Genetics and environment contributions to craniofacial phenotypes of Belgians

Hum Biol. 2008 Dec;80(6):637-54.

Contribution of genetics and environment to craniofacial anthropometric phenotypes in Belgian nuclear families.

Jelenkovic A, Poveda A, Susanne C, Rebato E.

In this study we estimate relative genetic and environmental influences on head-related anthropometric phenotypes. The subject group consisted of 119 nuclear families living in Brussels, Belgium, and included 238 males and 236 females, ages 17 to 72 years. Two factor analyses with varimax rotation (the first one related to facial measurements and the second one to overall head morphology) were used to analyze 14 craniofacial size traits. The resulting four synthetic traits [HFCF, VFCF, HDF1, and HDF2-horizontal (breadth) and vertical (height) facial factors and two head horizontal (breadth) factors, respectively] were used as summary variables. Maximum heritabilities (H2) were estimated for all studied traits, and variance components analysis was applied to determine the contribution of genetics and environment on the four craniofacial factors. In addition, we examined the covariations between the face (HFCF and VFCF) and head-related factors (HDF1 and HDF2), separately. Quantitative genetic analysis showed that HFCF, VFCF, HDF1, and HDF2 variation was appreciably attributable to additive genetic effects, with heritability (h2) estimates of 67.62%, 54.97%, 70.76%, and 65.05%, respectively. The three variance components reflecting a shared familial environment were nonsignificant for these four phenotypes. Bivariate analysis revealed significant additive and residual correlations for both pair of traits. The results confirm the existence of a significant genetic component determining the four craniofacial synthetic traits, and common genetic and environmental effects shared by the two face-related phenotypes and by the head-related ones.

Link

Craniometric evidence for Slavic-Finnic admixture in medieval Novgorod

The two main sources of the Russian population are well known by genetic evidence, but it is nice to see the historical process of admixture between Slavs and Finns visible in the anthropological record as well. The evidence for the presence of a Baltic component is more surprising in the light of genetic evidence, but at present diagnostic markers of Baltic admixture in uniparentally inherited markers do not appear to be available. Certainly, the high-resolution study of variation in the common N1c an R1a1 Y-chromosome haplogroups may reveal whether differences between Slav, Balt, or Finn (a) still exist, (b) do not exist because of a common substratu, (c) do not exist due to gene flow between the three linguistic groups.

From the paper:

Groups from 13th–14th century burials at Slavenka and Konezerie, and from 14th–16th century burials in Pskov are morphologically heterogeneous, and the variation exceeds that seen in non-admixed groups. Certain crania are markedly Caucasoid, displaying large and dolichocranic braincases, a sharp horizontal facial profile, a high face and a sharply protruding nose. Others are gracile, brachycranic, and have flattened low faces and flattened noses. The former are far fewer than the latter; most individuals are intermediate. The correlation coefficients also attest to heterogeneity; some of them, while concerning morphologically independent traits, are highly significant, and the same heterogeneity is revealed by the principal component analysis (Sankina, 2000).

...

According to the Mahalanobis distance values, Baltic parallels are especially marked for early Novgorodian groups, whereas Finnic parallels are typical of late groups. While the early and the late groups are very different, continuity between them is evidenced by a combination of intercorrelated traits discovered in the late groups from the upper Luga, Pskov, and the Ingrian Plateau. Speaking of the resemblance between the late Novgorodians and the Finns, it should not be overlooked that most of the former either had absorbed the Finnic substratum or were assimilated descendants of the local Finns. This concerns a group from Slantsy district, certain late groups of the Ingrian Plateau, and many others which, judging by archaeological evidence, were influenced by the traditions of the Baltic Finns.

While the presence of the Finnic element, which manifests itself in late Novgorodian groups, which cannot be disputed, the “Baltic” tendency of early Novgorodians is more difficult to explain. Large-scale Baltic presence in the Novgorodian territory during the pre-Slavic period (Early Iron Age) is evidenced by both archaeological and toponymical data. Recent archaeological and linguistic findings suggest that by the time of the Slavic colonization (7th century AD), Balts and Finns lived in the territory of northwestern Russia side by side, and the Balts which were numerically predominant, migrated to this territory several times, both from the east (the Dnieper basin) and from the west (the Vistula basin) (Vasiliev, 2008). Certain Baltic groups were apparently assimilated by the Slavs. Notably, among the fourteen 10th–13th century eastern Slavic groups from other territories, only three resemble the Balts. Another explanation may be that Balts, Slavs and Finns had absorbed the same ancient European substratum, which had been widely distributed in the past.

Of course, some non-Slavic elements may have participated in the population history of medieval Novgorod in more recent times. For instance, it is hardly accidental that the early group from Pskov is similar to populations of southeastern Estonia, which borders on the Pskov region.

Archaeology, Ethnology and Anthropology of Eurasia

Volume 37, Issue 2, June 2009, Pages 119-134

THE ETHNIC HISTORY OF MEDIEVAL NOVGOROD (BASED ON CRANIOMETRIC DATA)

S.L. Sankina

Cranial series from cemeteries on the territory of the medieval Novgorod Republic were subjected to multivariate analysis. Northwestern Russia is the region where important population changes occurred in the early 2nd millennium AD. As a rule, earlier groups (11th – early 13th centuries) are dolichocranic and exhibit a sharp horizontal facial profile. In those series whose lower chronological limit is 11th–12th centuries, diachronic morphological changes can be traced. In later groups (13th–14th centuries), the cranial index is higher than in earlier ones (11th – early 13th centuries), whereas cranial height and nasal protrusion angle decrease, and the orbits become narrower. Series from the 13th– 16th century cemeteries apparently attest to an admixture. A combination of traits, correlated mostly at the between- group level (orbital breadth, nasal height, and nasal prominence angle), points to the presence of two components. This combination separates early and late Novgorod groups, at the same time opposing neighboring non-Slavic populations. While early groups (11th–13th centuries) resemble the 10th–18th century Balts, late ones (late 13th – early 20th centuries) resemble various Finnic groups of the same period.

Link

Balloux in Heredity on Mitochondrial Phylogeography

Francois Balloux has some scathing criticism on mitochondrial phylogeography as it is currently practiced (doi: 10.1038/hdy.2009.122). I recommend reading the whole thing. The beginning:

Let us assume I gave a seminar. I would tell the audience about my latest results on the population history of the pigmy shrew. My findings would be based on a stretch of DNA comprising several metabolic genes, showing no signs of genetic recombination. Armed with sequences from a large number of individuals sampled over a broad geographical area, I would make some inference on the colonization routes and times. To make life easier, I would restrict my analysis to the mutations I liked best, with nice names having been given to related sequences, rather than relying on dull mathematical quantities. As I reach one of the key conclusions of the lecture, which would go as follows: 'It is obvious from the distribution of haplotypes Amanda, Eugenie* and Hector_2 that the Outer Hebrides were colonised about 50,000 years ago, this was followed by considerable population fluctuations, a bottleneck during the last Ice Age, a swift recovery and a dramatic recent expansion over the last 200 years and...'. Imagine that, at that climactic stage I was interrupted by someone in the audience. The impertinent would say, 'Sir, can I just ask you whether this confidence in your conclusions may not be misplaced; your analysis is based on a single genetic marker, which comprises genes with a central role in metabolism and is thus likely to have been affected by natural selection'. An awkward silence may ensue, as I would find it difficult to dismiss this criticism easily.

and the end:

Despite mitochondrial sequence variation covarying with climate in humans (Balloux et al., 2009), there are better ways to measure temperature. And, I would argue there are also better genetic markers than mtDNA to infer past population history. I fully appreciate that mtDNA has given us some of the most fundamental results on human evolution at a time when using mtDNA was the only realistic option at hand. I do not question the value of mtDNA in forensics and pedigree reconstruction. It is also likely to remain a valuable tool for inference at a localized geographical scale, particularly when testing specific hypotheses rather than making quantitative inferences on the age or size of the populations studied. It is convenient to type and analyse, and its use in humans raises no serious ethical or societal issue. But all these qualities do not counterbalance the fact that a single locus likely to be under selection is inappropriate for population inference at large geographical scales (or over long periods of time in the context of ancient DNA analysis). We have reached an era in which publicly available data sets of large numbers of complete human genomes are a tangible prospect, and I believe it is now time to move on from the excessive reliance on uniparental markers. Exploiting these new resources of autosomal variation will present significant challenges, but it will not help overcoming them if a large fraction of the community of human population biologists persists in sticking to mtDNA as the marker of choice.

The utility of mtDNA for studying modern populations is indeed limited now that we can study hundreds of thousands of markers per individual. However, it is still a very useful marker for ancient DNA, both because it is often the only game in town because of the relative ease with which it can be typed due to its large copy count, and also because it has proven itself to be capable of generating interesting results, as in the recently discovered discontinuity between Paleolithic and Neolithic Central Europeans, studying the mtDNA diversity of Neandertals compared to humans, or detecting sex-biased gene flow in relatively recently admixed populations.

See some of my previous criticisms on facile correlations between mtDNA time depth and archaeological-historical correlations:

• On the mtDNA molecular clock (Endicott et al. 2009)
• Time-dependency of the human mtDNA evolutionary mutation rate

UPDATE:

John Hawks also comments at length on the paper. An excerpt:

So what can we do? Fortunately we have lots of options. We can test the proposed demographic hypotheses against the historical record. When we make observations that show that people 1000 years ago had very different frequencies of common haplotypes, well, we know it was selection. There hasn't been any genetically significant bottleneck in the last 1000 years! When we see small Neolithic population samples dominated by haplotypes that are very rare today, again, no historically possible bottleneck could have caused that.

I am fundamentally in agreement that bottlenecks, so often invoked in the mtDNA literature, are really a non-issue. Consider why this is the case: every mtDNA paper normally takes a random sample of a few tens or hundreds of people from a population that usually numbers in the thousands or millions. The assumption is that such a small random sample generally preserves -within confidence limits- the haplogroup frequencies in the population. But a bottleneck is exactly such a random sample. You can't, at the same time, use a sample of 100 people to infer haplogroup frequencies, and claim that a bottleneck that reduces the population to a 100 people will radically shift haplogroup frequencies. And, of course, there is absolutely no evidence that any major post-Neolithic human population, save for the Andaman Islanders, the Samaritans, or various such populations ever underwent a bottleneck anywhere near that severity.

However, I am in disagreement that a change of haplotype frequencies across 1,000 years is evidence of selection. A different explanation is that of migration, the introduction of a new population element.

Sometimes, migration is easy to infer. For example, we can be fairly certain that modern Europeans are different from Paleolithic Europeans because of Neolithic and post-Neolithic migration into Europe, because there is an introduction of new haplotypes that were absent in the Paleolithic population. One possible explanation is that instead of "absent" we should say "possibly present at very low frequencies". But, once we see that these haplotypes were present on the early Neolithic migrants, it doesn't take much to put 2+2 together and infer that migration is a likelier explanation.

The same process of migration could be inferred for the Neolithic populations of the Lake Baikal district, where a postulated hiatus in occupation, followed by recolonization by immigrants, proposed on archaeological grounds, coincides with the discovery of a sharp difference between pre- and post-hiatus populations in mtDNA haplotype frequencies. Similarly, the absence of Mongoloid mtDNA before the 7th c. BC in Central Asian samples, followed by its introduction after it, can be parsimoniously explained by admixture, since that admixture is evident also in anthropological and autosomal studies.

In other cases, selection may be a more plausible possibility. For example, the reduction in the frequency of haplogroup I in Denmark since the Viking and Iron Age, or changes of frequency in haplogroups in England since the 11th c. AD, such as the reduction of U5a1 and the increase in H may in fact be due to selection. H was present -although not very frequent- in Neolithic farmers from Central Europe, Corded Ware people from Eulau, and its very high present-day frequency in Europeans (roughly 50%) as there is no plausible source or mechanism that would have brought large numbers of it in Europe.

In conclusion, both migration and selection may help explain shifts in haplotype frequencies over time. As we plug in the holes in our knowledge of the mtDNA distribution across space and time, we will be able to decide between the two.

Y chromosome and mtDNA of goats in North Africa

Mol Biol Evol. 2009 Sep 3. [Epub ahead of print]

Tracing the history of goat pastoralism: new clues from mitochondrial and Y chromosome DNA in North Africa.

Pereira F, Queirós S, Gusmão L, Nijman IJ, Cuppen E, Lenstra JA; the Econogene Consortium, Davis SJ, Nejmeddine F, Amorim A.

Valuable insights into the history of human populations have been obtained by studying the genetic composition of their domesticated species. Here we address some of the long-standing questions about the origin and subsequent movements of goat pastoralism in Northern Africa. We present the first study combining results from mitochondrial DNA (mtDNA) and Y chromosome loci for the genetic characterization of a domestic goat population. Our analyses indicate a remarkably high diversity of maternal and paternal lineages in a sample of indigenous goats from the northwestern fringe of the African continent. Median-joining networks and a multidimensional scaling of ours and almost 2000 published mtDNA sequences revealed a considerable genetic affinity between goat populations from the Maghreb (Northwest Africa) and the Near East. It has been previously shown that goats have a weak phylogeographic structure compatible with high levels of gene flow, as demonstrated by the worldwide dispersal of the predominant mtDNA haplogroup A. In contrast, our results revealed a strong correlation between genetic and geographical distances in 20 populations from different regions of the world. The distribution of Y chromosome haplotypes in Maghrebi goats indicates a common origin for goat patrilines in both Mediterranean coastal regions. Taken together, these results suggest that the colonization and subsequent dispersal of domestic goats in Northern Africa was influenced by the maritime diffusion throughout the Mediterranean Sea and its coastal regions of pastoralist societies whose economy included goat herding. Finally, we also detected traces of gene flow between goat populations from the Maghreb and the Iberian Peninsula corroborating evidence of past cultural and commercial contacts across the Strait of Gibraltar.

Link

Variable genetic ancestry in Brazilians

Braz J Med Biol Res. 2009 Sep 11. pii: S0100-879X2009005000026.

DNA tests probe the genomic ancestry of Brazilians.

Pena SD, Bastos-Rodrigues L, Pimenta JR, Bydlowski SP.

We review studies from our laboratories using different molecular tools to characterize the ancestry of Brazilians in reference to their Amerindian, European and African roots. Initially we used uniparental DNA markers to investigate the contribution of distinct Y chromosome and mitochondrial DNA lineages to present-day populations. High levels of genetic admixture and strong directional mating between European males and Amerindian and African females were unraveled. We next analyzed different types of biparental autosomal polymorphisms. Especially useful was a set of 40 insertion-deletion polymorphisms (indels) that when studied worldwide proved exquisitely sensitive in discriminating between Amerindians, Europeans and Sub-Saharan Africans. When applied to the study of Brazilians these markers confirmed extensive genomic admixture, but also demonstrated a strong imprint of the massive European immigration wave in the 19th and 20th centuries. The high individual ancestral variability observed suggests that each Brazilian has a singular proportion of Amerindian, European and African ancestries in his mosaic genome. In Brazil, one cannot predict the color of persons from their genomic ancestry nor the opposite. Brazilians should be assessed on a personal basis, as 190 million human beings, and not as members of color groups.

Link

On the mtDNA molecular clock (Endicott et al. 2009)

This is an excellent paper to read on the technicalities and controversies surrounding the human mtDNA clock. The authors argue against over-reliance on the human chimpanzee splitting as a calibration point, both because of uncertainty about the age of that event, and also because of limitations of the ρ statistic which is widely used to associate the accumulation of genetic diversity with time (e.g., its performance under selection). They further argue that existing mtDNA age estimates are largely over-estimates for such events such as sapiens-Neanderthal divergence, and the arrival of modern humans in various parts of the world. Their concluding remarks:

Further research is needed to improve our confidence in
molecular estimates of human evolutionary timescales.
First, the most reliable calibrations within the human tree
need to be identified. For mitochondrial DNA, this depends
on finding well-defined haplogroups that can be precisely
associated with dated palaeoanthropological evidence [17].
Second, the variation in observed rates across different
timescales needs to be accurately quantified [16–18].
Third, these patterns of rate variation need to be investigated
for nuclear data, including the Y-chromosome and
short tandem repeats.

The chief recommendation arising from the current
state of knowledge in the field is for a movement away
from reliance on the human-chimpanzee calibration;
instead, calibrations within the human tree are preferred
(but see [14]). There are several recent examples of estimates
made using archaeological calibrations [15–17,35],
extending the efforts of earlier authors [3,60]. Considering
recent advances in phylogenetic methodology, there is now
a compelling motivation to employ statistical models that
take into account rate heterogeneity among sites and
among lineages, that correct for multiple substitutions
(saturation), and that incorporate directly the uncertainty
in the ages of calibrations used. Some methods also allow
the statistical evaluation of competing demographic
models, which can have an important influence on estimates
of rates and timescales [17,23].

I have my own misgivings about the possibility of archaeologial calibration of the mtDNA clock. Archaeology provides us with evidence that the arrival of modern humans in a part of the world could not have been later than X years ago, the age of the earliest archaeological or osteological finds.

But, it does not really tell us how many of them arrived, or what their own mtDNA time depth was: if a small number of migrants arrive, it is possible that either their own common ancestor lived fairly close to the time of migration, or that only one of them -due to genetic drift in the small population- will leave matrilineal descendants. In other words, if a small number of migrants participates in the early colonization of a region, chances increase that their mtDNA time depth will be close to the time of their arrival; conversely, known time of arrival -from archaeology- calibrates the molecular clock. Indeed, if the population stays small for a long time after arrival, the common matrilineal ancestor may "reset" several times, and the population's antiquity (based on mtDNA diversity) will appear to be much younger than it really is.

However, if the number of migrants is not small, then in all likelihood the common ancestor precedes the migration substantially, and calibration of the molecular clock by the visible migration would lead to an overestimate in the rate in which mtDNA diversity accumulates, and a molecular clock that produces more recent ages than the true ones.

Many existing works make the assumption of neutrality about mtDNA evolution in humans. This means that no mtDNA lineage has an advantage over any other; and subsequently, the fact that we are all descended from a relatively small number of "mothers" (like the "Daughters of Eve") becomes difficult to explain. Massive disappearance of other lineages (besides the few surviving mothers) is only possible under conditions of strong genetic drift in small populations. Hence, the conclusion, reiterated time and again in the literature about humans being reduced to a few hundred or a few thousand individuals, which has sparked the new mythos of a "small band of humans surviving to colonize the entire world".

In reality, our descent from a small number of "mothers" can be reconciled with a large human population under the assumption that mtDNA is under substantial natural selection. If that is the case, the limited number of surviving lineages is not due to drift in a small population, but to selection in a large one.

My personal guess is that the molecular clock won't be calibrated by reliance to archaeology, but by improvements in the affordability of sequencing. At present it is not really affordable to do full mtDNA genome scans in a few thousand mother-daughter pairs to obtain reliable mutation rate estimates, but this is likely to eventually change, leading to better estimates of the splitting times of various mtDNA lineages.

Some previous topics on the question:

• mtDNA time depth of humanity more recent than previously thought
• Time-dependency of the human mtDNA evolutionary mutation rate
• Purifying selection and the mtDNA clock (Soares et al. 2009)

Trends in Ecology and Evolution doi:10.1016/j.tree.2009.04.006

Evaluating the mitochondrial timescale of human evolution

Phillip Endicott, Simon Y.W. Ho, Mait Metspalu and Chris Stringer

Abstract

Different methodologies and modes of calibration have produced disparate, sometimes irreconcilable, reconstructions of the evolutionary and demographic history of our species. We discuss how date estimates are affected by the choice of molecular data and methodology, and evaluate various mitochondrial estimates of the timescale of human evolution in the context of the contemporary palaeontological and archaeological evidence for key stages in human prehistory. We contend that some of the most widely-cited mitochondrial rate estimates have several significant shortcomings, including a reliance on a human-chimpanzee calibration, and highlight the pressing need for revised rate estimates.

Link

Independent horse domestication event in China

See also: Origin of ancient Chinese horses from ancient DNA

Anim Genet. doi:10.1111/j.1365-2052.2009.01950.x

Multiple maternal origins of native modern and ancient horse populations in China

Lei CZ, Su R, Bower MA, Edwards CJ, Wang XB, Weining S, Liu L, Xie WM, Li F, Liu RY, Zhang YS, Zhang CM, Chen H.

Summary To obtain more knowledge of the origin and genetic diversity of domestic horses in China, this study provides a comprehensive analysis of mitochondrial DNA (mtDNA) D-loop sequence diversity from nine horse breeds in China in conjunction with ancient DNA data and evidence from archaeological and historical records. A 247-bp mitochondrial D-loop sequence from 182 modern samples revealed a total of 70 haplotypes with a high level of genetic diversity. Seven major mtDNA haplogroups (A-G) and 16 clusters were identified for the 182 Chinese modern horses. In the present study, nine 247-bp mitochondrial D-loop sequences of ancient remains of Bronze Age horse from the Chifeng region of Inner Mongolia in China (c. 4000-2000a bp) were used to explore the origin and diversity of Chinese modern horses and the phylogenetic relationship between ancient and modern horses. The nine ancient horses carried seven haplotypes with rich genetic diversity, which were clustered together with modern individuals among haplogroups A, E and F. Modern domestic horse and ancient horse data support the multiple origins of domestic horses in China. This study supports the argument that multiple successful events of horse domestication, including separate introductions of wild mares into the domestic herds, may have occurred in antiquity, and that China cannot be excluded from these events. Indeed, the association of Far Eastern mtDNA types to haplogroup F was highly significant using Fisher's exact test of independence (P = 0.00002), lending support for Chinese domestication of this haplogroup. High diversity and all seven mtDNA haplogroups (A-G) with 16 clusters also suggest that further work is necessary to shed more light on horse domestication in China.

Geographic patterning of goats from Greece, Albania, and Italy

BMC Ecol. 2009 Sep 2;9(1):20. [Epub ahead of print]

Geographical patterning of sixteen goat breeds from Italy, Albania and Greece assessed by Single Nucleotide Polymorphisms.

Pariset L, Cuteri A, Ligda C, Ajmone-Marsan P, Valentini A, Consortium E.

ABSTRACT: BACKGROUND: SNP data of goats of three Mediterranean countries were used for population studies and reconstruction of geographical patterning. 496 individuals belonging to Italian, Albanian and Greek breeds were genotyped to assess the basic population parameters. RESULTS: A total of 26 SNPs were used, for a total of 12,896 genotypes assayed. Statistical analysis revealed that breeds are not so similar in terms of genetic variability, as reported in studies performed using different markers. The Mantel test showed a strongly significant correlation between genetic and geographic distance. Also, PCA analysis revealed that breeds are grouped according to geographical origin, with the exception of the Greek Skopelos breed. CONCLUSION: Our data point out that the use of SNP markers to analyze a wider breed sample could help in understanding the recent evolutionary history of domestic goats. We found correlation between genetic diversity and geographic distance. Also PCA analysis shows that the breeds are well differentiated, with good correspondence to geographical locations, thus confirming the correlation between geographical and genetic distances. This suggests that migration history of the species played a pivotal role in the present-day structure of the breeds and a scenario in which coastal routes were easier for migrating in comparison with inland routes. A westward coastal route to Italy through Greece could have led to gene flow along the Northern Mediterranean.

Link

"Mother goddess" figurines theory demolished

I can't say I ever bought into the whole "Mother goddess" theory. It reeks of a pacifistic/New Age/feminist mindset, is heavy on theory, interpretation, and "symbolism" and light on objective facts.

Ancient figurines were toys not mother goddess statues, say experts as 9,000-year-old artefacts are discovered

Made by Neolithic farmers thousands of years before the creation of the pyramids or Stonehenge, they depict tiny cattle, crude sheep and flabby people.

In the 1960s, some researchers claimed the more rotund figures were of a mysterious large breasted and big bellied "mother goddess", prompting a feminist tourism industry that thrives today.

But modern day experts disagree.

They say the "mother goddess" figures - which were buried among the rubbish of the Stone Age town - are unlikely to be have been religious icons.

Many of the figures thought to have been women in the 1960s, are just as likely to be men.

...

Archaeologist Prof Lynn Meskell, of Stanford University, said: "The majority are cattle or sheep and goats. They could be representatives of animals they were dealing with - and they could have been teaching aides.

"All were found in the trash - and they were not in niches or platforms or placed in burials."

Out of the 2,000 figurines dug up at the site, less than five per cent are female, she told the British science Festival in Surrey University, Guildford.

"These are things that were made and used on a daily basis," she said. "People carried them around and discarded them."

Paleolithic flax fibres from Georgia (Kvavadze et al. 2009)

From BBC News:

A Georgian cave has yielded what scientists say are the earliest examples of humans making cords.

The microscopic fibres, discovered accidentally while scientists were searching for pollen samples, are around 30,000 years old.

A team reports in the journal Science that ancient humans probably used the plant fibres to carry tools, weave baskets or make garments.

Some of the fibres are coloured and appear to have been dyed.

Science Vol. 325. no. 5946, p. 1359 DOI: 10.1126/science.1175404

30,000-Year-Old Wild Flax Fibers

Eliso Kvavadze et al.

A unique finding of wild flax fibers from a series of Upper Paleolithic layers at Dzudzuana Cave, located in the foothills of the Caucasus, Georgia, indicates that prehistoric hunter-gatherers were making cords for hafting stone tools, weaving baskets, or sewing garments. Radiocarbon dates demonstrate that the cave was inhabited intermittently during several periods dated to 32 to 26 thousand years before the present (kyr B.P.), 23 to 19 kyr B.P., and 13 to 11 kyr B.P. Spun, dyed, and knotted flax fibers are common. Apparently, climatic fluctuations recorded in the cave’s deposits did not affect the growth of the plants because a certain level of humidity was sustained.

Link

Warfare rather than agriculture as a cause of fires in the Neolithic of northern Vietnam

PNAS doi:10.1073/pnas.0813258106

Warfare rather than agriculture as a critical influence on fires in the late Holocene, inferred from northern Vietnam

Zhen Li et al.

Fire has played an essential role in the development of human civilization. Most previous research suggests that frequent-fire regimes in the late Holocene were associated with intensification of human activities, especially agriculture development. Here, we analyze fire regimes recorded in the Song Hong delta area of Vietnam over the past 5,000 years. In the prehistoric period, 2 long-term, low-charcoal abundance periods have been linked to periods of low humidity and cool climate, and 5 short-term fire regimes of 100–150 years in duration occurred at regular intervals of ≈700 years. However, over the last 1,500 years, the number, frequency, and intensity of fire regimes clearly increased. Six intensified-fire regime periods in northern Vietnam during this time coincided with changes of Vietnamese dynasties and associated warfare and unrest. In contrast, agricultural development supported by rulers of stable societies at this time does not show a positive correlation with intensified-fire regime periods. Thus, warfare rather than agriculture appears to have been a critical factor contributing to fire regimes in northern Vietnam during the late Holocene.

Link

Genetic Ancestry, Social Classification, and Racial Inequalities in Blood Pressure in Southeastern Puerto Rico (Gravlee et al. 2009)

I had posted when this appeared in AAPA 2008, and now the full paper has been published.

Figure 1 shows the relationship between "color" and genetic ancestry. As can be seen, the "color" categories overlap in terms of genetic ancestry, even though their averages are in the right order:

The paper is a powerful reminder that social race is not the same as genomic ancestry, and that racial disparities in an observable trait do not necessarily reflect differential genetic proclivities.

PLoS ONE 4(9): e6821. doi:10.1371/journal.pone.0006821

Genetic Ancestry, Social Classification, and Racial Inequalities in Blood Pressure in Southeastern Puerto Rico

Clarence C. Gravlee et al.

Abstract

Background

The role of race in human genetics and biomedical research is among the most contested issues in science. Much debate centers on the relative importance of genetic versus sociocultural factors in explaining racial inequalities in health. However, few studies integrate genetic and sociocultural data to test competing explanations directly.

Methodology/Principal Findings

We draw on ethnographic, epidemiologic, and genetic data collected in southeastern Puerto Rico to isolate two distinct variables for which race is often used as a proxy: genetic ancestry versus social classification. We show that color, an aspect of social classification based on the culturally defined meaning of race in Puerto Rico, better predicts blood pressure than does a genetic-based estimate of continental ancestry. We also find that incorporating sociocultural variables reveals a new and significant association between a candidate gene polymorphism for hypertension (α2C adrenergic receptor deletion) and blood pressure.

Conclusions/Significance

This study addresses the recognized need to measure both genetic and sociocultural factors in research on racial inequalities in health. Our preliminary results provide the most direct evidence to date that previously reported associations between genetic ancestry and health may be attributable to sociocultural factors related to race and racism, rather than to functional genetic differences between racially defined groups. Our results also imply that including sociocultural variables in future research may improve our ability to detect significant allele-phenotype associations. Thus, measuring sociocultural factors related to race may both empower future genetic association studies and help to clarify the biological consequences of social inequalities.

Link

Reduced fecundity of fat women

J Womens Health (Larchmt). 2009 May;18(5):633-6.

The relationship between obesity and fecundity.

Yilmaz N, Kilic S, Kanat-Pektas M, Gulerman C, Mollamahmutoglu L.

OBJECTIVE: Obesity is an important factor that might reduce fecundity. In order to determine the underlying physiological mechanisms and risk factors, the obesity-fecundity association is investigated in relation to parity, menstrual cycle regularity, smoking habits, and age. METHODS: This was a retrospective cohort study of 22,840 women who gave birth between January 2006 and January 2007 in the Dr Zekai Tahir Burak Women's Health Research and Education Hospital. Age, parity, prepregnancy body mass index (BMI) values, time to pregnancy data related to smoking, and reproductive, medical, and gynecological history were obtained from the medical records. RESULTS: Fecundity was reduced for overweight and obese women compared with optimal weight women, and this reduction was more evident for obese primiparous women. Fecundity remained reduced for overweight and obese women with normal menstrual cycles. Obese and overweight women were found to smoke significantly more than the optimal weight group. CONCLUSIONS: Obesity was found to be associated with reduced fecundity for all weight-adjusted groups of women and persisted for women with regular cycles. Weight loss should be encouraged initially during the treatment of infertile overweight and obese women.

Link

Ancient mtDNA from Yayoi period Doigahama (Japan)

Journal of Human Genetics doi: 10.1038/jhg.2009.81

Mitochondrial DNA analysis of Yayoi period human skeletal remains from the Doigahama site

Kazunari Igawa et al.

We analyzed the mitochondrial DNA extracted from 14 human skeletal remains from the Doigahama site in Japan to clarify the genetic structure of the Doigahama Yayoi population and the relationship between burial style and kinship among individuals. The sequence types obtained in this study were compared with those of the modern Japanese, northern Kyushu Yayoi and ancient Chinese populations. We found that the northern Kyushu Yayoi populations belonged to the groups that include most of the modern Japanese population. In contrast, most of the Doigahama Yayoi population belonged to the group that includes a small number of the modern Japanese population. These results suggest that the Doigahama Yayoi population might have contributed less to the formation of the modern Japanese population than the northern Kyushu Yayoi populations. Moreover, when we examined the kinship between individuals in the Doigahama site, we found that the vicinal burial of adult skeletons indicated a maternal kinship, although that of juvenile skeletons did not. The vicinal burial style might have been influenced by many factors, such as paternal lineages, periods and geographical regions, as well as maternal lineages. In addition, skeletons considered to be those of shamans or leaders had the same sequence types. Their crucial social roles may have been inherited through maternal lineage.

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European admixture and obesity traits in African Americans

Obesity (Silver Spring). doi:10.1038/oby.2009.282

Admixture Mapping of Obesity-related Traits in African Americans: The Atherosclerosis Risk in Communities (ARIC) Study.

Cheng CY, Reich D, Coresh J, Boerwinkle E, Patterson N, Li M, North KE, Tandon A, Bailey-Wilson JE, Wilson JG, Kao WH.

Obesity is an important cause of morbidity and mortality worldwide. In the United States, the prevalence of obesity is higher in African Americans than whites, even after adjustment for socioeconomic status (SES). This leads to the hypothesis that differences in genetic background may contribute to racial/ethnic differences in obesity-related traits. We tested this hypothesis by conducting a genome-wide admixture mapping scan using 1,350 ancestry-informative single-nucleotide polymorphisms (SNPs) in 3,531 self-identified blacks from the Atherosclerosis Risk in Communities (ARIC) study. We used these markers to estimate the overall proportions of European ancestry (PEAs) for each individual and then scanned for the association between PEA and obesity-related traits (both continuous and dichotomous) at each locus. The median (interquartile range) PEA was 0.151 (0.115). PEA was inversely correlated with continuous BMI, weight, and subscapular skinfold thickness, even after adjusting for socioeconomic factors. In contrast, PEA was positively correlated with BMI-adjusted waist circumference. Using admixture mapping on dichotomized traits, we identified a locus on 2p23.3 to be suggestively associated with BMI (locus-specific lod = 4.11) and weight (locus-specific lod = 4.07). After adjusting for global PEA, each additional copy of a European ancestral allele at the 2p23.3 peak was associated with a BMI decrease of ~0.92 kg/m(2) (P = 2.9 x 10(-5)). Further mapping in this region on chromosome 2 may be able to uncover causative variants underlying obesity, which may offer insights into the control of energy homeostasis.

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Colin Renfrew video on the "Renfrew hypothesis" of Indo-European origin

A two-part video interview of Colin Renfrew; the discussion of Indo-European spans roughly 22:20 to 40:40 in the second part.

Part I



Part II