Int J Legal Med DOI 10.1007/s00414-009-0406-z

The mtDNA composition of Uzbekistan: a microcosm of Central Asian patterns

Jodi A. Irwin et al.

Abstract

In order to better characterize and understand the mtDNA population genetics of Central Asia, the mtDNA control regions of over 1,500 individuals from Uzbekistan
have been sequenced. Although all samples were obtained from individuals residing in Uzbekistan, individuals with direct ancestry from neighboring Central Asian countries are included. Individuals of Uzbek ancestry represent five distinct geographic regions of Uzbekistan: Fergana, Karakalpakstan, Khorezm, Qashkadarya, and Tashkent. Individuals with direct ancestry in nearby countries originate from Kazakhstan, Kyrgyzstan, Russia, Afghanistan, Turkmenistan, and Tajikistan. Our data reinforce the evidence of distinct clinal patterns that have been described among Central Asian populations with classical, mtDNA, and Y-chromosomal markers. Our data also reveal hallmarks of recent demographic events. Despite their current close geographic proximity, the populations with ancestry in neighboring countries show little sign of admixture and retain the primary mtDNA patterns of their source populations. The genetic distances and haplogroup distributions among the ethnic populations are more indicative of a broad east–west cline among their source populations than of their relatively small geographic distances from one another in Uzbekistan. Given the significant mtDNA heterogeneity detected, our results emphasize the need for heightened caution in the forensic interpretation of mtDNA data in regions as historically rich and genetically diverse as Central Asia.

Link

It is interesting that only haplogroup Q was found in the (admittedly limited) sample of nomads. I am pretty sure that there is plentiful haplogroup O (the dominant Han group) in the region today and C (the dominant Mongolian one), just as haplogroup R1a which was dominant in the earliest inhabitants of the Tarim basin has lost its special place there.

Hopefully we will be seeing more ancient Y chromosome results from the eastern half of the Eurasian continuum in the future.

Journal of Human Genetics advance online publication 26 February 2010; doi: 10.1038/jhg.2010.8

Ancient DNA from nomads in 2500-year-old archeological sites of Pengyang, China

Yong-Bin Zhao et al.

Larry David 37% "Native American" and Jessica Alba only 13%?

Methinks this is due to inflated Native American DNA estimates, a problem which has plagued this particular test. As far as I know Larry David is Jewish in ancestry, so I would expect a much higher "European" component.

Alba is apparently half white Canadian and half Mexican American. A figure of about 1/3 Amerindian ancestry has been estimated for a sample of US Hispanics from New Mexico which would seem consistent with Alba's estimated ancestry estimate.

All in all, I would say that these results tend to confirm that while the AncestryByDNA test tends to provide reasonable admixture estimates (within its statistical limitations) for actual admixed persons, it is less valuable for non-admixed individuals who are not a good match for the four chosen ancestral sample groups.

Current Biology has several articles in its current issue (23 February, 2010 Volume 20, Issue 4). Will comment on them in this space. Just listing the titles for now:

Am J Hum Biol. 2010 Feb 12.

This appears to be a published study by the same team which appeared in a recent National Geographic documentary on the Tarim mummies. The site of Xiaohe (of the current study) is earlier and to the southeast of Urumqi.

The finding that the Bronze Age population, like that of Krasnoyarsk Siberians belonged exclusively -as far as sampling allows- to Y-chromosome haplogroup R1a1 is extremely interesting as it raises the issue of when and how exactly the diverse extant Y-chromosome gene pool of Central Asia came about.

The dominant haplogroup in the Xiaohe people was the East Eurasian lineage C, shared by 14 Xiaohe individuals who were associated with two different mtDNAhaplotypes (S1 and S2). According to the coding region 11969 A to G, all lineage C found in the Xiaohe people were further classified to subhaplogroup C4, which had D-loop group-specific polymorphisms at nucleotide positions (np) 16298 (T to C) and16327 (C to T) [18].

...

Besides the East Eurasian lineage, two West Eurasian mtDNA haplogroups H and K were found among the Xiaohe people. H lineage is the most common mtDNAhaplogroup in West Eurasia [20], but haplogroup H with a 16260T was shared by only nine modern people in Genbank, including one Italian, one German, one Hungarian,one Portuguese, one Icelander and four English people. Haplogroup K, a western Eurasian–specific haplogroup, is mainly distributed in Europe, central Asia, and Iran [20, 21]. However, haplogroup K with 16134T, found in the Xiaohe people, has not been found in modern people to our knowledge.

...

Among the Xiaohe people, three sequences with the unique HVRI motif 16189–16192–16311 formed a subcluster (Figure 2) and were not shared by modern people. [...] The results showed that they are related neither to the West Eurasian haplogroups UK, TJ, HV, R11and R1, nor to the East Eurasian haplogroups B and F. So we designated them as haplogroup R*temporarily. Another sequence with motif 16223–16304, shared by some people fromEast Asia, India, and Europe, was assigned to haplogroup M*.

It's not clear to me how Carthaginians disposed of sacrificial victims, so I'd say that absence of evidence is not evidence of absence.

I don't think it's unlikely that the occurrence of child sacrifice may have been "inflated" by hostile observers, but Diodorus Siculus gives a very specific description of what took place there, which I think is unlikely to have been pure invention.

14 Therefore the Carthaginians, believing that the misfortune had come to them from the gods, betook themselves to every manner of supplication of the divine powers; and, because they believed that Heracles, who was worshipped in their mother city,29 was exceedingly angry with them, they sent a large sum of money and many of the most expensive offerings to Tyre. 2 Since they had come as colonists from that city, it had been their custom in the earlier p179period to send to the god a tenth of all that was paid into the public revenue; but later, when they had acquired great wealth and were receiving more considerable revenues, they sent very little indeed, holding the divinity of little account. But turning to repentance because of this misfortune, they bethought them of all the gods of Tyre. 3 They even sent from their temples in supplication the golden shrines with their images,30 believing that they would better appease the wrath of the god if the offerings were sent for the sake of winning forgiveness. 4 They also alleged that Cronus31 had turned against them inasmuch as in former times they had been accustomed to sacrifice to this god the noblest of their sons, but more recently, secretly buying and nurturing children, they had sent these to the sacrifice; and when an investigation was made, some of those who had been sacrificed were discovered to have been supposititious. 5 When they had given thought to these things and saw their enemy encamped before their walls, they were filled with superstitious dread, for they believed that they had neglected the honours of the gods that had been established by their fathers. In their zeal to make amends for their omission, they selected two hundred of the noblest children and sacrificed them publicly; and others who were under suspicion sacrificed themselves voluntarily, in number not less than three hundred. 6 There was in their city a bronze image of Cronus, extending its hands, palms up and sloping toward the ground, so that each of the children when placed p181thereon rolled down and fell into a sort of gaping pit filled with fire.

Rogue Classicist also has reservations about the way the story is presented in the media.

The number of published complete genomes is starting to grow exponentially it seems. Pretty soon, I'm guessing, once most major groups are covered by at least one individual, they will cease to be paper-worthy, and we will move on to the era of full-genome population studies.

Even though the paper casts serious doubt on the identification of the relics with St. Birgitta and her daughter, it is still interesting as it gives us two late medieval sequences from Sweden:

16189C, 263G, 315.1C, 3010A, 16519C
16126C, 16294T, 16296T, 16304C, 73G, 263G, 309.1C, 315.1C, 16519C

PLoS ONE doi:10.1371/journal.pone.0008986

Analysis of the Putative Remains of a European Patron Saint–St. Birgitta

Martina Nilsson et al.

Abstract

Saint Birgitta (Saint Bridget of Sweden) lived between 1303 and 1373 and was designated one of Europe's six patron saints by the Pope in 1999. According to legend, the skulls of St. Birgitta and her daughter Katarina are maintained in a relic shrine in Vadstena abbey, mid Sweden. The origin of the two skulls was assessed first by analysis of mitochondrial DNA (mtDNA) to confirm a maternal relationship. The results of this analysis displayed several differences between the two individuals, thus supporting an interpretation of the two skulls not being individuals that are maternally related. Because the efficiency of PCR amplification and quantity of DNA suggested a different amount of degradation and possibly a very different age for each of the skulls, an orthogonal procedure, radiocarbon dating, was performed. The radiocarbon dating results suggest an age difference of at least 200 years and neither of the dating results coincides with the period St. Birgitta or her daughter Katarina lived. The relic, thought to originate from St. Birgitta, has an age corresponding to the 13th century (1215–1270 cal AD, 2σ confidence), which is older than expected. Thus, the two different analyses are consistent in questioning the authenticity of either of the human skulls maintained in the Vadstena relic shrine being that of St. Birgitta. Of course there are limitations when interpreting the data of any ancient biological materials and these must be considered for a final decision on the authenticity of the remains.

Link

Human Genetics doi:10.1007/s00439-010-0798-3

A genome-wide survey does not show the genetic distinctiveness of Basques

Hafid Laayouni et al.

Abstract

Basques are a cultural isolate, and, according to mainly allele frequencies of classical polymorphisms, also a genetic isolate. We investigated the differentiation of Spanish Basques from the rest of Iberian populations by means of a dense, genome-wide SNP array. We found that F ST distances between Spanish Basques and other populations were similar to those between pairs of non-Basque populations. The same result is found in a PCA of individuals, showing a general distinction between Iberians and other South Europeans independently of being Basques. Pathogen-mediated natural selection may be responsible for the high differentiation previously reported for Basques at very specific genes such as ABO, RH, and HLA. Thus, Basques cannot be considered a genetic outlier under a general genome scope and interpretations on their origin may have to be revised.

Link

Related:

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

BMC Evolutionary Biology doi:10.1186/1471-2148-10-36

A worldwide correlation of lactase persistence phenotype and genotypes

Yuval Itan et al.

Abstract (provisional)

Background
The ability of adult humans to digest the milk sugar lactose - lactase persistence - is a dominant Mendelian trait that has been a subject of extensive genetic, medical and evolutionary research. Lactase persistence is common in people of European ancestry as well as some African, Middle Eastern and Southern Asian groups, but is rare or absent elsewhere in the world. The recent identification of independent nucleotide changes that are strongly associated with lactase persistence in different populations worldwide has led to the possibility of genetic tests for the trait. However, it is highly unlikely that all lactase persistence-associated variants are known. Using an extensive database of lactase persistence phenotype frequencies, together with information on how those data were collected and data on the frequencies of lactase persistence variants, we present a global summary of the extent to which current genetic knowledge can explain lactase persistence phenotype frequency.

Results
We used surface interpolation of Old World lactase persistence genotype and phenotype frequency estimates obtained from all available literature and perform a comparison between predicted and observed trait frequencies in continuous space. By accommodating additional data on sample numbers and known false negative and false positive rates for the various lactase persistence phenotype tests (blood glucose and breath hydrogen), we also apply a Monte Carlo method to estimate the probability that known lactase persistence-associated allele frequencies can explain observed trait frequencies in different regions.

Conclusion
Lactase persistence genotype data is currently insufficient to explain lactase persistence phenotype frequency in much of western and southern Africa, southeastern Europe, the Middle East and parts of central and southern Asia. We suggest that further studies of genetic variation in these regions should reveal additional nucleotide variants that are associated with lactase persistence.

Link

From a related NY Times story:

The Greenlander belonged to a Paleo-Eskimo culture called the Saqqaq by archaeologists. On the basis of his genome, the Saqqaq man’s closest living relatives are the Chukchis, people who live at the easternmost tip of Siberia. His ancestors split apart from Chukchis some 5,500 years ago, according to genetic calculations, implying the Saqqaq people’s ancestors must have traveled across the northern edges of North America until they reached Greenland.

...

The Saqqaq man’s genome is so complete that the Danish researchers have been able to reconstruct his probable appearance and susceptibility to disease from the genetic information in his genome. They predict he would have had brown eyes because of variations, at four positions along his DNA, that are associated with brown eye color in East Asians.

He has the East Asian version of a gene known as EDAR, which endows people with hair that is thicker than that of most Europeans and Africans. Another gene suggests he would have had dry earwax, as do Asians and Native Americans, not the wet earwax of other ethnic groups.

Perhaps reflecting the so far somewhat limited reach of personal genomics, the researchers note that the ancient Greenlander was at risk for baldness, a surprising assessment given that all that remains of him is his hair. Dr. Rasmussen said he assumed the man died young.

Nature 463, 757-762 doi:10.1038/nature08835

Ancient human genome sequence of an extinct Palaeo-Eskimo

Morten Rasmussen

Mediterranean diet may lower risk of brain damage that causes thinking problems

ST. PAUL, Minn. – A Mediterranean diet may help people avoid the small areas of brain damage that can lead to problems with thinking and memory, according to a study released today that will be presented at the American Academy of Neurology's 62nd Annual Meeting in Toronto April 10 to April 17, 2010.

The study found that people who ate a Mediterranean-like diet were less likely to have brain infarcts, or small areas of dead tissue linked to thinking problems.

The Mediterranean diet includes high intake of vegetables, legumes, fruits, cereals, fish and monounsaturated fatty acids such as olive oil; low intake of saturated fatty acids, dairy products, meat and poultry; and mild to moderate amounts of alcohol.

For the study, researchers assessed the diets of 712 people in New York and divided them into three groups based on how closely they were following the Mediterranean diet. Then they conducted MRI brain scans of the people an average of six years later. A total of 238 people had at least one area of brain damage.

Those who were most closely following a Mediterranean-like diet were 36 percent less likely to have areas of brain damage than those who were least following the diet. Those moderately following the diet were 21 percent less likely to have brain damage than the lowest group.

"The relationship between this type of brain damage and the Mediterranean diet was comparable with that of high blood pressure," said study author Nikolaos Scarmeas, MD, MSc, of Columbia University Medical Center in New York and a member of the American Academy of Neurology. "In this study, not eating a Mediterranean-like diet had about the same effect on the brain as having high blood pressure."

Previous research by Scarmeas and his colleagues showed that a Mediterranean-like diet may be associated with a lower risk of Alzheimer's disease and may lengthen survival in people with Alzheimer's disease. According to the present study, these associations may be partially explained by fewer brain infarcts.

International Journal of Legal Medicine doi:10.1007/s00414-009-0406-z

The mtDNA composition of Uzbekistan: a microcosm of Central Asian patterns

Jodi A. Irwin et al.

Abstract

In order to better characterize and understand the mtDNA population genetics of Central Asia, the mtDNA control regions of over 1,500 individuals from Uzbekistan have been sequenced. Although all samples were obtained from individuals residing in Uzbekistan, individuals with direct ancestry from neighboring Central Asian countries are included. Individuals of Uzbek ancestry represent five distinct geographic regions of Uzbekistan: Fergana, Karakalpakstan, Khorezm, Qashkadarya, and Tashkent. Individuals with direct ancestry in nearby countries originate from Kazakhstan, Kyrgyzstan, Russia, Afghanistan, Turkmenistan, and Tajikistan. Our data reinforce the evidence of distinct clinal patterns that have been described among Central Asian populations with classical, mtDNA, and Y-chromosomal markers. Our data also reveal hallmarks of recent demographic events. Despite their current close geographic proximity, the populations with ancestry in neighboring countries show little sign of admixture and retain the primary mtDNA patterns of their source populations. The genetic distances and haplogroup distributions among the ethnic populations are more indicative of a broad east–west cline among their source populations than of their relatively small geographic distances from one another in Uzbekistan. Given the significant mtDNA heterogeneity detected, our results emphasize the need for heightened caution in the forensic interpretation of mtDNA data in regions as historically rich and genetically diverse as Central Asia.

Link

Coll Antropol. 2009 Dec;33(4):1323-8.

The frappe analysis for K=7 using ~16k and ~19k X chromosome (top) and Chromosome 16 (bottom) SNPs is shown. The pattern is almost identical.

This showcases the fallacy of a common objection to the concept of "race", namely that it is "trait-specific" and by looking at one trait (or locus) we will arrive at one racial classification, while looking at another wew will arrive at another.

The fact that by looking at two completely independently inherited pieces of DNA we arrive at the same conclusion is strong visual evidence that race is neither (a) a subjective property which depends on which part of the genome we look at, nor (b) a holistic property that can only be inferred by looking at the individual in toto.

Genome Biology doi:10.1186/gb-2010-11-1-r10

Characterization of X-Linked SNP genotypic variation in globally-distributed human populations

Amanda M Casto et al.

Abstract

Background
The transmission pattern of the human X chromosome reduces its population size relative to the autosomes, subjects it to disproportionate influence by female demography, and leaves X-linked mutations exposed to selection in males. As a result, the analysis of X-linked genomic variation can provide insights into the influence of demography and selection on the human genome. Here we characterize the genomic variation represented by 16,297 X-linked SNPs genotyped in the CEPH human genome diversity project samples.

Results
We found that X chromosomes tend to be more differentiated between human populations than autosomes with several notable exceptions. Comparisons between genetically distant populations also showed an excess of X-linked SNPs with large allele frequency differences. Combining information about these SNPs with results from tests designed to detect selective sweeps, we identified two regions that were clear outliers from the rest of the X chromosome for haplotype structure and allele frequency distribution. We were also able to more precisely define the geographical extent of some previously described X-linked selective sweeps.

Conclusions
The relationship between male and female demographic histories is likely to be complex as evidence supporting different conclusions can be found in the same dataset. Although demography may have contributed to the excess of SNPs with large allele frequency differences observed on the X chromosome, we believe that selection is at least partially responsible. Finally, our results reveal the geographical complexities of selective sweeps on the X chromosome and argue for the use of diverse populations in studies of selection.

Link

Am J Phys Anthropol doi:10.1002/ajpa.21252

Mitochondrial DNA patterns in the Iberian Northern plateau: Population dynamics and substructure of the Zamora province

Luis Alvarez et al.

ABSTRACT

Several studies have shown the importance of recent events in the configuration of the genetic landscape of a specific territory. In this context, due to the phenomena of repopulation and demographic fluctuations that took place in recent centuries, the Iberian Northern plateau is a very interesting case study. The main aim of this work is to check if recent population movements together with existing boundaries (geographical and administrative) have influenced the current genetic composition of the area. To accomplish this general purpose, mitochondrial DNA variations of 214 individuals from a population located in the Western region of the Iberian Northern plateau (the province of Zamora) were analyzed. Results showed a typical Western European mitochondrial DNA haplogroup composition. However, unexpected high frequencies of U5, HV0, and L haplogroups were found in some regions. The analyses of microdifferentiation showed that there are differences between regions, but no geographic substructure organization can be noticed. It can be stated that the differences observed in the genetic pool of the sampled area at regional level results from the mixture of different populations carrying new lineages into this area at different points in history.

Link

Not very surprising given his nationality. I guess there is a small chance of a non-paternity event in 4 transmission events, so the result is probably not as good as e.g., exhuming Charles Darwin himself and testing him directly, but that's probably just nitpicking.

This ties in with what I've written before, namely, that complex phenotypes don't have a set of population-common genetic causes, but are caused by different combinations of "commodity" alleles.

Just as you can drink water from a cup, or a glass, or a bucket, or a spoon, or your hands, i.e., you can achieve the same functional effect by very different means, so you can achieve the same phenotypic effect (e.g., intelligence) by very different genetic means.

International Journal of Osteoarchaeology doi:10.1002/oa.1150

Anthropological analysis of the osteological material from an ancient tomb (Early Bronze Age) from the middle Euphrates valley, Terqa (Syria)

J. Tomczyk et al.

Abstract

Terqa, situated on the right bank of the Middle Euphrates, is known to have been a site already in the third and second millennium BC. Excavations which take place in this region aim to provide answers for numerous significant issues connected with the origins of human civilisation. In 2008 season we found a tomb dated 2650-2450 BC, consisting of two chambers with stone domes. The smaller chamber contained many luxury grave goods. The other one was bigger and contained human skeletons.