October 28, 2016

The destiny of a cave lion: to serve as decoration


Spanish researchers have concluded that a carpet or other comparable fur ornament (a tapestry?, a cape?) is why a late cave lion remains, the latest ones known in Iberia, were found in an otherwise human (Magdalenian) context in the cave of La Garma (Asturias, Spain): it was a fur, claws included, used as decoration of some sort.

Marian Cueto et al., Under the Skin of a Lion: Unique Evidence of Upper Paleolithic Exploitation and Use of Cave Lion (Panthera spelaea) from the Lower Gallery of La Garma (Spain). PLoS ONE, 2016. Open accessLINK [doi:10.1371/journal.pone.0163591]


Pleistocene skinning and exploitation of carnivore furs have been previously inferred from archaeological evidence. Nevertheless, the evidence of skinning and fur processing tends to be weak and the interpretations are not strongly sustained by the archaeological record. In the present paper, we analyze unique evidence of patterned anthropic modification and skeletal representation of fossil remains of cave lion (Panthera spelaea) from the Lower Gallery of La Garma (Cantabria, Spain). This site is one of the few that provides Pleistocene examples of lion exploitation by humans. Our archaeozoological study suggests that lion-specialized pelt exploitation and use might have been related to ritual activities during the Middle Magdalenian period (ca. 14800 cal BC). Moreover, the specimens also represent the southernmost European and the latest evidence of cave lion exploitation in Iberia. Therefore, the study seeks to provide alternative explanations for lion extinction in Eurasia and argues for a role of hunting as a factor to take into account.

Fig 4. Cave lion distal phalanxes from the Lower Gallery of La Garma.
Note that only eight of nine specimens are depicted in the figure.

Above: the claws that are the only remnants found of said lion, whose cut marks are fully coincident with skinning techniques used in more recent times with similar decorative purpose. They are believed to be all anterior claws and that one is missing therefore. That is why they imagine the fur to have been cut with an aesthetic interest, because the hind claws would not be visible if the fur was, for example, hang on the wall, so they were probably cut off.

Whether hunting of lions by humans was a decisive, contributing or negligible factor in cave lion extinction remains unclear.

October 27, 2016

Mitochondrial DNA from post-Neolithic Santimamiñe (Basque Country)

Four human remains dated to the Bronze Age were sequenced for mitochondrial DNA in Santimamiñe cave (Kortezubi, Biscay, Basque Country), along with single instances from the Neolithic, Chalcolithic and Roman period.

J.C. López Quintana et al., NUEVOS DATOS SOBRE LA SECUENCIA DE USO SEPULCRAL DE LA CUEVA DE SANTIMAMIÑE (KORTEZUBI, BIZKAIA). Arqueología y Prehistoria del Interior Peninsular (ARPI), 2016. Freely accessible (PDF) → LINK [no DOI]

The mtDNA study is not "brand new" but a synthesis of a previous doctoral thesis and advance publications:

Un primer avance de este estudio fue publicado en la monografía de las campañas de 2004 a 2006 de Santimamiñe (Cardoso et al. 2011), incluyendo el conjunto completo en la Tesis Doctoral de L. Palencia Madrid (Palencia 2015).

So we are talking of relatively old data, that has partly remained within the (sometimes absurdly greedy and anti-social) academic circles until now. The relative antiquity of the DNA study is important when assessing it, because genetic analysis is evolving very fast and, in most cases in the rather closed and under-budgeted Spanish universitary circles, they tend to do things "the old way", so we are almost certainly dealing here with HVS-I sequencing, something that is not explicit in the paper (I'm searching for Leire Palencia's thesis to make sure but no luck until now). 

If I am correct in this (and I should be), then we must understand that it is impossible in many cases to determine the exact haplogroup in the crucial R0 upper tier haplogroup, which includes HV and the extremely common H. Lacking the original HVS-I sequences by the moment, I can't but take the authors labels at face value but I must warn here that where it reads "R0" it is almost certainly H (HV0 or V are easy to recognize with this method, as is R0a) and where it reads "H1" it is probably H1 but not 100% certain. 

For more details see the relevant PhyloTree page, where the HVS-I markers are the last bloc in blue, beginning always with the sequence "16" (the other markers in blue of lower numerical value are HVS-II, more rarely used, and the ones in black are the coding region markers, which are in this case fundamental for proper assignment).

The mtDNA haplogroups (as reported) are:

  • Neolithic:
    • U5a2a (S2011-M2, c. 5100 BCE)
  • Chalcolithic:
    •  T2b (S-1, c. 2000 BCE)
  • Bronze Age:
    • U5b (S2011-M1 c. 1700 BCE) 
    • H1 (S2011-M4, c. 1700 BCE)
    • R0 (S2011-M6, c. 1500 BCE)
    • U3a (S2011-M3 c. 1300 BCE)
  • Roman period: 
    • R0 (S2011-M5, c. 300 CE)

Interpretation attempts

It's difficult to extract conclusions from them but they should be compared with other sequences from the area, for which I recommend my 2013 synthesis. In general, treat "R0" as meaning "H", even if I chose to use a different color (magenta instead of red) for exactitude. 

In order to aid that analysis, I reproduce here my 2013 graphic:

We cannot compare the single Neolithic and Roman Era individuals but we can compare the Satimamiñe Chalcolithic+Bronze group of five sequences with the peripheral Chalcolithic large dataset of De La Rúa:

  1. R*+H (very similar):
    1. Peripheral "Basque" Chalcolithic: ~40%
    2. Santimamiñe Chalcolithic+Bronze: 40% 
    3. Santimamiñe Bronze only: 50%
  2. U(xK) (very different):
    1. Peripheral "Basque" Chalcolithic: ~15%
    2. Santimamiñe Chalcolithic+Bronze: 40%
    3. Santimamiñe Bronze only: 50%
  3. Other lineages (all them of certain Neolithic immigrant origin, very different too):
    1. Peripheral "Basque" Chalcolithic: ~45%
    2. Santimamiñe Chalcolithic+Bronze: 20%
    3. Santimamiñe Bronze only: 0%

However one of the U(xK) lineages in Santimamiñe is U3, which is also quite certain to be of Neolithic immigrant origin, and one is an important figure when n=5 so we can also see it this way:
  1. Paleolithic lineages:
    1. Peripheral "Basque" Chalcolithic: ~55%
    2. Santimamiñe Chalcolithic+Bronze: 60%
    3. Santimamiñe Bronze only: 75%
  2. Neolithic lineages:
    1. Peripheral "Basque" Chalcolithic:  ~45%
    2. Santimamiñe Chalcolithic+Bronze: 40%
    3. Santimamiñe Bronze only: 25%

The comparison of #1 with #2 is much more similar. This could be important, because Santimamiñe is not anymore a "peripheral" site, as are those from De La Rúa's dataset, but a rather central one with a extremely long and uninterrupted Paleolithic sequence, dating to Neanderthal-made Chatelperronian culture. It is still a single site with a small number of samples but it does provide a counterpoint that, in one approach could produce similar results. 

But, surprisingly, when we consider a distinct Bronze Age category, comparing not anymore with #2 but with #3 everything changes, suggesting a totally different interpretation of the available dataset, in which, the "Chalcolithic interlude" (if real at all, more data is needed) would be reversed quickly with the onset of the Bronze Age. 

I am sorry but I cannot lean for either interpretation: the data is just not extensive enough to allow for conclusions. I am tempted to support the continuity hypothesis, allowing only for lesser changes to happen, and keep the Chalcolithic dataset under a big question mark, but the question mark is admittedly a bit smaller now: something in terms demographic may have happened in the Chalcolithic period and may have been reversed in the Bronze Age. But "may" is not "for sure", we need more data points.

Feel free to discuss in good mood, as always.

Thanks for the heads up to Jean Lohizun (again).

October 22, 2016

The 300 (improved) genomes project

I must make mention here of this study, which seems an attempt to improve the available datasets of global human genetics, particularly the widely used 1000 Genomes Project. It has some less striking but still interesting highlights.

Swapan Mallick et al., The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature, 2016. Pay per viewLINK [doi:10.1038/nature18964]


Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.

The genomes and some other information seem to be available in their dedicated webpage.

One of the highlights is explicit in the abstract: the single African origin of Homo sapiens and the single out-of-Africa migration episode are confirmed. I didn't have any doubt but there have been occasional speculations, based on nothing worth considering, on the conjecture of more than one migration out of Africa before the Holocene, maybe affecting Australasian peoples. Not at all: it's all based on mere misunderstanding on how "racial" traits evolved, those remote isolated peoples basically allow us for a glimpse on the plausible phenotypes of the early Eurasian migrants, which were probably quite dark in skin pigmentation and most often had thinly curled hair like that of most Africans. In fact, I have argued on occasion that it is very possible that straight hair and its less extreme variants, wavy and widely curly hair, are Neanderthal genetic and phenotype influences, positively selected for some unclear reason, and not part of our African Homo sapiens heritage. 

The other highlight that I appreciate is that they find some errors in the 1000 Genomes Project, particularly affecting Australasians, Andamanese and some Africans (quite extreme among the Khoisan particularly). This is very apparent in this map and might explain some misleading and often puzzling conclusions made by some researchers, academic or amateur alike:

Otherwise I do not find their reconstructions of the paleo-history of Humankind, based only on autosomal DNA (not the best tool for such deep incursions, really), too helpful. But the most important thing is the existence and availability of a new, allegedly improved, global dataset.

October 21, 2016

Wisent co-existed with true bison already in the Paleolithic

A fascinating story this one indeed: the European bison or wisent has some ancestry related to the cow, evident in its mitochondrial DNA. This was already known but what wasn't known is that this distinct "hybrid" species of bison dated to the Upper Paleolithic. Thanks to the excellent records of anonymous prehistorical biologists who recorded them in Southwestern European rock art with great detail and naturalism, modern researchers have realized that the wisent, with its bovid heritage, existed already in the Upper Paleolithic. Ancient DNA recovery has now confirmed the artist's impression.

Julien Soubrier et al. Early cave art and ancient DNA record the origin of European bison. Nature communications, 2016. Open access → LINK [doi:10.1038/ncomms13158]


The two living species of bison (European and American) are among the few terrestrial megafauna to have survived the late Pleistocene extinctions. Despite the extensive bovid fossil record in Eurasia, the evolutionary history of the European bison (or wisent, Bison bonasus) before the Holocene (< 11.7 thousand years ago (kya)) remains a mystery. We use complete ancient mitochondrial genomes and genome-wide nuclear DNA surveys to reveal that the wisent is the product of hybridization between the extinct steppe bison (Bison priscus) and ancestors of modern cattle (aurochs, Bos primigenius) before 120 kya, and contains up to 10% aurochs genomic ancestry. Although undetected within the fossil record, ancestors of the wisent have alternated ecological dominance with steppe bison in association with major environmental shifts since at least 55 kya. Early cave artists recorded distinct morphological forms consistent with these replacement events, around the Last Glacial Maximum (LGM, ∼21–18 kya).

The depictions of both types of bison are rather distinct but it seems nobody had noticed the difference until now, as the researchers explain in this article.

Fig. 1 - (a) Reproduction from Lascaux cave (France), from the Solutrean or early Magdalenian period (20,000 kya—picture adapted from ref. 53). (b) Reproduction from the Pergouset cave (France), from the Magdalenian period (<17,000 kya—picture adapted from ref. 54).

The ancient wisents sequenced now carry a distinct mtDNA haplogroup, called "clade X", which is sister to that of modern wisents (all descending from just 12 survivors). This wisent macro-haplogroup forms a clade with that of bovine cattle (cows of all sorts, both taurine and indicine) but they are joined only at the root, suggesting that the hybridization event that created the wisents as distinct species is very old, just a bit more recent than the divergence of cow and bison.

Fig. 2 - (a) Phylogenetic tree inferred from bovine mitochondrial control region sequences, showing the new clade of bison individuals. The positions of the newly sequenced individuals are marked in red for CladeX. (b) Bovine phylogeny estimated from whole-mitochondrial genome sequences, showing strong support for the grouping of wisent and CladeX with cattle (cow) and zebu. For both trees (a,b) numbers above branches represent the posterior probabilities from Bayesian inference, numbers below branches represent approximate likelihood ratio test support values from maximum-likelihood analysis and scale bars represent nucleotide substitutions per site from the Bayesian analysis. (c) Maximum-clade-credibility tree of CladeX and wisent estimated using Bayesian analysis and calibrated with radiocarbon dates associated with the sequenced bones. Dates of samples older than 50 kyr were estimated in the phylogenetic reconstruction. (d) Map showing all sampling locations, using the same colour code (red for CladeX, orange for wisent and blue for steppe bison).

So it is not random auroch hybridization but a very specific and very ancient episode of admixture between the ancestors of bisons and cows.

The two species appear to have distinct ecological niches:

The detailed records of the southern Ural sites allow the timing of the population replacements between steppe bison and wisent to be correlated with major palaeoenvironmental shifts, revealing that the wisent was associated with colder, more tundra-like landscapes and absence of a warm summer.

This pattern seems to correspond with the periods in which the two species are portrayed in rock art, as two of the researchers explain in this video (third part):

Post-statement: I must say that, on second thought, I'm not really convinced by the claim of wisent corresponding to colder periods. In fig. 1 above it is apparent that it is the steppe bison which corresponds to the last glacial maximum (LGM) in Southwestern Europe and not the wisent, which only shows up after the end of this coldest period. 

I wonder if the researchers are explaining themselves well enough on this aspect or if it is a case of wishful thinking, maybe caused by different conditions in SW Europe (where the rock art is) and the Southern Urals (where most of the archaeogenetic and paleontological data comes from). 

At the very least, judging on fig. 1, it would be the steppe bison the one corresponding with the coldest spell and the wisent the one corresponding to more temperate conditions. Can someone explain me what is going on here?

Armintxe: new rock art site discovered in the Basque Country

A week ago a new rock art site was revealed to exist right in the town of Lekeitio (Biscay). The art, estimated to be from some 14,000 years ago (Magdalenian culture), is made up of several groups of engraved animals: bisons, horses, goats and deers. The cave is not far from other known sites like Lumentxa, Atxurra and Santa Catalina.

Video of the cave and art[es]:

More information:
Pileta de Prehistoria[es] (has several videos and news from several sources, quite extensive)

October 9, 2016

A 14.000 year old human settlement in Argentina


Although the paper claims this site as the signature of arrival of our species to the South Cone (southern region of South America), there is another site with quite apparently older dates: Monte Verde (Chile), that cannot be ignored. In any case, it is a quite interesting data point for the peopling of America and the oldest one known East of the Andes.

Gustavo G. Politis et al., The Arrival of Homo sapiens into the Southern Cone at 14,000 Years Ago. PLoS ONE, 2016. Open accessLINK [doi:10.1371/journal.pone.0162870]


The Arroyo Seco 2 site contains a rich archaeological record, exceptional for South America, to explain the expansion of Homo sapiens into the Americas and their interaction with extinct Pleistocene mammals. The following paper provides a detailed overview of material remains found in the earliest cultural episodes at this multi-component site, dated between ca. 12,170 14C yrs B.P. (ca. 14,064 cal yrs B.P.) and 11,180 14C yrs B.P. (ca. 13,068 cal yrs B.P.). Evidence of early occupations includes the presence of lithic tools, a concentration of Pleistocene species remains, human-induced fractured animal bones, and a selection of skeletal parts of extinct fauna. The occurrence of hunter-gatherers in the Southern Cone at ca. 14,000 cal yrs B.P. is added to the growing list of American sites that indicate a human occupation earlier than the Clovis dispersal episode, but posterior to the onset of the deglaciation of the Last Glacial Maximum (LGM) in the North America.

September 8, 2016

Genetic structure in South-Eastern Africa


Another quite interesting paper on Khoesan and Southern African genetics:

Caitlin Uren et al., Fine-Scale Human Population Structure in Southern Africa Reflects Ecogeographic Boundaries. Genetics 2016. Freely accessibleLINK [doi:10.1534/genetics.116.187369]


Recent genetic studies have established that the KhoeSan populations of southern Africa are distinct from all other African populations and have remained largely isolated during human prehistory until ∼2000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about their population history. We examine new genome-wide polymorphism data and whole mitochondrial genomes for >100 South Africans from the ≠Khomani San and Nama populations of the Northern Cape, analyzed in conjunction with 19 additional southern African populations. Our analyses reveal fine-scale population structure in and around the Kalahari Desert. Surprisingly, this structure does not always correspond to linguistic or subsistence categories as previously suggested, but rather reflects the role of geographic barriers and the ecology of the greater Kalahari Basin. Regardless of subsistence strategy, the indigenous Khoe-speaking Nama pastoralists and the N|u-speaking ≠Khomani (formerly hunter-gatherers) share ancestry with other Khoe-speaking forager populations that form a rim around the Kalahari Desert. We reconstruct earlier migration patterns and estimate that the southern Kalahari populations were among the last to experience gene flow from Bantu speakers, ∼14 generations ago. We conclude that local adoption of pastoralism, at least by the Nama, appears to have been primarily a cultural process with limited genetic impact from eastern Africa.
Figure 2
Five spatially distinct ancestries indicate deep population structure in southern Africa. Using global ancestry proportions inferred from ADMIXTURE k = 10, we plot the mean ancestry for each population in southern Africa. The five most common ancestries in southern Africa, from the Affymetrix HumanOrigins data set, are shown separately in A–E. The x- and y-axes for each map correspond to latitude and longitude, respectively. Black dots represent the sampling location of populations in southern Africa. The third dimension in each map (depth of color) represents the mean ancestry proportion for each group for a given k ancestry, calculated from ADMIXTURE using unrelated individuals, and indicated in the color keys as 0–100% for five specific k ancestries. Surface plots of the ancestry proportions were interpolated across the African continent.

See also:

August 29, 2016

Gobero (Green Sahara key site) documentary

This site of Gobero (Niger) was news in the archaeology and anthropology circles a few years ago and today I stumbled on this quite nice video documentary on it that I believe will be of interest for many readers: