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Friday, March 22, 2013

A revised timescale for human evolution + new revelations about Paleolithic European mtDNA

Doubts have been raised about one of Europe's most talked about ancient DNA results, the mtDNA haplogroup H sequence from the Paglicci Cave remains. A preprint at Current Biology suggests the Paleolithic sample was contaminated with modern DNA:

To further evaluate the authenticity of the ancient DNA we calculated the proportion of nucleotide misincorporations arising from DNA damage, a quantity that is known to increase over time after the death of an individual [12] and has been used as an indication of authenticity in previous work [10]. It was suggested that bone samples 100 years and older have a minimum of 20% C to T misincorporations concentrated at the 50 end of the molecule [13]. Using this criterion, we excluded Paglicci Str. 4b from further analysis as the rate of C to T misincorporation at the 50 end was only 8.8%, thus making an ancient origin for the DNA in this sample uncertain [14].

Another sample thought to be from a Paleolithic European, dubbed "Cro-Magnon 1" and belonging to haplogroup T2b1, was also eliminated from the study after radiocarbon dating revealed it to be of medieval origin. What this means is that all Paleolithic European remains successfully tested to date belong to mtDNA haplogroup U, including six new samples featured in this paper.

It has been argued that hg U5 is the most ancient subhaplogroup of the U lineage, originating among the first early modern humans in Europe [18]. Our results support this hypothesis because we find that the two Dolni Vestonice individuals radiocarbon dated to 31.5 kya carry a type of mtDNA that is as yet uncharacterized, sits close to the root of hg U, and carries two mutations that are specific to hg U5. With our recalibrated molecular clock, we date the age of the U5 branch to approximately 30 kya, thus predating the LGM. Because the majority of late Paleolithic and Mesolithic mtDNAs analyzed to date fall on one of the branches of U5 (see also [15]), our data provide some support for maternal genetic continuity between the pre- and post-ice age European hunter-gatherers from the time of first settlement to the onset of the Neolithic.

Oh yeah, the paper also shows a revised timescale for human evolution based on most of the ancient mtDNA sequences listed above. However, I'd say this timescale will probably be revised a few more times as more aDNA samples become available.

Fu et al., A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes, Current Biology (2013),


Maju said...

Regardless of Paglicci. Does that timescale make any sense to you? It would indicate that H. sapiens and H. neanderthalensis diverged ONLY 400 Ka ago, what makes no sense to me on light of the archaeological evidence available.

Not being privy to the details (PPV paper, are they using ONLY HVS-I again?) I can't but be quite skeptic.

In any case it must be reminded that haplogroup H has been sequenced with almost 100% certainty (coding region) in two Paleolithic individuals from Cantabria (Northern Spain), one Epipaleolithic individual from Gipuzkoa (Basque Country) and another Epipaleolithic one from Karelia, adding plausibility for previously studied (HVS-only) pre-Neolithic sequences from Portugal (Epipaleolithic), Northern Morocco (Oranian-Late UP) and Sughir (Russia, Gravettian).

Kristiina said...

This research forced me to re-evaluate my ideas about the human migration out of Africa. It is true that people often believe in what they want to believe and I am not an exception. I have eagerly supported the earlier exit of Homo Sapiens Sapiens out of Africa for several reasons:
1. There are important archaelogical sites in Qafseh, Arabian peninsula, dated 90-130 kya
2. Climate was hospitable in Arabia 90-130 kya, and the best places were there where we have the archaelogical sites above. It is strange that people would have migrated and expanded just when the climate got worse everywhere.
3. The structure of mtdna and ydna is complicated and there are strange divisions
4. Eurasian people have Neanderthal and even Denisovan admixture
5. The modern Homo Sapiens is found in China 100,000 y.o., Zhirendong jaw
According to this new method, the age of M+N seems to be 62 – 95 kya and L3 is little older. The upper HPD limit is c. 115 kya. Isn’it possible that Qafseh and Arabian settlers were of haplogrup L3. M arose only later on, possibly in India 70 kya and N perhaps in Qafseh or nearby somewhat earlier. According to the research ”separation of non-Africans from the most closely related sub-Saharan African mitochondrial DNAs (haplogroup L3) … occurred less than 62–95 kya.” Now I am wondering if the worsening of climate in Arabia forced people to move away from there c. 70 kya and in fact the lowering of sea level would have made it easier to hop from Arabia into Africa and it was these L3 carriers who back-migrated to Africa. L3 has several subclades and there is for example the ancestor of L3b’f which could have arisen in Arabia and migrated to Africa.