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Monthly Archives: March 2013

Neanderthal mtDNA in alleged Italian hybrid from late Mousterian context

The alleged hybrid characteristics are only attributed to morphological data of the bones (the bulk of the paper), what is always subject of great debate. Otherwise most people would just think in terms of Neanderthal, as the individual from Monte Lessini is also from a Mousterian context. By this I do not mean there was no interbreeding in the Neanderthal direction, just that without clear genetic data, I fail to see such morphometric speculations as conclusive in any way.
S. Condemi et al., Possible Interbreeding in Late Italian Neanderthals? New Data from the Mezzena Jaw (Monti Lessini, Verona, Italy). PLoS ONE 2013. Open accessLINK [doi:10.1371/journal.pone.0059781]

Abstract

In this article we examine the mandible of Riparo Mezzena a Middle Paleolithic rockshelter in the Monti Lessini (NE Italy, Verona) found in 1957 in association with Charentian Mousterian lithic assemblages. Mitochondrial DNA analysis performed on this jaw and on other cranial fragments found at the same stratigraphic level has led to the identification of the only genetically typed Neanderthal of the Italian peninsula and has confirmed through direct dating that it belongs to a late Neanderthal. Our aim here is to re-evaluate the taxonomic affinities of the Mezzena mandible in a wide comparative framework using both comparative morphology and geometric morphometrics. The comparative sample includes mid-Pleistocene fossils, Neanderthals and anatomically modern humans. This study of the Mezzena jaw shows that the chin region is similar to that of other late Neanderthals which display a much more modern morphology with an incipient mental trigone (e.g. Spy 1, La Ferrassie, Saint-Césaire). In our view, this change in morphology among late Neanderthals supports the hypothesis of anatomical change of late Neanderthals and the hypothesis of a certain degree of interbreeding with AMHs that, as the dating shows, was already present in the European territory. Our observations on the chin of the Mezzena mandible lead us to support a non abrupt phylogenetic transition for this period in Europe.

While there is little reason to doubt the Neanderthal attribution of these remains, the method of using only HVS-I is a bit antiquated and prone to errors and uncertainties. Follows table S10, with the genetic data (HVS-I) of this and other Neanderthal mtDNA sequences:

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Table S10.
Fossil specimen
Country
mtDNA region
Length (bp)
Diagnostic Neanderthals trasversion in HVR1 according to
Reference
Feldhofer 1
Germany
Complete mtDNA
16565
16139 A/T
16256 C/A
Insertion 16263 A
Feldhofer 2
Germany
Complete mtDNA
16565
16139 A/T
16256 C/A
Insertion 16263 A
Mezmaiskaya
Russia
Complete mtDNA
16565
16139 A/T
16256 C/A
Insertion 16263 A
Vindija 75
Croatia
HVR1
357
16139 A/T
16256 C/A
Insertion 16263 A
Vindija 77
Croatia
HVR1
31
16256 C/A
Vindija 80 (33.16)
Croatia
Complete mtDNA
31
16139 A/T
16256 C/A
Insertion 16263 A
Vindija 33.25
Complete mtDNA
16565
16139 A/T
16256 C/A
Insertion 16263 A
Engis 2
Belgium
HVR1
31
16256 C/A
Le Chapelle-aux-Saint
France
HVR1
31
16256 C/A
Rochers de Villenueve
France
HVR1
31
16256 C/A
Scladina
Belgium
HVR1
123
16256 C/A
Monte Lessini
Italy
HVR1
378
16139 A/T
16256 C/A
Insertion 16263 A
Monte Lessini Mandibula
Italy
HVR1
31
16256 C/A
This paper
El Sidron SD-441
Spain
HVR1
47
16256 C/A
El Sidron SD-1252
Spain
HVR1
303
16139 A/T
16256 C/A
Insertion 16263 A
EL Sidron 1253
Spain
Complete MtDNA
16565
16139 A/T
16256 C/A
Insertion 16263 A
Valdegoba
Spain
HVR1
303
16139 A/T
16256 C/A
Insertion 16263 A
Teshik Tash
Uzbekistan
HVR1
190
16139 A/T
16256 C/A
Insertion 16263 A
Okladnikov
Russia
HVR1
348
16139 A/T
16256 C/A
Insertion 16263 A
 

Trebiño: major flint stone quarry of the Upper Paleolithic

Trebiño (also Treviño in Spanish), just south of Vitoria-Gasteiz, Western Basque Country, includes de the sierra of Araiko, which was, we get to know now, in the Upper Paleolithic one of the main sources of flint stone of SW Europe, “exporting” to most of the Franco-Cantabrian Region, the core of Late UP Europe. 
The quarry left rather massive remains, hard to discern today, as they have been reclaimed by Nature again, such as 300m long ditches and rubble piles seven meters tall. Mining tools have also been found. The high quality Trebiñese flint stone was used by most Upper Paleolithic peoples in the region, underlining the notion of extense socio-economic networks already in those times, and the site continued in exploitation through the Neolithic and Chalcolithic eras. 
The archaeological site is in danger because of the planned erection of a wind energy generation park right atop of it. Update: the wind park planned on it was actually suspended on October 2012, it seems.
Source: Diario de Burgos[es] (via Pileta[es]).
 

Epipaleolithic site dug in Sudan

Archaeologist watches a lioness head
not mentioned in the sources
A late hunter-gatherer necropolis has been discovered and researched by Czech scientists. The area of Sabalonka, some 80 Km north of Khartoum, includes a large necropolis of some 400-450 burials, believed to be from 8-10,000 years ago. Along with the burials, still awaiting radiocarbon dating, the archaeologists found a network of nearby settlements.
So far 30 skeletons have been recovered, many with personal ornaments made of shells, ostrich egg and bone. Other objects found are bone needles and domestic tools made of bone and horn.
The site is at risk in the mid-run because of a planned dam, also the researchers are somewhat concerned about funding, even though the project is low-cost. 
Sources[es]: Paleorama en Red, Radio Praga
 
 

SE Iberian pollution in the Metal Ages

One of the earliest cases of overexploitation and pollution in Europe has been found in SE Iberia, a key center of Early Bronze in Western Europe (Argaric civilization). The sediments of a lake in Sierra Nevada (Andalusia), known as Laguna de Río Seco (pictured), have provided the evidence for important pollution c. 3900 years ago, just when the Bronze Age began in the region. This is attributed mostly not to industry but to increase in fires and deforestation.
However, as we get into the Late Bronze (post-Argaric culture) and Iron age (Iberian culture), the evidence speaks of a type of pollution which can only be attributed to manufacture: lead. This kind of pollution reached a peak c. 2900 years ago (beginnings of Iron Age) and then again in the Roman era (as well as in the Industrial Age).
It is worth mentioning that lead pollution has decreased in the last decades, caused no doubt by the environmental awareness of these times and derived normative, like banning lead from gasoline.
Sources: SINC[es], Paleorama en Red[es].
Ref. A. García Alix et al., Anthropogenic impact and lead pollution throughout the Holocene in Southern Iberia. Science of the Total Environment 2013. Pay per viewLINK [doi:10.1016/j.scitotenv.2013.01.081]

 

Rare early North Chinese skull suggests inbreeding depression

Again very quickly on a matter that seems to be of some interest:
Xiu-Jie Wu, Song Xing & Erik Trinkaus, An Enlarged Parietal Foramen in the Late Archaic Xujiayao 11 Neurocranium from Northern China, and Rare Anomalies among Pleistocene Homo. PLoS ONE, 2013. Open accessLINK [doi:10.1371/journal.pone.0059587]

Abstract


We report here a neurocranial abnormality previously undescribed in Pleistocene human fossils, an enlarged parietal foramen (EPF) in the early Late Pleistocene Xujiayao 11 parietal bones from the Xujiayao (Houjiayao) site, northern China. Xujiayao 11 is a pair of partial posteromedial parietal bones from an adult. It exhibits thick cranial vault bones, arachnoid granulations, a deviated posterior sagittal suture, and a unilateral (right) parietal lacuna with a posteriorly-directed and enlarged endocranial vascular sulcus. Differential diagnosis indicates that the perforation is a congenital defect, an enlarged parietal foramen, commonly associated with cerebral venous and cranial vault anomalies. It was not lethal given the individual’s age-at-death, but it may have been associated with secondary neurological deficiencies. The fossil constitutes the oldest evidence in human evolution of this very rare condition (a single enlarged parietal foramen). In combination with developmental and degenerative abnormalities in other Pleistocene human remains, it suggests demographic and survival patterns among Pleistocene Homo that led to an elevated frequency of conditions unknown or rare among recent humans.

The authors argue, according to previous research that Xujiayao remains are neither Homo erectus nor early Homo sapiens but it’s difficult to say, as the Chinese Academy tends to be ambiguous on these matters and so is Trinkaus.
The most recent datings (OSL) for the site suggest MIS 4 ages (60±8 and 69±8 ka BP). However earlier datings (U-Th series) claimed a much older age: 104-125 Ka BP (MIS 5). The later dates would certainly fit with my expectations for the arrival of H. sapiens to the area.
Whatever the case, the authors conclude that this EPF anomaly is in line with a long list of Paleolithic cases of developmental anomalies that they suspect caused by inbreeding within the parameters of small hunter-gatherer populations. 

To the extent that these abnormalities can be considered congenital or
cannot be securely diagnosed, these considerations raise questions
regarding the population dynamics of Pleistocene humans. To what extent
could this pattern reflect small, highly inbred populations, which were
also demographically unstable, resulting in both the increased
appearance of congenital deleterious conditions and in their subsequent
disappearance through local population extinction? Demographic
instability appears to have been characteristic of most Pleistocene
human populations [78][80].
It remains unclear, and probably untestable, to what extent these
populations were inbred, but close genetic relationships have been
suggested for one Neandertal sample [81] and some Upper Paleolithic burial groups [76], [82], [83].

 
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Posted by on March 25, 2013 in China, East Asia, health, Middle Paleolithic

 

Nearly complete sequence of a Neanderthal from Altai

A 99.9% complete Neanderthal genome from a toe bone found at Denisova Cave (Altai, Southern Siberia).

A high-quality Neandertal genome sequence


The genome sequence was generated from a toe bone discovered in Denisova Cave in southern Siberia in 2010. The bone is described in Mednikova (Ethnology & Anthropology of Eurasia 2011. 39: 129-138).


DNA sequences were generated on the Illumina HiSeq platform and constitute an average 50-fold coverage of the genome. 99.9% of the 1.7GB of uniquely mappable DNA sequences in the human genome are covered at least ten times.
Contamination with modern human DNA, estimated from mitochondrial and nuclear DNA sequences, is around 1%.


The figure shows a tree relating this genome to the genomes of Neandertals from Croatia, from Germany and from the Caucasus as well as the Denisovan genome recovered from a finger bone excavated at Deniosva Cave. It shows that this individual is closely related to these other Neandertals. Thus, both Neandertals and Denisovans have inhabited this cave in southern Siberia, presumably at different times. 

One may wonder: how can they know it is a Neanderthal and not a “Denisovan”? Because of the close genetic affinity with other Neanderthals from Europe:

It is still possible, considering its position in the tree that the Altai Neanderthal had minor “Denisovan” admixture. But it would be very minor in any case. 

 
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Posted by on March 25, 2013 in aDNA, Altai, Denisova, Neanderthal

 

Millet Mesolithic and Early Neolithic in Northern China

Panicum miliaceum
(GFDL by Kurt Stüber)
I’m getting my backlog up to date, so you will have to excuse some lack of in depth analysis in this and some entries to follow. My most sincere apologies because I’d really like to be able to offer an in-depth analysis in every other entry but the harsh reality is that my mind and my energies only reach that far.
This one is a paper from a year ago but that has some interest regarding the Mesolithic (wild cereal harvesting) transition to Neolithic (agriculture)  in China.
Xiaoyang Yang  et al., Early millet use in northern China. PNAS 2012. Freely accessibleLINK [doi:10.1073/pnas.1115430109]

Abstract

It is generally understood that foxtail millet and broomcorn millet were initially domesticated in Northern China where they eventually became the dominant plant food crops. The rarity of older archaeological sites and archaeobotanical work in the region, however, renders both the origins of these plants and their processes of domestication poorly understood. Here we present ancient starch grain assemblages recovered from cultural deposits, including carbonized residues adhering to an early pottery sherd as well as grinding stone tools excavated from the sites of Nanzhuangtou (11.5–11.0 cal kyBP) and Donghulin (11.0–9.5 cal kyBP) in the North China Plain. Our data extend the record of millet use in China by nearly 1,000 y, and the record of foxtail millet in the region by at least two millennia. The patterning of starch residues within the samples allow for the formulation of the hypothesis that foxtail millets were cultivated for an extended period of two millennia, during which this crop plant appears to have been undergoing domestication. Future research in the region will help clarify the processes in place.



Conclusions

The data from these studies extends the archaeobotanical record of millet exploitation to 11 cal kyBP in East Asia. The presence of the starch grains on processing tools is a strong indicator that millet seeds were ground into flour or meal using stone tools, then cooked in earthenware vessels as early as 10 cal kyBP. Other grasses and geophytes were also part of the diet during this time in the North China Plain. We believe these data may indicate that the domestication of foxtail millet occurred over an extended period, perhaps two millennia or more. Future research in this region should help clarify the trajectory of this important crop plant.

 
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Posted by on March 25, 2013 in China, East Asia, Mesolithic, Neolithic

 

African MSA

As I mentioned recently, I am collaborating in a joint series of articles in Spanish language which try to explore the expansion of Homo sapiens from the double viewpoint of archaeology and population genetics. The series, hosted by Noticias de Prehistoria – Prehistoria al Día, began this past Thursday with David Sánchez’ article on the African MSA, earliest fossils of H. sapiens and other early African cultures like the Lupemban and Aterian. In the next week I plan to explore the genetic aspects, in line with what has been published in this blog and its predecessor Leherensuge.
But so far let’s try to synthesize the most important aspects of David’s entry at his blog. First and foremost is this map, which I believe is of great interest because of its synthetic informative value:


Legend translation:
· Fossil remains of Homo sapiens (195-90 Ka BP)
· Aterian sites (170*-40 Ka BP)
· Nubian complex [MSA] sites (115-37 Ka BP)
· Lupemban sites (230-130 Ka BP)
· Undetermined MSA
· South African [MSA] sites (165-59 Ka BP)
· Some early MSA sites
[* personally I am a bit skeptic about the oldest Aterian dates but well…]

It’s possible that it’s not totally complete (feel free to add to our unavoidably limited knowledge) but it does gather in a quick view most of the African Middle Paleolithic (MSA, Aterian and Lupemban). The site of Katanda which has a special interest because of the harpoons, the earliest known ever, was absent in the version first uploaded but this has been corrected now.
This synthetic map, together with the extensive bibliography (in several languages) that David links at the bottom of his article are, I believe, an interesting reference for all those interested in the origins of Homo sapiens and its first prehistory in the African continent.

Paleolithic mattresses

Most readers are probably at least somewhat familiar with the many, often impressive and revealing, South African sites but, besides the already mentioned Katanda harpoons, what really impressed me a lot was the finding in Sibudu, Northern Mozambique, near Lake Malawi, of fragments of ancient fossilized mattresses made up of vegetation that has bug-repealing properties (→ news article at El Mundo[es]). Apparently the owners, some 73,000 years ago, burnt them now and then in order to destroy parasites. Since c. 58,000 BP the number of mattresses, fires and ashes grew, surely indicating greater population densities, at least locally. 
The ancient inhabitants of that area of Mozambique are also known to have milled and processed, some 100,000 years ago, a diverse array of plants, including sorghum, “African potato” (medicinal), wine palm, false banana, pigeon peas, etc.
 

Comment moderation again

I have decided to banish TerryT from the comments section. He’s just manipulating all I say and throwing insults and accusations. I have been extremely patient for many many years but I have really grow tired of all that almost every day. There is another person (guess who) just one step from going down the drain.
In consequence, I have decided to moderate comments for a week or so, establishing that way a buffer of comfort for myself. 
The list of people banned from commenting in this blog (from memory) is:
  • German Dziebel – cause: smartass trolling
  • Octavià Alexandre – cause: smartass trolling, personal attacks
  • DDeden – cause: some sort of mental problems apparently
  • Onur – cause: stubborn racism under a varnish of “scientific terminology”
  • TerryT – cause: smartass trolling, personal attacks, insistently putting words in my mouth that have nothing to do with reality, abusing without any consideration my dedication to this blog, etc.
Sorry for the inconvenience to all readers and commenters of good will, who are the vast majority.

 
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Posted by on March 22, 2013 in blogging

 

Khoesan and Coloured autosomal DNA in context

There has been a number of studies coming out recently on Khoesan genetics but this one does not seem to be just redundant, providing some extra information instead.

Desiree C. Petersen et al., Complex Patterns of Genomic Admixture within Southern Africa. PLoS Genetics 2013. Open accessLINK [doi:10.1371/journal.pgen.1003309]


Abstract


Within-population genetic diversity is greatest within Africa, while between-population genetic diversity is directly proportional to geographic distance. The most divergent contemporary human populations include the click-speaking forager peoples of southern Africa, broadly defined as Khoesan. Both intra- (Bantu expansion) and inter-continental migration (European-driven colonization) have resulted in complex patterns of admixture between ancient geographically isolated Khoesan and more recently diverged populations. Using gender-specific analysis and almost 1 million autosomal markers, we determine the significance of estimated ancestral contributions that have shaped five contemporary southern African populations in a cohort of 103 individuals. Limited by lack of available data for homogenous Khoesan representation, we identify the Ju/’hoan (n = 19) as a distinct early diverging human lineage with little to no significant non-Khoesan contribution. In contrast to the Ju/’hoan, we identify ancient signatures of Khoesan and Bantu unions resulting in significant Khoesan- and Bantu-derived contributions to the Southern Bantu amaXhosa (n = 15) and Khoesan !Xun (n = 14), respectively. Our data further suggests that contemporary !Xun represent distinct Khoesan prehistories. Khoesan assimilation with European settlement at the most southern tip of Africa resulted in significant ancestral Khoesan contributions to the Coloured (n = 25) and Baster (n = 30) populations. The latter populations were further impacted by 170 years of East Indian slave trade and intra-continental migrations resulting in a complex pattern of genetic variation (admixture). The populations of southern Africa provide a unique opportunity to investigate the genomic variability from some of the oldest human lineages to the implications of complex admixture patterns including ancient and recently diverged human lineages.

The array of Khoesan populations senso stricto analyzed in this study is much smaller than that of Schebusch 2010 but this study has the advantage of including Cape Coloureds and their Baster relatives, partially descendants from the otherwise extinct pastoralist Khoekhoe (Hottentots, now considered a derogative term) who lived in much of Southern Africa upon the arrival of Bantu and Europeans, as well as the amaXhosa, a Bantu people which clearly display marked Khoesan admixture.

Figure 1. Map of southern Africa
showing distribution of sampling per population identifier and
significant historical events that likely shaped ancestral
contributions.

There is brief mention of maternal and paternal DNA. Just to mention that mtDNA being mostly aboriginal (L0d/L0k) among the Khoesan (86-100%), the Coloureds (68%) and even the Xhosa (47%, all L0d), while aboriginal Y-DNA (essentially A2b and A2c2, plus occasional B2) is concentrated among the Ju/’hoan, with the !Xun being instead dominated by E1b1-M275, of putative East African (Nilotic?) origins. This is consistent with the !Xun being historically pastoralists. European patrilineages, notably R1b, are dominant among the Baster (92%) and Cape Coloured (71%).
Coloureds only make up some 9% of South African population but they dominate the countryside in much of the former Cape Province. Namibian Basters are a subset of them who migrated northwards in 1868.

Figure 2.  PCA and STRUCTURE analysis (click to expand)
We can see in the graphics above how the North Cape Coloured and Baster only display minor Bantu admixture, being essentially a variable mix of European and Khoesan ancestry, with probably also some Malay input (apparent in the increase of the blue component relative to the European reference). Instead East Cape and Cape Town (D6) Coloured appear to have greater apportion of Bantu ancestry and, especially the later, a notable increase of the East Asian input.
The STRUCTURE graph, particularly at K=9, is also informative about other African populations but I won’t dwell in that here. 
The authors also made an interesting exercise of analysis using Ancestry Informative Markers with the !Xun and Xhosa:

Figure 4. Ju/’hoan-Yoruba ancestry
informative markers (AIMs) defined ancestral contributions to the !Xun
and amaXhosa, providing evidence for two distinct !Xun lineages with
differing ancestral contributions.
It seems evident that much of the !Xun ancestry (up to 70%) does not fall in either (Ju/’hoan-Yoruba) category but it is something else, probably specific to this people. The Xhosa Khoesan ancestry also seems closer to the pastoralist !Xun than to the (likely more genuinely ancient) Ju/’hoan. 

There is some more info in the paper but I feel that the essentials are sufficiently covered here. 

See also: