BARCODE and the dating of sub-haplogroups

A new paper introduces BARCODE, a new software program that can be used to infer the age of different sub-haplogroups. The age is presented as a fraction of the time for the entire haplogroup, thus allowing for the comparative dating of the antiquity of lineages. Below is the dating of several sub-haplogroups within Y-haplogroups E, J, and I.



Human Genetics (Online first)

Independent methods for evolutionary genetic dating provide insights into Y-chromosomal STR mutation rates confirming data from direct father–son transmissions

Francesca Luca et al.

Abstract Five datasets consisting of samples jointly typed for Y-chromosomal Unique Event Polymorphism (UEP) and simple tandem repeat (STR) markers were re-examined with independent methods for dating the different UEP-defined lineages. We report on the results obtained with an original program which performs comparative dating (BARCODE) in comparison with coalescent analyses performed with BATWING under various prior conditions. For the first time these are equalized across datasets. We also report on the results concerning STR mutability as obtained with both methods. The dating results for the entire series of sub-haplogroups are highly correlated. Within coalescent analyses, dating-estimates under a wide range of priors tend to converge. As to STR mutation rates the main findings are: (1) large variations among loci within the same dataset with both methods, also when the same prior was used for all loci; (2) figures in most cases above 1×10−3 and often above 2×10−3; (3) a few loci that mutate differently across studies. These results closely match those obtained from direct observation of father–son transmissions. Overall, this work supports the use of genetic dating procedures that take into account the complexity of the phenomenon, with a repertoire of priors tailored on the particular dataset.

Link

Blind test of DNA BioScience

DNA Bioscience is a British firm which offers (among other things) the Ancestry By DNA test. Recently, the company was featured in a Guardian story, in which four journalists from the paper submitted their DNA samples and the company predicted their skin color and ethnic origin. Person A was an Eastern European Jew who was predicted as being European with East Asian admixture, a reasonable finding, since both Ashkenazi Jews and eastern Slavs have some degree of Asian admixture. Person B was a Sub-Saharan African who was classified as such, again a reasonable result. Person C was a native Briton who was however given minor Native American ancestry, again underscoring the tendency of the test to wrongly predict such ancestry in persons without any possible Native American connection. Person D was a native Indian. The company shrewdly inferred his origin, even though a European-East Asian-Sub-Saharan-Native American mix does not reflect the origin of Indians. The suggestions that the individual had East Asian grandparents or his ancestors reached Britain through Africa (to explain the Sub-Saharan component) are of course rationalizations, and a good example of a case where this type of test is not useful.

All in all, this small test establishes once again the strength of admixture testing in predicting majority ancestry, its overreporting of minority ancestry that does not exist, and its difficulty in dealing with populations that fall outside the group of a priori chosen populations.

Stability of British height in England since the Neolithic

Medieval ancestors measured up to our height standards

OUR ANCESTORS were as tall as we are, contrary to popular belief. Over the past five millennia the average height of men in Britain has remained stable at about 170cm (5ft 7in), and that of women at 160cm (5ft 3in).

Link

Botai and horse domestication

See also the updated entry on the redating of the Dereivka stallion, including some comments from Dr. David Anthony. Now that Dereivka has been redated as belonging to the Scythian Iron Age, the Botai (east of the Urals) represents the earliest evidence of possible horse riding. Levine writes:

Another example of this commitment to an earliest date is Anthony’s argument that the domesticated horse was present in the Ukraine earlier than in Kazakhstan. His evidence for this comes from bitwear studies of two samples of lower second premolars from two Eneolithic sites, Botai in northern Kazakhstan (5 from a total of 19 teeth) and Dereivka in the Ukraine (2 from a total of 6 teeth). He implies from this that horse domestication spread from west to east (Anthony 1995).

The redating of the Dereivka stallion casts doubt on the idea that horse domestication spread from west to east. Certainly it might have, but there is no direct evidence for the prior existence of domesticated horses in Ukraine than in Kazakhstan (Botai). But is the pattern of tooth wear interpreted as bit wear unambiguous evidence of horse riding? Levine writes:

The question of whether the wear pattern described by Anthony and Brown could have had other causes has not been adequately addressed. Their unbitted sample of feral horses consisted of 20 individuals from two North American populations (mustangs from the mountains of Nevada and barrier island ponies from the Atlantic Coast). They have generalized from this small sample that unbitted horses could not manifest the wear pattern they describe as unique to bitwear. On the other hand, Angela von den Driesch (personal communication) has observed
that similar, if not identical, wear on the lower second premolar can result from abnormal occlusion with the upper second premolar.

As far as we know, then, beveling on the anterior part of the lower P2 masticatory surface could be caused by bitwear or abnormal occlusion. Either a domesticated horse or a wild one that had been tamed could be bitted. The absence of bitwear could indicate that a horse had not been ridden recently or regularly before its death, that it was ridden unbitted, or that it never was ridden. We must conclude from this that bitwear should not be used without corroboration as proof of domestication. This is not to say that bitwear studies should not be carried out. On the contrary, their use should be much more widespread, but in conjunction with other methods of analysis.

From the conclusions:

The results of the analyses carried out on the data from Dereivka and Botai suggest that the vast majority of the horses from those sites were killed in the hunt. Different hunting techniques were employed at each of them: stalking or chasing at Dereivka and driving or surrounding at Botai. The possibility that some of the horses might have been tamed or domesticated, as suggested by Anthony and Brown’s bitwear studies, is certainly not excluded. However, the possibility that the wear pattern they define as bitwear could have other causes has not been disproved.

See also Domestication, Breed Diversification and Early History of the Horse.

Journal of Anthropological Archaeology
Volume 18, Issue 1 , March 1999, Pages 29-78

Botai and the Origins of Horse Domestication

Marsha A. Levine

Abstract

This paper explores some issues related to the origins of horse domestication. First, it focuses on methodological problems relevant to existing work. Then, ethnoarchaeological and archaeozoological methods are used to provide an alternative approach to the subject. Ethnological, ethological, and archaeological data are used to construct a series of population structure models illustrating a range of human–horse relationships. Analysis of assemblages from the Eneolithic sites of Botai (northern Kazakhstan) and Dereivka (Ukraine) suggests that horses at these sites were obtained largely by hunting.

Link

UPDATE

Dr. Anthony writes in the comments section. I have placed his comments in the blog entry because haloscan comments get deleted after a few months.

1. I have argued that horse domestication spread from west to east because the cultures of Ukraine and the the Volga-Ural region certainly had domesticated animals (cattle and sheep) before 5000 calBC, while the cultures of northern Kazakhstan remained foragers until at least 3500 calBC (when they probably adopted horse-herding), and perhaps until 2500 calBC (when they finally began to adopt domesticated cattle and sheep, 2500 years after the cultures of the western steppes). Horses were included with cattle and sheep in funeral sacrifices in the western steppes between 5000-4500 calBC and were portrayed there in mobile art, while in the eastern (Kazakh) steppes horses played no special role in ritual or in art until the Botai culture appeared, about 3500 BCE. Botai was a radically new kind of culture in the Kazakh steppes, with large settlements and dense deposits of animal bone consisting of 70-90% horse bones. This specialized horse hunting economy appeared with bit wear and stabling soils full of horse dung in the settlement of Botai. Bit wear also appeared at the related settlement of Kozhai 1. The Botai people were foragers who rode domesticated horses to hunt wild horses, a peculiar adaptation that existed only in Kazakhstan and only between 3500-3000 calBC.

2. Levine is incorrect in stating that what we have defined as bit wear can appear on the teeth of wild horses; her description of our sample size is incorrect; and her statement that bit wear could have other causes is an unsupported speculation. In a forthcoming paper in a BAR volume edited by Sandra Olsen we describe a new sample of 74 never-bitted Pleistocene equid teeth, studied with our methods. None of them shows a bevel measurement of 3mm, our threshold for bit wear. No one, including von den Dreisch and Levine, has described a population of wild horses that exhibits this kind of wear facet as the result of natural wear. Bit wear clearly distinguishes bitted from never-bitted populations at better than the .001 level of confidence. Levine's criticism of our bit wear statistics in the Journal of Anthropological Anthropology confused the issue by comparing our median measurement for bitted horses to our maximum measurement for never-bitted horses, implying that only .5mm separated them. This was a basic error. Comparing median to median and maximum to maximum, the statistical separation is very good.

3. Levine distinguishes between horses that are merely 'tamed' and those that are 'domesticated'. Tamed horses might have been ridden regularly in the hunt and in war, but this is unimportant in her scheme if they do not show the measurements she expects for a 'domesticated' horse. Culturally, this turns anthropological zoology upside down. When people began to ride horses regularly the world was changed. Whether leg bone measurements changed at the same time is an interesting question, but not nearly as interesting as identifying ridden horses.

Y chromosome haplogroups in Byelorussians

Genetika. 2005 Aug;41(8):1132-6.

[Frequencies of Y chromosome binary haplogroups in Belarussians]

[Article in Russian]

[No authors listed]

The compositions and frequencies of Y-chromosome haplogroups identified by genotyping 23 biallelic loci of its nonrecombining region (YAP, 92R7, DYF155S2, 12f2, Tat, M9, M17, M25, M89, M124, M130, M170, M172, M174, M173, M178, M201, M207, M242, M269, P21, P25, and P37) have been determined in a sample of 68 Belarussians. Eleven haplogroups have been found in the Belarussian gene pool (E, F*, G, I, I1b, J2, N3a*, Q*, R1*, R1a1, and R1b3). Haplogroup R1a1 is the most frequent; it includes 46% of all Y chromosomes in this sample. The frequencies of haplogroups I1b and I are 17.6 and 7.3%, respectively. Haplogroup N3a* is the next in frequency. The frequencies of haplogroups E, J2, and R1b3 are 4.4% each; that of R1* is 3%; and those of F*, G, and Q* are 1.5% each.

Link

Haplogroup frequency correlations in Southeastern Europe (part II)

I've added five new populations to my previous dataset (SIT: Southern Italians, ESC: East Sicilians, SWS: Southwest Sicilians, NWS: Northwest Sicilians, CYP: Cyprus), taken from this recent paper. The resulting principal components plot again shows the J2/R1b/E3b "coastal" vs. I/R1a1 "continental" groupings along the first principal component (right vs. left respectively).

Viruses, mitochondria, cells, etc.

Carl Zimmer posts a fascinating description on new research about the ever-more-fascinating stuff that is found in our cells. It was first thought that cells are nice containers, designed to keep our DNA safely shielded in their nuclei, but it turns out that our cells contain DNA fragments of quite diverse origins, which have managed to strike up an alliance for their joint proliferation:

Here’s the history as they now see it: the free-living, oxygen-breathing ancestors of mitochondria were infected with some nasty T3/T7 viruses. Most of the time the viruses were fatal. But some mutant tried to replicate itself inside a proto-mitochondrion and failed. Its genes were trapped in the genome of its host. Its host was able to reproduce, and one of its descendants took up residence inside the cell of a eukaryote. At some point after this merger, a mutation caused the virus’s DNA and RNA copying genes to come back online. They took over the job of making these molecules, and the mitochondria’s own genes for this job were later stripped out of its genome.

It’s a plausible hypothesis for a number of reasons. Filee and Forterre didn’t just pull the notion that viral genes can become active again out of a hat; this sort of viral resurrection has been documented in other species. Not only is the hypothesis plausible, but it’s a tantalizing as well. It suggests that we are chimeras built from the DNA of eukaryotes, bacteria, and viruses, all mixed together through a natural version of genetic engineering. Forterre even argues that these sorts of results are going to turn out to be the tip of the iceberg. Like many scientists, he believes that before life was based on DNA, the Earth was inhabited by RNA-based life. He argues that DNA was an invention of viruses of these RNA-based organisms, which the RNA-based organisms then seized for their own use. All this may not make you any fonder of the chickenpox you may have had as a kid, but it may at least give you a feeling of kinship.

Y chromosome perspective on Mediterranean populations

Capelli et al. have written an important new article on Y-chromosomal variation in the Mediterranean basin. This is the most comprehensive study yet on the region, using a combination of biallelic polymorphisms defining haplogroups and microsatellites over several Mediterranean populations, including many population samples taken from the literature. Moreover, mtDNA and autosomal data are also included, and these tend to support the authors' broad findings.

The key finding is that Mediterranean populations can be grouped into four main clusters: North Africa, Arab, Central-East, and West Mediterranean. The North African cluster exhibits high frequencies of North African specific haplotypes within haplogroup E3b. The Arab cluster exhibits high frequencies of J*(xJ2), which is rarer elsewhere.

According to the authors, there has been very little gene flow from North Africa into Europe. Moreover, Near Eastern populations should not be considered a unity, but are differentiated depending on the extent of Arab admixture exemplified by J*(xJ2) chromosomes. Modern Near Easterners are thus not representative of the early Neolithic people who migrated into Europe. J*(xJ2) chromosomes associated with Arabs are also present in North Africans, but North Africans have maintained their own Y-chromosomal peculiarities, typified by haplogroup E3b haplotypes.

It is unfortunate that a mainland Greek sample was not included, but to make up for it, there is a Cypriot sample, in addition to three Sicilian samples. These populations which are largely of Greek origin are very similar to Greeks in general, and belong to the Central-East cluster. Their inclusion also allow us to test my previously expressed hypothesis that haplogroup R1a1 was rare in ancient Greek populations. Indeed, this haplogroup is found at a frequency of 1.8-3.1% in Sicilians, Cypriots and Southern Italians, thus essentially confirming my idea. On the other hand, haplogroup I*(xI1b2) is found at frequencies from 3.4-15.7%, and is thus (as I have said before), much more likely to have been present in the ancient Greek population.

The study also examines briefly the origins of the Jews. Sephardic Jews are shown to resemble Mediterraneans more, while Ashkenazi resemble Arabs more.

The table of frequencies also allows us to ascertain the prevalence of Negroid admixture in Sicily, a popular subject in certain circles, and one which is shown to be without any basis in fact. In 212 Sicilians in total, no haplogroup A, E3a, or E*(xE3a,E3b) chromosomes were detected. Two haplogroup A chromosomes were detected in Cyprus, one in Sardinia, and two E3a, E*(xE3b, E3a) chromosomes in Malta. This is about the extent of male Sub-Saharan African introgression in the Mediterranean: 5 out of 656.

From the conclusions:

The significant genetic structuring of populations facing the Mediterranean basin into three groupings, Near Eastern Arab, Mediterranean and North African, is related to the demographic processes that have occurred since first populating the area. The distribution of Neolithic technologies was probably paralleled by demographic expansion in the Mediterranean basin, and subsequent westward migration by Phoenicians and Greeks contributed to the distribution of Y chromosome types of most likely Near East origin. The Arab conquest in particular appears to have had a dramatic influence on the East and South Mediterranean coasts, with differential sex-related gene flow playing a major role in the distribution of genetic variation. The presence of Arab Y chromosome lineages in the Middle East suggests that most have experienced substantial gene flow from the Arabian peninsula. This result raises the issue of the correctness of identifying all Near Eastern populations as reliable representations of the original Neolithic groups that expanded from the Middle East towards the European peninsula.

Annals of Human Genetics (online early)

Population Structure in the Mediterranean Basin: A Y Chromosome Perspective

C. Capelli et al.

Abstract

The Mediterranean region has been characterised by a number of pre-historical and historical demographic events whose legacy on the current genetic landscape is still a matter of debate. In order to investigate the degree of population structure across the Mediterranean, we have investigated Y chromosome variation in a large dataset of Mediterranean populations, 11 of which are first described here. Our analyses identify four main clusters in the Mediterranean that can be labelled as North Africa, Arab, Central-East and West Mediterranean. In particular, Near Eastern samples tend to separate according to the presence of Arab Y chromosome lineages, suggesting that the Arab expansion played a major role in shaping the current genetic structuring within the Fertile Crescent.

Link

Allele for light pigmentation has been positively selected in Europeans

A new paper shows that a polymorphism on the AIM1 locus which is associated with human pigmentation has been under strong positive selection in Europeans, reaching almost fixation in tested European populations (0.89 in South Africans and 0.96 in Germans), while being rare elsewhere. The derived allele is associated with lighter overall pigmentation. This contrasts to the situation with the MC1R locus in which the ancestral variant is maintained by selection in Negroids, but multiple unrelated mutations outside Africa have resulted in lighter-skinned phenotypes. Unlike the MC1R where relaxation of selection constraints were observed in non-Africans, the new AIM1 polymorphism has been positively selected.

The time of the common ancestor of alleles bearing the haplotype is estimated to be 10,965 years, although the 95% confidence interval is wide from 1,328 to 39,609 years. We should probably not speculate on what triggered the selection based on this very uncertain dating, but the repopulation of Europe after the last glaciation may be a candidate. As humans spread to higher latitudes, they may have been subjected to higher selective pressures for light pigmentation. It would be interesting to determine the frequency of the polymorphism in different Caucasoid populations and determine the most likely ancestral populations.


Molecular Biology and Evolution (published online)

Evidence for Recent Positive Selection at the Human AIM1 Locus in a European Population

Mikiko Soejima et al.

Abstract

Two missense polymorphisms (E272K and L374F) of the AIM1 locus, encoding a melanocyte differentiation antigen, were shown to have a clear association with human ethnicities. These two nonpathogenic SNPs may be associated with human pigmentation variation. In this study, we investigated sequence variation in the coding region and exon-flanking sequence and found low genetic variation only in subjects of European descent. All four statistical tests applied to the 7.55-kb region surrounding the L374F polymorphism detected statistically significant deviations from selective neutrality in Europeans. In addition, haplotype analysis revealed that one haplotype carrying 374F was overrepresented in this population, and the low rate of variation, with some features of selective sweeps, was shown to be statistically significant. These results suggest that positive selection recently has been acting or has acted on at least this region of the melanogenic gene and that an advantageous haplotype spread rapidly in Europe.

Link

Horses were not ridden in the fifth millennium BC

The first domesticated horses were used for meat and for drawing wheeled vehicles. The idea that horses were ridden before the 1st millennium BC is one of the arguments of the adherents of the Pontic steppe thesis of Indo-European origins, because ridden horses would give a significant military advantage, and thus allow the steppe people to overwhelm the settled agricultural populations of Old Europe.

There are however no depictions of horse riding in art before the 1st millennium BC, or in the earliest texts of Indo-European speakers. So, some archaeologists have sought alternative ways of establishing that horses were ridden. To ride a horse, one needs a bit which is put in the horse's mouth and reins by which the horse is controlled. The teeth of a horse that have a hard bit will show evidence of wear in a distinctive pattern, and this will allow us to infer that it was ridden.

The following excerpt from a recent review of Robert Drews' Early riders: the beginning of mounted warfare in Asia and Europe by Karlene Jones-Bley in Journal of Indo-European Studies vol 33, no. 1/2 shows how this ingenuous hypothesis has not survived radiocarbon dating.

Nevertheless, the entire bit wear thesis collapsed once the skull of the "cult stallion" was subjected to radiocarbon dating and was found to have died before 700 and 200BC. Thus, even if the evidence for bit wear were valid (and there are those who still question even this), it didn't happen at Dereivka until the Iron Age when no one doubts the existence of horse riding and hard bits.

UPDATE

Dr. David Anthony, who proposed the bit wear hypothesis has sent me an e-mail in which he gives some additional information.

The date of the domestication of the horse is still poorly understood, but horses certainly were domesticated and used for riding in the northern Eurasian steppes by the middle of the fourth millennium BCE, and they were grouped with cattle, sheep, and humans in funeral rituals that excluded obviously wild animals during the fifth millennium BCE. The 3500BCE date for riding is supported at Khvalynsk in northern Kazakhstan, dated 3500-3000 BCE, where in addition to bit wear on horse premolars, stabling soils full of horse dung were found, and whole horse carcasses were regularly brought into the settlement for butchering as a regular practice over the course of hundreds of years. The occupants had no cattle or sheep, no draft animals other than horses, so if the horses at Botai were wild it is difficult to understand how they were brought into the settlement. The inclusion of horses in human graves dated 4500 BCE is documented at Khvalynsk on the middle Volga, a cemetery where the sacrificed animals included parts of 52 sheep/goat, 23 cattle, and 11 horses, and no obviously wild animals. Khvalynsk sites also have yielded stone maceheads shaped like horseheads and bone plaques carved in the shape of horses. The bit-worn horse teeth at Dereivka were re-dated to 700-200 BCE by me, the same person who identified the bit wear, but the article in which I announced the re-dating of the Dereivka teeth also described the evidence from Botai and Khvalynsk. Dereivka was not the only site with early bit wear in the steppes. No credible or accurate criticisms of bit wear analysis have yet been published, so the detection of bit wear remains a valid way to identify bitted horses in the archaeological record. Please see Anthony, David W. and Dorcas Brown, 2000, "Eneolithic horse exploitation in the Eurasian steppes: diet, ritual and riding," Antiquity 74: 75-86.

Bones

John Hawks reports on Bones, a new TV drama series about forensic anthropologists. Inspired be real-life forensic anthropologist and writer Kathy Reichs.

The Myths of the 20th century

The first half of the 20th century was dominated by the myth of human inequality. According to this myth, human beings could be ordered in a scale of worth, with some individuals and groups being deemed superior and others inferior.

The second half of the 20th century was dominated by the myth of human identity. According to this myth, human beings were inherently the same, except for cosmetic external differences and the sexual differences necessary for procreation. Any observable differences in health, intelligence, personality, or beauty were deemed to stem from prejudices of the observer or the effects of environmental influences.

The first myth was a consequence of widespread means of transportation, which enabled the meeting of races and cultures. It was also a consequence of quantitative anthropology which enabled the measurement of human beings, and their classification according to measurable quantities such as the cephalic index or the facial angle.

The second myth was a result of the great emancipation movements. Previously marginalized groups, such as women and minorities found themselves in possession of the same rights as white males. It was believed that their previously socially inferior position would soon be changed, and that once people became unprejudiced and educated, then all genders and races would exhibit similar outcomes in life.

The myth of human inequality was the common-sense reaction to the previous Christian worldview of equality of men. People could no longer hold that view once faced with the dramatic differences in appearance, culture, and behavior between different groups. It was common-sense, but wrong, because human beings are not single-dimensional entities and cannot be ordered on a unique scale.

The myth of human identity was the moral reaction to the old society which subjugated a good portion of its population. It was wrong, because the power structures of society are not only the result of prejudice, oppression, and opportunity, but also a manifestation of innate differences between human individuals and groups.

Today, neither human inequality, nor human identity are any longer tenable positions. So, what will be our new myths for the 21st century?

Φόρουμ ΑΝΘΡΩΠΟΣ

Για τη διευκόλυνση της επικοινωνίας στα Ελληνικά όσων ενδιαφέρονται για θέματα ανθρωπολογίας, γενετικής, ιστορίας, κτλ. μπορείτε να συμμετάσχετε στις συζητήσεις στη διαδικτυακή κοινότητα ΑΝΘΡΩΠΟΣ. Προφανώς αρχικά δεν υπάρχουν αρκετά μέλη, αλλά ελπίζω πως με τον καιρό θα μαζευτούνε εκεί όσοι και όσες ενδιαφέρονται για φιλική συζήτηση πάνω σε αυτά τα αντικείμενα στην Ελληνική γλώσσα.

Were modern humans neighbors to Neanderthals?

A pretty good article on the controversy of modern human-Neanderthal interactions. The conventional orthodoxy that moderns and Neanderthals co-existed in Europe has been shaken by the fact that none of the Aurignacian archaeological assemblages, which were once believed to have been created by modern humans, are actually associated with modern human bones. So, the only way to associate them with modern humans is to claim that their sophistication makes it unlikely that they were created by Neanderthals, i.e., to presuppose that Neanderthals were dumber than modern humans and could not have created those artifacts. But, some of the Neanderthals' genes may persist in modern Europeans, so we shouldn't assume that Neanderthals were genetic dead-ends that had nothing (cultural or genetic) to offer to the first anatomically modern humans during their arrival in Europe.

On a somewhat related note, John Hawks writes about a recent conference on Rethinking the Human Revolution.

Ancient British mtDNA

One more paper added to the growing list of studies of ancient DNA. This time around, scientists have studied the mtDNA of Britons from the 4th to 11th century AD. The scope of the study is one of the largest I've seen so far, with 319 dental samples and 156 individuals in total. The haplogroup frequencies are shown below; the ancient sample is also split into Early and Late Saxon periods.



UPDATE

The comparative modern mtDNA were taken from the following regions. It is a bit peculiar that more continental European samples are missing, while Armenians and Palestinians are listed.

The comparative data set from modern populations of Europe for the founder and genetic distance analyses consisted of mtDNA HVS-I sequences from the following populations: Armenia (N=191), England (N=258), Estonia (N=149), northern France (N=101), Finland (N=176), Iceland (N=467), Norway (N=565), northern Germany (N=107), Palestine (N=117), Saami (N=176), Scotland (N=981), Spain (N=181) and Western Isles (N=181).

Molecular Biology and Evolution (advance access)

Tracing the Phylogeography of Human Populations in Britain Based on 4th-11th Century mtDNA Genotypes

A. Töpf et al.

Abstract

Some of the transitional periods of Britain during the first millennium AD are traditionally associated with the movement of people from continental Europe, composed largely of invading armies (e.g. the Roman, Saxon and Viking invasions). However, the extent to which these were migrations (as opposed to cultural exchange) remains controversial. We investigated the history of migration by women by amplifying mtDNA from ancient Britons who lived between approximately 300-1,000 AD, and compared these with 3,549 modern mtDNA database genotypes from England, Europe and the Middle East. The objective was to assess the dynamics of the historical population composition by comparing genotypes in a temporal context. Towards this objective we test and calibrate the use of rho-statistics to identify relationships between founder and source populations. We find evidence for shared ancestry between the earliest sites (predating Viking invasions) with modern populations across the north of Europe from Norway to Estonia, possibly reflecting common ancestors dating back to the last glacial epoch. This is in contrast with a late Saxon site in Norwich, where the genetic signature is consistent with more recent immigrations from the south, possibly as part of the Saxon invasions.

Link

Stop the presses... huge papers on brain evolution in recent humans

I am very sure that a set of new papers (one two) in Science will generate a huge amount of buzz. I will blog in more detail about them later, but for now, this Red Nova story covers the findings pretty well. The interesting part:

The team also observed geographic differences. For haplogroup D of ASPM, they found that it occurs more frequently in Europeans and surrounding populations including, North Africans, Middle Easterners, and South Asians, and at a lower incidence in East Asians, New World Indians and sub-Saharan Africans. For microcephalin, the researchers found that haplogroup D is more abundant in populations outside of sub-Saharan Africa.

For now, from the papers:



Fig. 3. Global frequencies of Microcephalin haplogroup D chromosomes (defined as having the derived C allele at the G37995C diagnostic SNP) in a panel of 1184 individuals.



Fig. 1. Worldwide frequencies of ASPM haplogroup D chromosomes (defined as having the derived G allele at the A44871G diagnostic polymorphism), based on a panel of 1186 individuals.

UPDATE

Here is what these studies mean:

• Microcephalin and ASPM are genes involved in regulating brain size
• A variant of Microcephalin has reached very high frequencies in non-Sub-Saharan Africans in the last 37,000 years.
  
• A variant of ASPM has reached very high frequencies especially in Caucasoids but also in some southern Mongoloids and Australoids in the last 5,800 years.
  
• It is almost inconceivable that these two factors were caused by random factors (drift). Therefore selection has acted on these two genes, favoring the new Microcephalin variant in non-Sub-Saharan Africans and the ASPM especially in Caucasoids, but also to a lesser extent in some southern Mongoloid and Australoid groups.
• We know absolutely nothing about what the new Microcephalin and ASPM variants actually do. What we do know is that they confer some substantial advantage that has caused them to grow in numbers. Perhaps, they confer some cognitive or behavioral ability.
  

These are the facts. The interpretation of the facts must wait until we have more information. However, the dates for the expansion of the two variants are extremely suggestive.

In a recent article, Erik Trinkaus has surveyed the human paleoanthropological record, and wrote that:

The earliest candidates for human anatomical modernity, those between ca. 150,000 and 195,000 years B.P. in Africa, are best considered as bridging a morphological gap between late archaic and early modern humans.

...

The spread of modern humans thoughout Africa and into Eurasia occurred after 50,000 years B.P. and probably after 40,000 years B.P., 100,000 years after their appearance.

Now, it may be a coincidence that the spread of humans throughout Africa and into Eurasia happened at around the same time that the new Microcephalin variant appeared, but the timing is certainly suggestive.

The question is: why did the new variant not get selected in Sub-Saharan Africans? There are only two possible explanations:

• There is something in the Sub-Saharan African environment which did not allow the variant to be selected; in other words: the variant did not confer an advantage in Africa itself.
• The gene pool of most Sub-Saharan Africans did not possess the new Microcephalin variant. Hence the variant did not get selected because it was lacking in the Sub-Saharan African gene pool.
  

Now, it is well known that the greatest difference in modern human genetic variation is between Sub-Saharan Africans and non-Sub-Saharan Africans. This is the result of the fact that humans originated in Africa, and possess only a subset of the variation that exists there.

As I have written before, there is good reason to believe that a human group originated in eastern Africa ("Afrasians") and came to colonize the rest of the world in relatively recent times. But, the rest of the African continent was already inhabited by pre-existing anatomically modern humans ("Paleoafricans") since at least 150,000 years in the past. These "Paleoafricans" were separated from the "Afrasians", as evidenced by the fact that typical "Paleoafrican" markers, originating long before the 40,000BP cutoff date, such as Y-haplogroups A and B and mtDNA haplogroups L0-L2 are not found in Eurasia.

If my theory is correct, then we don't need to propose some unquantifiable peculiarity of the African environment. Rather, the new Microcephalin variant has a low frequency in Sub-Saharan Africans precisely because it emerged in the Afrasians of eastern Africa that started colonizing the world around 40,000BP and was later added to the Paleoafrican populations of Sub-Saharan Africa. It simply has not had enough time to spread in most of Africa!

The second variant (of ASPM) is even more impressive, because it started to spread only 5,800 years ago, although the confidence margins are wide. The only movement which could have affected so many populations of Eurasia, regardless of language, in the last few millennia is the Neolithic expansion, followed by population growth in the first civilizations of the Near East and China.

It seems all by certain that the variant first appeared in Western Eurasia. It could have been carried easily to the east by the Near Eastern Neolithic people who reached India. It would only take a small step to make the jump to the Mongoloid world; once introduced into the population, it would also undergo the same selection process that made it so frequent among Caucasoids. However, agriculture begins much later among Mongoloids and even later among Australoids. So, the low frequency of the new variant in these populations is a consequence of the fact that it has had less time to spread among these populations.

The new ASPM variant is lacking in Sub-Saharan Africans and Native Americans. These results can be easily explained:

• Sub-Saharan African agriculture is late, and moreover there has been almost no gene flow from Eurasia into Sub-Saharan Africa, with a few occasional exceptions. So, the ASPM variant did not exist in the Sub-Saharan African gene pool, and could thus have not been selected.
• Native Americans migrated into the New World in Paleolithic times. Naturally, the ASPM variant was not present in their ancestral gene pool yet, so it could not have been selected.

The importance of these new papers is that cognitive evolution in Homo sapiens did not stop after our lineage became anatomically modern, and it did not stop when a subet of anatomically modern humans set out to colonize the world 40,000 years ago from eastern Africa, and it did not stop when Neolithic man appeared 10,000 years ago. Evolution has continued, and the proof for it is in the genetic variation of living human populations.

Science, Vol. 309 No. 5741

Microcephalin, a Gene Regulating Brain Size, Continues to Evolve Adaptively in Humans

Patrick D. Evans et al.

The gene Microcephalin (MCPH1) regulates brain size and has evolved under strong positive selection in the human evolutionary lineage. We show that one genetic variant of Microcephalin in modern humans, which arose ~37,000 years ago, increased in frequency too rapidly to be compatible with neutral drift. This indicates that it has spread under strong positive selection, although the exact nature of the selection is unknown. The finding that an important brain gene has continued to evolve adaptively in anatomically modern humans suggests the ongoing evolutionary plasticity of the human brain. It also makes Microcephalin an attractive candidate locus for studying the genetics of human variation in brain-related phenotypes.

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Ongoing Adaptive Evolution of ASPM, a Brain Size Determinant in Homo sapiens

Nitzan Mekel-Bobrov et al.

The gene ASPM (abnormal spindle-like microcephaly associated) is a specific regulator of brain size, and its evolution in the lineage leading to Homo sapiens was driven by strong positive selection. Here, we show that one genetic variant of ASPM in humans arose merely about 5800 years ago and has since swept to high frequency under strong positive selection. These findings, especially the remarkably young age of the positively selected variant, suggest that the human brain is still undergoing rapid adaptive evolution.

Link