/ Liujiang skull dated to at least 68,000 BP and possibly as old as 159,000 BP.

Pdf.

 

 Nauwalabila I, Australia.

 Oldest thermoluminescence date of 60,300+6,700 years on stone tools .

Malakunanja II, Australia.

Thermoluminescence dates of prior to 50,000 BP. There’s also a claimed but very poorly provenenced date of 116k in a site in Kimberly.

Topper site, S. Carolina, USA.

Site dated  ~50,000 BP with C14.

Pedra Furada, Brazil.

Oldest date for site occupation 60,000 BP ,according to the archaeologist.

Kota Tampan, Malaysia.

Pebble tools associated with modern humans dating back to 75,000 BP. The pebble tools were found in a later burial with a modern human (Perak man).

Niah Cave, Borneo.

Skull dated to 40,000 to 42,000 BP.

Üçağızlı Cave, Turkey

EUP site about 43,000 BP.

Ksar ‘Akil, Lebanon.

EUP site dated to 45,000 BP

 And Dr Stephen Oppenheimer has worked out it woukd take about 20,000 years for modern humans to work their way into Australia from Africa. so add that on to any Australian and American sites for a minimum OOA date.

There are probably a few I’ve missed. Some of the Indian sites under the Toba ash are claimed as modern human sites, but there’s a lack of bones so I won’t include those, although I suspect they are right. Some are on this pdf, with more detail from this paper, Modern Human Origins and the Evolution of Behavior in the Later Pleistocene Record of South Asia. From this a few snippets..

A number of mtDNA lineages (specifically U2i, M2,and R5) share coalescence dates of 50,000–70,000 yearsago (Kivisild et al. 2000, Metspalu et al. 2004) and may represent an India-specific subcladerelated to the initial dispersal of modern humans into the peninsula.

A Middle Paleolithic scraper-based industry from Patpara in the Middle Son Valley is dated to~103,000 years ago (Blumenschine, Brandt, and Clark 1983, Williams and Clarke1995), while dates of 75,000 and160,000 years ago areassociated with artifacts recovered from Samnapur (Nar-mada Valley) and Balotra (Luni River valley) (Mishra etal. 1999, Misra et al. 1990). The dating of miolites in the Hiran Valley places assemblages classed as Middle Paleolithic at 69,000–56,000 years ago (Baskaran et al.1986). The earliest assemblage classified as Upper Paleolithic is currently Site 55, Pakistan, where the loess overlying the occupational horizon has been dated to ca 45,000 years before present(Dennell et al. 1992).

One of my main objections to a more recent OOA date is that it doesn’t make sense with the dates of the backmigration mt DNA into Africa and the mt DNA in early Europeans. In a nutshell, there was a back migration of mt U and M1 from Asia, which appears to have been accompanied by Y chromosome R1, somewhere from 40,000 to 35,000 BP- supported by stone tool cultures and later dates of mt DNA in the same area matching the cultural epxansions. The problem with a more recent OOA date is that you have to skip impossibly quickly from L3 to U if the exit date is around the 40,000 mark. The same is true for the migrations into Europe where much later haplotypes are found relatively quickly in time and it just wouldn’t allow enough time to get from L3 to pre HV. There’s also not enough time for Y chromosome R1 to appear with the more recent OOA dates. The estimated dates on the mt DNA make a lot more sense when compared to an OOA date of 100k, and the Y chromosome date estimates are starting to get old enough to be an acceptable match. Which is why I’m taking the side that supports humans being on the other side of Asia when the Toba eruption occurred.

I’m in good company at least. Cavalli Sforza’s estimated date for the separation of African and non African populations was 146,000 BP.

The first estimate gave a separation time of the first migrants out of Africa of 146,000 years ago

I’ve seen at one other paper where the date was 120,ooo. My guess would be that modern humans were inhabiting North Africa and particularly the Nile delta (which as far as I know never dried out) for a while before a move into Asia was made. The structure of this Aterian population was wiped out by the later backmigrations from West Asia, and no North African mt DNA dates back prior to this era.

And now I have an evil headache. I’ll have a better look at the Petraglia pdf later…

Skhul/Qafzeh early modern human hand function

Behavioral inferences from the SkhulyQafzeh early modern human hand remains.

Two groups of humans are found in the Near East ~100,000 years ago, the late archaic Neanderthals and the early modern Skhul/ Qafzeh humans. Observations that Neanderthals were more heavily muscled, had stronger upper-limb bones, and possessed unusual shapes and orientations of some upper-limb joint complexes relative to the Skhul/Qafzeh hominids, have led some researchers to conclude that significant between-group upper limb- related behavioral differences must have been present, despite the  association of the two groups with similar Middle Paleolithic archeological complexes. A three-dimensional morphometric analysis of the hand remains of the Skhul/Qafzeh hominids, Neanderthals, early and late Upper Paleolithic humans, and Holocene humans supports the dichotomy. The Skhul/Qafzeh carpometacarpal remains do not have any unique morphologies relative to the other fossil samples remains examined. However, in the functionally significant metacarpal 1 and 3 bases they resemble Upper Paleolithic humans, not Neanderthals. Furthermore, the
Skhul/Qafzeh sample differs significantly from the  Neanderthals in many other aspects of hand functional anatomy. Given the correlations between changes in tool technologies and functional adaptations seen in the hands of Upper Paleolithic humans, it is concluded that the  Skhul/Qafzeh hand remains were adapted to Upper Paleolithic-like manipulative repertoires. These results support the inference of significant behavioral differences between Neanderthals and the Skhul/Qafzeh hominids and indicate that a significant shift in human manipulative behaviors was associated with the earliest stages of the emergence of modern humans.

A little prep work for my list of before 40k sites where modern Humans are found out of Africa.

The fossil remains from the ‘80,000- to 100,000-year-old site of Skhul (5) and the  100,000-year-old site of Qafzeh (1, 2), both in Israel, are craniofacially more modern and less muscular than Neanderthals.

These features, plus the results just presented, demonstrate that the Skhul/Qafzeh and Neanderthal samples are distinct from each other in the most functionally significant regions of the hand and that the Skhul/Qafzeh hand remains are morphologically and functionally within the range of the combined EUP/LUP samples.

Although there is some arguing about who these people were, the general agreement is that they were modern humans, dated to about 100k ago in Israel. There are shell beads  dated to 100,000 -130,000 years from this site.

Reconstruction of an early European skull

By Dr Richard Neave. I believe (though I can’t find anything saying this specifically) this is the Peştera cu Oase 2   crania from Romania (edit: John Hawkes also says it this one), which is 40,000 years old and was found by potholers. I can’t find any other crania of this age or date from Romania, so by a process of elimination this would be it. They don’t know if the skull is male or female.

Peştera cu Oase 2 crania.

First of all let me comment my objection to this recon is entirely to do with the really dark skin colour of the head. My main point is that even Southern Africans have a skin colour a lot lighter than this. Modern humans were also resident across North Africa from about 130k ago, and into the near East from about 100k ago- 60k prior to the entry into Europe, so the reason behind the UV-resistant equatorial skin tone escapes me as that area (equator) was left behind about 90k prior to entering Europe. The Khoisan people in the area believed to be where humans evolved are much lighter. I’m also a little unsure as to why he made the nose quite so flared, as the shape seems half way betwen European and African. But then, I have seen some Irish guys with nostrils like that.

Also needing to be taken into consideration is that the European hair colour mutations for fair/brown and red hair date back to over 80k, and that the red hair genes at least  will have had a lightening affect on skin tone. Lighter eye colours also lighten skin colour, and although blue is recent and fairly limited in distribution, other eye colours are much older and wider distributed, even as far as the Ainu and the Hmong.

On the other hand; it has the brow ridges, heavy jaw and wider nose you typical of more archaic samples, as seen in this 26,000 year old ivory head from Europe. The average prognathism in the Paleolithic samples is greater than in modern populations, and probably has a lot to do with the much larger teeth humans had prior to the Neolithic farming revolution.

Judging from the scant art objects the Europeans had straight hair. So.. give him hazel brown eyes and dark brown hair and a lighter Khoisan-ish skin tone and you’d probably be close to an accurate reconstruction of the face.