January 31, 2013

Y chromosome and mtDNA study of modern Middle Eastern populations (Badro et al. 2013)

I will just briefly comment on the occurrence of L3* mtDNA in the Near East. This is a critical haplogroup because of its age of ~70ky. If all L3* in the Near East represents African migrants, then only the M and N macrogroups appeared in Eurasia, and a good case can be made for a "late" OoA event.

On the other hand, it is quite possible that some of the L3* in the Near East does not represent recent admixture, but rather native forms of L3 with deep ancestry in the region. If that is the case, then the Near East will emerge as the origin of L3, with M, N representing Out-of-Near East-into-Eurasia founders, and the various L3*(xM, N) representing Out-of-Near East-into-Africa founders.

It is difficult to say at present what will turn out to be the case. Ancient DNA has the potential of resolving this issue, because if L3*(xM, N) in Eurasia is really recent (e.g., associated with Islamic/Arab dispersals spanning Africa and Eurasia), then it ought to be missing from the earliest genetic layers.

Also of interest the geographical distribution of Y-haplogroups; nothing much new here, but still useful as a reference:

PLoS ONE 8(1): e54616. doi:10.1371/journal.pone.0054616

Y-Chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations 

Danielle A. Badro et al.

The Middle East was a funnel of human expansion out of Africa, a staging area for the Neolithic Agricultural Revolution, and the home to some of the earliest world empires. Post LGM expansions into the region and subsequent population movements created a striking genetic mosaic with distinct sex-based genetic differentiation. While prior studies have examined the mtDNA and Y-chromosome contrast in focal populations in the Middle East, none have undertaken a broad-spectrum survey including North and sub-Saharan Africa, Europe, and Middle Eastern populations. In this study 5,174 mtDNA and 4,658 Y-chromosome samples were investigated using PCA, MDS, mean-linkage clustering, AMOVA, and Fisher exact tests of FST's, RST's, and haplogroup frequencies. Geographic differentiation in affinities of Middle Eastern populations with Africa and Europe showed distinct contrasts between mtDNA and Y-chromosome data. Specifically, Lebanon's mtDNA shows a very strong association to Europe, while Yemen shows very strong affinity with Egypt and North and East Africa. Previous Y-chromosome results showed a Levantine coastal-inland contrast marked by J1 and J2, and a very strong North African component was evident throughout the Middle East. Neither of these patterns were observed in the mtDNA. While J2 has penetrated into Europe, the pattern of Y-chromosome diversity in Lebanon does not show the widespread affinities with Europe indicated by the mtDNA data. Lastly, while each population shows evidence of connections with expansions that now define the Middle East, Africa, and Europe, many of the populations in the Middle East show distinctive mtDNA and Y-haplogroup characteristics that indicate long standing settlement with relatively little impact from and movement into other populations.

Genetic diversity of modern horses

Some very distinctive groupings of modern breeds emerge in this survey of modern horse breed genetic variation, and some of these groups have clear geographical associations.

Horses are very mobile, and can also be traded; much of their existing variation may also be the result of artificial breeding which might have included both selection for particular desirable traits as well as mixing different populations.

Now that there is a fairly clear picture of modern variation, it will be useful to explore how this has emerged over time. It'll be interesting to see how ancient horses fit into the modern picture: will they prove ancestral to those living in the same regions, or is there a process of continuous renewal, with multiple episodes of turnover, as good breeds emerge somewhere across the geographical range of the animal, and quickly replace less advantageous ones?
PLoS ONE 8(1): e54997. doi:10.1371/journal.pone.0054997

Genetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data

Jessica L. Petersen et al.

Horses were domesticated from the Eurasian steppes 5,000–6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. FST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection.


January 30, 2013

Breeding a (part-/quasi-) Neandertal the old-fashioned way

Razib has an interesting suggestion about how one could breed a Neandertal:
The most humane and viable manner in which you might do this is simply start a religion in a Bene Gesserit fashion where the prophesied Kwisatz Haderach is a Neandertal. Over the generations by selecting individuals within the population (which could draw in converts) enriched for Neandertal ancestry to mate assortatively one could slowly increase the proportion of that ancestral component. 
The idea is simple: if you mate two persons with x% and y% Neandertal ancestry, you will get (in the expected sense) a baby with 0.5(x+y)% Neandertal ancestry. In actuality the baby's Neandertal ancestry will be a random variable z with mean 0.5(x+y) and some variation around that mean.

Now, if x and y are very different from each other (e.g., at the limit you had crossed a full Neandertal with x=100% and a full sapiens with y=0%), then z will always be in-between x and y.

But, if x and y are fairly close to each other, it's possible that thanks to the wonders of recombination it will happen that z will be greater than both x and y, because the offspring might actually happen -by chance- to inherit many Neandertal alleles from both mom and dad.

Project the above procedure over the millennia, and it's easy to see how one might incrementally increase the proportion of Neandertal ancestry in the gene pool to an arbitrary degree: individuals might start with, say, 2% Neandertal ancestry, and given enough crossings per generation (so that enough individuals with >2% Neandertal ancestry will be produced), and enough generations, the number will inch along, and converge to 100%.

But, actually, reaching a 100% Neandertal might be impossible. To see why, consider that while many Neandertal alleles introgressed into the modern human population a few tens of thousands of years ago, surviving down to the present, some of them did not introgress and some that did were culled away by either drift or natural selection. 

Moreover, we might not be able to utilize all extant Neandertal alleles because we can mostly identify Neandertal-ness with respect to ancient DNA samples.

In other words, the modern human gene pool has a lot of Neandertal alleles floating around, but some of these don't look like Neandertal alleles (because we didn't find them in any ancient specimen yet), while others are simply long gone.

Such a breeding program would therefore not produce a Neandertal in the end, for the same reason that you cannot produce a grey hue by mixing different shades of red and blue: you also need some yellow. The modern human gene pool may have lots of Neandertal alleles but it may not have enough.

In any case, it would still be possible to create a, say, 50% Neandertal, or whatever the proportion of Neandertal alleles still in existence is. But, will such an individual be a Neandertal in the physical sense?

Which were the alleles that conferred Neandertal-ness to their bearers? We don't know, but this property may very well have involved both (i) combinations of alleles that exist in modern humans, and, (ii) alleles we no longer possess.

As an analogy, imagine that in the future, polar bears are extinct, but some of their DNA introgressed into other bear populations. Future zoologists might breed specimens that have a lot of polar bear alleles, but will lack the alleles conferring white coat color. Such a hypothetical breed of bear might possess a high degree of genome-wide similarity to actual polar bears, but it won't be the same where it counts.

Thus, it may very well be possible to create individuals from extinct human populations (be they archaic hominins such as Neandertals, or even admixed modern humans such as Tainos), but one might not get a 100% replica of such populations by breeding alone. Even if one was able to reconstruct a great part of such creatures' genome, the most important portions might still be missing.

January 26, 2013

Indonesian mega-study (Tumonggor et al. 2013)

A new comprehensive survey of Y chromosome/mtDNA variation in Indonesia has just appeared online. From the paper:
The first stage of Indonesian prehistory represents the archipelago’s initial settlement as part of the African dispersal ~50 kya. The geography of the region was then markedly different from today. Sea levels were much lower, most modern islands had merged into larger landmasses, and the westernmost parts of Indonesia were physically contiguous with mainland Asia. This first stage is recorded by deep mtDNA lineages (M17a, M73, M47, N21, N22, R21, R22 and R23), which trace back to the main branching of macrohaplogroups M and N, and have a spotty distribution across both mainland and island southeast Asia today.
The second stage reflects recurrent colonization events from mainland Asia throughout the later Paleolithic. Many haplogroups (B4a, B4b, B4c, B4c1b3, B5a, B5b, B5b1, D and E) show origin dates of 10-40 kya (Supplementary Table 6) 25, 63 and are distributed across a wide range of mainland and island southeast Asian populations. 
The third stage represents Neolithic movements into and around island southeast Asia. Some of these may involve population dispersals from (and perhaps to) Taiwan, while others reflect movements between Indonesian island groups. Representative haplogroups include M7b3, E1a1a, M7c3c and Y2. Autosomal data strongly supports large demic movements of Asian populations into eastern Indonesia from around 4 kya 67.
and, finally:
The fourth stage reflects historic movements into Indonesia, largely involving trade and the associated spread of major religions from India, Arabia and China 71. Although found at relatively low frequency today, Y chromosome lineages representing these movements occur across Indonesia 20, notably in the west, such as the Hindu dominated island of Bali
It would be useful to study Indonesian haplogroups as a means of testing the hypothesis of Indian settlement in Australia, since it is difficult to see any such settlement that would not have passed through the Indonesian archipelago.

Of the lineages found in Indonesia, the deepest ancestry appears to be associated with mtDNA haplogroups P (54+/-16ky) and Q (38+/-9ky), both of which appear to have clear "Australo-Melanesian" associations. Of the B subclades that are lately of interest due to the publication of Tianyuan ancient DNA, the oldest one appears to be B4a (33+/-13ky).

One of the major puzzles in prehistory is the co-occurrence of mtDNA macro-haplogroups M and N in the eastern portion of Eurasia vs. the dominance of N in the western part thereof. The peninsulas of Arabia and India probably hold a key to this riddle, although in both cases the situation is obscured by subsequent events: in Arabia, there has probably been substantial population turnover during its "desert" phases, while in India there has been recent admixture between the aboriginal population and West Eurasian-derived inhabitants.

Journal of Human Genetics , (24 January 2013) | doi:10.1038/jhg.2012.154

The Indonesian archipelago: an ancient genetic highway linking Asia and the Pacific 

Meryanne K Tumonggor et al.

Indonesia, an island nation linking mainland Asia with the Pacific world, hosts a wide range of linguistic, ethnic and genetic diversity. Despite the complexity of this cultural environment, genetic studies in Indonesia remain surprisingly sparse. Here, we report mitochondrial DNA (mtDNA) and associated Y-chromosome diversity for the largest cohort of Indonesians examined to date—2740 individuals from 70 communities spanning 12 islands across the breadth of the Indonesian archipelago. We reconstruct 50 000 years of population movements, from mitochondrial lineages reflecting the very earliest settlers in island southeast Asia, to Neolithic population dispersals. Historic contacts from Chinese, Indians, Arabs and Europeans comprise a noticeable fraction of Y-chromosome variation, but are not reflected in the maternally inherited mtDNA. While this historic immigration favored men, patterns of genetic diversity show that women moved more widely in earlier times. However, measures of population differentiation signal that Indonesian communities are trending away from the matri- or ambilocality of early Austronesian societies toward the more common practice of patrilocal residence today. Such sex-specific dispersal patterns remain even after correcting for the different mutation rates of mtDNA and the Y chromosome. This detailed palimpsest of Indonesian genetic diversity is a direct outcome of the region’s complex history of immigration, transitory migrants and populations that have endured in situ since the region’s first settlement.


Facial shape uncorrelated with aggression

Of interest is the calculation of sexual dimorphism for a variety of indices in different datasets (Figure 1; left). The figure caption:
Box and whisker plots of global sexual dimorphism computed across the different databases. Indices that differed significantly among sexes (after t-test for independent samples) are shown in solid grey. A) Howells database; b) Pucciarelli database, c) 2D Geometric Morphometric database, d) 3D Geometric Morphometric database, e) Patagonian groups database. Square: median; box: 25%–75%; whisker: minimum-maximum values.
Also of interest Figure S1 (bottom right), which breaks down the sexual dimorphism in different populations. The caption reads:
Box and whisker plots of fWHR depicting inter-sexual differences across the populations of each database. a) Howells database; b) Pucciarelli database, c) 2D Geometric Morphometric database, d) 3D Geometric Morphometric database, e) Patagonian groups database. Square: median; box: 25%–75%; whisker: minimum-maximum values. Orange: females, blue: males. Populations showing significantly greater male fWHR (after t-test for independent samples) are marked with grey boxes.
It would be nice if more anthropometric datasets were publicly available. Perhaps some of the above-mentioned are, but I didn't see any mention of how to obtain them in the paper itself.

PLoS ONE 8(1): e52317. doi:10.1371/journal.pone.0052317

Lack of Support for the Association between Facial Shape and Aggression: A Reappraisal Based on a Worldwide Population Genetics Perspective

Jorge Gómez-Valdés et al.

Antisocial and criminal behaviors are multifactorial traits whose interpretation relies on multiple disciplines. Since these interpretations may have social, moral and legal implications, a constant review of the evidence is necessary before any scientific claim is considered as truth. A recent study proposed that men with wider faces relative to facial height (fWHR) are more likely to develop unethical behaviour mediated by a psychological sense of power. This research was based on reports suggesting that sexual dimorphism and selection would be responsible for a correlation between fWHR and aggression. Here we show that 4,960 individuals from 94 modern human populations belonging to a vast array of genetic and cultural contexts do not display significant amounts of fWHR sexual dimorphism. Further analyses using populations with associated ethnographical records as well as samples of male prisoners of the Mexico City Federal Penitentiary condemned by crimes of variable level of inter-personal aggression (homicide, robbery, and minor faults) did not show significant evidence, suggesting that populations/individuals with higher levels of bellicosity, aggressive behaviour, or power-mediated behaviour display greater fWHR. Finally, a regression analysis of fWHR on individual's fitness showed no significant correlation between this facial trait and reproductive success. Overall, our results suggest that facial attributes are poor predictors of aggressive behaviour, or at least, that sexual selection was weak enough to leave a signal on patterns of between- and within-sex and population facial variation.


Paternal origins of Chinese cattle

The taurine/indicine north/central vs. south China makes sense. Also of interest, the dominance (within the taurine group) of Y2 over Y1 haplogroup. I had wished for more eastern data points when Edwards et al. was published and it now appears clear that at least in the case of China there is a predominance of the Y2 (southern) haplogroup within the taurine group of patrilineages.

Anim Genet. 2013 Jan 24. doi: 10.1111/age.12022. [Epub ahead of print]

Paternal origins of Chinese cattle.

Li R, Zhang XM, Campana MG, Huang JP, Chang ZH, Qi XB, Shi H, Su B, Zhang RF, Lan XY, Chen H, Lei CZ.

logy, Northwest A&F University, Yangling, Shaanxi, 712100, China. Abstract

To determine the genetic diversity and paternal origin of Chinese cattle, 302 males from 16 Chinese native cattle breeds as well as 30 Holstein males and four Burma males as controls were analysed using four Y-SNPs and two Y-STRs. In Chinese bulls, the taurine Y1 and Y2 haplogroups and indicine Y3 haplogroup were detected in seven, 172 and 123 individuals respectively, and these frequencies varied among the Chinese cattle breeds examined. Y2 dominates in northern China (91.4%), and Y3 dominates in southern China (90.8%). Central China is an admixture zone, although Y2 predominates overall (72.0%). The geographical distributions of the Y2 and Y3 haplogroup frequencies revealed a pattern of male indicine introgression from south to north China. The three Y haplogroups were further classified into one Y1 haplotype, five Y2 haplotypes and one Y3 haplotype in Chinese native bulls. Due to the interplay between taurine and indicine types, Chinese cattle represent an extensive reservoir of genetic diversity. The Y haplotype distribution of Chinese cattle exhibited a clear geographical structure, which is consistent with mtDNA, historical and geographical information.


Beware of who you kiss

Forensic Sci Int Genet. 2013 Jan;7(1):124-8. doi: 10.1016/j.fsigen.2012.07.007. Epub 2012 Aug 20.

Prevalence and persistence of male DNA identified in mixed saliva samples after intense kissing.

Kamodyová N, Durdiaková J, Celec P, Sedláčková T, Repiská G, Sviežená B, Minárik G.


Identification of foreign biological material by genetic profiling is widely used in forensic DNA testing in different cases of sexual violence, sexual abuse or sexual harassment. In all these kinds of sexual assaults, the perpetrator could constrain the victim to kissing. The value of the victim's saliva taken after such an assault has not been investigated in the past with currently widely used molecular methods of extremely high sensitivity (e.g. qPCR) and specificity (e.g. multiplex Y-STR PCR). In our study, 12 voluntary pairs were tested at various intervals after intense kissing and saliva samples were taken from the women to assess the presence of male DNA. Sensitivity-focused assays based on the SRY (single-copy gene) and DYS (multi-copy gene) sequence motifs confirmed the presence of male DNA in female saliva after 10 and even 60min after kissing, respectively. For specificity, standard multiplex Y-STR PCR profiling was performed and male DNA was found in female saliva samples, as the entire Y-STR profile, even after 30min in one sample. Our study confirms that foreign DNA tends to persist for a restricted period of time in the victim's mouth, can be isolated from saliva after prompt collection and can be used as a valuable source of evidence.


Ancestry Composition to be fixed

From the explanation at the relevant thread:
Ancestry Composition (AC) works by learning (training) a set of useful features from reference individuals with known ancestry (the training set) and then using these features to predict the ancestry of our customers.

Our set of reference individuals consists in part of customers who reported their 4 grandparents were born in the same country. Remember that we also remove the outliers, or people whose genetic ancestry doesn't match their survey answers. From this set, AC learns to associate certain haplotypes with their geographical origin. AC is then able to recognize similar haplotypes and thus to predict the ancestry of other customers.

However, when predicting the ancestry of reference individuals, AC suffers from overfitting, a problem common to many supervised learning methods. As a consequence, AC predicts the ancestry of most reference individuals as being 100% from their grandparents’ birthplace.

We addressed this issue using a method inspired from cross-validation. We divided the training set into 5 folds, each containing 20% of the reference individuals. We then trained 5 AC models in which each fold in turn is excluded from the set of reference individuals. So each of these models is learned using 80% of the reference individuals. Additionally, we retain the model that was trained using all the reference individuals. From this process, we end up with 6 different models from which we can predict the ancestry of our customers.

Now, when predicting the ancestry of a customer, we start by figuring out if he/she is a reference individual. If yes, we identify the fold in which the customer belongs, and we use the corresponding model for prediction. If not, we use the fold containing all of the reference data. This way, we ensure that AC was never trained using the haplotypes of the individual it tries to predict.
I had proposed basically the same solution about a month ago, and it's great that the issue is being addressed so soon after it first appeared. If any of the people who had written to me/commented on the topic get their new updated results and want to comment, feel free to do so in this post.

I am not sure how 23andMe plans to handle their Ancestry Composition feature in the future, but I would suggest that they periodically re-update it as they get more samples. According to a recent estimate, there are over 180,000 people in their database at the moment, a fraction of which meets the twin requirements of: (i) having 4 grandparents from the same country, and (ii) not being an outlier. As this number increases over time, it might be a good idea to occasionally re-partition the sample and re-calculate participants' ancestry composition results.

The fact that they are ready to roll out their updated results so soon after the initial ones tells me that they do have the computing power to do so, and it might be a good idea to update Ancestry Composition periodically, say on a quarterly basis or when a certain increase in the training set (say, 10%) is achieved. Eventually the admixture estimates may stabilize, in which case the way forward may involve rethinking the choice of ancestral populations currently in use.

January 25, 2013

The case for earlier Out-of-Africa (Boivin et al. 2013)

An informative review critical of the ~60kya coastal-Out-of-Africa hypothesis. On the left, the authors' estimate of the distribution of hominin groups during MIS5.

From the paper:
Another under-appreciated issue is the anomalous nature of the genetic evidence for a rapid spread of modern humans from Africa to Asia. Echoing the fossil date anomaly, the mtDNA branch lengths for sampled populations are longest for those which are farthest east, in Near Oceania, and shortest in the Asian areas that would have been encountered first (Merriwether et al., 2005; Oppenheimer, 2009). The real problem, however, is that the variation in branch lengths suggests that a single genotype engaged in the expansion actually existed for 30 ka, which does not support a rapid expansion. The anomaly can be explained by what we call an an ‘M buffer’ effect (see Supplementary material A) which implies that the branch ages we observe are considerable underestimates of the time of arrival of the genotype to these areas. Such anomalously long-lived genotypes have been directly observed through ancient DNA in species such as the Iberian lynx (Dalen et al., 2011).
We have focused here on the possibility that the modern human exit recorded by fossil evidence in the Levant in MIS 5 does not represent a failed dispersal, and that in fact our species was not only in the Levant but also the Arabian peninsula during this marine isotope stage, and spread to India before the Toba eruption at 74 ka (Petraglia et al., 2007). Another valid hypothesis we do not explore here is that H. sapiens was able to leave Africa in MIS 6 via a grassland corridor (Frumkin et al., 2011; see also Scally and Durbin, 2012). Yet another is that our species dispersed out of Africa shortly after its first appearance c. 195 ka, in MIS 7 (Dennell and Roebroeks, 2005: 1102). One other possibility is that there were several, separate dispersals of our species out of Africa (Dennell and Petraglia, 2012). At the same time, we acknowledge that major demographic changes occurred in MIS 4 and MIS 3, perhaps explaining the relatively young mtDNA coalescence age in living populations. The increasing evidence for complexity as well as the clear patterns of bias for all records, whether archaeological, fossil or genetic, suggests the need for an open mind to multiple scenarios for Out of Africa, as well as for more rather than less complex models of H. sapiens dispersal across Eurasia.
Quaternary International doi:10.1016/j.quaint.2013.01.008

Human Dispersal Across Diverse Environments of Asia during the Upper Pleistocene

Nicole Boivin et al.

The initial out of Africa dispersal of H. sapiens, which saw anatomically modern humans reach the Levant in Marine Isotope Stage 5, is generally regarded as a ‘failed dispersal’. Fossil, archaeological and genetic findings are seen to converge around a consensus view that a single population of H. sapiens exited Africa sometime around 60 thousand years ago (ka), and rapidly reached Australia by following a coastal dispersal corridor. We challenge the notion that current evidence supports this straightforward model. We argue that the fossil and archaeological records are too incomplete, the coastal route too problematic, and recent genomic evidence too incompatible for researchers not to remain fully open to other hypotheses. We specifically explore the possibility of a sustained exit by anatomically modern humans, drawing in particular upon palaeoenvironmental data across southern Asia to demonstrate its feasibility. Current archaeological, genetic and fossil data are not incompatible with the model presented, and appear to increasingly favour a more complex out of Africa scenario involving multiple exits, varying terrestrial routes, a sub-divided African source population, slower progress to Australia, and a degree of interbreeding with archaic varieties of Homo.


Diverse occupants of Hungarian kurgan

Antiquity Volume: 86 Number: 334 Page: 1097–1111

Immigration and transhumance in the Early Bronze Age Carpathian Basin: the occupants of a kurgan

Claudia Gerling

You never know until you look. The authors deconstruct a kurgan burial mound in the Great Hungarian Plain designated to the Yamnaya culture, to find it was actually shared by a number of different peoples. The Yamnaya were an influential immigrant group of the Late Copper Age/Early Bronze Age transition. The burials, already characterised by their grave goods, were radiocarbon dated and further examined using stable isotope analysis on the human teeth. The revealing sequence began with a young person of likely local origin buried around or even before the late fourth millennium BC—a few centuries before the arrival of the Yamnaya. It ended around 500 years later with a group of different immigrants, apparently from the eastern mountains. These are explained as contacts built up between the mountains and the plain through the practice of transhumance.


January 24, 2013

Upcoming Richard III documentary

From Channel 4:
With the support of historians, the University of Leicester's archaeologists identified a possible location of the monastery as the car park for Leicester City Council's Social Services department. However as Richard Buckley, Head of the University of Leicester's Archaeology Services tells the programme: "...the chance of finding Richard was, I don't know, a million to one." Yet the dig commenced and on the very first day a male skeleton was discovered - which careful examination would later reveal to have curvature of the spine and battle injuries including a head wound.

For the last three months, the remains has been subjected to some of the most cutting edge technology and forensic testing in existence - with Channel 4 capturing every moment. In specialist labs in Leicester and across the country, the bones have been subjected to CT scans, they have been carbon-dated, DNA has been extracted to be compared to that of one his living descendants, the source of the spinal curvature has been investigated - and the entire body has been subjected to rigorous testing to reveal blow-by-blow how this individual died and how he was buried.

Perhaps most fascinating of all, using technology developed to identify human remains in crime investigations, scientists have been busily re-creating the face these bones belong to - this image will be revealed exclusively in the programme the night it airs. And of course, Richard III: The King in the Car Park will reveal the results of what could be one of the most astonishing archaeological discoveries in recent history - whether England's missing king has indeed been recovered.
This will air on Feb 4.

January 23, 2013

Dog food

Diet Shaped Dog Domestication
The analysis turned up 36 regions, with 122 genes in all, that may have contributed to dog evolution, the team reports online today in Nature. Nineteen of these regions contain genes important for the brain, eight of which are involved with nervous system development, which makes sense given the importance of behavioral changes in the transition to becoming man's best friend, Axelsson notes.

More surprising were genes for digesting starch. Dogs had four to 30 copies of the gene for amylase, a protein that starts the breakdown of starch in the intestine. Wolves have only two copies, one on each chromosome. As a result, that gene was 28-fold more active in dogs, the researchers found. More copies means more protein, and test-tube studies indicate that dogs should be fivefold better than wolves at digesting starch, the chief nutrient in agricultural grains such as wheat and rice. The number of copies of this gene also varies in people: Those eating high carbohydrate diets -- such as the Japanese and European Americans -- have more copies than people with starch-poor diets, such as the Mbuti in Africa. "We have adapted in a very similar way to the dramatic changes that happened when agriculture was developed," Axelsson says.
Nature (2013) doi:10.1038/nature11837

The genomic signature of dog domestication reveals adaptation to a starch-rich diet

Erik Axelsson et al.

The domestication of dogs was an important episode in the development of human civilization. The precise timing and location of this event is debated1, 2, 3, 4, 5 and little is known about the genetic changes that accompanied the transformation of ancient wolves into domestic dogs. Here we conduct whole-genome resequencing of dogs and wolves to identify 3.8 million genetic variants used to identify 36 genomic regions that probably represent targets for selection during dog domestication. Nineteen of these regions contain genes important in brain function, eight of which belong to nervous system development pathways and potentially underlie behavioural changes central to dog domestication6. Ten genes with key roles in starch digestion and fat metabolism also show signals of selection. We identify candidate mutations in key genes and provide functional support for an increased starch digestion in dogs relative to wolves. Our results indicate that novel adaptations allowing the early ancestors of modern dogs to thrive on a diet rich in starch, relative to the carnivorous diet of wolves, constituted a crucial step in the early domestication of dogs.


Genetic evidence for the colonization of Australia

Quaternary International Volume 285, 8 February 2013, Pages 44–56

Genetic evidence for the colonization of Australia

Sheila van Holst Pellekaan et al.

Mitochondrial DNA (mtDNA), Y-chromosome and, more recently, genome studies from living people have produced powerful evidence for the dispersal of modern human populations. The prevailing model of global dispersion assumes an African origin in which Australia and the American continents represent some of the extreme regions of human migration, though the relative timing of dispersal events remains debatable. Here, a focus on Australia and New Guinea discusses currently available genetic evidence from the two regions, compared with that from Asia. Mt haplotypes indicate ancient ancestry for both Australia and New Guinea peoples, with evidence of some shared genetic connection and other unshared haplogroups apparently specific to both places. Migration into Sahul from south-east Asia may have been by more complex routes than only along a ‘southern coastal route’, raising the question of possible common ancestry in central or northern Asia for some Australian and American peoples for which current genetic evidence is tenuous. Although current dating methods for genetic diversity rely heavily on several assumptions, best estimates provide support for archaeological dates, indicating that, relative to the colonization of America, Australia was inhabited very early. Genetic diversity of living descendants of Australia’s founding populations is informative for dispersal within Australia and for understanding complex population histories of Asia.


Genomic history of Denmark

An announcement from the GeoGenetics centre:

The Genomic History of Denmark.
The centre has received a 36 mill. DKK grant from Univ. of Copenhagen's dedicated 2016-program. Researchers from GeoGenetics in close cooperation with collegues from the National Museum of Denmark and institutes at the University of Copenhagen will make Denmark the first country in the world to map its evolutionary, demographic and health history - from the earliest settlers through to modern times.

DNA and proteins extracted from a Danish collection of archaeological skeletons from the Older Stone Age (5000-3000 BC) will be analysed in order to learn more about the Danish cultural heritage and health history.

Professor and director of the Centre for GeoGenetics Eske Willerslev is project leader.

January 21, 2013

Ancient DNA from Tianyuan Cave

Another new PNAS paper that hasn't yet appeared in the journal website. Still, from this description at ScienceNews this appears to be Very Important, as it pertains to a 40,000-year-old modern human, which, if I'm not mistaken is the oldest modern human tested so far:
Ancient DNA from cell nuclei and maternally inherited mitochondria indicates that this individual belonged to a population that eventually gave rise to many present-day Asians and Native Americans, says a team led by Qiaomei Fu and Svante Paabo, evolutionary geneticists at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. 
The partial skeleton, unearthed in Tianyuan Cave near Beijing in 2003, carries roughly the same small proportions of Neandertal and Denisovan genes as living Asians do (SN: 8/25/12, p. 22), the scientists report online January 21 in the Proceedings of the National Academy of Sciences.
The Max Planck press release adds some information:
The genetic profile reveals that this early modern human was related to the ancestors of many present-day Asians and Native Americans but had already diverged genetically from the ancestors of present-day Europeans.
This is an important finding because some published demographic models had Europeans and East Eurasians diverging as recently as ~20 thousand years ago. It now appears that they did so already at around the time of the Upper Paleolithic revolution, when unambiguous evidence of modern humans across Eurasia exists.

UPDATE I: While we wait for this paper to appear on the PNAS website, it might be useful to wonder whether the Tianyuan sample might fall on the East Asian/Amerindian group or the more general "Ancestral South Indian" (ASI)/East Eurasian group.

According to current dating, haplogroup M itself is ~50 thousand years old, and most of the subclades therein coalesce to younger than 40ky times. It's possible that the Tianyuan sample dates from a period where ASI/East Asian differentiation had only just begun or was just about to begin.

The press release makes clear that Tianyuan was already "Asian" rather than generalized Eurasian, proving that East/West Eurasian differentiation had begun by ~40kya. It will be interesting to see whether it can be placed on a more specific "East Eurasian" group rather than a generalized "Asian" one.

UPDATE II: The paper is now online.

UPDATE III: From the paper:
Thus, it is related to the mtDNA that was ancestral to present-day haplogroup B (Fig. 1), which has been estimated to be around 50,000 y old (18) (50. 7 ka BP; 95% CI: 38.1–68.3 ka BP). We note that the age of the Tianyuan individual is compatible with this date.
So, it appears to be within macro-haplogroup N, with haplogroup B being, I think, a fairly unambiguously East Asian/Native American clade of the phylogeny. It will certainly be interesting to see how the much more successful -and younger- M subclades ended up dominating East Eurasia.

UPDATE IV: The TreeMix analysis clearly places Tianyuan within the Asian group, but does not resolve whether Papuans are an outgroup to East Asians/Tianyuan:

I guess that is expected (see my UPDATE I), since Tianyuan dates from a period where within-Asia differentiation had only just begun or was about to begin.

UPDATE V: With respect to sharing of alleles with archaic Eurasian hominins, the Tianyuan sample is within the modern range of variation.

PNAS doi: 10.1073/pnas.1221359110

DNA analysis of an early modern human from Tianyuan Cave, China

Qiaomei Fu et al.

Hominins with morphology similar to present-day humans appear in the fossil record across Eurasia between 40,000 and 50,000 y ago. The genetic relationships between these early modern humans and present-day human populations have not been established. We have extracted DNA from a 40,000-y-old anatomically modern human from Tianyuan Cave outside Beijing, China. Using a highly scalable hybridization enrichment strategy, we determined the DNA sequences of the mitochondrial genome, the entire nonrepetitive portion of chromosome 21 (~30 Mbp), and over 3,000 polymorphic sites across the nuclear genome of this individual. The nuclear DNA sequences determined from this early modern human reveal that the Tianyuan individual derived from a population that was ancestral to many present-day Asians and Native Americans but postdated the divergence of Asians from Europeans. They also show that this individual carried proportions of DNA variants derived from archaic humans similar to present-day people in mainland Asia.


Sweet potato genome provides link between South America and Polynesia

The actual PNAS paper seems to be still under embargo, but here's a news story in Science about the new research:

By analyzing genetic markers specific to sweet potatoes in both modern samples of the plant and older herbarium specimens, the researchers discovered significant differences between varieties found in the western Pacific versus the eastern Pacific. This finding supports the so-called tripartite hypothesis, which argues that the sweet potato was introduced to the region three times: first through premodern contact between Polynesia and South America, then by Spanish traders sailing west from Mexico, and Portuguese traders coming east from the Caribbean. The Spanish and Portuguese varieties ended up in the western Pacific, while the older South American variety dominated in the east, which would explain the genetic differences the French team saw.
Apart from the famous Heyerdahl voyage (which has recently become the subject of a 2012 movie), there was some other research regarding the introduction of Polynesian chickens to Chile. I have not followed the genetics of that part of the world very closely, but it's my impression that such a link between Polynesia and South America has not been found in the human populations of the two regions.

January 17, 2013

Deep mtDNA substructure in southern Africa (Barbieri et al. 2013)

The Khoisan have been used in many different ways in reconstructions of human history.

Being probably the most genetically diverse modern human population, they are occasionally viewed as akin to the ur-humans, with everyone else shedding diversity via founder effects as they moved away from a south African modern human urheimat.

They are also sometimes viewed as a basal branch of the human family tree, and they probably are -if modern humans are made to fit a tree model. But, modern humans didn't really evolve tree-like (some African farmers have Khoisan-like admixture, and the Khoisan themselves have relatively "shallow" common ancestry with other Africans and many Eurasians on account of their possession of a respectable frequency of Y-haplogroup E).

I have sometimes noted that in the case of South African groups were are lucky that the Khoisan exist as a discrete set of populations, making it easier to discern the legacy of South African hunter-gatherers in the genomes of immigrant farmers and pastoralists who converged southwards over the last few thousand years. This can be contrasted with the presumable situation in places like West Africa (the cradle of Sub-Saharan African farming), in which any indigenous hunter-gatherer groups have ceased to exist as distinct entities a long time ago.

A new AJHG paper sample south African genomes extensively and arrives at a startling conclusion. In the words of the authors:
Overall, the results of this analysis indicate that it is very unlikely that the highly divergent L0k1b/L0k2 lineages were incorporated into the Bantu-speaking populations via gene flow from a population that was ancestral to a Khoisan population in our sample but subsequently lost from the Khoisan population via drift. Instead, these results support the hypothesis that the ancestors of the Bantu-speaking populations carrying the divergent L0k lineages (who now live mainly in Zambia) experienced gene flow from a pre-Bantu population that is nowadays extinct. Alternatively, it is possible that descendants from this pre-Bantu population do exist but have not yet been included in population genetic studies; however, our extensive sampling of populations from Botswana, Namibia, andWest Zambia (which includes representatives of nearly all known Khoisan groups) makes it highly unlikely that this pre-Bantu Khoisan population has not yet been sampled.
In other words, we must resist the tendency to think of the Khoisan as representatives of all pre-Bantu south Africans. The Khoisan are certainly descendants of old south Africans, and represent a part of the pre-Bantu genetic landscape that retained its cultural distinctiveness (and hence can be nowadays sampled as a distinct population). But, there were other, now submerged, peaks in that landscape that are no longer extant in distinct form, but only in absorbed form in the gene pool of south African farmers.

This is fairly interesting in itself, and certainly ought to change our belief about what Africa looked like pre-Bantu expansion. We ought to think of, perhaps, a cornucopia of groups: many of them may have gone extinct; some may have been completely absorbed into more successful ones, and perhaps only a handful survive as distinct entities. Such a view would agree with the conclusions of physical anthropology about the persistence of archaic-leaning groups in parts of Africa down to the Holocene boundary.

The American Journal of Human Genetics, 17 January 2013 doi:10.1016/j.ajhg.2012.12.010

Ancient Substructure in Early mtDNA Lineages of Southern Africa

Chiara Barbieri et al.

Among the deepest-rooting clades in the human mitochondrial DNA (mtDNA) phylogeny are the haplogroups defined as L0d and L0k, which are found primarily in southern Africa. These lineages are typically present at high frequency in the so-called Khoisan populations of hunter-gatherers and herders who speak non-Bantu languages, and the early divergence of these lineages led to the hypothesis of ancient genetic substructure in Africa. Here we update the phylogeny of the basal haplogroups L0d and L0k with 500 full mtDNA genome sequences from 45 southern African Khoisan and Bantu-speaking populations. We find previously unreported subhaplogroups and greatly extend the amount of variation and time-depth of most of the known subhaplogroups. Our major finding is the definition of two ancient sublineages of L0k (L0k1b and L0k2) that are present almost exclusively in Bantu-speaking populations from Zambia; the presence of such relic haplogroups in Bantu speakers is most probably due to contact with ancestral pre-Bantu populations that harbored different lineages than those found in extant Khoisan. We suggest that although these populations went extinct after the immigration of the Bantu-speaking populations, some traces of their haplogroup composition survived through incorporation into the gene pool of the immigrants. Our findings thus provide evidence for deep genetic substructure in southern Africa prior to the Bantu expansion that is not represented in extant Khoisan populations.


Warlike Minoans

War was central to Europe's first civilization, contrary to popular belief
Research from the University of Sheffield has discovered that the ancient civilisation of Crete, known as Minoan, had strong martial traditions, contradicting the commonly held view of Minoans as a peace-loving people.

The research, carried out by Dr Barry Molloy of the University of Sheffield's Department of Archaeology, investigated the Bronze Age people of Crete, known by many as the Minoans, who created the very first complex urban civilisation in Europe.

"Their world was uncovered just over a century ago, and was deemed to be a largely peaceful society," explained Molloy. "In time, many took this to be a paradigm of a society that was devoid of war, where warriors and violence were shunned and played no significant role.

"That utopian view has not survived into modern scholarship, but it remains in the background unchallenged and still crops up in modern texts and popular culture with surprising frequency.
Personally, I'm not very surprised about this re-appraisal of the relationship of Minoans with war. There are multiple lines of evidence for Minoan power (e.g., the Thucydidean thalassocracy, the belief in Minos and Rhadamanthys as judges in Hades, the Theseus/Minotaur/Attican tributes legend) that have always suggested to me that the Bronze Age Cretans did not achieve pre-eminence only due to the attractiveness of their culture and/or their trading acumen, but also because they actually projected power by force.

One of the biggest arguments for Minoan pacifism was the lack of fortifications in Minoan sites. But, I've never found that argument convincing, because this lack might actually signify an excess of power (strong nations having no need of fortifications), and we need not forget that other unfortified city called Sparta, which, hopefully, no one could ever mistake as a champion of pacifism.

The Annual of the British School at Athens, 107, pp 87-142doi:10.1017/S0068245412000044


Barry P.C. Molloy

Together with politics, economics and religion, war is one of the fundamental factors that canshape a society and group identities. In the prehistoric world, the sources for the study of war are disparate and their interpretation can be inconsistent and problematic. In the case of Cretein the Bronze Age, a systematic analysis of the evidence will be undertaken for the first time inthis paper, and this opportunity is used to critically evaluate the most effective ways of employing the widely agreed sets of physical correlates for ancient war in the archaeological record. A further objective in exploring the diachronic roles of war in these societies is to movethe discussion from a niche field to a more integrated, and systematic, social analysis. Theexistence and character of a warrior identity is examined, and it is proposed that it oftenconstituted a conspicuous element of male identity. The varying scales and time spans throughwhich war can influence a society are discussed, and a broad framework for understanding war in social process, practices and events is proposed.


Assortative mating for height in the UK

PLoS ONE 8(1): e54186. doi:10.1371/journal.pone.0054186

Are Human Mating Preferences with Respect to Height Reflected in Actual Pairings?

Gert Stulp et al.

Pair formation, acquiring a mate to form a reproductive unit, is a complex process. Mating preferences are a step in this process. However, due to constraining factors such as availability of mates, rival competition, and mutual mate choice, preferred characteristics may not be realised in the actual partner. People value height in their partner and we investigated to what extent preferences for height are realised in actual couples. We used data from the Millennium Cohort Study (UK) and compared the distribution of height difference in actual couples to simulations of random mating to test how established mate preferences map on to actual mating patterns. In line with mate preferences, we found evidence for: (i) assortative mating (r = .18), (ii) the male-taller norm, and, for the first time, (iii) for the male-not-too-tall norm. Couples where the male partner was shorter, or over 25 cm taller than the female partner, occurred at lower frequency in actual couples than expected by chance, but the magnitude of these effects was modest. We also investigated another preference rule, namely that short women (and tall men) prefer large height differences with their partner, whereas tall women (and short men) prefer small height differences. These patterns were also observed in our population, although the strengths of these associations were weaker than previously reported strength of preferences. We conclude that while preferences for partner height generally translate into actual pairing, they do so only modestly.


Complete mtDNA sequences and the history of Slavs

PLoS ONE 8(1): e54360. doi:10.1371/journal.pone.0054360

The History of Slavs Inferred from Complete Mitochondrial Genome Sequences

Marta Mielnik-Sikorska et al.

To shed more light on the processes leading to crystallization of a Slavic identity, we investigated variability of complete mitochondrial genomes belonging to haplogroups H5 and H6 (63 mtDNA genomes) from the populations of Eastern and Western Slavs, including new samples of Poles, Ukrainians and Czechs presented here. Molecular dating implies formation of H5 approximately 11.5–16 thousand years ago (kya) in the areas of southern Europe. Within ancient haplogroup H6, dated at around 15–28 kya, there is a subhaplogroup H6c, which probably survived the last glaciation in Europe and has undergone expansion only 3–4 kya, together with the ancestors of some European groups, including the Slavs, because H6c has been detected in Czechs, Poles and Slovaks. Detailed analysis of complete mtDNAs allowed us to identify a number of lineages that seem specific for Central and Eastern Europe (H5a1f, H5a2, H5a1r, H5a1s, H5b4, H5e1a, H5u1, some subbranches of H5a1a and H6a1a9). Some of them could possibly be traced back to at least ~4 kya, which indicates that some of the ancestors of today's Slavs (Poles, Czechs, Slovaks, Ukrainians and Russians) inhabited areas of Central and Eastern Europe much earlier than it was estimated on the basis of archaeological and historical data. We also sequenced entire mitochondrial genomes of several non-European lineages (A, C, D, G, L) found in contemporary populations of Poland and Ukraine. The analysis of these haplogroups confirms the presence of Siberian (C5c1, A8a1) and Ashkenazi-specific (L2a1l2a) mtDNA lineages in Slavic populations. Moreover, we were able to pinpoint some lineages which could possibly reflect the relatively recent contacts of Slavs with nomadic Altaic peoples (C4a1a, G2a, D5a2a1a1).


Moldavian Y-chromosomes

The most salient feature is probably the absence of E-V13 (which is modal in Balkan populations) in Ukrainians. The position of Moldavians in the MDS plot of haplogroup frequencies is as expected, with a clear differentiation of "southern" populations from Italy, Greece/Albania, and Anatolia, and "northern" ones from the west Balkans (ex-Yugoslavs) and eastern Europe: Moldavians occupy an intermediate position along this second group of populations.

PLoS ONE 8(1): e53731. doi:10.1371/journal.pone.0053731

Paleo-Balkan and Slavic Contributions to the Genetic Pool of Moldavians: Insights from the Y Chromosome

Alexander Varzari et al.

Moldova has a rich historical and cultural heritage, which may be reflected in the current genetic makeup of its population. To date, no comprehensive studies exist about the population genetic structure of modern Moldavians. To bridge this gap with respect to paternal lineages, we analyzed 37 binary and 17 multiallelic (STRs) polymorphisms on the non-recombining portion of the Y chromosome in 125 Moldavian males. In addition, 53 Ukrainians from eastern Moldova and 54 Romanians from the neighboring eastern Romania were typed using the same set of markers. In Moldavians, 19 Y chromosome haplogroups were identified, the most common being I-M423 (20.8%), R-M17* (17.6%), R-M458 (12.8%), E-v13 (8.8%), R-M269* and R-M412* (both 7.2%). In Romanians, 14 haplogroups were found including I-M423 (40.7%), R-M17* (16.7%), R-M405 (7.4%), E-v13 and R-M412* (both 5.6%). In Ukrainians, 13 haplogroups were identified including R-M17 (34.0%), I-M423 (20.8%), R-M269* (9.4%), N-M178, R-M458 and R-M73 (each 5.7%). Our results show that a significant majority of the Moldavian paternal gene pool belongs to eastern/central European and Balkan/eastern Mediterranean Y lineages. Phylogenetic and AMOVA analyses based on Y-STR loci also revealed that Moldavians are close to both eastern/central European and Balkan-Carpathian populations. The data correlate well with historical accounts and geographical location of the region and thus allow to hypothesize that extant Moldavian paternal genetic lineages arose from extensive recent admixture between genetically autochthonous populations of the Balkan-Carpathian zone and neighboring Slavic groups.


January 15, 2013

Climate and history (in Eastern Europe)

PNAS doi: 10.1073/pnas.1211485110

Filling the Eastern European gap in millennium-long temperature reconstructions

Ulf Büntgen et al.

Tree ring–based temperature reconstructions form the scientific backbone of the current global change debate. Although some European records extend into medieval times, high-resolution, long-term, regional-scale paleoclimatic evidence is missing for the eastern part of the continent. Here we compile 545 samples of living trees and historical timbers from the greater Tatra region to reconstruct interannual to centennial-long variations in Eastern European May–June temperature back to 1040 AD. Recent anthropogenic warming exceeds the range of past natural climate variability. Increased plague outbreaks and political conflicts, as well as decreased settlement activities, coincided with temperature depressions. The Black Death in the mid-14th century, the Thirty Years War in the early 17th century, and the French Invasion of Russia in the early 19th century all occurred during the coldest episodes of the last millennium. A comparison with summer temperature reconstructions from Scandinavia, the Alps, and the Pyrenees emphasizes the seasonal and spatial specificity of our results, questioning those large-scale reconstructions that simply average individual sites.


Ancient mtDNA from Santimamiñe Cave

I see press releases and news stories on this cave from time to time, but I haven't actually located any published studies. If anyone is aware of more information, feel free to leave a comment.

Genetic research reveals that current population of Urdaibai probably descended from cave dwellers at Santimamiñe

The comparison of DNA extracted from a Homo sapiens who inhabited the Santimamine Cave (in the Basque province of Biscay) some 4,000 years ago, and from 6 other bone remains found in the same cave, with the DNA of 158 persons currently living in the surrounding Urdaibai region, has shown that current individuals have maternal lineages very similar to the archaeological remains. The findings enable putting forward the hypothesis that the current population is descended from the ancient denizens of the Santimamine Cave. 
The research received funding from the Department of Culture of the Provincial Government of Bizkaia, as well as from the Urdaibai District Authority. Once the research in Urdabai is concluded, it is hoped that, shortly, it will be extended to other regions of the Basque Country, using new studies of funerary sites from the same period and from other eras (the Copper Age, the Bronze Age, etc.) thus enabling extending the knowledge we currently have on the special characteristics of the Basque population. This populational group has sparked enormous scientific interest for its distinctive characteristics regarding the preservation of its pre-Indo-European language and its relative isolation from the influence of other peoples and cultures.

January 14, 2013

Gene flow between Indian populations and Australasia ~4,000 years ago

Only the press release is available so far, I will add the paper abstract when I see it on the PNAS website:

Researcher Irina Pugach and colleagues now analysed genetic variation from across the genome from aboriginal Australians, New Guineans, island Southeast Asians, and Indians. Their findings suggest substantial gene flow from India to Australia 4,230 years ago. i.e. during the Holocene and well before European contact. “Interestingly,” says Pugach, “this date also coincides with many changes in the archaeological record of Australia, which include a sudden change in plant processing and stone tool technologies, with microliths appearing for the first time, and the first appearance of the dingo in the fossil record. Since we detect inflow of genes from India into Australia at around the same time, it is likely that these changes were related to this migration.” 
Their analyses also reveal a common origin for populations from Australia, New Guinea and the Mamanwa – a Negrito group from the Philippines – and they estimated that these groups split from each other about 36,000 years ago. Mark Stoneking says: “This finding supports the view that these populations represent the descendants of an early ‘southern route’ migration out of Africa, while other populations in the region arrived later by a separate dispersal.“ This also indicates that Australians and New Guineans diverged early in the history of Sahul, and not when the lands were separated by rising sea waters around 8,000 years ago.
A relationship between Indian and Australasian populations has long been suspected on various grounds (e.g., HGDP Papuans often show membership in a "South Asian" ancestral component at low levels of resolution). It will be interesting to see the model proposed in the new paper about the admixture event leading to modern Australasians.

UPDATE: Ed Yong covers the story in Nature News:

Some aboriginal Australians can trace as much as 11% of their genomes to migrants who reached the island around 4,000 years ago from India, a study suggests. Along with their genes, the migrants brought different tool-making techniques and the ancestors of the dingo, researchers say1.
From World News Australia:

The study suggests that in addition to an earlier northern route of migration out of Africa, into Asia, and then South East Asia about 60,000 to 70,000 years ago, the second wave occurred much later, arriving during the Holocene period about 4,230 years ago.
“About that point in the archaeological record, there were significant changes in the use of stone tools, in hunting techniques and significantly, the introduction of the dingo,” Professor Cooper said.
There are other theories that may support the evidence of a more recent influx of migrants from India, including that they brought with them a disease of epidemic proportions that wiped out earlier Aboriginal populations.

UPDATE II: I added the abstract.

PNAS doi: 10.1073/pnas.1211927110

Genome-wide data substantiate Holocene gene flow from India to Australia 

Irina Pugach et al.

The Australian continent holds some of the earliest archaeological evidence for the expansion of modern humans out of Africa, with initial occupation at least 40,000 y ago. It is commonly assumed that Australia remained largely isolated following initial colonization, but the genetic history of Australians has not been explored in detail to address this issue. Here, we analyze large-scale genotyping data from aboriginal Australians, New Guineans, island Southeast Asians and Indians. We find an ancient association between Australia, New Guinea, and the Mamanwa (a Negrito group from the Philippines), with divergence times for these groups estimated at 36,000 y ago, and supporting the view that these populations represent the descendants of an early “southern route” migration out of Africa, whereas other populations in the region arrived later by a separate dispersal. We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact, contrary to the prevailing view that there was no contact between Australia and the rest of the world. We estimate this gene flow to have occurred during the Holocene, 4,230 y ago. This is also approximately when changes in tool technology, food processing, and the dingo appear in the Australian archaeological record, suggesting that these may be related to the migration from India.


Haplotype of Neandertal origin in OAS gene cluster in Eurasians


Mol Biol Evol (2013) doi: 10.1093/molbev/mst004

Neandertal origin of genetic variation at the cluster of OAS immunity genes

Fernando L. Mendez et al.

Analyses of ancient DNA from extinct humans reveal signals of at least two independent hybridization events in the history of non-African populations. To date there are very few examples of specific genetic variants that have been rigorously identified as introgressive. Here we survey DNA sequence variation in the OAS gene cluster on chromosome 12 and provide strong evidence that a haplotype extending for ~185 kb introgressed from Neandertals. This haplotype is nearly restricted to Eurasians and is estimated to have diverged from the Neandertal sequence ~125 kya. Despite the potential for novel functional variation, the observed frequency of this haplotype is consistent with neutral introgression. This is the second locus in the human genome, after STAT2, carrying distinct haplotypes that appear to have introgressed separately from both Neandertals and Denisova.


Multiplex determination of eye and hair color

From the paper:
Sample S24 represents a controversial case from the Benedictine Abbey in  Tyniec near Krakow. During the work undertaken in the crypt of the St. Peter and Paul  church belonging to the Abbey, 17 skeletons of alleged abbots were found. The burial was  dated to the period of the 12th to 14th centuries. Unexpectedly, the anthropological  examination revealed that two skeletons may be of female origin, which indeed was  confirmed by DNA analysis (data not shown), while only male monks were expected. One of the two DNA samples was sufficiently preserved to enable analysis of other nuclear markers  (data not shown) and was used here for HIrisPlex analysis. The mysterious woman was  predicted to have dark blond/brown hair (accuracy of 78.5%) and brown eyes (accuracy of 90.4%), (Table 2 and Figure 2B). 
Two medieval  skeletons were found under the floor between the chancel and the nave of the church. Based  on historical markers the grave was dated to originate from the 14th century. Further  anthropological examinations indicated that the S25 male died at the approximate age of 60,  whereas the S26 male was approximately 75 years old at the time of death. It is alleged that  the skeletons belong to members of the Teczynski family, representing noble Polish magnates  of medieval times. The tooth collected from the deeper burial (S25) was found to be seriously  affected by decay, which was reflected by a very low DNA concentration (3 pg/µl) and  incomplete autosomal and Y chromosome STR profiles (NGM and Yfiler). Complete  mtDNA HVI and HVII profiles were generated in both teeth (data not shown). From these  data it was possible to conclude that both skeletons are of male origin and are unrelated in  both maternal and paternal lines. From the partial HIrisPlex profile ascertained from S25 we  successfully inferred blue eye colour (P = 0.899, accuracy of 95.6%), but hair colour could  not be inferred because of missing genotypes at three DNA variants (N29insA, rs1805005,  rs2228479). The sample S26 revealed a prediction of blond hair colour (P = 0.784) together  with a light hair colour shade (P = 0.918) concluding that the individual had light blond hair  (accuracy of 69.5%). Eye colour prediction of S26 revealed blue eyes (P = 0.919, accuracy of  97.4%) (Table 2).
Wikipedia article on Tęczyński family.

Investigative Genetics 2013, 4:3 doi:10.1186/2041-2223-4-3

Bona fide colour: DNA prediction of human eye and hair colour from ancient and contemporary skeletal remains

Jolanta Draus-Barini

Abstract (provisional)


DNA analysis of ancient skeletal remains is invaluable in evolutionary biology for exploring the history of species, including humans. Contemporary human bones and teeth, however, are relevant in forensic DNA analyses that deal with the identification of perpetrators, missing persons, disaster victims or family relationships. They may also provide useful information towards unravelling controversies that surround famous historical individuals. Retrieving information about a deceased person's externally visible characteristics can be informative in both types of DNA analyses. Recently, we demonstrated that human eye and hair colour can be reliably predicted from DNA using the HIrisPlex system. Here we test the feasibility of the novel HIrisPlex system at establishing eye and hair colour of deceased individuals from skeletal remains of various post-mortem time ranges and storage conditions.


Twenty-one teeth between 1 and approximately 800 years of age and 5 contemporary bones were subjected to DNA extraction using standard organic protocol followed by analysis using the HIrisPlex system.


Twenty-three out of 26 bone DNA extracts yielded the full 24 SNP HIrisPlex profile, therefore successfully allowing model-based eye and hair colour prediction. HIrisPlex analysis of a tooth from the Polish general W[latin small letter l with stroke]adys[latin small letter l with stroke]aw Sikorski (1881 to 1943) revealed blue eye colour and blond hair colour, which was positively verified from reliable documentation. The partial profiles collected in the remaining three cases (two contemporary samples and a 14th century sample) were sufficient for eye colour prediction.


Overall, we demonstrate that the HIrisPlex system is suitable, sufficiently sensitive and robust to successfully predict eye and hair colour from ancient and contemporary skeletal remains. Our findings, therefore, highlight the HIrisPlex system as a promising tool in future routine forensic casework involving skeletal remains, including ancient DNA studies, for the prediction of eye and hair colour of deceased individuals.


January 11, 2013

Neandertal origin of Châtelperronian; likely modern human origin of Châtelperronian body ornamentation


PNAS doi: 10.1073/pnas.1212924109

Radiocarbon dates from the Grotte du Renne and Saint-Césaire support a Neandertal origin for the Châtelperronian

Jean-Jacques Hublin et al.

The transition from the Middle Paleolithic (MP) to Upper Paleolithic (UP) is marked by the replacement of late Neandertals by modern humans in Europe between 50,000 and 40,000 y ago. Châtelperronian (CP) artifact assemblages found in central France and northern Spain date to this time period. So far, it is the only such assemblage type that has yielded Neandertal remains directly associated with UP style artifacts. CP assemblages also include body ornaments, otherwise virtually unknown in the Neandertal world. However, it has been argued that instead of the CP being manufactured by Neandertals, site formation processes and layer admixture resulted in the chance association of Neanderthal remains, CP assemblages, and body ornaments. Here, we report a series of accelerator mass spectrometry radiocarbon dates on ultrafiltered bone collagen extracted from 40 well-preserved bone fragments from the late Mousterian, CP, and Protoaurignacian layers at the Grotte du Renne site (at Arcy-sur-Cure, France). Our radiocarbon results are inconsistent with the admixture hypothesis. Further, we report a direct date on the Neandertal CP skeleton from Saint-Césaire (France). This date corroborates the assignment of CP assemblages to the latest Neandertals of western Europe. Importantly, our results establish that the production of body ornaments in the CP postdates the arrival of modern humans in neighboring regions of Europe. This new behavior could therefore have been the result of cultural diffusion from modern to Neandertal groups.


Decoding Neanderthals

I finished watching Decoding Neandertals (trailer below):

Much of what was mentioned in the program would not be new to readers of this blog. A couple of things that stood out for me was the demonstration of "Neanderthal pyrotechnics" by Wil Roebroeks. Related articles:

John Hawks also mentioned his findings about differential Neandertal admixture across Eurasia on the basis of the 1000 Genomes data, with Europeans having more than East Asians, and Tuscans having the most. This seems superficially at odds with the findings of Meyer et al. (2012), according to which:
We estimate that the proportion of Neandertal ancestry in Europe is 24% lower than in eastern Asia and South America (95% C.I. 12-36%).
It will be interesting to see Dr. Hawks's study when it is published. But, it seems to me that there might not be a real difference between the Hawks and Meyer et al. findings, because the former seem to be counting shared derived alleles, and Europeans would have more of those than East Asians, simply because they are more heterozygous across the genome, and Italians more than Britons. An ASHG 2012 abstract  also seems to  find more Neandertal-derived alleles in Europeans than in East Asians. So, it might seem that Europeans have inherited a more varied set of "stuff" from Neandertals, but East Asians inherited a larger portion of their ancestry from Neandertals overall.

On the topic of documentaries, I found the recent Prehistoric Autopsy to be extremely good, and you can probably find it fairly easily online if you don't happen to live in the UK.

January 10, 2013

Genetic variation in gorillas quantified (Scally et al. 2013)

The allele frequency spectrum (Figure 3) from the paper is shown on the left. From the paper:

Figure 3 shows the resulting mean conditional AFS for nine western lowland gorillas (excluding the three lowest-coverage samples as above), and comparable samples from three human populations whose ancestry derives from Africa, Asia and Europe [22]. In a population whose effective size has remained constant, the theoretical expectation for such a conditional AFS is a straight line of constant negative slope [23], shown by the dashed line in Figure 3. Compared to this, western lowland gorillas show a deficit of rare alleles, consistent with their having undergone genetic drift due to a bottleneck or other reduction in effective population size during their demographic history. The similar signal in non-African human populations has been attributed to population contraction associated with the out-of-Africa event [24]. By contrast to the gorillas and the non-African humans, the African YRI population in Figure 3 shows an excess of rare alleles, consistent with population expansion and again similar to the signal seen in other African human data [24]. 

A population bottleneck culls rare alleles, and thus leads to a "dip" in the AFS on the left. An allele that occurs at, say, 10% frequency in a very small population is more likely to go extinct "by accident" than one which occurs at exactly the same frequency in a large population. You can think of this by taking the two extreme cases:

  1. if an allele exists in exactly one physical copy (i.e., 1 copy in 5 diploid individuals = 10% frequency), then its bearer must survive, must reproduce, and the allele must be inherited by one offspring in order for it survive.
  2. if the population has infinite size, then 10% frequency is still = infinite number of physical copies, hence the allele will survive no matter what [unless it always kills its unlucky bearer, but then how did it end up at 10% frequency in the first place?]

On the other hand, low-frequency alleles become more prevalent when the population expands in the recent past, because there is an ever growing number of bodies, an ever growing number of mutated alleles, but not enough time for these new alleles to grow in frequency.

A different mechanism whereby low-frequency alleles appear in excess in a population is admixture. African Americans, for example, have ~20% European ancestry, so any alleles that are present in Europeans and absent in Sub-Saharan Africans would tend to appear as low-frequency alleles in African Americans.

It is an open question to what degree modern human differences in the presence of low-frequency alleles are due to bottlenecks (such as the Out-of-Africa event) and to what degree they are due to admixture with other non-modern groups. A recent paper discovered a signal of Neandertal admixture when one considered alleles with 10% or less frequency in Europeans.

In the case of African Americans, we can tell that some of their low-frequency alleles were acquired by admixture with Europeans, because we have European samples; and, in the case of Europeans, we can tell that some of their low-frequency alleles were acquired by admixture with Neandertals, because we have a Neandertal genome. But, we don't have many of the genomes of archaic human groups that may have contributed variants to modern humans (and in some cases, like the Denisovans, we did not even know they existed in the first place!), so we must always keep in mind the possibility that such alleles may lurk on the left side of the AFS.

arXiv:1301.1729 [q-bio.PE]

A genome-wide survey of genetic variation in gorillas using reduced representation sequencing

Aylwyn Scally et al.

All non-human great apes are endangered in the wild, and it is therefore important to gain an understanding of their demography and genetic diversity. To date, however, genetic studies within these species have largely been confined to mitochondrial DNA and a small number of other loci. Here, we present a genome-wide survey of genetic variation in gorillas using a reduced representation sequencing approach, focusing on the two lowland subspecies. We identify 3,274,491 polymorphic sites in 14 individuals: 12 western lowland gorillas (Gorilla gorilla gorilla) and 2 eastern lowland gorillas (Gorilla beringei graueri). We find that the two species are genetically distinct, based on levels of heterozygosity and patterns of allele sharing. Focusing on the western lowland population, we observe evidence for population substructure, and a deficit of rare genetic variants suggesting a recent episode of population contraction. In western lowland gorillas, there is an elevation of variation towards telomeres and centromeres on the chromosomal scale. On a finer scale, we find substantial variation in genetic diversity, including a marked reduction close to the major histocompatibility locus, perhaps indicative of recent strong selection there. These findings suggest that despite their maintaining an overall level of genetic diversity equal to or greater than that of humans, population decline, perhaps associated with disease, has been a significant factor in recent and long-term pressures on wild gorilla populations.


Blue eyes, facial shape, and perceived trustworthiness

A new paper suggests that Czechs tend to view brown-eyed people as more trustworthy than blue-eyed ones, although the difference seems to be due to differences in facial structure between brown- and blue-eyed people; an article in Scientific American covers this new paper fairly well.

I will add that the location of the sample (Czech Republic) is interesting, as it is intermediate between the Baltic area (where light eye pigmentation reaches quasi-fixation, and, hence, presumably, light eyes are not viewed with any suspicion) and southeastern Europe and Anatolia (where there is well-documented folklore about the association of eye pigmentation with the "evil eye").

I had encountered an explanation for this phenomenon in a work by P.G. Maxwell-Stuart on ancient color terminology, in which an argument was made that in predominantly dark-eyed peoples, light eyes -because of their rarity- may have an indirect association with glaucoma and viewed suspiciously for that reason -perceived chance of morbidity; the Wikipedia article suggests the phenomenon is explained on the basis of encounters with light-eyed foreigners who might be unaware of cultural norms against direct staring. But, the frequency of different eye colors in Czechs today is probably fairly balanced, making either explanation unsatisfactory.

Getting back to the article at hand, it appears that -at least in men- blue eyes are associated with a suite of other facial features. Razib offers the suggestion that the possible disadvantage conferred by reduced "trustworthiness" may be compensated in another way through pleiotropy, and the authors suggest:
The trade-off between a preference for colorful and visible physical features and the advantage of a trustworthy-looking face might have contributed to the high variability of European eye and hair color.
But, I'll get back to the possibility that the phenomenon may be driven by a historical process, i.e., the encounter between peoples who differed statistically in eye pigmentation and other facial features.

The picture on the left is from the Gospel Book of Otto III and is about 1,000 years old. Now, all eyes appear conventionally painted as brown dots here, but we can notice that the different provinces are painted with different hair color, with Sclavinia being darker than Germania and lighter than Gallia and Roma. This might make some sense, since Germanic peoples are thought to have originated in northern Germany/southern Scandinavia, and Slavs in C/E Europe (perhaps somewhere between Poland and Ukraine).

This raises the possibility that early Slavs were phenotypically somewhere in the middle of the European pigmentation continuum, although their exact position therein might only be determined with ancient DNA evidence. Today, the lighter-pigmented Slavs are probably those close to the Baltic (e.g., Russians and Poles), the darker ones from the Balkans, perhaps indicating different types of gene flow ("northern" Germanic/Baltic/Finno-Ugrian vs. "southern" Thraco-Illyrian-Greek).

If this is correct, then the slightly negative association of blue eyes in the present Czechs might be a culturally-transmitted vestige of inter-ethnic contact during the medieval period. A possible test would be to repeat the experiment with the Czechs' German neighbors, in which the process ought to operate in reverse -if my hypothesis is correct.

PLoS ONE 8(1): e53285. doi:10.1371/journal.pone.0053285

Trustworthy-Looking Face Meets Brown Eyes

Karel Kleisner et al.

We tested whether eye color influences perception of trustworthiness. Facial photographs of 40 female and 40 male students were rated for perceived trustworthiness. Eye color had a significant effect, the brown-eyed faces being perceived as more trustworthy than the blue-eyed ones. Geometric morphometrics, however, revealed significant correlations between eye color and face shape. Thus, face shape likewise had a significant effect on perceived trustworthiness but only for male faces, the effect for female faces not being significant. To determine whether perception of trustworthiness was being influenced primarily by eye color or by face shape, we recolored the eyes on the same male facial photos and repeated the test procedure. Eye color now had no effect on perceived trustworthiness. We concluded that although the brown-eyed faces were perceived as more trustworthy than the blue-eyed ones, it was not brown eye color per se that caused the stronger perception of trustworthiness but rather the facial features associated with brown eyes.