Category Archives: Paleolithic

Ancient Native Americans related to modern ones

Sequencing of ancient Native American remains from British Columbia (Canada), dated to c. 5-6000 years ago, shows that many modern local natives are their apparent descendants or otherwise related.
Yinqiu Cui et al. Ancient DNA Analysis of Mid-Holocene Individuals from the Northwest Coast of North America Reveals Different Evolutionary Paths for Mitogenomes. PLoS ONE 2013. Open accessLINK [doi:10.1371/journal.pone.0066948]

To gain a better understanding of North American population history, complete mitochondrial genomes (mitogenomes) were generated from four ancient and three living individuals of the northern Northwest Coast of North America, specifically the north coast of British Columbia, Canada, current home to the indigenous Tsimshian, Haida, and Nisga’a. The mitogenomes of all individuals were previously unknown and assigned to new sub-haplogroup designations D4h3a7, A2ag and A2ah. The analysis of mitogenomes allows for more detailed analyses of presumed ancestor–descendant relationships than sequencing only the HVSI region of the mitochondrial genome, a more traditional approach in local population studies. The results of this study provide contrasting examples of the evolution of Native American mitogenomes. Those belonging to sub-haplogroups A2ag and A2ah exhibit temporal continuity in this region for 5000 years up until the present day. Of possible associative significance is that archaeologically identified house structures in this region maintain similar characteristics for this same period of time, demonstrating cultural continuity in residence patterns. The individual dated to 6000 years before present (BP) exhibited a mitogenome belonging to sub-haplogroup D4h3a. This sub-haplogroup was earlier identified in the same general area at 10300 years BP on Prince of Wales Island, Alaska, and may have gone extinct, as it has not been observed in any living individuals of the Northwest Coast. The presented case studies demonstrate the different evolutionary paths of mitogenomes over time on the Northwest Coast.

Figure 2. Phylogeny of complete mitochondrial genomes sequenced in this study.
are transitions unless specified. Transversions are indicated by an A,
G, C, or T after the nucleotide position. Insertions are indicated by an
“i”, deletions are indicated by a “d”, recurrent mutations are
underlined, and mutations back to the rCRS nucleotide are designated by a
“@”. The C stretch length polymorphism in region 303–315 was
disregarded in the tree. The sample “Haida 9″ was analyzed in Schurr et
al. (2012). All other samples were analyzed in this study.
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Posted by on July 7, 2013 in aDNA, America, mtDNA, Native Americans, Paleolithic


Reconstructing human demographic history from IBS segments

Figure 1. An eight base-pair tract of identity by state (IBS).
Identity-by-state (IBS) segments are those located between any two SNPs (polymorphisms, letters that vary among individuals). According to this new paper, they seem to be evolutionarily neutral and therefore their length, modified by recombination events each new generation, is a good trail to reconstruct human demographic history.
Kelley Harris & Rasmus Nielsen, Inferring Demographic History from a Spectrum of Shared Haplotype Lengths. PLoS Genetics 2013. Open accessLINK [doi:10.1371/journal.pgen.1003521]


There has been much recent excitement about the use of genetics to elucidate ancestral history and demography. Whole genome data from humans and other species are revealing complex stories of divergence and admixture that were left undiscovered by previous smaller data sets. A central challenge is to estimate the timing of past admixture and divergence events, for example the time at which Neanderthals exchanged genetic material with humans and the time at which modern humans left Africa. Here, we present a method for using sequence data to jointly estimate the timing and magnitude of past admixture events, along with population divergence times and changes in effective population size. We infer demography from a collection of pairwise sequence alignments by summarizing their length distribution of tracts of identity by state (IBS) and maximizing an analytic composite likelihood derived from a Markovian coalescent approximation. Recent gene flow between populations leaves behind long tracts of identity by descent (IBD), and these tracts give our method power by influencing the distribution of shared IBS tracts. In simulated data, we accurately infer the timing and strength of admixture events, population size changes, and divergence times over a variety of ancient and recent time scales. Using the same technique, we analyze deeply sequenced trio parents from the 1000 Genomes project. The data show evidence of extensive gene flow between Africa and Europe after the time of divergence as well as substructure and gene flow among ancestral hominids. In particular, we infer that recent African-European gene flow and ancient ghost admixture into Europe are both necessary to explain the spectrum of IBS sharing in the trios, rejecting simpler models that contain less population structure.

The most interesting graph, synthesizing the result for standard HapMap European and African proxy samples is figure 7. However I have major issues with the age estimates, which seem to be half what is needed to be realistic according to archaeological and other genetic data (unlineal haplogroup history, for example). Therefore I have annotated it with a revised timeline, so it fits better with the objective data:

Figure 7. A history inferred from IBS sharing in Europeans and Yorubans.
This is the simplest history we found to satisfactorily explain IBS tract sharing in the 1000 Genomes trio data. It includes ancient ancestral population size changes, an out-of-African bottleneck in Europeans, ghost admixture into Europe from an ancestral hominid, and a long period of gene flow between the diverging populations.
(Right margin annotations by Maju).

Indeed the simplest revision of the time-scale was to double it. I guess it can be refined a bit more than that, maybe pushing it a bit further into the past, but the alternative time-scale I propose fits closely enough with known archaeological data like the time of the OoA to Arabia and Palestine or the spread of Acheulean (and therefore H. ergaster, common ancestor of Neanderthals and H. sapiens) out of Africa c. 1 Ma ago to illustrate that the reconstruction seems pretty much correct overall but fails when estimating the dates (because of scholastic-autistic academic biases that are too common in the field of human population genetics).

Update: even Dienekes agrees, on his own well documented reasoning, with a x2 mutation rate being necessary for the above graph.


Submerged rock art from Papua

In the World-famous diving paradise of Raja Ampat, just West of the Bird’s Head peninsula of Papua (aka New Guinea), there is more than one of the greatest biodiversity areas of the planet. It has been found recently that off the shore of Misool, one of the major islands of the archipelago, there is also abundance of beautifully conserved Paleolithic murals.

The now submerged rock art is found in 13 different sites (so far), most of them sharing an intriguing pattern of location:
  • a large and rather high cliff;
  • a cavity, cave, overhang or hole around the foot of the cliff;
  • a main coloured (red-yellow to red-brown) wide strip pouring out, or reaching down to the cavity;
  • a (facultative) step-bank (coral or karst platform) at the foot. 
The art was obviously above the water level until the sea flooded all that area at the end of the Ice Age. 
Sources: World Archaeological Congress, Stone Pages’ Archaeonews.

Update (Feb 24): after being down for days, causing perplexity among some readers and myself, the WAC source site is up again. Exactly as it was four days ago. Just in case this time I’ll upload the images here. 

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Posted by on February 18, 2013 in Oceania, Paleolithic, Papua, rock art


Echoes from the Past (Dec 26)

Before the year is over, here there is a bunch of stuff I wanted to mention:
Lower and Middle Paleolithic

Humans may have originated near rivers – Technology & science – Science – LiveScience – – neither savanna nor jungle, beach (river banks) was the favored ecosystem even for old good Ardi, it seems.
Pileta de Prehistoria: 180 prehistoric sites located around Atapuerca[es] – not just Neanderthal ones: a bit of everything (located just outside Burgos city, Atapuerca is a key pass between the Upper Ebro basin and the Northern Iberian Plateau, which must have played an ecological and socio-political role always, and hence attracted people towards it).
Upper Paleolithic and Epipaleolithic 

The boulders at lake Huron were to trap the reindeer (caribou)
Remains found of the culture which inhabited Northern Chile 11,000 years ago – Terrae Antiqvae[es] – they exploited a quartz deposit for their tools in the middle of Atacama desert, which then was probably quite milder.
Simultaneous ice melt in Antarctic and Arctic at the end of the last Ice Age.
Neolithic and Chalcolithic
El Neolítico en Europa: una simulación del proceso | Neolítico de la Península Ibérica – Iberian Neolithic – exposition and criticism in Spanish language of yet another paper simulating the Neolithic ‘colonization’ (Lemmen 2011).

Metal Ages and Historical periods

Iruina blog: doubts about the ability of the Basque Autonomous Police to  analyze the Iruña-Veleia pieces[es] – the Spanish Guardia Civil police force already declared themselves unable to do the tests. The defense asks to send the remains to one of the few international laboratories able to do the tests and has even offered to pay the cost of it. Also at Diario de Noticias de Alava[es].
An intimate look at ancient Rome – – a journey through the hygienic practices of Ancient Rome.
Scientists unlock the mystery surrounding a tale of shaggy dogs – Native Americans used dog hair for textiles (among other components).
The Archaeology News Network: Real Mayan apocalypse may have been their own fault -overexploitation of the jungle biome caused desertification.

Some of these open access papers surely deserved a deeper look at… I did not have time or energies for that however.

BBC News – Liking a lie-in in people’s genes, researchers say – long sleeping is a genetic need: tell your boss next time you are late. I am among those who need to sleep 9-10 hours per day (normally) though I have also met people who only sleep 4-5 hours.
The Spittoon » Find Your Inner Neanderthal (I retract what I said before: the results are coherent, even if Africans still get too much too often I guess that’s part of the margin of error. However there is another “free online” genetic test that is misleading).

Biology and psychology
Of mice and men, a common cortical connection – a nice comparison to better understand brain regions. To the right: F/M: frontal/motor cortex, S1: primary somatosensory cortex, A1: primary audtive cortex and V1: primary visual cortex. Mice have a much more developed somatosensory cortex (surely related to whiskers, smell, etc.) but a much less developed frontal/motor cortex (related to willpower and rationality).
Brain Scans Reveal Difference Between Neanderthals and Us | LiveScience – something about the sense of smell, not too clear.

Primates are more resilient than other animals to environmental ups and downs – diversification and flexibility is the key to long-term success.

Prehistoric Aquitaine: exposition at Baiona (Bayonne)

The Basque Museum of Baiona (Bayonne in French) will welcome for two months the exposition Aquitaine préhistorique – Historiaurreko Akitania (Prehistoric Aquitaine), gathering some of the most fascinating stuff and information from European prehistory. 
Among the elements in this educative show are the famous Lady of Brassempouy (left) and more than 2,000 other  archaeological objects from the heartland of European Paleolithic.
For example this beautiful engraving of an auroch from Erango cave (Lower Navarre):

The exhibition will be at Baiona between March 22nd and May 22nd and has already been at Bordeaux’ Museum of Aquitaine.

More Austronesian genetics: Dayaks are mostly pre-Austronesian (as most other Austronesians)

I just had to mention a paper on Austronesian genetics at one of the great open access publications, Bio Med Central (BMC), and now I have to mention another at the other major open access magazine: Public Library of Science (PLoS):
Because good things always come in batches, right?
Well whatever the case, the Sea Dayaks or Iban people do not cluster well with Taiwan Aborigines or other possible source populations for the fabled Austronesian colonization of Island SE Asia. Nope, they cluster best with mainland SE Asia, notably Vietnamese, Thais and peninsular Malays.
For example, for autosomal DNA, we get the following graph (fig 2):
Where the Iban cluster best with some Indonesian (but not others) and Thais (again some but not others) but not with Taiwan Aborigines (and only poorly with Filipinos).
Not convinced? I cannot blame you because PC analysis suck and specially for autosomal genetics. They also provide a K=3 admixture analysis (fig. S1):
Here we can spot three components, neither of which is too specific. Still the red component seems strongest among Malaysian (not the Iban however), the blue component is most common among some Indonesians, while the green component is widespread by dominant in the mainland if anything (specially Japan/North China). Not too clear anyhow but for deeper clustering you probably want something else, like the HUGO paper.
Let’s see the Y-DNA then (fig. 3):
This is more clear, right: here the Iban are almost like Vietnamese and then like other Sundaland Malays but not like Taiwan Aborigines nor Filipinos. So Y-DNA-wise they do not look particularly Austronesian recent arrivals but older arrivals from Indochina if anything.
MtDNA? Let’s see:
Seems not again: Philippines and Taiwan are far away, while Sundaland, Orang Asli, Thais and Chinese are closer.
The authors conclude:

The majority of mtDNA haplogroups and the greatest proportion of NRY lineages identified in our Iban sample are associated with population movements that occurred prior to this expansion. More NRY haplogroups than mtDNA haplogroups were introduced into this population during the Neolithic expansion, but the proportion of NRY haplogroups attributed to this more recent event is still less than half of the total NRY haplogroups identified. Therefore, it appears that migrations during the Neolithic did not eradicate pre-Neolithic groups.

Another blow against Neolithic replacement nonsense.


Posted by on February 1, 2011 in autosomal DNA, Malaysia, mtDNA, Neolithic, Paleolithic, SE Asia, Y-DNA


Modeling cultural diversity, local extinctions, etc.

Before I forget, just a quick mention of another potentially interesting paper published at PLoS ONE this week:

L.S. Premo and S.L. Kuhn, Modeling Effects of Local Extinctions on Culture Change and Diversity in the Paleolithic. PLoS ONE 2010. Open access.

The persistence of early stone tool technologies has puzzled archaeologists for decades. Cognitively based explanations, which presume either lack of ability to innovate or extreme conformism, do not account for the totality of the empirical patterns. Following recent research, this study explores the effects of demographic factors on rates of culture change and diversification. We investigate whether the appearance of stability in early Paleolithic technologies could result from frequent extinctions of local subpopulations within a persistent metapopulation. A spatially explicit agent-based model was constructed to test the influence of local extinction rate on three general cultural patterns that archaeologists might observe in the material record: total diversity, differentiation among spatially defined groups, and the rate of cumulative change. The model shows that diversity, differentiation, and the rate of cumulative cultural change would be strongly affected by local extinction rates, in some cases mimicking the results of conformist cultural transmission. The results have implications for understanding spatial and temporal patterning in ancient material culture.

This mention is not adhesion. I find the modeling potentially interesting in its essentials but I surely have many discrepancies on issues such as assuming tiny “populations” of some 25 individuals in black and white (life or death) states. Such size is ok with operative hunter-gatherer bands but these are not “sovereign” units but just dynamic and fluctuating economic ones, integrated in larger groups. Probably a better size would be something like 100 or 200 people but again integrated into larger units of several hundreds to several thousands (tribes or nations).

Also we have to consider that people change “clans”, for example when marrying. So cultural, as well genetic flow is persistent at least within the borders of the ethnicity, which are anyhow generally open. So I guess that the modeling needs a lot of refinement but still it is a curious speculation – or exploration if you wish.

Something I do agree is in the authors founding their research on previous works that strongly suggest that population size and specially connectivity is critical in driving and maintaining the rhythm of innovation.