Category Archives: evolution

So, non-Africans are definitely part Neanderthal

Finally the DNA evidence is in from Paabo ect. I thought I detected signs of a back track last year when he said they had probably had sex.

Neanderthal Genome Yields Insights Into Human Evolution and Evidence of Interbreeding With Modern Humans

 “We can now say that, in all probability, there was gene flow from Neanderthals to modern humans,” said the paper’s first author, Richard E. (Ed) Green of the University of California, Santa Cruz.

I’m trying to locate the full text for the Science article later. But my PC time is a bit limited today. However, I am officially entering smug mode now. Told you so.

I image there are a few anthropologists hopping up and down like excited orangutans right now at the news. To quote John Hawks:

Out-of-Africa movement was a major mechanism of recent human evolution. The genetic ancestry of living people is multiregional.


It does define all non-Africans today as an interspecific hybrid population.

From the article..

“The scenario is not what most people had envisioned,” Green said. “We found the genetic signal of Neanderthals in all the non-African genomes, meaning that the admixture occurred early on, probably in the Middle East, and is shared with all descendants of the early humans who migrated out of Africa.”

Which would suggest that the Levant, where modern humans and Neanderthals co-existed for some time about 120k ago was a mixing place for the two. According to the article, between 1% nd 4% of the genomes of non-Africans in Neanderthal in origin, which pretty much tallies with some of the older studies done (they are on the blog if you want to hunt them down).

The estimate of the time of admixture is around 50,000-80,000 years, however I’m not really sure why that should be correct, seeing as they first encountered each other prior to the ‘beach buggy’ colonisation of S/SE Asia, which would kind of place 80k as a bare minimum age, and more like 100k as there is some evidence of modern humans in SE Asia 74k ago under the Toba ash (necessitating a dispersal date for SE Asian populations of about 95k min). I also wonder what implications this has for the route out of Africa, as an exit via the Gate of Tears would make it less likely they’d come into contact with the Med coast Neanderthals of the era. I wonder if the number is more a composite of the very early mix in the Levant, followed by a later addition of Neanderthal DNA in Europe.

Having a happy day 🙂


IQ Population Genetics: It’s not as Simple as You Think

IQ Population Genetics: It’s not as Simple as You Think

A paper I came across while blog surfing. While the IQ stuff is interesting, what really caught my attention was the section on the out of Africa date.

Both genetic evidence (Ingman et al., 2000; Underhill et al., 2001; Zhivotovsky et al., 2003) and the fossil record (White et al., 2003) point to Africa as the likely homeland of our species. According to the most widely accepted scenario, one or more subgroups of early modern humans left Africa between 120,000 and 100,000 years ago to become the ancestors of the non- African populations

Which makes a pleasant change after reading an idiot paper earlier today that was hitting the 40k date. Again.

 And something I didn’t know..

Genes, like drugs, have many side effects. This is called pleiotropy. For example, the average IQ of nearsighted people is 6 to 8 points higher than the average for normal-sighted people.

Although I am familiar with a medical condition called torsion dystonia that raises the IQ of the sufferer by an average of 10 points. An interesting read.

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.

Neanderthal genome decoded


Their lives may have been nasty, brutish and short but their DNA has survived long enough to be almost fully decoded in a pioneering study that has revealed just how closely related the Neanderthals were to modern humans.

For the first time scientists have deciphered the genetic sequence of the Neanderthal genome. It is the first genetic blueprint of an extinct human species and a tour de force in terms of the scientific techniques used to recover tiny strands of ancient DNA from fragments of fossilised bones tens of thousand of years old.

Although scientists are far from answering the many questions about the last of our relatives known to live alongside modern humans, they believe that the research is close to finding out what it is, genetically, that made us human.

Prof Svante Paabo of the Max Planck Institute for Evolutionary Anthropology in Leipzig was to reveal at the American Association for the Advancement of Science in Chicago this weekend that he and his colleagues had deciphered 60 percent of the Neanderthal genome and used it to calculate that the last common, ape-like ancestor of modern man and the Neanderthals lived about 830 000 years ago.

The project took more than two-and-a-half years of research on dozens of Neanderthal bones from 40 000-70 000 years old and excavated from four archaeological sites in Europe, stretching from southern Russia and Croatia to Germany and Spain.

They extracted enough DNA from an analysis of 70 fossilised bones to build up a library of Neanderthal DNA covering 3.7 billion “base pairs” – the individual letters of the genetic code – and in the process discovered that the extinct humans were very closely related to modern people.

The Neanderthals are so closely related to us that they fall into our genetic variation, Paabo said. In other words, it would be difficult to distinguish Neanderthal DNA from the DNA of a modern European, Asian or African.

The last Neanderthals died out about 30,000 years after sharing the same European landscape with modern humans for many thousands of years.

It has been an enduring mystery as to why they disappeared and whether they ever interbred with their close human cousins – although the latest evidence from the DNA suggests they did not.

“What we have looked at, from the point of view of variation today, is the contribution from Neanderthals to the human gene pool. That was very little, if anything. Our data shows that, if there was a contribution, it was very small,” Paabo said.

“But the cool thing is that interbreeding was a two-way street. For the first time we can look at whether there was a contribution from human ancestors to Neanderthals because, for the first time, we have a Neanderthal genome,” he said.

Another question is whether Neanderthals could speak.

Although they are known to have a hyoid bone in the throat, which is anatomically important for articulating words, the only other evidence comes from an analysis of a gene called FOXP2, which is known to be critical to speech development in modern humans.

Paabo said that the Neanderthal FOXP2 gene shares two changes to its DNA sequence that is also seen in modern humans but not in chimpanzees. These two changes support the view that Neanderthals may have been able to communicate verbally.

Other insights gained from a preliminary analysis of the Neanderthal genome are that the species could not drink milk as adults – they have the same lactose intolerance seen in the majority of modern humans – and they also have a mutation in the gene involved in brain development seen in modern-day Africans.

Just a thought… if, as it says “The Neanderthals are so closely related to us that they fall into our genetic variation,” how did they come to the conclusion they didn’t contribute to the modern gene pool? Confused.

I have to point out here that the average North American is only about 4% native American, so any contribution from a nearly wiped out group can be just a trace; the same goes for the very ancient North Africans and Australoid South Americans, of whom no genetic trace has been found (modern humans).

The lactase-persistence-associated allele in early Neolithic Europeans

The lactase-persistence-associated allele in early Neolithic Europeans

Lactase persistence (LP), the dominant Mendelian trait conferring the ability to digest the milk sugar lactose in adults, has risen to high frequency in central and northern Europeans in the last 20,000 years. This trait is likely to have conferred a selective advantage in individuals who consume appreciable amounts of unfermented milk. Some have argued for the “culture-historical hypothesis,” whereby LP alleles were rare until the advent of dairying early in the Neolithic but then rose rapidly in frequency under natural selection. Others favor the “reverse cause hypothesis,” whereby dairying was adopted in populations with preadaptive high LP allele frequencies. Analysis based on the conservation of lactase gene haplotypes indicates a recent origin and high selection coefficients for LP, although it has not been possible to say whether early Neolithic European populations were lactase persistent at appreciable frequencies. We developed a stepwise strategy for obtaining reliable nuclear ancient DNA from ancient skeletons, based on (i) the selection of skeletons from archaeological sites that showed excellent biomolecular preservation, (ii) obtaining highly reproducible human mitochondrial DNA sequences, and (iii) reliable short tandem repeat (STR) genotypes from the same specimens. By applying this experimental strategy, we have obtained high-confidence LP-associated genotypes from eight Neolithic and one Mesolithic human remains, using a range of strict criteria for ancient DNA work. We did not observe the allele most commonly associated with LP in Europeans, thus providing evidence for the culture-historical hypothesis, and indicating that LP was rare in early European farmers.

Just an archived item- I’ve posted a news  item on this before but it’s nice to have the paper. The lactose tolerance seems to only about 8,000 years old, and has occured independantly in several different pastoralist groups around the world. I guess retention of a juvenille trait is an easy mutation for the genome to make. Last time I looked it was worked out on a computer simulation to have spread with the  Linearbandkeramik culture

Probable human hair found in a fossil hyaena coprolite from Gladysvale cave, South Africa

Probable human hair found in a fossil hyaena coprolite from Gladysvale cave, South Africa.

Journal of Archaeological Science

Until now, the oldest known human hair was from a 9,000 year old South American mummy. Here we report fossil hairs of probable human origin that exceed that age by about 200,000 years. The hairs have been discovered in a brown hyaena (Parahyaena brunnea) coprolite from Gladysvale cave in South Africa. The coprolite is part of a hyaena latrine preserved in calcified cave sediment dated between 195,000 and 257,000 years ago. This find supports the hypothesis that hyaenas accumulated some of the early hominin remains found in cave sites, and provides a new source of information on Pleistocene mammals in the Sterkfontein Valley

Hyaenas will eat anything. If I ever get full access to the article I’ll post it, but that’s all for now.

The Aterian of North Afrca, and the Solutrean of the Iberian peninsula:was there contact between them in the upper Paleothic

The Aterian of North Africa, and the Solutrean of the Iberian peninsula-was there contact between them in the upper Paleothic?

En Espanol desafortunadamente… Anyone who feels like translating the finer details let me know.
We present a state of the question on the North African Aterian, examining different hypotheses that posit some kind of relationship of this technocomplex with the Solutrean of the Iberian Peninsula, via the Strait of Gibraltar. Despite the fact that palaeoenvironmental conditions of the Strait area during the last glaciation would have allowed the movement of humans in several moments, the current archaeological record, besides some techno-typological similarities, does not allow us to conclude any kind of Aterian contribution in the formation of the peninsular Solutrean industries. Furthermore, some reflections about the evolution of the lithic industries from the Initial Upper Palaeolithic are made, pointing out the necessity of undertaking a theoretical and methodological renovation, in order to gain a better understanding of the processes of technological evolution in the Upper Paleolithic, and their relationships with prior contexts.


mtDNA Variation in the South African Kung and Khwe—and Their Genetic Relationships to Other African Populations

mtDNA Variation in the South African Kung and Khwe—and Their Genetic Relationships to Other African Populations

The mtDNA variation of 74 Khoisan-speaking individuals (Kung and Khwe) from Schmidtsdrift, in the Northern Cape Province of South Africa, was examined by high-resolution RFLP analysis and control region (CR) sequencing. The resulting data were combined with published RFLP haplotype and CR sequence data from sub-Saharan African populations and then were subjected to phylogenetic analysis to deduce the evolutionary relationships among them. More than 77% of the Kung and Khwe mtDNA samples were found to belong to the major mtDNA lineage, macrohaplogroup L* (defined by a HpaI site at nucleotide position 3592), which is prevalent in sub-Saharan African populations. Additional sets of RFLPs subdivided macrohaplogroup L* into two extended haplogroups—L1 and L2—both of which appeared in the Kung and Khwe. Besides revealing the significant substructure of macrohaplogroup L* in African populations, these data showed that the Biaka Pygmies have one of the most ancient RFLP sublineages observed in African mtDNA and, thus, that they could represent one of the oldest human populations. In addition, the Kung exhibited a set of related haplotypes that were positioned closest to the root of the human mtDNA phylogeny, suggesting that they, too, represent one of the most ancient African populations. Comparison of Kung and Khwe CR sequences with those from other African populations confirmed the genetic association of the Kung with other Khoisan-speaking peoples, whereas the Khwe were more closely linked to non–Khoisan-speaking (Bantu) populations. Finally, the overall sequence divergence of 214 African RFLP haplotypes defined in both this and an earlier study was 0.364%, giving an estimated age, for all African mtDNAs, of 125,500–165,500 years before the present, a date that is concordant with all previous estimates derived from mtDNA and other genetic data, for the time of origin of modern humans in Africa.

I’m going through a lot of DNA studies atthe moment looking for evidence of M1 and M. Apparently one  HG, L3a, seems closely related to it, as L3a is the precursor to M.

The Asian mtDNA phylogeny is subdivided into two macrohaplogroups, one of which is M. M is delineated by a DdeI site at np 10394 and an AluI site of np 10397. The only African mtDNA found to have both of these sites is the Senegalese haplotype AF24. This haplotype branches off African subhaplogroup L3a (figs.2 and3), suggesting that haplogroup M mtDNAs might have been derived from this African mtDNA lineage; however, it is also possible that this particular haplotype is present in Africa because of back-migration from Asia.

I was entertained to see someone was using this to claim M1 was African in origin on another site.. leaving out the inconvenient back-migration from Asia at the end of the quote. Since M itself seems absent in Africa, and M1 traces the path of U in North and East Africa pretty closely, it’s now pretty much a done deal that M1 arrived in North Africa from West Asia. The real mystery is the lack of L3 and M in India, but the Toba eruption could easily have caused a wipe out across India that erased the first immigrants there. I’d like to observe that this L3a seems to have followed the North African population movements that curved southwards down into the West coast of Africa, so I think that its from the back migration may be possible, or at least dating to the expansion from upper Egypt about 24k ago with a origin from the Nile area. I shall have a dig into L3a distribution, something I should have done a while ago.

Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans

Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans

Recent advances in the understanding of the maternal and paternal heritage of southand southwest Asian populations have highlighted their role in the colonization of Eurasia byanatomically modern humans. Further understanding requires a deeper insight into the topology ofthe branches of the Indian mtDNA phylogenetic tree, which should be contextualized within thephylogeography of the neighboring regional mtDNA variation. Accordingly, we have analyzedmtDNA control and coding region variation in 796 Indian (including both tribal and castepopulations from different parts of India) and 436 Iranian mtDNAs.

 The results were integratedand analyzed together with published data from South, Southeast Asia and West Eurasia.Results: Four new Indian-specific haplogroup M sub-clades were defined. These, in combinationwith two previously described haplogroups, encompass approximately one third of the haplogroupM mtDNAs in India. Their phylogeography and spread among different linguistic phyla and socialstrata was investigated in detail. Furthermore, the analysis of the Iranian mtDNA pool revealedpatterns of limited reciprocal gene flow between Iran and the Indian sub-continent and allowed theidentification of different assemblies of shared mtDNA sub-clades.

Conclusions: Since the initial peopling of South and West Asia by anatomically modern humans,when this region may well have provided the initial settlers who colonized much of the rest ofEurasia, the gene flow in and out of India of the maternally transmitted mtDNA has been surprisingly limited. Specifically, our analysis of the mtDNA haplogroups, which are shared betweenIndian and Iranian populations and exhibit coalescence ages corresponding to around the earlyUpper Paleolithic, indicates that they are present in India largely as Indian-specific sub-lineages. Incontrast, other ancient Indian-specific variants of M and R are very rare outside the sub-continent

mt-dna-india m-maps u-map-india 

Click to enlarge all images.

The quest for finding the origin of haplogroup M and a plausible scenario for the peopling of Eurasia.

Based on the high frequency and diversity of haplogroupM in India and elsewhere in Asia, some authors have suggested (versus [3]) that M may have arisen in SouthwestAsia [16,17,31]. Finding M1 or a lineage ancestral to M1 in India, could help to explain the presence of M1 inAfrica as a result of a back migration from India. Yet, to date this has not been achieved [15], this study). Therefore, one cannot rule out the still most parsimonious scenario that haplogroup M arose in East Africa [3].Furthermore, the lack of L3 lineages other than M and N(indeed, L3M and L3N) in India is more consistent withthe African launch of haplogroup M. On the other hand,one also observes that: i) M1 is the only variant of haplo-group M found in Africa; ii) M1 has a fairly restricted phy-logeography in Africa, barely penetrating into sub-Saharan populations, being found predominantly inassociation with the Afro-Asiatic linguistic phylum – afinding that appears to be inconsistent with the distribu-tion of sub-clades of haplogroups L3 and L2 that havesimilar time depths. That, plus the presence of M1 without accompanying L lineages in the Caucasus [32] and [ourunpublished data], leaves the question about the origin of haplogroup M still open.

The paper gives the age of M2 at about 70k, with 21k either way.  Reading through it there seems to be more of a case for M appearing in the Arabian area, the same for the later M1 and U. Call me mad but I think the absence of M in general could be down to the Toba eruption, which must have had some serious impact in South Asia as it put down ash 2m thick all over India.