July 31, 2009

The Map of Altinum, Ancestor of Venice (Ninfo et al. 2009)

I had posted about the discovery of Altinum last year. Now, a new paper in Science presents a map of the ancient Roman city that was a precursor of Venice. Rogue Classicist has several links that cover the story. On the left is an aerial view of the site (top) and its reconstructed map (bottom) from the paper.

From ScienceNow:
Archaeologists have known for decades that Altinum, a Roman trading center that thrived between the 1st and 5th centuries C.E., lay below these farm fields. Raised 2 to 3 meters above the surrounding marshy lagoon by centuries of human habitation, the city was approximately the size of Pompeii. Its history could stretch back to the Bronze Age, and it dominated the region for at least 600 years before it became a part of the Roman Empire.

But all traces of Altinum's buildings have long since disappeared, either stolen as building material or swamped by rising water levels in the surrounding lagoon. So how to map a city with no visible ruins? In July 2007, during a severe drought, Paolo Mozzi, a geomorphologist at the University of Padua in Italy, and his team took aerial photos of the site in several wavelengths of visible light and in near-infrared, with a resolution of half a meter.

When the images were processed to tease out subtle variations in plant water stress, a buried metropolis emerged. The researchers discovered that the crops planted on the land were in different stages of ripening, thanks to differences in the amount of water in the soil. Lighter crops traced the outlines of buildings--including a basilica, an amphitheater, a forum, and what may have been temples--buried at least 40 centimeters below the surface. To the south of the city center runs a wide strip of riper crops. They were growing above what clearly used to be a canal, an indication that Venice's Roman forebears were already incorporating waterways into their urban fabric.

In fact, Altinum's end may have been Venice's beginning. The first century Roman historian Strabo mentions Altinum's importance: Its location near both heavily traveled sea routes and along roads running north to the edges of the Roman Empire made it a critical mercantile center. But as waves of barbarians invaded, Altinum was a ripe target. Finally, in the 7th century C.E., a Lombard invasion pushed the city's beleaguered residents onto the defensible islands of the Venice lagoon.

This is what Strabo had to say (5.1):
These cities, then, are situated considerably above the marshes; and near them is Patavium, the best of all the cities in that part of the country, since this city by recent census,23 so it is said, had five hundred knights, and, besides, in ancient times used to send forth an army of one hundred and twenty thousand. And the quantities of manufactured goods which Patavium sends to Rome to market — clothing of all sorts and many other things — show what a goodly store of men it has and how skilled they are in the arts. Patavium offers an inland voyage from the sea by a river which runs through the marshes, two hundred and fifty stadia from a large harbour; the harbour, like the river, is called Medoacus. The largest city in the marshes, however, is Ravenna, a city built entirely of wood24 and coursed by rivers, and it is provided with thoroughfares by means of bridges and ferries. At the tides the city receives no small portion of the sea, so that, since p315the filth is all washed out by these as well as the rivers, the city is relieved of foul air. At any rate, the place has been found to be so healthful that the rulers have given orders to feed and train the gladiators there. Now this is indeed one of the marvellous things at Ravenna, I mean the fact that the air in a marsh is harmless (compare the Egyptian Alexandria, 214where, in summer, the lake25 loses its baneful qualities by reason of the overflow of the Nile and the disappearance of the standing waters), but the behaviour of the vine is also a thing fit to marvel at; for although the marshes support it and make it fruit quickly and in great quantities, it dies within four or five years. Altinum too is in a marsh, for the portion it occupies is similar to that of Ravenna. Between the two cities is Butrium, a town belonging to Ravenna, and also Spina, which though now only a small village, long ago was a Greek city of repute.a At any rate, a treasury26 of the Spinitae is to be seen at Delphi; and everything else that history tells about them shows that they were once masters of the sea. Moreover, it is said that Spina was once situated by the sea, although at the present time the place is in the interior, about ninety stadia distant from the sea. Furthermore, it has been said that Ravenna was founded by the Thessalians; but since they could not bear the wanton outrages of the Tyrrhenians, they voluntarily took in some of the Ombrici,27 which latter still now hold the city, whereas the Thessalians themselves returned home. p317These cities, then, are for the most part surrounded by the marshes, and hence subject to inundations.

Science doi:10.1126/science.1174206

The Map of Altinum, Ancestor of Venice

Andrea Ninfo, Alessandro Fontana, Paolo Mozzi, Francesco Ferrarese

Processing and interpretation of July 2007 digital visible and near-infrared aerial photographs, coupled by a digital terrain model, has allowed for detailed reconstruction of the topography and the paleoenvironmental setting of the Roman city of Altinum, shedding new light on the far origins of Venice. Images were taken during severe dry conditions, which stressed the maize and soy crops. The city walls and doors, the street network, dwellings, theaters, amphitheater, forum, emporia, basilica, and a complex network of rivers and canals have been mapped.


July 30, 2009

mtDNA from pre-Columbian Peru

Yet another case in which differentiation of ancient with modern inhabitants is established. The paper discusses this issue:
The significant differentiation between the ancient Peruvian coastal populations (Shimada et al., 2004; this study) to the ancient highland and modern Peruvian populations cannot be explained satisfyingly in this moment. Although a recent work of Lewis (2009) shows that for genetic differences between the ancient and contemporary Andean populations genetic drift cannot be rejected as a cause, especially when only relying on mitochondrial haplogroup data, this explanation does not fit for the observed coast-highland differentiation. When the Palpa data is compared diachronically, new haplogroups and haplotypes appear and the overall genetic variability in all studied populations is high. Beside the genetic data, the insights in the cultural dynamic processes show that there were relatively large populations, dynamic processes of spatial and intercultural exchange. All those observations definitely are not compatible with the genetic drift scenario. But, the influences of the evolutionary forces on the observed genetic distribution patterns have to be taken into account and can not be utterly rejected. When compared with more mitochondrial datasets from South America, the Palpa populations show a high affinity to the contemporary indigenous populations of the Southern Andes and Tierra del Fuego like the Mapuche, Pehuenche, and Yaghan in Chile (Moraga et al., 2000). All the three populations show high frequencies of haplogroups C (41%–48%) and D (46%–52%) comparable with the prehistoric Palpa and Paracas Peninsula populations (cf. Table 4).
The current paper is a great step forward in the study of South American prehistory, as the large samples allow us to speak quite confidently about gene pool compositions.

A real problem faced by ancient DNA studies is that of inference of population movements based on modern haplogroup frequencies. Is the similarity between prehistoric Palpa and Paracas Peruvians (high C and D, almost non-existent A) with modern Southern Andeans and Tierra del Fuegoans the result of a genetic relationship? It is hard to arrive at any conclusions until we see what prehistoric Southern Andeans and Tierra del Fuegoans looked like.

The same problem was faced in the study of Etruscans, where relationships of modern Tuscans or ancient Etruscans with the modern Near East were discovered, but such relationships have a question mark next to them until we study the ancient Near East directly.

Hopefully, in the coming years, it will become more feasible to fill up the map of ancient mtDNA gene pools in several locations around the world, allowing us both to understand facets of mtDNA evolution, as well as to correct our inferences of population movements based on modern-day haplogroup distributions.

American Journal of Physical Anthropology doi:10.1002/ajpa.21135

Pre-Columbian population dynamics in coastal southern Peru: A diachronic investigation of mtDNA patterns in the Palpa region by ancient DNA analysis

Lars Fehren-Schmitz et al.


Alternative models have been proposed to explain the formation and decline of the south Peruvian Nasca culture, ranging from migration or invasion to autochthonous development and ecological crisis. To reveal to what extent population dynamic processes accounted for cultural development in the Nasca mainland, or were influenced by them, we analyzed ancient mitochondrial DNA of 218 individuals, originating from chronologically successive archaeological sites in the Palpa region, the Paracas Peninsula, and the Andean highlands in southern Peru. The sampling strategy allowed a diachronic analysis in a time frame from approximately 800 BC to 800 AD. Mitochondrial coding region polymorphisms were successfully analyzed and replicated for 130 individuals and control region sequences (np 16021-16408) for 104 individuals to determine Native American mitochondrial DNA haplogroups and haplotypes. The results were compared with ancient and contemporary Peruvian populations to reveal genetic relations of the archaeological samples. Frequency data and statistics show clear proximity of the Nasca populations to the populations of the preceding Paracas culture from Palpa and the Peninsula, and suggest, along with archaeological data, that the Nasca culture developed autochthonously in the Rio Grande drainage. Furthermore, the influence of changes in socioeconomic complexity in the Palpa area on the genetic diversity of the local population could be observed. In all, a strong genetic affinity between pre-Columbian coastal populations from southern Peru could be determined, together with a significant differentiation from ancient highland and all present-day Peruvian reference populations, best shown in the differential distribution of mitochondrial haplogroups.


July 29, 2009

Demographic history of African farmers and hunters (Cox et al. 2009)

From the paper:
Median times since the onset of population growth are 1,863 (513–6,625), 1,027 (97–6,656), and 901 (38–6,497) generations ago, for the San, Biaka and Mandenka, respectively. Given a generation interval of 28 years [21], these values correspond to chronological dates of 52, 29 and 25 thousand years ago (or 37, 21 and 18 kya if we assume a 20-year generation interval). We obtain similar results with our larger Yoruban dataset. We infer a growth rate of 1.7×10−4 per generation (4.3×10−6–6.6×10−2), and a time of onset of growth at 1,280 (28–6,780) generations ago (or 36 kya), and 5-fold growth from ancestral size (Table 2)


The data from the three surveyed non-African populations (French Basque, Chinese Han, and Melanesians) are inconsistent with the simple growth model, presumably because they reflect more complex demographic histories. In contrast, data from all four sub-Saharan African populations fit the two-phase growth model, and a range of onset times and growth rates is inferred for each population. Interestingly, both hunter-gatherers (San and Biaka) and food-producers (Mandenka and Yorubans) best fit models with population growth beginning in the Late Pleistocene.
I am very doubtful of low-level exponential growth sustained over hundreds of generations, very doubtful that modern-day human gene pools contain a strong enough signal of past demographic history, and very doubtful that the demography of Eurasians is more complex than that of Africans. The paper could probably be improved by taking into account admixture processes in Africa itself, i.e., the fact that both African farmers and hunter-gatherers are the result of fairly recent admixture events, with introgressing of "farmer" genes in both San and Pygmies being particularly important.

The observed difference in inferred demography for Eurasians and Africans certaintly means something, but it's hard to evaluate how strong the case is for the scenario proposed in this paper.

UPDATE: The authors consider a simple 2-way admixture model for either recent cryptic admixture, or the Bantu expansion (3kya):
In the presence of gene flow or admixture (or a combination of both), our inference methods would tend to overestimate the effects of population growth, thus leading us to infer slightly older and stronger growth than actually occurred.
But, what about more ancient admixture? The recent Tishkoff et al. paper suggests substantial structure and admixture in African populations that goes well beyond a simple Bantu+Hunter-gatherer model. Even clusters that appear to be homogeneous in that study may reflect stabilized blends of earlier admixture events. If Europeans came into contact with Africans after Pygmies and San had disappeared (as seems likely to happen eventually), we would not even know that such peoples ever existed. How many more small hunter groups were absorbed by expanding African populations (pre-Neolithic or Neolithic), leaving no trace today?

Unlike the authors, I think Eurasian demography is fairly simple in comparison to the African one. There is nothing metaphysical about this guess: Africa, being the cradle of Homo sapiens, is likely to have had the largest human populations, for the longest time. These populations did not sit idly for so long, waiting to be discovered by outsiders, but experienced growth, admixture, competition leading to extinction or absorption, etc.

PLoS ONE 4(7): e6366. doi:10.1371/journal.pone.0006366

Autosomal Resequence Data Reveal Late Stone Age Signals of Population Expansion in Sub-Saharan African Foraging and Farming Populations

Murray P. Cox et al.



A major unanswered question in the evolution of Homo sapiens is when anatomically modern human populations began to expand: was demographic growth associated with the invention of particular technologies or behavioral innovations by hunter-gatherers in the Late Pleistocene, or with the acquisition of farming in the Neolithic?

Methodology/Principal Findings

We investigate the timing of human population expansion by performing a multilocus analysis of≥20 unlinked autosomal noncoding regions, each consisting of ~6 kilobases, resequenced in ~184 individuals from 7 human populations. We test the hypothesis that the autosomal polymorphism data fit a simple two-phase growth model, and when the hypothesis is not rejected, we fit parameters of this model to our data using approximate Bayesian computation.


The data from the three surveyed non-African populations (French Basque, Chinese Han, and Melanesians) are inconsistent with the simple growth model, presumably because they reflect more complex demographic histories. In contrast, data from all four sub-Saharan African populations fit the two-phase growth model, and a range of onset times and growth rates is inferred for each population. Interestingly, both hunter-gatherers (San and Biaka) and food-producers (Mandenka and Yorubans) best fit models with population growth beginning in the Late Pleistocene. Moreover, our hunter-gatherer populations show a tendency towards slightly older and stronger growth (~41 thousand years ago, ~13-fold) than our food-producing populations (~31 thousand years ago, ~7-fold). These dates are concurrent with the appearance of the Late Stone Age in Africa, supporting the hypothesis that population growth played a significant role in the evolution of Late Pleistocene human cultures.


July 28, 2009

Ancestry informative marker set for determining continental origin (Nassir et al. 2009)

UPDATE: This PCA plot from the paper is very instructive:

In PC1 vs PC2 (top left), the five major races (Caucasoids, East Asian Mongoloids, Amerindians, Australoids, Negroids) are clearly separable, but their relationships are not very clear. Australoids are somewhere between Caucasoids and East Asians. If we were to go by this figure alone, we might even infer that they are some type of mix of the two. But, look at PC3 vs PC4 (top right). Here it is the case that Australoids are not intermediate between Caucasoids and Mongoloids, but occupy their own space, and we can conclude that they are not in fact such a mix.

Compare with Mexicans (bottom left), who occupy the same space as East Asians in PC1 vs PC2. Does that mean that they are East Asians? An alternative explanation is that they are a mix of Caucasoids and Amerindians, since they occupy an intermediate position between the two groups, which happens to coincide with the position of East Asians. But, if we look at PC3 vs P4 (bottom right), it is clear that Mexicans are indeed better explained as a Caucasoid-Amerindian mix, as they occupy an intermediate position between Caucasoids and Columbians/Quechuans (who are on the left), and not at all that of East Asians (who are on the right).

Next, consider African Americans. In PC1 vs PC2 they occupy an intermediate position between Negroids and Caucasoids (bottom left), as expected by their known ancestry. But, what if we didn't know about their history, and we wanted to infer their origin based on their genomes, as we did with Australoids? Unlike Australoids, in PC3 vs PC4, African Americans do not form a cluster of their own, but overlap with both Caucasoids and Negroids who occupy the same space in these two dimensions. Thus, we are more certain that they are indeed a Caucasoid-Negroid mixed population.

Next, consider Mozabites and South Asians, both of which deviate from Caucasoids, in a Negroid, and Mongoloid direction respectively (top left). North African Mozabites may indeed by Negroid-influenced, as is evident in the STRUCTURE analysis of this paper. South Asian Indians, however, who show "admixture" with the East Asian cluster at K=5 in the STRUCTURE analysis, are revealed to form a cluster of their own at higher K (pink), suggesting that they are not, in fact a Caucasoid-Mongoloid mixed population.

The important lesson from all of this, is to use as much information as possible when trying to examine population relationships from graphical plots, because things may not always be "what they seem", and a number of alternative explanations may result in identical two-dimensional plots.

BMC Genetics 2009, 10:39doi:10.1186/1471-2156-10-39

An ancestry informative marker set for determining continental origin: validation and extension using human genome diversity panels

Rami Nassir et al.

Abstract (provisional)


Case-control genetic studies of complex human diseases can be confounded by population stratification. This issue can be addressed using panels of ancestry informative markers (AIMs) that can provide substantial population substructure information. Previously, we described a panel of 128 SNP AIMs that were designed as a tool for ascertaining the origins of subjects from Europe, Sub-Saharan Africa, Americas, and East Asia.


In this study, genotypes from Human Genome Diversity Panel populations were used to further evaluate a 93 SNP AIM panel, a subset of the 128 AIMS set, for distinguishing continental origins. Using both model-based and relatively model-independent methods, we here confirm the ability of this AIM set to distinguish diverse population groups that were not previously evaluated. This study included multiple population groups from Oceana, South Asia, East Asia, Sub-Saharan Africa, North and South America, and Europe. In addition, the 93 AIM set provides population substructure information that can, for example, distinguish Arab and Ashkenazi from Northern European population groups and Pygmy from other Sub-Saharan African population groups.


These data provide additional support for using the 93 AIM set to efficiently identify continental subject groups for genetic studies, to identify study population outliers, and to control for admixture in association studies.


mtDNA points to population increase in South Asia at the same time as the development of microlithic technology

The paper includes free supporting information (pdf), which focus rather on the archaeology than the mtDNA evidence.

PNAS doi:10.1073/pnas.0810842106

Population increase and environmental deterioration correspond with microlithic innovations in South Asia ca. 35,000 years ago

Michael Petraglia et al.


Genetic studies of South Asia's population history have led to postulations of a significant and early population expansion in the subcontinent, dating to sometime in the Late Pleistocene. We evaluate this argument, based on new mtDNA analyses, and find evidence for significant demographic transition in the subcontinent, dating to 35–28 ka. We then examine the paleoenvironmental and, particularly, archaeological records for this time period and note that this putative demographic event coincides with a period of ecological and technological change in South Asia. We document the development of a new diminutive stone blade (microlithic) technology beginning at 35–30 ka, the first time that the precocity of this transition has been recognized across the subcontinent. We argue that the transition to microlithic technology may relate to changes in subsistence practices, as increasingly large and probably fragmented populations exploited resources in contracting favorable ecological zones just before the onset of full glacial conditions.


July 27, 2009

Skeletal trauma before death in Cretans and South Africans

A a couple of days after I mentioned that levels of violence in populations could be studied by counting traumas, a new study does just that, albeit for much more recent populations.

International Journal of Osteoarchaeology doi:10.1002/oa.1096

Analysis of ante mortem trauma in three modern skeletal populations

M. Steyn et al.


When archaeological skeletons are assessed, the prevalence (and patterns of bone involvement) of trauma is important. The number and pattern of fractures can be used to gain insight into the occurrence of interpersonal violence, workload and living conditions. However, the question remains as to how these results should be interpreted - such as what constitutes high or low levels of trauma? The aim of this study was to investigate the occurrence of trauma in a population of modern Greeks living in Crete, as well as South African (SA) whites and blacks in the Pretoria Bone and Raymond Dart collections. The sample comprised mostly of older individuals (n = 90-100 within a sex-population group). Each skeleton was studied for healed trauma. For the vertebrae, only spondylolysis was assessed. In the Greek sample, it was found that 42% of the males and 46% of females had at least one fracture, with corresponding figures of 63 and 44% for SA whites and 83 and 69% for SA blacks. Radius, rib and femur fractures were most common in Greeks, with skull, radius and ribs most common in SA whites and skull, ulna and ribs in SA blacks. These prevalences of trauma are high, but the composition of the samples (mostly of lower socio-economic origin) should be kept in mind. It may also be questioned whether these individuals reflect the society as a whole. It seems that the fractures in Greeks are mostly related to old age due to falls and accidents (radius and hip fractures), while the SA black sample reflects high prevalences of interpersonal violence (such as cranial vault and ulna fractures). The SA white sample follows a comparatively moderate pattern of trauma. These comparative figures may be useful when assessing trauma in other skeletal populations.


July 25, 2009

Genetic diversity and every-day health in humans

From the paper:
These results provide some support for an association between genetic diversity and a measure of general, everyday health in humans. We found a small, but significant, effect of nonMHC genetic diversity, measured as standardized mean-d2, on health. Individuals with greater nonMHC-d2 reported significantly fewer symptoms over a four-month period than less diverse individuals, with nonMHC-d2 accounting for 3% of the variance in health. This relationship suggests that the previously observed male preferences for the faces of females with high levels of nonMHC-d2 would be adaptive for obtaining a healthier mate [46].
PLoS ONE doi:10.1371/journal.pone.0006391

Does Genetic Diversity Predict Health in Humans?

Hanne C. Lie et al.


Genetic diversity, especially at genes important for immune functioning within the Major Histocompatibility Complex (MHC), has been associated with fitness-related traits, including disease resistance, in many species. Recently, genetic diversity has been associated with mate preferences in humans. Here we asked whether these preferences are adaptive in terms of obtaining healthier mates. We investigated whether genetic diversity (heterozygosity and standardized mean d2) at MHC and nonMHC microsatellite loci, predicted health in 153 individuals. Individuals with greater allelic diversity (d2) at nonMHC loci and at one MHC locus, linked to HLA-DRB1, reported fewer symptoms over a four-month period than individuals with lower d2. In contrast, there were no associations between MHC or nonMHC heterozygosity and health. NonMHC-d2 has previously been found to predict male preferences for female faces. Thus, the current findings suggest that nonMHC diversity may play a role in both natural and sexual selection acting on human populations.


Major Histocompatibility Complex (MHC) diversity and human facial attractiveness

Previous research has shown that faces of MHC heterozygous males are judged more attractive. The new study confirms the findings of the earlier one, by finding a preference of females to MHC heterozygous males, with MHC heterozygosity being predictive of facial averageness in both sexes.

Evolution Volume 62 Issue 10, Pages 2473 - 2486


Hanne C. Lie et al.


From an evolutionary perspective, human facial attractiveness is proposed to signal mate quality. Using a novel approach to the study of the genetic basis of human preferences for facial features, we investigated whether attractiveness signals mate quality in terms of genetic diversity. Genetic diversity in general has been linked to fitness and reproductive success, and genetic diversity within the major histocompatibility complex (MHC) has been linked to immunocompetence and mate preferences. We asked whether any preference for genetic diversity is specific to MHC diversity or reflects a more general preference for overall genetic diversity. We photographed and genotyped 160 participants using microsatellite markers situated within and outside the MHC, and calculated two measures of genetic diversity: mean heterozygosity and standardized mean d2. Our results suggest a special role for the MHC in female preferences for male faces. MHC heterozygosity positively predicted male attractiveness, and specifically facial averageness, with averageness mediating the MHC-attractiveness relationship. For females, standardized mean d2 at non-MHC loci predicted facial symmetry. Thus, attractive facial characteristics appear to provide visual cues to genetic quality in both males and females, supporting the view that face preferences have been shaped by selection pressures to identify high-quality mates.


The missing mtDNA link in the southern route out of Africa

In order to substantiate the southern route hypothesis of the settlement of Australia, a link between Australia and coastal populations of Asia is needed. Australian mtDNA belongs largely to the same Out-of-Africa subclades M and N, but it is not clearly a branch of a more derived clade that would allow us to pinpoint a specific Eurasian location as a place of origin.

This paper makes the case that Australian mtDNA haplogroup M42 shares two polymorphisms with a set of Indian M sequences, suggesting more recent common ancestry between these Indians and Australians than the generic "Out of Africa" M. The simplest explanation for this is that the M42 ancestors of Australians ultimately originated in India, and were thus part of the "southern route" dispersal of humans from Africa.

BMC Evolutionary Biology 2009, 9:173doi:10.1186/1471-2148-9-173

Reconstructing Indian-Australian phylogenetic link.

Satish Kumar et al.


An early dispersal of biologically and behaviorally modern humans from their African origins to Australia, by at least 45 thousand years via southern Asia has been suggested by studies based on morphology, archaeology and genetics. However, mtDNA lineages sampled so far from south Asia, eastern Asia and Australasia show non-overlapping distributions of haplogroups within pan Eurasian M and N macrohaplogroups. Likewise, support from the archaeology is still ambiguous.

In our completely sequenced 966-mitochondrial genomes from 26 relic tribes of India, we have identified seven genomes, which share two synonymous polymorphisms with the M42 haplogroup, which is specific to Australian Aborigines.

Our results showing a shared mtDNA lineage between Indians and Australian Aborigines provides direct genetic evidence of an early colonization of Australia through south Asia, following the "southern route".


July 24, 2009

Demography and selection in the spread of Lactase persistence in Europe (Gerbault et al. 2009)

Simply put, the frequency of the Lactase Persistence (LP) allele in most of southern Europe can be explained by demography alone, as the result of genetic drift during the Neolithic diffusion from the Near East. In Europe itself, there is a very strong correlation of this allele with latitude, and it is in Northwestern populations where the allele finds its higher frequency. This is more compatible with the calcium assimilation hypothesis, since lactase persistence is beneficial in low sunshine (high latitude) regions than with the gene-cultural co-evolution hypothesis, according to which pastoralists become LP because of their need to rely on animal milk.

These results can of course be improved by sampling more populations and micro-sampling communities that have traditionally practiced pastoralism vs. agricultural ones, where available, e.g., in the Balkans. However, they do suggest that the hypothesis of LP spreading during the Neolithic, and being selected at higher latitudes (south-to-north) is more attractive than its spread by pastoralists who were genetically adapted to consume milk in adulthood, as is the case in Africa.

PLoS ONE doi:10.1371/journal.pone.0006369

Impact of Selection and Demography on the Diffusion of Lactase Persistence

Pascale Gerbault et al.



The lactase enzyme allows lactose digestion in fresh milk. Its activity strongly decreases after the weaning phase in most humans, but persists at a high frequency in Europe and some nomadic populations. Two hypotheses are usually proposed to explain the particular distribution of the lactase persistence phenotype. The gene-culture coevolution hypothesis supposes a nutritional advantage of lactose digestion in pastoral populations. The calcium assimilation hypothesis suggests that carriers of the lactase persistence allele(s) (LCT*P) are favoured in high-latitude regions, where sunshine is insufficient to allow accurate vitamin-D synthesis. In this work, we test the validity of these two hypotheses on a large worldwide dataset of lactase persistence frequencies by using several complementary approaches.


We first analyse the distribution of lactase persistence in various continents in relation to geographic variation, pastoralism levels, and the genetic patterns observed for other independent polymorphisms. Then we use computer simulations and a large database of archaeological dates for the introduction of domestication to explore the evolution of these frequencies in Europe according to different demographic scenarios and selection intensities.


Our results show that gene-culture coevolution is a likely hypothesis in Africa as high LCT*P frequencies are preferentially found in pastoral populations. In Europe, we show that population history played an important role in the diffusion of lactase persistence over the continent. Moreover, selection pressure on lactase persistence has been very high in the North-western part of the continent, by contrast to the South-eastern part where genetic drift alone can explain the observed frequencies. This selection pressure increasing with latitude is highly compatible with the calcium assimilation hypothesis while the gene-culture coevolution hypothesis cannot be ruled out if a positively selected lactase gene was carried at the front of the expansion wave during the Neolithic transition in Europe.


July 23, 2009

mtDNA of Tunisians and Moroccans

Forensic Sci Int Genet. 2009 Jun;3(3):166-72

Polymorphisms of mtDNA control region in Tunisian and Moroccan populations: an enrichment of forensic mtDNA databases with Northern Africa data.

Turchi C, Buscemi L, Giacchino E, Onofri V, Fendt L, Parson W, Tagliabracci A.

Current forensic mitochondrial (mt)DNA databases are limited in representative population data of African origin. We investigated HVS-I/HVS-II sequences of 120 Tunisian and Moroccan healthy male donors applying stringent quality criteria to assure high quality of the data and phylogenetic alignment and notation of the sequences. Among 64 Tunisians, 56 different haplotypes were observed and the most common haplotype (16187T 16189C 16223T 16264T 16270T 16278T 16293G 16311C 73G 152C 182T 185T 195C 247A 263G 309.1C 315.1C; haplogroup (hg) L1b) was shared by four individuals. 56 Moroccans could be assigned to 52 different haplotypes where the most common haplotype was of West Eurasian origin with the hg H sequence motif 263G 315.1C and variations in the HVS-II polyC-stretch (309.1C 309.2C) shared by six samples. The majority of the observed haplotypes belong to the west Eurasian phylogeny (50% in Tunisians and 62.5% in Moroccans). Our data are consistent with the current phylogeographic knowledge displaying the occurrence of sub-Saharan haplogroup L sequences, found in 48.4% of Tunisians and 25% of Moroccans as well as the presence of the two re-migrated haplogroups U6 (7.8% and 1.8% in Tunisians and Moroccans, respectively) and M1 (1.6% in Tunisians and 8.9% in Moroccans).


July 22, 2009

Did Homo sapiens kill Shanidar 3?

The evidence suggests that modern humans were responsible for this Paleolithic murder mystery, although it's not one of those cases were the evidence is strong enough to "stand up in court", so to speak.

I think that if modern humans and Neandertals ever crossed paths -- and the evidence is very clear that they were very close to each other, at least in Europe -- then inter-species violence is almost a given. Humans have been known to kill all sorts of animals, including members of their own species, so it would have been really difficult to imagine them not killing Neanderthals, if given the opportunity.

But, occasional conflict is not the same as annihilation. So, even if Shanidar 3 did die of a modern human hand, the conclusion is far from certain that Neanderthals as a species did.

Elsewhere on the web: MSNBC, Science Daily.

John Hawks has a thorough review:
Plugging into Bayes' theorem, that means that an encounter rate of 1 modern human for every 28 Neandertals would yield a five percent chance that a modern human was the culprit. Did Shanidar 3 encounter one modern human for every 28 of his own? If not, we have to conclude its very unlikely -- less than five percent -- that his wounds were caused by a modern human.
Arriving at a probability relies at many guesstimates of parameters; this is why I said that the authors' case wouldn't stand up in court. One of Prof. Hawks's hypotheses is:
We don't know the probability that Shanidar 3 encountered modern humans. We'll assume that Shanidar 3 would have been attacked with equal probability by whomever he encountered.
This hypothesis is probably as good as any, but the actual probability could very well be either higher or lower. For example, in a first contact scenario, within-group violence might decline in the face of a common "Other". A classical example is the temporary banding together of Greeks in the face of advancing Persians. While Greeks had a good chance of killing each other before and after the early 5th c. BC, the inter-Greek violence probability experienced a dip in order to face the Persian danger.

In a long-term cohabitation scenario, we might be tempted to assign slightly higher probability to inter-group than to intra-group violence. But this is far from a certain conclusion, since groups may differ in their average tendency to violence. Members of the more violent group may actually have a higher probability of being attacked by one of their own than by a member of a more peaceful group: put 100 mercenaries and 100 Buddhist monks together, and each mercenary will have a higher probability of being attacked by another mercenary than by a monk.

Were modern humans and Neandertals different in their tendency to violence? Did modern human succeed so well because they expanded peacefully and weren't held back by constant bickering? Or did their expansion result from them being warlike and prone to arguments and divisions that eventually led some of them to the ends of the earth? Perhaps, by a careful counting of spear points and traumas, we will, one day, be able to answer that question.

Journal of Human Evolution doi:10.1016/j.jhevol.2009.05.010

Shanidar 3 Neandertal rib puncture wound and paleolithic weaponry

Steven E. Churchill et al.


Since its discovery and initial description in the 1960s, the penetrating lesion to the left ninth rib of the Shanidar 3 Neandertal has been a focus for discussion about interpersonal violence and weapon technology in the Middle Paleolithic. Recent experimental studies using lithic points on animal targets suggest that aspects of weapon system dynamics can be inferred from the form of the bony lesions they produce. Thus, to better understand the circumstances surrounding the traumatic injury suffered by Shanidar 3, we conducted controlled stabbing experiments with replicas of Mousterian and Levallois points directed against the thoraces of pig carcasses. Stabs were conducted under both high and low kinetic energy conditions, in an effort to replicate the usual impact forces associated with thrusting spear vs. long-range projectile weapon systems, respectively.

Analysis of the lesions produced in the pig ribs, along with examination of goat ribs subjected primarily to high kinetic energy stabs from an independent experiment, revealed consistent differences in damage patterns between the two conditions. In the case of Shanidar 3, the lack of major involvement of more than one rib, the lack of fracturing of the affected and adjacent ribs, and the lack of bony defects associated with the lesion (such as wastage, hinging, and radiating fracture lines) suggests that the weapon that wounded him was carrying relatively low kinetic energy.

While accidental injury or attack with a thrusting spear or knife cannot absolutely be ruled out, the position, angulation, and morphology of the lesion is most consistent with injury by a low-mass, low-kinetic energy projectile weapon. Given the potential temporal overlap of Shanidar 3 with early modern humans in western Asia, and the possibility that the latter were armed with projectile weapon systems, this case carries more than simple paleoforensic interest.


July 21, 2009

mtDNA and Y chromosomes of Eurasian cattle

Heredity doi:10.1038/hdy.2009.68.

Maternal and paternal genealogy of Eurasian taurine cattle (Bos taurus).

Kantanen J et al.

Maternally inherited mitochondrial DNA (mtDNA) has been used extensively to determine origin and diversity of taurine cattle (Bos taurus) but global surveys of paternally inherited Y-chromosome diversity are lacking. Here, we provide mtDNA information on previously uncharacterised Eurasian breeds and present the most comprehensive Y-chromosomal microsatellite data on domestic cattle to date. The mitochondrial haplogroup T3 was the most frequent, whereas T4 was detected only in the Yakutian cattle from Siberia. The mtDNA data indicates that the Ukrainian and Central Asian regions are zones where hybrids between taurine and zebu (B. indicus) cattle have existed. This zebu influence appears to have subsequently spread into southern and southeastern European breeds. The most common Y-chromosomal microsatellite haplotype, termed here as H11, showed an elevated frequency in the Eurasian sample set compared with that detected in Near Eastern and Anatolian breeds. The taurine Y-chromosomal microsatellite haplotypes were found to be structured in a network according to the Y-haplogroups Y1 and Y2. These data do not support the recent hypothesis on the origin of Y1 from the local European hybridization of cattle with male aurochsen. Compared with mtDNA, the intensive culling of breeding males and male-mediated crossbreeding of locally raised native breeds has accelerated loss of Y-chromosomal variation in domestic cattle, and affected the contribution of genetic drift to diversity. In conclusion, to maintain diversity, breeds showing rare Y-haplotypes should be prioritised in the conservation of cattle genetic resources.


July 20, 2009

Aristotle on heterogeneity as a cause of civil war

Aristot. Pol. 5.1303a
A difference of race (1) is also conducive to civil war, until they acquire a common spirit: just as a city (2) cannot come into being by a chance multitude, nor in a chance length of time: this is why, whoever has accepted co-settlers either in the beginning or later (3), most of the time they revolted.

στασιωτικὸν δὲ καὶ τὸ μὴ ὁμόφυλον, ἕως ἂν συμπνεύσῃ: ὥσπερ γὰρ οὐδ᾽ ἐκ τοῦ τυχόντος πλήθους πόλις γίγνεται, οὕτως οὐδ᾽ ἐν τῷ τυχόντι χρόνῳ: διὸ ὅσοι ἤδη συνοίκους ἐδέξαντο ἢ ἐποίκους, οἱ πλεῖστοι διεστασίασαν

1. A. is not speaking of a difference of race (τὸ μὴ ὁμόφυλον) in the modern sense of continental groups; his examples following this passage all involve different Greek peoples who were involved in a common settlement. Indeed, the very word translated as "conducive to civil war" (στασιωτικὸν) refers to inter-Hellenic conflicts (cf. Plat. Rep. 5.470c, where the terminology of στασιάζειν is applied to "unnatural" inter-Hellenic conflicts, while war itself (πόλεμον) is reserved for inter-ethnic conflicts.)

2. Note that by city (πόλις), A. is not speaking only of the physical entity of a city, but rather its political identity, i.e., a city-state. A physical city can certainly exist with a "chance multitude", but A. warns that a city-state cannot, until a sufficient length of time has transpired for the different elements in it to acquire a common spirit.

3. A. uses the words συνοίκους and ἐποίκους. The first one denotes those who live together, and is usually used for those who participate in the act of foundation of a city-state. The second term denotes those who are later added to the population, after the city has already been established.

Aristotle's emphasis on common descent (ὁμόφυλον) as a preventive factor against war seems strange by present-day norms, especially since he is speaking of the co-existence of different sets of Greeks, rather than the co-existence of different ethnic groups, or even different races.

This is why he does not suggest that the possibility of peaceful cohabitation is inherently impossible, but that it takes a long time, until the constituent elements "acquire a common spirit" (ἕως ἂν συμπνεύσῃ).

It appears that Aristotle did believe in inherent differences between nations (cf. Aristot. Pol. 1.1252b, 7.1327b) which would presumably make the possibility of acquiring a "common spirit" even more remote, if not impossible. States with a Greek and non-Greek citizen body were unheard of at his time, so the issue does not seem to have even crossed his mind.

July 19, 2009

Regional homogeneity of mtDNA in Sweden

Int J Legal Med. 2009 Jul 10.

Homogeneity in mitochondrial DNA control region sequences in Swedish subpopulations.

Tillmar AO et al.

In order to promote mitochondrial DNA (mtDNA) testing in Sweden we have typed 296 Swedish males, which will serve as a Swedish mtDNA frequency database. The tested males were taken from seven geographically different regions representing the contemporary Swedish population. The complete mtDNA control region was typed and the Swedish population was shown to have high haplotype diversity with a random match probability of 0.5%. Almost 47% of the tested samples belonged to haplogroup H and further haplogroup comparison with worldwide populations clustered the Swedish mtDNA data together with other European populations. AMOVA analysis of the seven Swedish subregions displayed no significant maternal substructure in Sweden (F (ST) = 0.002). Our conclusion from this study is that the typed Swedish individuals serve as good representatives for a Swedish forensic mtDNA database. Some caution should, however, be taken for individuals from the northernmost part of Sweden (provinces of Norrbotten and Lapland) due to specific demographic conditions. Furthermore, our analysis of a small sample set of a Swedish Saami population confirmed earlier findings that the Swedish Saami population is an outlier among European populations.


July 18, 2009

Metric and non-metric variation of Ainu

Am J Hum Biol. 2009 Jul 10.

Metric and nonmetric dental variation and the population structure of the Ainu.

Hanihara T.

Gene flow and genetic drift are important factors affecting geographic variations in human phenotypic traits. In the present study, the effects of gene flow from an outside source on the pattern of within- and among-group variation of the Ainu from Sakhalin Island and three local groups of Hokkaido are examined by applying an R-matrix approach to metric and nonmetric dental data. The comparative samples consist of their ancestral and neighboring populations, such as the Neolithic Jomon, the subsequent Epi-Jomon/Satsumon, the Okhotsk culture people who migrated from Northeast Asia to the northeastern part of Hokkaido during a period 1600-900 years B.P., and modern non-Ainu Japanese. The results obtained by using the census population sizes of the regional groups of the Ainu as an estimate of relative effective population size suggest the possibility of an admixture between the Okhotsk culture people and the indigenous inhabitants in Hokkaido, at least in the coastal region along the Sea of Okhotsk. Such gene flow from Northeast Asian continent may have exerted an effect on the genetic structure of the contemporary Ainu. The present findings indicate that the population structure, as represented by genetic drift and gene flow, tend to be obscured in the results obtained by standard statistical methods such as Mahalanobis' generalized distance and Smith's MMDs. The present extension of the R-matrix approach to metric and nonmetric dental data provide results that can be interpreted in terms of a genetically, archaeologically, and prehistorically suggested pattern of gene flow and isolation.


July 17, 2009

Intermarriage and the risk of divorce in the Netherlands

Prompted by my recent post on Constantinus Porphyrogenitus and inter-ethnic marriage.

From the paper:
We therefore introduce two hypotheses. The first hypothesis is the main-effects hypothesis, which argues that the more traditional the value orientation of a religious or national origin group, the lower the risk of divorce.


Our second hypothesis concerns the effect of the spouses’ religion and national origin, and argues that when the religions or national origins of the two spouses are dissimilar, the risk of divorce is higher.We call this the heterogamy hypothesis. Assumingthat the main-effects hypothesis is valid, we need to decide what constitutes evidence for the heterogamy hypothesis. If the divorce risk of a mixed marriage (between, say, a member of group A and a member of group B) is higher than the divorce risk of AA marriages but lower than the divorce risk of BB marriages, we argue that adaptation is taking place. The behaviour of those couples is in between the two groups, and one can argue that this is simply the average of the two group effects and not a heterogamy effect (Jones 1996). To analyse real heterogamy effects, we employ both a strong and a weak form of the heterogamy hypothesis. According to the strong heterogamy hypothesis, AB marriages will have a divorce risk that is higher than the maximum divorce risk of AA and BB marriages. For example, we expect that a marriage between a Catholic and an unaffiliated person will have a divorce risk that is higher than the (already) high risk for unaffiliated couples. According to the weak heterogamy hypothesis, AB marriages will have a divorce risk that is higher than the average risk of AA and BB marriages. In our example, the risk of the mixed group will be higher than the average of the low risk for Catholics and the high risk for unaffiliated couples.
The data is supportive of the strong heterogamy hypothesis, according to which an AB has a higher chance of a divorce than the highest of AA and BB:
Are there effects of heterogamy on the risk of divorce? Table 8 shows that the answer is clear: most mixed combinations have a risk of divorce that is higher than the highest level of divorce in the two homogamous groups. The average ratio is 2.02, indicating that mixed marriages have a risk of divorce twice as high as that of the maximum level of divorce in the two corresponding groups. This effect is quite strong and clearly supports the strong heterogamy hypothesis.


We also find variations in the magnitude of the effects that are consistent with our hypothesis about value orientations. Combinations of Dutch and Turkish or Moroccan persons reveal a stronger heterogamy effect than combinations involving Dutch and Western European persons. The effects for combinations involving Southern Europeans are in between the combinations with Turks or Moroccans and the combinations with Western Europeans. When looking at combinations involving
minority men, the differences are quite strong. The ratio is 4.7 for combinations involving Turkish men, 2.4 for combinations involving Moroccan men, and 1.5 for combinations involving Western European men. Because European groups are more similar than Moroccan and Turkish groups to the Dutch in values and lifestyle, this finding is consistent with theoretical interpretations of the heterogamy effect
in terms of value similarity.
The paper has detailed tables on the various combinations of intermarriage between different Dutch religious denominations and national origins. What seems clear is that Constantinus' ideas about religious and ethnic homogamy as more conducive to harmonious cohabitation seem to be supported by the data.

Population Studies, Vol. 59, No. 1, 2005, pp. 71-85

Intermarriage and the risk of divorce in the Netherlands: The effects of differences in religion and in nationality, 1974-94

Matthijs Kalmijn et al.

A textbook hypothesis about divorce is that heterogamous marriages are more likely to end in divorce than homogamous marriages. We analyse vital statistics on the population of the Netherlands, which provide a unique and powerful opportunity to test this hypothesis. All marriages formed between 1974 and 1984 (nearly 1 million marriages) are traced in the divorce records and multivariate logistic regression models are used to analyse the effects on divorce of heterogamy in religion and national origin. Our analyses confirm the hypothesis for marriages that cross the Protestant-Catholic or the Jewish-Gentile boundary. Heterogamy effects are weaker for marriages involving Protestants or unaffiliated persons. Marriages between Dutch and other nationalities have a higher risk of divorce, the more so the greater the cultural differences between the two groups. Overall, the evidence supports the view that, in the Netherlands, new group boundaries are more difficult to cross than old group boundaries.


Analysis of five Neandertal Genomes (Briggs et al. 2009)

This is a very exciting paper, both for the apparent advance in ancient DNA technology, and for the finding of a smaller effective population size for Neandertals. The reduced mtDNA diversity in Neandertals might be the result of selection. Even among current cold-adapted populations, mtDNA diversity is reduced, and this is due to bioenergetic adaptation for a cold climate.

Chemistry World has some details on the new technical advance:
Now, Pääbo and colleagues have created a quicker, less expensive, and less wasteful method to reconstruct the genomes of ancient specimens. 'The samples we used in this new project were even more poorly preserved than that original sample [analysed last year], meaning that the shotgun method would have cost hundreds of millions of pounds,' says graduate student Adrian Briggs who helped pioneer the new technique. 'Hence the need for our new targeted retrieval method - primer extension capture (PEC).'

'We have managed to immortalise a precious DNA source, for example a Neanderthal DNA extract, by making many thousands of copies of every original DNA molecule in that source,' says Briggs. In doing so, ancient DNA sequences can be stored in a 'library' they can be used again and again. The technique uses 5'- biotinylated oligonucleotide primers and a DNA polymerase that isolate Neanderthal mtDNA sequences from the plethora of contaminant DNA. Sequences of interest are then directly extracted from this amplified library of degraded DNA before the sequencing step. 'This saves on experimental time and costs by several thousand fold,' Briggs adds.

Eske Willerslev, an expert on ancient DNA at the University of Copenhagen, Denmark, thinks this is an important technological breakthrough. 'The capture approach makes it possible to retrieve very short pieces of DNA (50-70bp) that is difficult if not impossible using regular [ approaches,' he comments. 'This means that the chances of retrieving endogenous rather than contaminant DNA increases significantly.'
The much publicized Neandertal DNA data from Vindija cave were taken from an almost ideal sample in terms of preservation.

LiveScience has some details on the implications for the demography of Neandertals:
In fact, new genetic evidence from the remains of six Neanderthals (Homo neanderthalensis) suggests the population hovered at an average of 1,500 females of reproductive age in Europe between 38,000 and 70,000 years ago, with the maximum estimate of 3,500 such female Neanderthals.

"It seems they never really took off in Eurasia in the way modern humans did later," said study researcher Adrian Briggs of the Max-Planck Institute for Evolutionary Anthropology in Germany.

The research, which will be published in the July 17 issue of the journal Science, suggests the small population size of our ancestral cousins may have been a factor in their demise.

"Because there never really were millions of them, they probably were more susceptible to some event that made them go extinct, which to me, suspiciously coincides with the emergence of modern humans," Briggs told LiveScience.

Ian Tattersall, curator of anthropology at the American Museum of Natural History in New York, who was not involved in the current research, said the study "does support notions that toward the end of last ice age, the Neanderthal population was declining as a result of harsh circumstances." He added, "I don't believe Neanderthals would've gone extinct if it wasn't for this new element, the Homo sapiens competing for the same resources."
I really find it hard to believe that Neandertals died out beause of competition with Homo sapiens. After all, a population of a few thousand could quite easily have been accommodated in Paleolithic Europe; population density was so low, that there were plenty of resources for modern humans and Neandertals alike.

There are plenty of scenaria for the disappearance of the Neandertals, ranging from absorption by modern humans (although recent estimates of introgression are usually from modest to very low) to cannibalism, to contracting diseases brought by Homo sapiens and for which they had no immunity. We don't even know how long the co-existence between the species was before the disappearance of Neandertals. The argument for a causative role of modern humans in Neandertal demise is weakened if the latter persisted for many thousands of years after the arrival of the former.

If, however, Neandertals were so limited in numbers, perhaps there was no major reason for their disappearance. It could very well have been a statistical accident as random fluctuations in population size may have driven them to a non-viable demographic size from which they may not have been able to recover.

As usual for a Science paper, there are plentiful open access supplementary data.

Science doi:10.1126/science.1174462

Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes

Adrian W. Briggs et al.


Analysis of Neandertal DNA holds great potential for investigating the population history of this group of hominins, but progress has been limited due to the rarity of samples and damaged state of the DNA. We present a method of targeted ancient DNA sequence retrieval that greatly reduces sample destruction and sequencing demands and use this method to reconstruct the complete mitochondrial DNA (mtDNA) genomes of five Neandertals from across their geographic range. We find that mtDNA genetic diversity in Neandertals that lived 38,000 to 70,000 years ago was approximately one-third of that in contemporary modern humans. Together with analyses of mtDNA protein evolution, these data suggest that the long-term effective population size of Neandertals was smaller than that of modern humans and extant great apes.


July 16, 2009

mtDNA from the Carpathian Highlands

Hum Biol. 2009 Feb;81(1):43-58.

Mitochondrial DNA sequence variation in the boyko, hutsul, and lemko populations of the carpathian highlands.

Nikitin AG et al.

Abstract Genetic studies of the distribution of mitochondrial DNA (mtDNA) haplogroups in human populations residing within the Carpathian Mountain range have been scarce. We present an analysis of mtDNA haplogroup composition of the Boykos, Hutsuls, and Lemkos, three population groups of the Carpathian highlands. In our study Hutsuls had the highest frequency of subhaplogroup H1 in central and eastern Europe. Lemkos shared the highest frequency of haplogroup I ever reported and the highest frequency of haplogroup M(*) in the region. MtDNA haplogroup frequencies in Boykos were different from most modern European populations. We interpreted these unique mtDNA frequencies to be evidence of diverse and dynamic population histories in the Carpathian highland region.


July 15, 2009

Constantinus Porphyrogenitus on inter-ethnic marriage

Constantinus VII was a 10th c. Byzantine Emperor.

Constantinus Porphyrogenitus, De administrando imperio, Ch. 13
Because each nation has different customs and divergent laws and institutions, it must hold its own things, and perform the associations necessary for the continuation of life from the same nation. As every animal mixes with those of the same genus, so has it been established as a just thing for every nation to form marriage partnerships not with people of a different race and language, but of the same genus and speech. Because, herein grows sameness of mind, and intercourse, and friendly discourse, and cohabitation. But different customs and divergent laws give birth rather to dislikes and conflicts and hatreds and civil wars, which do not bring about friendship and intercourse, but enmity and dissent.

ἕκαστον γὰρ ἔθνος διάφορα ἔχον ἔθη καὶ διαλλάττοντας νόμους τε καὶ θεσμοὺς ὀφείλει τὰ οἰκεῖα κρατεῖν καὶ ἀπὸ τοῦ αὐτοῦ ἔθνους τὰς πρὸς ἀνάκρισιν βίου κοινωνίας ποιεῖσθαι καὶ ἐνεργεῖν. ὥσπερ γὰρ ἕκαστον ζῷον μετὰ τῶν ὁμογενῶν τὰς μίξεις ἐργάζεται, οὕτω καὶ ἕκαστον ἔθνος οὐκ εξ ἀλλοφύλων καὶ ἀλλογλώσσων ἀλλ’ ἐκ τῶν ὁμογενῶν τε καὶ ὁμοφώνων τὰ συνοικέσια τῶν γάμων ποιεῖσθαι καθέστηκε δίκαιον. ἐντεῦθεν γὰρ καὶ ἡ πρὸς ἀλλήλους ὁμοφροσύνη καὶ συνομιλία καὶ προσφιλὴς συνδιατριβὴ και συμβίωσις περιγίνεσθαι πέφυκε· τὰ δε ἀλλότρια ἔθη καὶ διαλλάττοντα νόμιμα ἀπεχθείας μᾶλλον καὶ προσκρούσεις καὶ μίση καὶ στάσεις εἴωθεν ἀπογεννᾶν, ἅπερ οὐ φιλίας καὶ κοινωνίας ἀλλ’ ἔχθρας καὶ διαστάσεις φιλεῖ ἀπεργάζεσθαι.

The punishment of treason in ancient Athens

"Archeptolemus son of Hippodamus, the Agrylian, and Antiphon son of Sophilus, the Rhamnusian, being both present in court, are condemned of treason. And this was to be their punishment: that they should be delivered to the eleven executioners, their goods confiscated, the tenth part of them being first consecrated to Athene; their houses to be levelled with the ground, and in the places where they stood this inscription to be engraved on brass, '[The houses] of Archeptolemus and Antiphon, traitors.'

That Archeptolemus and Antiphon should neither of them be buried in Athens, nor anywhere else under that government. And besides all this, that their posterity should be accounted infamous, bastards as well as their lawful descendants;  and he too should be held infamous who should adopt any one of their descendants for his son. And that all this should be engraved on a brass tablet, and that tablet should be placed where that stands on which is engraved the decree concerning Phrynichus."


Andreas Willi on Macedonia

Andreas Willi has written a rebuttal of sorts (pdf) to the letter of the Macedonia Evidence Initiative. It is an extremely interesting piece of doublethink, and as such, it is useful to address in some detail.

Willi (henceforth W.) writes:
The internet documentation which is referred to in the letter may be right when it sees nothing but “a personal grudge” behind Demosthenes’ calling Philip II a “barbarian,” but to cite Herodotus 5.22 as conclusive evidence that Alexander the Great was “thoroughly and indisputably Greek” is seriously misleading, since Herodotus’ statement “I happen to know that [the forefathers of Alexander] are Greek” is triggered precisely by the existence of a dispute over the matter, long before the age of Demosthenes.
Indeed, there was a dispute over the matter, but the key point is that the dispute was resolved in favor of the Macedonian claims of Hellenicity. So, if the Hellanodikai of ancient Olympia accepted the Macedonian king as a Hellene, what reason does W. have to doubt them? Indeed, this acceptance occurred a century and a half at least before the ascent of Macedonians as a great power, so there is no reason to think that the judges' acceptance was the result of pressure.

Thus, we know that Alexander affirmed his Hellenicity --by choosing to compete at the Olympic games-- and this affirmation (and that of his successors who also competed) were affirmed by the other Greeks. We have both a proclamation and an acceptance of his Hellenicity.

W. writes:
As for (b), the question “Why was Greek the lingua franca all over Alexander’s empire if he was a ‘Macedonian’?” cannot be adequately answered with the words “[Because] Alexander the Great was Greek,” given that we have numerous examples of ancient empires in which the lingua franca was not the language of the ruler.
The unnamed examples of "ancient empires" notwithstanding, it is the case that Empires usually spread their own language. The Romans much esteemed Greek as a language of learning, but they spread Latin, not Greek to most of their Empire. Centuries later, the Europeans, who much esteemed Latin, spread Spanish or English to their empires.

Languages are spread by people, and Empires spread the languages of their peoples. What wondrous miracle would result in myriads of Macedonians settling throughout Asia not to leaving a single trace of their non-Hellenic presence? Did the Macedonians decide to abandon their language at precisely the time of their own triumph? A simpler explanation is that they did not.

But, here comes the doublethink, as W. writes of the ancient Paionians:
What is at the core of the letter is a mistaken and unhealthy notion of historical identity. “While it is true that the Paionians were subdued by Philip II, father of Alexander, in 358 B.C. they were not Macedonians and did not live in Macedonia”—but is that really so? How many Paionians did we ask about it, and at what point in history?
Thus, W. questions the letter's statement that the Paionians were not Macedonians. None of the ancient sources ever confuse the two people, or assert that the Paionians were Macedonians. But, let us grant, for the sake of argument, that at some point in their history, the Paionians felt like Macedonians.

But, if feelings sufficed, then how can W. deny the feelings of the Macedonian kings to be Hellenes? If Paionians may be Macedonians since they may have considered themselves to be such, how can W. simultaneously cast doubt to the claims of the Macedonian kings to be Hellenes, when they certainly did consider themselves to be such.

W. continues:
The comparison with Egypt is awkward, for at least after the incorporation of “Paionia” under Antigonos Gonatas (249 BCE) a territorially continuous political unity had come into being which survived as such in the Roman provincial administration. That the case of Egypt is rather different in this respect need hardly be stressed.
Suppose that Paionians did start feeling like Macedonians during Roman times. Certainly, in Strabo's time, who lived after the Roman conquest, the Paionians continue to be reckoned as a different people, while Macedonia is reckoned as part of Hellas. But, let's suppose that indeed a "Macedonian identity" formed.

But, then, in Byzantine times, the Macedonian theme, consisted of a completely different region, in Thrace. So, whatever, "Macedonian" identity may have formed, it was no lasting thing, having disappeared by medieval times, and transferred to Thrace. Thus, the argument that FYROM Slavs can be seen as inheritors of a distinctive "Macedonian" identity from antiquity collapses. Their only relationship to Macedonia is that they happen to live in what was the Ottoman province of Macedonia.

W. writes:
Moreover, to use an ancient but immediately relevant analogy, are we really to think that Thucydides got it all wrong when he wrote that, decades before the conquest of Paionia, the term “Macedonia” also applied to lands not inhabited by “ethnic” Macedonians (Thuc. 2.99)?
But, Thucydides statement actually opposes W's argument:
Assembling in Doberus, they prepared for descending from the heights upon Lower Macedonia, where the dominions of Perdiccas lay; [2] for the Lyncestae, Elimiots, and other tribes more inland, though Macedonians by blood and allies and, dependents of their kindred, still have their own separate governments. [3] The country on the sea coast, now called Macedonia, was first acquired by Alexander, the father of Perdiccas, and his ancestors, originally Temenids from Argos. This was effected by the expulsion from Pieria of the Pierians, who afterwards inhabited Phagres and other places under Mount Pangaeus, beyond the Strymon (indeed the country between Pangaeus and the sea is still called the Pierian gulf) of the Bottiaeans, at present neighbors of the Chalcidians, from Bottia, [4] and by the acquisition in Paeonia of a narrow strip along the river Axius extending to Pella and the sea; the district of Mygdonia, between the Axius and the Strymon, being also added by the expulsion of the Edonians. [5] From Eordia also were driven the Eordians, most of whom perished, though a few of them still live round Physca, and the Almopians from Almopia. [6] These Macedonians also conquered places belonging to the other tribes, which are still theirs--Anthemus, Crestonia, Bisaltia, and much of Macedonia proper. The whole is now called Macedonia, and at the time of the invasion of Sitalces, Perdiccas, Alexander's son, was the reigning king.
It is clear from this passage that Macedonians e.g., the Lyncestae) existed outside the Macedonian state, while some people who lived within it were not reckoned as Macedonians. Macedonians and the "Kingdom of Macedonia" are not conterminous entities. Thucydides does not assert that the non-Macedonians within the Macedonian state become, by reason of their inclusion in this state, Macedonians.

Thus, there were non-Macedonians within the Kingdom of Macedonia, and none of the independent self-governing Macedonians listed by Thucydides lived in present-day FYROM.

W. writes:
But to call Cleopatra a “Macedonian” gives away what constitutes true identity in the eyes of the letter’s authors: to them, identity seems defined by ancestry and blood-lines, by the past more than the present. Are we then to conclude that, for example, John F. Kennedy—or George W. Bush or Barack Obama, for that matter—were never real Americans? And if John F. Kennedy’s ancestors spoke Irish at one point, is it preposterous for all English-speaking Americans to use him today in their construction of a national identity because of that?
On what basis was Cleopatra not a Macedonian? She was a Macedonian by blood, and indeed by a fairly inbred pedigree full of Macedonians. But, suppose we discount, for the sake of argument, the importance of ancestry. Why, still, was Cleopatra not a Macedonian?

According to W. the conquered Paionians became Macedonians on account of them being conquered, but Cleopatra, the descendant of the conquerors of Egypt became a non-Macedonian, and, presumably, an Egyptian.

In W's strange world of doublethink, it appears that conquerors become the conquered (Cleopatra becomes an Egyptian), and the conquered become the conquerors (Paionians become Macedonians).

W. continues the JFK analogy:
By coming to America John F. Kennedy’s ancestors chose to become Americans (with Irish roots); but why could the Slavs coming to Macedonia then not become Macedonians (with Slavic roots)?
The analogy is false, for several reasons. First of all, JFK's ancestors came to the US as peaceful immigrants while the Slavs came to Macedonia as enemies of the local inhabitants. One needs to read the Miracula Sancti Demetrii to see what the local Macedonians thought of Slavs during the time of their arrival.

But, for the sake of argument, let's accept that the Slavs after several centuries, and because they live in part of Ottoman Macedonia, have some reason to consider themselves some kind of Macedonian. If this was all they did, no Greek would mind; after all, Greeks speak of Turkocretans, or Turkocypriots, or Slavomacedonians.

No, the real issue is that the Slavs of FYROM want to usurp the rights to the use of Macedonians exclusively for Slavs. Consider the official FYROM state policy about the existence of a "Macedonian" minority in Greece, which is -supposedly- oppressed by Greeks.

Going back to the Irish immigrants example, imagine if Irish immigrants not only started calling themselves Americans, but also started speaking about an American minority (by which they meant Americans of Irish origin) oppressed by "Anglos." That is, they tried to dispossess the original bearers of the name and take it as their property. Yet, this is precisely what FYROM Slavs are attempting to do.

W. writes:
No matter what its ethnic mix was—and what serious scholar would nowadays want to argue that the only “good” states are ethnically “pure” states, in which everyone must speak the same language?—the tendentiously-labeled “pseudo-greater Macedonia,” far from being a recent invention, did exist as a real recent invention, did exist as a real identitarian concept well before the 20th century. And in a sense its roots can be traced back to the conquests of Philip II, Alexander the Great and their successors in “Paionia”; for if those conquests had never taken place, the history of the region would have looked different and the territory of “Paionia” might not have shared the fate and fortune of “Aegean” Macedonia for long stretches of its history. Thus, unless one subscribes to a dangerous “blood-and-soil ideology,” there is no reason why the modern Slavic Macedonians should not be allowed to continue to call their country “Macedonia” and to pride themselves in Alexander the Great just as much as the modern Hellenic Greeks do. What does it matter if Alexander “was Greek, not Slavic,” as long as no one claims the opposite?
This is a truly peculiar argument. Alexander's conquests influenced the history of much of the known world, so, should they all be called Macedonians on account of being conquered by the actual Macedonians?

Also, what can one make of the statement about sharing the "fate and fortune"? Was a Macedonian Greek in any case closer to a Skopje Slav because they both happened to live in a territory that Ottoman Sultans claimed to be Macedonia? Was he not closer --Ottoman borders notwithstanding-- to a Thessalian or Thracian Greek? If we abandon the "blood-and-soil ideology", should we replace it with a "borders-and-history ideology", whereby an annexation of Paionia 23 centuries ago has forever marked the territory as Macedonia?

FYROM Slavs may, of course, feel pride that the ancient Paionians were conquered by Philip and Alexander a thousand years before their linguistic ancestors came to Macedonia. I don't feel particular pride that Greece was conquered by the Romans or the Ottomans or the Nazis, but there's no accounting for taste.

One cannot fail to notice, however, how thoroughly un-Macedonian this attitude is. Philip and Alexander loved Greek culture, and proudly proclaimed their Greekness, while these modern "Macedonians" despise Greeks, and proudly proclaim their non-Greekness. I submit this as exhibit A in the case that they are not, indeed, Macedonians at all.

July 14, 2009

Restricted geographical distribution of Q* Y-chromosome paragroup in Americas

Am J Phys Anthropol doi:10.1002/ajpa.21133

Restricted geographic distribution for Y-Q* paragroup in South America

Graciela Bailliet et al.


We analyzed 21 paragroup Q* Y chromosomes from South American aboriginal and urban populations. Our aims were to evaluate the phylogenetic status, geographic distribution, and genetic diversity in these groups of chromosomes and compare the degree of genetic variation in relation to Q1a3a haplotypes. All Q* chromosomes from our series and five samples from North American Q* presented the derivate state for M346, that is present upstream to M3, and determined Q1a3* paragroup. We found a restrictive geographic distribution and low frequency of Q1a3* in South America. We assumed that this low frequency could be reflecting extreme drift effects. However, several estimates of gene diversity do not support the existence of a severe bottleneck. The mean haplotype diversity expected was similar to that for South American Q1a3* and Q1a3a (0.478 and 0.501, respectively). The analysis of previous reports from other research groups and this study shows the highest frequencies of Q* for the West Corner and the Grand Chaco regions of South America. At present, there is no information on whether the phylogenetic status of Q* paragoup described in previous reports is similar to that of Q1a3* paragroup though our results support this possibility.


July 13, 2009

mtDNA of Hakka and Chaoshanese

Am J Phys Anthropol doi:10.1002/ajpa.21124

Tracing the origins of Hakka and Chaoshanese by mitochondrial DNA analysis

Wen-Zhi Wang et al.


Hakka and Chaoshanese are two unique Han populations residing in southern China but with northern Han (NH) cultural traditions and linguistic influences. Although most of historical records indicate that both populations migrated from northern China in the last two thousand years, no consensus on their origins has been reached so far. To shed more light on the origins of Hakka and Chaoshanese, mitochondrial DNAs (mtDNAs) of 170 Hakka from Meizhou and 102 Chaoshanese from Chaoshan area, Guangdong Province, were analyzed. Our results show that some southern Chinese predominant haplogroups, e.g. B, F, and M7, have relatively high frequencies in both populations. Although median network analyses show that Hakka/Chaoshanese share some haplotypes with NH, interpopulation comparison reveals that both populations show closer affinity with southern Han (SH) populations than with NH. In consideration of previous results from nuclear gene (including Y chromosome) research, it is likely that matrilineal landscapes of both Hakka and Chaoshanese have largely been shaped by the local people during their migration southward and/or later colonization in southern China, and factors such as cultural assimilation, patrilocality, and even sex-bias in the immigrants might have played important roles during the process.


July 12, 2009

Y chromosome and mtDNA of eastern Aleuts

Ann Hum Biol. 2009 Jul 8:1-16. [Epub ahead of print]

Mitochondrial DNA and Y-chromosome variation in five eastern Aleut communities: Evidence for genetic substructure in the Aleut population.

Zlojutro M, Rubicz R, Crawford MH.

Since Russian contact in 1741, the Aleut communities of southwestern Alaska have undergone a series of demographic upheavals stemming from forced relocations, disease epidemics, population bottlenecks, and pervasive admixture with European populations. This study investigates the impact of key historical events on the genetic structure of the Aleut population through analysis of mitochondrial and Y-chromosome DNA variation in five eastern Aleut communities. Results from HVS-I sequencing and Y-chromosome typing reveal patterns of variability that exhibit east-west geographic differentiation for the major Aleut haplogroups. This finding is underscored by SAMOVA and Monmonier analyses that identify genetic discontinuities between eastern and western Aleut populations. The majority of Aleut Y-chromosomes were characterized to haplogroups of mostly Russian, Scandinavian and Western European origin (approximately 85%), which is in stark contrast to the 3.6% of Aleut mtDNA lineages identified as non-Native American, and thus indicating a large degree of asymmetrical gene flow between European men and Aleut women. Overall, this study identifies a significant relationship between geography and genetic variation in the Aleut population, with a distinct substructure along an east-west axis that reflects the combined effects of founder events in aggregate island communities, male-biased gene flow from European populations, and the original peopling of the Aleutian Archipelago.


July 11, 2009

Human remains from the Moravian Gravettian

International Journal of Osteoarchaeology doi:10.1002/oa.1088

Human remains from the Moravian Gravettian: morphology and taphonomy of additional elements from Dolní Vestonice II and Pavlov I

E. Trinkaus et al.


Zooarchaeological analysis of the earlier Mid Upper Paleolithic (MUP) (Pavlovian) assemblages from Dolní Vstonice II and Pavlov I, southern Moravia, have yielded 11 additional remains from Dolní Vstonice II (five of which may be associated) and 20 remains from Pavlov I (16 of which come from a pair of hands, Pavlov 31). These remains are those of early modern humans, albeit with a few generally archaic features. At least two of them represent very tall individuals, among the tallest known for the Upper Paleolithic. These remains also raise the question, previously posed, as to the nature of differential treatment of the dead among MUP humans, given the presence of ritual burials, isolated bones and (with Pavlov 31) selected associated anatomy. Copyright © 2009 John Wiley & Sons, Ltd.


July 10, 2009

Annotated Korean genomic sequence

The first Korean genome was presented recently. The present paper on the annotated Korean genome includes some freely available supplementary material.

Nature doi:10.1038/nature08211

A highly annotated whole-genome sequence of a Korean individual

Jong-Il Kim et al.


Recent advances in sequencing technologies have initiated an era of personal genome sequences. To date, human genome sequences have been reported for individuals with ancestry in three distinct geographical regions: a Yoruba African, two individuals of northwest European origin, and a person from China1, 2, 3, 4. Here we provide a highly annotated, whole-genome sequence for a Korean individual, known as AK1. The genome of AK1 was determined by an exacting, combined approach that included whole-genome shotgun sequencing (27.8times coverage), targeted bacterial artificial chromosome sequencing, and high-resolution comparative genomic hybridization using custom microarrays featuring more than 24 million probes. Alignment to the NCBI reference, a composite of several ethnic clades5, 6, disclosed nearly 3.45 million single nucleotide polymorphisms (SNPs), including 10,162 non-synonymous SNPs, and 170,202 deletion or insertion polymorphisms (indels). SNP and indel densities were strongly correlated genome-wide. Applying very conservative criteria yielded highly reliable copy number variants for clinical considerations. Potential medical phenotypes were annotated for non-synonymous SNPs, coding domain indels, and structural variants. The integration of several human whole-genome sequences derived from several ethnic groups will assist in understanding genetic ancestry, migration patterns and population bottlenecks.


Two comments on ancient mtDNA from Native American coprolites

They are referring to the paper by Thomas et al. which detected mtDNA haplogroups A2 and B2 in pre-Clovis Americans. The arguments are highly technical, so I won't express an opinion on who of the two is right.

My default position is to have a question-mark next to every ancient DNA study, whether it has been formally criticized or not. Only when a large number of such studies from a similar time/place and by different researchers produce similar results, will we be justified, I think, to remove that question mark.

Science 10 July 2009:
Vol. 325. no. 5937, p. 148
DOI: 10.1126/science.1168182

Comment on "DNA from Pre-Clovis Human Coprolites in Oregon, North America"

Hendrik Poinar et al.

Gilbert et al. (Reports, 9 May 2008, p. 786) analyzed DNA from radiocarbon-dated paleofecal remains from Paisley Cave, Oregon, which ostensibly demonstrate a human presence in North America predating the well-established Clovis complex. We question the authenticity of their DNA results and argue that in the absence of intact stratigraphy and diagnostic artifacts, and in view of carbon isotope anomalies, the radiocarbon dates of the oldest specimens are unreliable.


Science 10 July 2009:
Vol. 325. no. 5937, p. 148
DOI: 10.1126/science.1168457

Response to Comment by Poinar et al. on "DNA from Pre-Clovis Human Coprolites in Oregon, North America"

M. Thomas et al.

The arguments of Poinar et al. neither challenge our conclusions nor would contribute to the verification of our data. We counter their questions about the authenticity of our ancient DNA results and the reliability of the radiocarbon data and stand by the conclusion that our data provide strong evidence of pre-Clovis Native Americans.


July 09, 2009

Climate has driven mtDNA variation in humans

Yann Klimentidis points me to this very exciting new paper. Some of its authors also contributed to another recent paper which investigated the role of climate in shaping human cranial variation.

The authors compared autosomal, X chromosome and Y chromosome genetic variation with that of mtDNA. For example an impressive 85% of autosomal microsatellite diversity in worldwide humans can be explained by their distance from Africa, but no apparent effect is seen for climate. The effect of distance from Africa is only 18% for HVS-I of human mtDNA, and a strong effect of climate measures (such as temperature) is seen. On the contrary, human Y chromosomes show no relationship with climate.

The effect of climate is also resilient to accounting for distance from Africa (which is very hot, and thus distance from it might be expected to correlate with a decrease in temperature; it is not), and by removing populations living in extreme arctic conditions, for which thermoregulation is of the utmost importance.

I would say that this paper represents the best evidence so far of selection acting on the human Y chromosome.

The implications of this are manifold, and they relate:

(i) to the use of mtDNA to assess population relationships. For example, South Asians have a strong affinity with West Eurasians in their Y-chromosomes and with East Asians in their mtDNA. Nonetheless they do not occupy an intermediate position between the two in autosomal DNA, but are predominantly aligned to West Eurasians.

(ii) to the overall mitochondrial time depth of humanity, i.e., the age of mitochondrial Eve, and what that implies about the recentness of our species (it may be older than its mtDNA time depth), and its possible admixture with other human populations such as Neandertals (it may have occurred, but the non-modern mtDNA may have been selected against)

(iii) to the potential of solving, at least in part, discrepancies between present-day and archaeological mtDNA gene pools, which may not in fact reflect processes of migration, but climate shifts over time.

Note that this is not the first time that adaptive evolution of human mtDNA has been proposed. For example five years ago, Ruiz-Pesini et al. noticed the conservation of internal branch amino acid substitutions at high latitudes, and made the case for energy-related climate adaptation in human mtDNA. The current paper makes a different argument, but arrives at a similar conclusion.

Proceedings of the Royal Society B doi:10.1098/rspb.2009.0752

Climate shaped the worldwide distribution of human mitochondrial DNA sequence variation

François Balloux et al.


There is an ongoing discussion in the literature on whether human mitochondrial DNA (mtDNA) evolves neutrally. There have been previous claims for natural selection on human mtDNA based on an excess of non-synonymous mutations and higher evolutionary persistence of specific mitochondrial mutations in Arctic populations. However, these findings were not supported by the reanalysis of larger datasets. Using a geographical framework, we perform the first direct test of the relative extent to which climate and past demography have shaped the current spatial distribution of mtDNA sequences worldwide. We show that populations living in colder environments have lower mitochondrial diversity and that the genetic differentiation between pairs of populations correlates with difference in temperature. These associations were unique to mtDNA; we could not find a similar pattern in any other genetic marker. We were able to identify two correlated non-synonymous point mutations in the ND3 and ATP6 genes characterized by a clear association with temperature, which appear to be plausible targets of natural selection producing the association with climate. The same mutations have been previously shown to be associated with variation in mitochondrial pH and calcium dynamics. Our results indicate that natural selection mediated by climate has contributed to shape the current distribution of mtDNA sequences in humans.