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 access → LINK [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:

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 view → LINK [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 access → LINK [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].

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).

Documents at Max Plank Institute for Evolutionary Anthropology, Department of Evolutionary Genetics.

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. 

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 accessible → LINK [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.

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 use of racist-like language under a varnish of "scientific terminology". Unbanned "on probation" Sep. 6th 2013 (original reason of bane edited after controversy).
• 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.

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 access → LINK [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:

• Khoisan autosomal genetics
• Khoesan genetics helping to understand the evolutionary history of Humankind as a whole
• Khoe-San matrilineages and prehistory
• The Neolithic site of Leopard Cave (Namibia) - for details on early pre-Bantu Neolithic in Southern Africa
  

Autosomal genetics of the Roma People

Some more information on the genetics of the Roma People.

Prija Moorjani et al., Reconstructing Roma History from Genome-Wide Data. PLoS ONE 2013. Open access → LINK [doi:10.1371/journal.pone.0058633]

Abstract

The Roma people, living throughout Europe and West Asia, are a diverse population linked by the Romani language and culture. Previous linguistic and genetic studies have suggested that the Roma migrated into Europe from South Asia about 1,000–1,500 years ago. Genetic inferences about Roma history have mostly focused on the Y chromosome and mitochondrial DNA. To explore what additional information can be learned from genome-wide data, we analyzed data from six Roma groups that we genotyped at hundreds of thousands of single nucleotide polymorphisms (SNPs). We estimate that the Roma harbor about 80% West Eurasian ancestry–derived from a combination of European and South Asian sources–and that the date of admixture of South Asian and European ancestry was about 850 years before present. We provide evidence for Eastern Europe being a major source of European ancestry, and North-west India being a major source of the South Asian ancestry in the Roma. By computing allele sharing as a measure of linkage disequilibrium, we estimate that the migration of Roma out of the Indian subcontinent was accompanied by a severe founder event, which appears to have been followed by a major demographic expansion after the arrival in Europe.

The claim of "80%" West Eurasian ancestry seems quite exaggerated on light of the ADMIXTURE data, where at least 40% is clearly of South Asian origin (maybe somewhat more as NW South Asians display some West Eurasian admixture). I guess that they are just speculating on the ANI/ASI (North-South Indian) issue and attributing ANI to a West Eurasian gene pool, what is most confusing to say the least.

Figure 1. Relationship of Roma with other worldwide populations.
(click to expand)

It is true in any case that FST distances are significantly higher with Gujarati Indians (GIH) than with Europeans (CEU, TSI), the former at 0.026, while the latter at only 0.016.

Whatever the case I'd focus on the Fig 1(a) ADMIXTURE graph, because in the (b) one the appearance of European affinity among many South Asians (in my understanding, a 50,000 years-old affinity highlighted only for lack of sufficient K-depth, K=3 only!) is only a factor of confusion. Following this criterion, Roma appear to be some 60% West Eurasian and 40% NW Indian.

Something I really miss in this paper is a more detailed comparison not just with South Asians (more K-depth please!) but also with West Asians, totally absent from the study.

See also: Romani mtDNA

The Katanda harpoons

Recently David Sánchez (of Noticias de Prehistoria - Prehistoria al Día[es]) asked me to collaborate in a series at his blog on the early prehistory and expansion of Homo sapiens, from the viewpoints of both archaeology and population genetics. I gladly accepted, of course. The first articles will be published in the next days/weeks at his blog (I plan to make synthesis of them in English here but not full translations - too much work). The bulk of the archaeological materials will be done by David, while I am taking responsibility mostly for the genetic aspects.

As he has been preparing the first article on the African Middle Stone Age, David stumbled upon a quite fascinating curiosity that was unknown to both and is probably of interest for the readers of this blog: the existence of well-finished proto-harpoons in the MSA of Katanda (North Kivu, D.R. Congo, near Uganda - not to be confused with another larger town named Katanda in the Kasaï-Oriental province) dated to some 110-80,000 years ago. 

I can only imagine that this quite unknown but fascinating materials should be of interest to the readers of this blog. 

Source: Dictionary of Ichtyology

The main direct reference for this unusual finding is:

J.E. Yellen et al., A middle stone age worked bone industry from Katanda, Upper Semliki Valley, Zaire. Science 1995. Pay per view → LINK [doi:10.1126/science.7725100]

Abstract

Three archaeological sites at Katanda on the Upper Semliki River in the Western Rift Valley of Zaire have provided evidence for a well-developed bone industry in a Middle Stone Age context. Artifacts include both barbed and unbarbed points as well as a daggerlike object. Dating by both direct and indirect means indicate an age of approximately 90,000 years or older. Together with abundant fish (primarily catfish) remains, the bone technology indicates that a complex subsistence specialization had developed in Africa by this time. The level of behavioral competence required is consistent with that of upper Paleolithic Homo sapiens sapiens. These data support an African origin of behaviorally as well as biologically modern humans.

This discovery has been mentioned later on by more accessible materials, for example: D'Errico & Stringer 2011, D'Errico 2006 (in French) or a book by Luis Raposo (in Spanish). 

Regardless of the speculations about the so-called "modern human behavior", what it clearly means is that those ancient Africans produced well-finished barbed proto-harpoons (not known of otherwise until Magdalenian times in Europe) and used them to fish in the Semliki river (being one of the earliest documented cases of this kind of economy).

Another SE Asian genetic adaption to Malaria

Malaria has been one of the greatest challenges to human survival in the tropics and subtropical areas, which make up the bulk of our early distribution as species. In response we have developed a number of genetic-biological strategies of which the best known is the allele that causes the sickle cell disease in homozygotes but protects heterozygotes against the deadly infection in a clear example of balancing selection. This is not however the only adaption against malaria.

A new study explores a SE Asian (including Southern Chinese) adaption that also seems to be a way to fight against the disease, which is a variant of Alpha-Thalassemia:

Qin-Wei Qiu et al., Evidence of recent natural selection on the Southeast Asian deletion (--SEA) causing alpha-thalassemia in South China. BMC Evolutionary Biology 2013. Open access → LINK [doi:10.1186/1471-2148-13-63]

Abstract (provisional)

Background

The Southeast Asian deletion (--SEA) is the most commonly observed mutation among diverse alpha-thalassemia alleles in Southeast Asia and South China. It is generally argued that mutation --SEA, like other variants causing hemoglobin disorders, is associated with protection against malaria that is endemic in these regions. However, little evidence has been provided to support this claim.

Results

We first examined the genetic imprint of recent positive selection on the --SEA allele and flanking sequences in the human alpha-globin cluster, covering a genomic region spanning ~410 kb, by genotyping 28 SNPs in a Chinese population consisting of 76 --SEA heterozygotes and 138 normal individuals. The pattern of linkage disequilibrium (LD) and the long-range haplotype test revealed a signature of positive selection. The network of inferred haplotypes suggested a single origin of the --SEA allele.

Conclusions

Thus, our data support the hypothesis that the --SEA allele has been subjected to recent balancing selection, triggered by malaria.

See also:

• Malaria and sickle cell anemia do not correlate well in Asia
• The other red cell disease that protects against the other malaria
• IL-4 genetic combo protects Indian hunter-gatherers from Malaria

Plants do use epigenetics to adapt to diverse environments

If you've ever grown plants that come from a distant land, you may be familiar with the fact that you may need an adaptive process of one or more generations to get the best of them. Oddly enough this time is often too short for genetic adaption to happen and sweep over, especially as most of the ill-adapted plants don't really die nor fail to reproduce (i.e. they are not too aggressively selected against). How does it happen then? Epigenetics may have the answer.

Robert J. Schmidt et al., Patterns of population epigenomic diversity. Nature 2013. Pay per view → LINK [doi:10.1038/nature11968]

Abstract

Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to such diversity, its interaction with genetic variation requires further investigation. Here we report population-wide DNA sequencing of genomes, transcriptomes and methylomes of wild Arabidopsis thaliana accessions. Single cytosine methylation polymorphisms are not linked to genotype. However, the rate of linkage disequilibrium decay amongst differentially methylated regions targeted by RNA-directed DNA methylation is similar to the rate for single nucleotide polymorphisms. Association analyses of these RNA-directed DNA methylation regions with genetic variants identified thousands of methylation quantitative trait loci, which revealed the population estimate of genetically dependent methylation variation. Analysis of invariably methylated transposons and genes across this population indicates that loci targeted by RNA-directed DNA methylation are epigenetically activated in pollen and seeds, which facilitates proper development of these structures.

From the body of the article:

Epiallele formation in the absence of genetic variation can result in phenotypic variation, which is most evident in the plant kingdom, as exemplified by the peloric and colorless non-ripening variants from Linaria vulgaris and Solanum lycopersicum, respectively^{6, 7}. Although rates of spontaneous variation in DNA methylation and mutation can be decoupled in the laboratory^{8, 9, 10, 11}, in natural settings, these two features of genomes co-evolve to create phenotypic diversity on which natural selection can act.

...

Similarly to the limited examples of pure epialleles (methylation variants that form independent of genetic variation), few examples of DNA methylation variants linked to genetic variants are known^{15, 16, 17}.

And the 'Conclusion remarks' (emphasis is mine):

Natural epigenomic variation is widespread within A. thaliana, and the population-based epigenomics presented here has uncovered features of the DNA methylome that are not linked to underlying genetic variation, such as all forms of SMPs and CG-DMRs. However, C-DMRs have positional association decay patterns similar to linkage disequilibrium decay patterns for SNPs and in some cases are associated with genetic variants, but the majority of C-DMRs were not tested by association mapping due to low allele frequencies and could result from rare sequence variants. Our combined analyses of genetic and methylation variation did not uncover a correlation between major effect mutations and genes silenced by RdDM, suggesting that this pathway may target these genes for another purpose. This purpose could be to restrict expression from vegetative tissues similarly to transposons. Another possible purpose of being targeted by RdDM could be to coordinate expression specifically in pollen and in seed to ensure proper gametophytic and embryonic development. Animals also use small RNA-directed DNA methylation and heterochromatin formation mechanisms to maintain the epigenome of the germ line through the use of Piwi-interacting RNAs³⁶. In both plants and animals these small RNAs are derived from the genome of companion cells, which are terminal in nature and can afford widespread reactivation of transposon and repeat sequences as they are not passed on to the next generation. Our study provides evidence that RdDM-targeted genes may have co-opted this transposon silencing mechanism to maintain their silenced state in vegetative tissues and transgenerationally, as well as to ensure proper expression important for pollen, seed and germ line development.

New Late Paleolithic(?) site discovered in Tianjin, China

[In red and crossed out text: editions to the first version. See update below]

A new Late Paleolithic site has been dug out in Northern China, more specifically in Tianjin, the port of Beijing. The site is known as Taiziling.

The information provided at PhysOrg, other than the images is scant, but it would seem to belong to the Late Middle Paleolithic made by Homo Sapiens (clearly much more advanced than the technologies of H. erectus in those areas). No datings are provided anyhow.

The stone assemblage includes cores (n=5), flakes (n=42), chunks (n=5) and retouched tools (n=6). Lithic raw materials exploited at the locality were locally available from ancient riverbeds, with chert being the predominant raw material (72.5%). The principal flaking technique was direct hammer percussion with core preparation, especially for microblade cores. Most stone artifacts were standardized in shape, finely retouched and small in size, and most tool blanks were flakes. Only three retouched tool types were identified: scrapers, points and picks. Modified tools appear to be retouched by hammer percussion and pressure techniques, with tools retouched primarily on the dorsal surface.

"It can be inferred from these materials that this stone assemblage shows a close relationship with the Flake Tool Industry (Main Industry) in North China, but bears some characteristics of the Microblade Industry there", said coauthor SHENG Lishuang, an archaeologist at the Preservation Center of Cultural Heritage in Tianjin.

Important Update (Mar 15):

The impression provided by the PhysOrg article is not concordant with what the source entry at the Institute of Vertebrate Paleontology and Paleoanthropology (Chinese Academy of Sciences) says.

In fact this one rather suggests a Late Pleistocene and even maybe Early Holocene dating and indicates, as some commenters have suggested, that some of the tools show an UP affinity rather than being typical Middle Paleolithic:

“It can be inferred from these materials that this stone assemblage shows a close relationship with the Flake Tool Industry (Main Industry) in North China, but bears some characteristics of the Microblade Industry there”, said coauthor SHENG Lishuang, an archaeologist at the Preservation Center of Cultural Heritage in Tianjin.

Geomorphological and chronological comparison within Jixian County indicates a Late Pleistocene or Early Holocene date.

Autosomal DNA of NE Europeans

A paper of some interest is available these days at the Public Library of Science:

Andrey V. Kruhnin et al., A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe. PLoS ONE 2013. Open access → LINK [doi:10.1371/journal.pone.0058552]

Abstract

Several studies examined the fine-scale structure of human genetic variation in Europe. However, the European sets analyzed represent mainly northern, western, central, and southern Europe. Here, we report an analysis of approximately 166,000 single nucleotide polymorphisms in populations from eastern (northeastern) Europe: four Russian populations from European Russia, and three populations from the northernmost Finno-Ugric ethnicities (Veps and two contrast groups of Komi people). These were compared with several reference European samples, including Finns, Estonians, Latvians, Poles, Czechs, Germans, and Italians. The results obtained demonstrated genetic heterogeneity of populations living in the region studied. Russians from the central part of European Russia (Tver, Murom, and Kursk) exhibited similarities with populations from central–eastern Europe, and were distant from Russian sample from the northern Russia (Mezen district, Archangelsk region). Komi samples, especially Izhemski Komi, were significantly different from all other populations studied. These can be considered as a second pole of genetic diversity in northern Europe (in addition to the pole, occupied by Finns), as they had a distinct ancestry component. Russians from Mezen and the Finnic-speaking Veps were positioned between the two poles, but differed from each other in the proportions of Komi and Finnic ancestries. In general, our data provides a more complete genetic map of Europe accounting for the diversity in its most eastern (northeastern) populations.

I'm not too sure of how to analyze this paper because, on one side, there's some missing data, especially in regards to the ADMIXTURE analysis (FST distances between components) and then for some reason the Chinese control was totally removed from further analysis as well, making very difficult for example to estimate if and how much East Asian admixture exists in these NE European populations. Then on the other side, nearly all Finno-Ugrian peoples (as well as the Mezen Russians, genetically Finno-Ugrian as well) are highly endogamous peoples, what almost invariably distorts ADMIXTURE analysis by creating many localized components of dubious relevance.

The ADMIXTURE analysis was presented, as often happens quite incorrectly, for values under the cross-validation optimum, which in this case is at least known: K=6 and K=7 (very similar lowest values):

Figure 4. ADMIXTURE clustering of individuals from the populations studied.

Results obtained at K = 2 to 5 are shown. Each individual is represented by a vertical line composed of colored segments, in which each segment represents the proportion of an individual’s ancestry derived from one of the K ancestral populations. Individuals are grouped by population (labeled on the bottom of the graph). In addition to populations used in principal component analysis, a Chinese sample (Han Chinese from Beijing [22]) was included. The results at K = 5 are also accompanied by average ancestral proportions by population (*). Population designations are the same as in Figure 1.

[From fig. 1:] Key: Komi_Izh – Izhemski Komi, Komi_Pr – Priluzski Komi, Rus_Tv – Russians from Tver, Rus_Ku – Russians from Kursk, Rus_Mu – Russians from Murom, Rus_Me – Russians from Mezen, Finns_He – Finns from Helsinki, Finns_Ku – Finns from Kuusamo, Rus_HGDP – Russians from the Human Genome Diversity Panel.

At least in the supplemental materials we find the missing K-values:

Figure S4. Results of ADMIXTURE clustering at K = 6 to 8. The number of populations and their order are the same as at Figure 4.
[Note: per fig. S5, the optimal K-values are K=6 and K=7]

Something that may call your attention is the relatively high value of the Chinese component in Italians (Tuscans, judging on the locator map). This anomalous effect (unheard of in other studies) may well be caused because a West Asian control is clearly missing and Italians have relatively high West Asian affinity, being otherwise relatively isolated within this Northern European sample. 

Notice also how every single endogamous Finno-Ugric population forms their own cluster: a generic Finno-Ugrian component at K=3 (red), a distinction between the Komi and the Finnic component at K=4 (red and purple), then at K=5 we get a mini-break with a more general North/South Europe distinction showing up (yellow and blue components), but at "optimal" K=6 and K=7, we still see other localized components forming: first Komi_Pr (brown) and then the Vepsian one (grey). So out of seven "optimal" components (K=7), four are local corresponding to highly endogamous populations. 

But I'm running a bit ahead of myself, admittedly. The endogamy index is analyzed as ROH values: nROH for the mean and cROH for the average:

Table 2. Summary of ROH statistics of 16 European populations.

We can see here that large and relatively cosmopolitan populations like Germans and Italians have low ROH values. Czechs and Central Russians come next, with Poles already showing a bit higher endogamy index. Latvians and Estonians are still relatively low but Northern Finno-Ugrian peoples (including Mezen Russians) deviate a lot, with values (at the non-asterisk columns) that are at best almost double than those for Estonians and, at worst, six times higher.

So in this particular case, and quite exceptionally, I'd say that K=2 or K=3 are the most realistic K-values, in spite of scoring quite poor in the cross-validation test. Of course that the N-S European distinction shown at K=5 is also real and not caused by any "effect" but otherwise the clusters showing up correspond to extreme drift caused by isolation and endogamy and therefore only tell us about that peculiarity of the European Far North. 

K=2 is surely the most informative level for East Asian genetic influence, except for  the already mentioned Italian anomaly (which may also affect to lesser extent Central Europeans). However because this study is so limited in this aspect, I'd encourage the development of more informative studies, which could for example ponder the FST distances between components, always informative, and/or use other population sampling strategies that better capture this aspect.

After all this is a study focused on Russia, even if that way it has also produced some valuable information for much of NE Europe.

Figure 3. Principal component analysis of the combined autosomal genotypic data of individuals from Russia and seven European countries (Finnland, Estonia, Latvia, Poland, Czech Republic, Germany [5] and Italia [22]).
The first two PCs are shown. The color legend for the predefined population labels is indicated within the plot. Population designations are the same as in Figure 1.

Appendix: Finno-Ugrian peoples/languages map by Marting/Nug (anti-copyright):