March 28, 2008

Which of these two women is more attractive? (updated)

There are separate polls for male and female readers. Comments will open when the results are announced.

UPDATE (March 31): The results are now in:

MEN: Left: 369 (77%), Right: 109 (23%)
WOMEN: Left: 125 (58%), Right: 89 (42%)

Feel free to give your explanations for the findings, voice your preferences and the reasons for them, or speculate about what each of these two women represent!

UPDATE (April 1):

The names for search engines: Katherine Heigl, Alessandra Ambrosio, Kate Beckinsale, Eva Mendes, Jessica Alba, Scarlett Johansson, Jessica Biel, Marisa Miller, Ginger Rogers, Joan Fontaine, Jennifer Jones, Joan Crawford, Olivia de Havilland, Loretta Young, Jane Wyman.

March 27, 2008

Christian and Muslim Lebanese do differ from each other after all

Like I said they did in 2007. BBC has a story about this:
The team analysed the Y chromosomes of 926 Lebanese males and found that patterns of male genetic variation in Lebanon fell more along religious lines than along geographical lines.

A genetic signature on the male chromosome called WES1, which is usually only found in European populations, was found among the Lebanese men included in the study.

"It seems to have come in from Europe and is found mostly in the Christian population," said Dr Spencer Wells, director of the Genographic Project.

"This is odd because typically we don't see this sort of stratification by religion when we are looking at the relative proportions of these lineages - and particularly immigration events."

He told BBC News: "Looking at the same data set, we saw a similar enrichment of lineages coming in from the Arabian Peninsula in the Muslim population which we didn't see [as often] in the Christian population."

Lebanese Muslim men were found to have high frequencies of a Y chromosome grouping known as J1. This is typical of populations originating from the Arabian Peninsula, who were involved in the Muslim expansion.

As I predicted, the finding of similarity between Christian and Muslim Lebanese in the older National Geographic story on Wells' and Zalloua's work was premature, based on their common possession of Y-haplogroup J, because it did not look at downstream markers which differentiate between Christians and Muslims. As I observed based on the work of Capelli et al., it is the overrepresentation of Y-haplogroup J*(xJ2), which comprises almost entirely of J1 chromosomes that is the mark of the Arab descent of Muslim Lebanese.

I will post the abstract of this study and any further comments when I see it.

UPDATE: The Genographic project has its own page on this research, as well as a link to the paper (pdf).

Y-Chromosomal Diversity in Lebanon Is Structured by Recent Historical Events

Pierre A. Zalloua et al.

Lebanon is an eastern Mediterranean country inhabited by approximately four million people with a wide variety of ethnicities and religions, including Muslim, Christian, and Druze. In the present study, 926 Lebanese men were typed with Y-chromosomal SNP and STR markers, and unusually, male genetic variation within Lebanon was found to be more strongly structured by religious affiliation than by geography.We therefore tested the hypothesis that migrations within historical times could have contributed to this situation. Y-haplogroup J*(xJ2) was more frequent in the putative Muslim source region (the Arabian Peninsula) than in Lebanon, and it was also more frequent in Lebanese Muslims than in Lebanese non-Muslims. Conversely, haplogroup R1b was more frequent in the putative Christian source region (western Europe) than in Lebanon and was also more frequent in Lebanese Christians than in Lebanese non-
Christians. The most common R1b STR-haplotype in Lebanese Christians was otherwise highly specific for western Europe and was unlikely to have reached its current frequency in Lebanese Christians without admixture.We therefore suggest that the Islamic expansion from the Arabian Peninsula beginning in the seventh century CE introduced lineages typical of this area into those who subsequently became Lebanese Muslims, whereas the Crusader activity in the 11th-13th centuries CE introduced western European lineages into Lebanese Christians.

March 26, 2008

Yeniseic - Na-Dene linguistic link

A previous post on Kets and other northern Eurasians. Interestingly, the Kets belong overwhelmingly to Y-haplogroup Q, the major Native American Y-haplogroup, with the remainder being mostly C, the other Y-haplogroup found in Native Americans.

Siberian, Native American Languages Linked -- A First
His research links the Old World language family of Yeniseic in central Siberia with the Na-Dene family of languages in North America.

The Yeniseic family includes the extinct languages Yugh, Kott, Assan, Arin, and Pumpokol. Ket is the only Yeniseic language spoken today. Less than 200 speakers remain and most are over 50, according to Vajda.

"Within a couple of generations, Ket will probably become extinct," he said.

Eyebrow position and attractiveness in females

Aesthetic Plast Surg. 2007 Mar-Apr;31(2):154-60.

Attractiveness of eyebrow position and shape in females depends on the age of the beholder.

Feser DK, Gründl M, Eisenmann-Klein M, Prantl L.

BACKGROUND: Great diversity exists among individuals with respect to eyebrow position and shape, and the notion of an "ideal" eyebrow has changed quite significantly over the past several decades. METHODS: This study compared three different variations of eyebrows. One variation was the arched eyebrow with the maximum height in the middle. The other two variations had their maximum height in the lateral third, but differed in their position (high vs low). For each of the seven female portraits presented, three variations were generated using morphing software. A total of 357 subjects 12 to 85 years of age compared these variations and ranked each woman individually with respect to perceived attractiveness. RESULTS: The data show that the preference for a specific eyebrow shape depends on a person's age. Young subjects up to 30 years of age preferred eyebrows in a lower position, and ruled out arched eyebrows. Subjects older than 50 years stated exactly the opposite preference. CONCLUSION: First, there is not one single beauty ideal for eyebrows, but at least three. The ideal a person prefers depends on his or her age. Second, because trends are generally introduced by young people and not by older individuals, and the young tend to prefer eyebrows in a lower position, it seems plausible to assume that the trend currently appears to be moving away from arched eyebrows toward lower positioned eyebrows with a maximum height in the lateral third.


March 25, 2008

Origins of the Uighur

Interesting bit from the paper:
Notably, the distribution of admixture proportions among UIG individuals is relatively even, with 48.7% the lowest admixture from European ancestry and the highest 62.2%. The standard deviation is only 3.8%, which is much smaller than the estimation for the African-American (AfA) population,58 suggesting a much longer history of admixture events for the Uyghur population compared with the AfA population.

The American Journal of Human Genetics, doi:10.1016/j.ajhg.2008.01.017

Analysis of Genomic Admixture in Uyghur and Its Implication in Mapping Strategy

Shuhua Xu et al.


The Uyghur (UIG) population, settled in Xinjiang, China, is a population presenting a typical admixture of Eastern and Western anthropometric traits. We dissected its genomic structure at population level, individual level, and chromosome level by using 20,177 SNPs spanning nearly the entire chromosome 21. Our results showed that UIG was formed by two-way admixture, with 60% European ancestry and 40% East Asian ancestry. Overall linkage disequilibrium (LD) in UIG was similar to that in its parental populations represented in East Asia and Europe with regard to common alleles, and UIG manifested elevation of LD only within 500 kb and at a level of 0.1 < style="font-weight: bold;">we estimated that the admixture event of UIG occurred about 126 [107∼146] generations ago, or 2520 [2140∼2920] years ago assuming 20 years per generation. In spite of the long history and short LD of Uyghur compared with recent admixture populations such as the African-American population, we suggest that mapping by admixture LD (MALD) is still applicable in the Uyghur population but ∼10-fold AIMs are necessary for a whole-genome scan.


mtDNA haplogroup E in Southeast Asia

Mol Biol Evol. 2008 Mar 21 [Epub ahead of print]

Climate Change and Post-Glacial Human Dispersals in Southeast Asia.

Soares P, Trejaut JA, Loo JH, Hill C, Mormina M, Lee CL, Chen YM, Hudjashov G, Forster P, Macaulay V, Bulbeck D, Oppenheimer S, Lin M, Richards MB.

Modern humans have been living in Island Southeast Asia (ISEA) for at least 50,000 years. Largely because of the influence of linguistic studies, however, which have a shallow time depth, the attention of archaeologists and geneticists has usually been focused on the last 6000 years - in particular, on a proposed Neolithic dispersal from China and Taiwan. Here we use complete mitochondrial DNA (mtDNA) genome sequencing to spotlight some earlier processes that clearly had a major role in the demographic history of the region but have hitherto been unrecognised. We show that haplogroup E, an important component of mtDNA diversity in the region, evolved in situ over the last 35,000 years and expanded dramatically throughout ISEA around the beginning of the Holocene, at the time when the ancient continent of Sundaland was being broken up into the present-day archipelago by rising sea levels. It reached Taiwan and Near Oceania more recently, within the last approximately 8000 years. This suggests that global warming and sea-level rises at the end of the Ice Age, 15,000-7000 years ago, were the main forces shaping modern human diversity in the region.


Long Live the 25th March 1821

March 21, 2008

Genomic admixture of Latin American Mestizos

PLoS Genetics has a new study on the origins of Latin American Mestizo populations.

PLoS Genetics doi:10.1371/journal.pgen.1000037

Geographic Patterns of Genome Admixture in Latin American Mestizos

Sijia Wang et al.

The large and diverse population of Latin America is potentially a powerful resource for elucidating the genetic basis of complex traits through admixture mapping. However, no genome-wide characterization of admixture across Latin America has yet been attempted. Here, we report an analysis of admixture in thirteen Mestizo populations (i.e. in regions of mainly European and Native settlement) from seven countries in Latin America based on data for 678 autosomal and 29 X-chromosome microsatellites. We found extensive variation in Native American and European ancestry (and generally low levels of African ancestry) among populations and individuals, and evidence that admixture across Latin America has often involved predominantly European men and both Native and African women. An admixture analysis allowing for Native American population subdivision revealed a differentiation of the Native American ancestry amongst Mestizos. This observation is consistent with the genetic structure of pre-Columbian populations and with admixture having involved Natives from the area where the Mestizo examined are located. Our findings agree with available information on the demographic history of Latin America and have a number of implications for the design of association studies in population from the region.


March 20, 2008

Y chromosome haplogroups of ancient Southern Siberians from Krasnoyarsk

The samples belonged to the Afanasyevo (which did not yield a result), Andronovo, Tagar, and Tachtyk cultures. The non-R1a1 individual belonged to haplogroup C(xC3) and the Andronovo culture; the 2 other Andronovo individuals belonged to R1a1. This is an interesting result which suggests the presence of an eastern element in steppe cultures that originated by all accounts in the west of the area in question.

Int J Legal Med. 2007 Nov;121(6):493-9.

First successful assay of Y-SNP typing by SNaPshot minisequencing on ancient DNA.

Bouakaze C, Keyser C, Amory S, Crubézy E, Ludes B.

In the present study, a set of 13 Y-chromosomal single nucleotide polymorphisms (Y-SNPs) selected for the identification of the most frequent Asian Y-haplogroups was included in an allele-specific primer extension assay. Single nucleotide polymorphism (SNP) genotyping was accomplished by co-amplification of these 13 DNA fragments within 2 multiplex PCRs followed by detection with 1 minisequencing reaction using the SNaPshottrade mark Multiplex kit and analysis of extension products by capillary electrophoresis. First developed on modern samples, the assay was optimized for the analysis of 11 ancient DNA (aDNA) samples from the Krasnoyarsk region (southern Siberia) that were dated from 5,500-1,800 years before present (YBP). SNP typing was successful for most of them, which were all assigned to Y-haplogroup R1a1 except one. These results show that SNPs are well-suited for the analysis of aged and degraded DNA samples. Moreover, we found that the SNaPshot minisequencing methodology is a convenient, robust, and efficient method for SNP typing. To our knowledge, this study reports the first successful investigation of Y-SNPs on aDNA samples. The potential use of Y-SNPs in both evolutionary and forensic fields is also discussed.


March 19, 2008

mtDNA haplogroup R and severe sepsis in Chinese Han population

Genet Med. 2008 Mar;10(3):187-92.

Mitochondrial DNA haplogroup R predicts survival advantage in severe sepsis in the Han population.

Yang Y, Shou Z, Zhang P, He Q, Xiao H, Xu Y, Li C, Chen J.

PURPOSE: To determine whether the main mitochondrial DNA (mtDNA) haplogroups of the Han people have an impact on long-term clinical outcome. METHODS: We prospectively studied 181 individuals who were sequentially admitted to the intensive care unit. Demographic and clinical data were recorded along with clinical outcome over 180 days. Follow-up was completed for all study participants. We then determined the mtDNA haplogroups of the patients and 570 healthy, age-matched Han people from Zhejiang province, Southeast China, by analyzing sequences of hypervariable mtDNA segments and testing diagnostic polymorphisms in the mtDNA coding region with DNA probes. RESULT: The frequency of the main subhaplogroups of the Han population in the study cohort did not differ significantly from the control group. mtDNA haplogroup R, one of the three main mtDNA haplogroups of the Han people, was a strong independent predictor for the outcome of severe sepsis, conferring a 4.68-fold (95% CI 1.903-10.844, P = 0.001) increased chance of survival at 180 days compared with those without the haplogroup R. CONCLUSION: In the Han population, mtDNA haplogroup R was a strong independent predictor for the outcome of severe sepsis, conferring an increased chance of long-term survival compared with individuals without the R haplogroup.


March 18, 2008

Divergence of modern humans and Neanderthals

The time of the split between Neanderthals and modern humans has been previously calculated by comparing modern human and Neanderthal DNA. In this paper, the authors use cranial morphology to arrive at an independent estimate of the divergence time between the two species. Modern human populations have differentiated cranially as they expanded from Africa. By comparing this differentiation with that observed between modern humans and Neanderthals, the authors were able to arrive at an estimate of the divergence between the two species.

From the UC Davis announcement:
New research led by UC Davis anthropologist Tim Weaver adds to the evidence that chance, rather than natural selection, best explains why the skulls of modern humans and ancient Neanderthals evolved differently. The findings may alter how anthropologists think about human evolution.

Weaver's study appears in the March 17 issue of the Proceedings of the National Academy of Sciences. It builds on findings from a study he and his colleagues published last year in the Journal of Human Evolution, in which the team compared cranial measurements of 2,524 modern human skulls and 20 Neanderthal specimens. The researchers concluded that random genetic change, or genetic drift, most likely account for the cranial differences.

Discovery and National Geographic also cover this. From the latter source:

Erik Trinkaus is a Neandertal expert at Washington University in St. Louis.

The new study by Weaver's team "is valid in indicating that those aspects of the human cranium that are likely to be governed by random processes, such as drift, are in agreement with … genetic analyses," he said.

"Both of them are [also] in general agreement with the fossil record, which indicates that you start getting divergent aspects of human anatomy in Africa and Europe 300,000 to 500,000 years ago."

An interesting tidbit from the MSNBC coverage of the article:
This finding may contradict a common belief that humans won out over Neanderthals because they acquired helpful physical changes in their skulls.


Erik Trinkaus, an anthropologist at Washington University in St. Louis who did not work on the study, said the research cannot establish absolutely that natural selection did not create skull differences between Neanderthals and modern humans, or even that the divergence date of 370,000 years is accurate, because both dating methods are only looking at chance mutations.

Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0709079105

Close correspondence between quantitative- and molecular-genetic divergence times for Neandertals and modern humans

Timothy D. Weaver et al.

Recent research has shown that genetic drift may have produced many cranial differences between Neandertals and modern humans. If this is the case, then it should be possible to estimate population genetic parameters from Neandertal and modern human cranial measurements in a manner analogous to how estimates are made from DNA sequences. Building on previous work in evolutionary quantitative genetics and on microsatellites, we present a divergence time estimator for neutrally evolving morphological measurements. We then apply this estimator to 37 standard cranial measurements collected on 2,524 modern humans from 30 globally distributed populations and 20 Neandertal specimens. We calculate that the lineages leading to Neandertals and modern humans split {approx}311,000 (95% C.I.: 182,000 to 466,000) or 435,000 (95% C.I.: 308,000 to 592,000) years ago, depending on assumptions about changes in within-population variation. These dates are quite similar to those recently derived from ancient Neandertal and extant human DNA sequences. Close correspondence between cranial and DNA-sequence results implies that both datasets largely, although not necessarily exclusively, reflect neutral divergence, causing them to track population history or phylogeny rather than the action of diversifying natural selection. The cranial dataset covers only aspects of cranial anatomy that can be readily quantified with standard osteometric tools, so future research will be needed to determine whether these results are representative. Nonetheless, for the measurements we consider here, we find no conflict between molecules and morphology.


March 16, 2008

Ithaca may be Homeric Ithaca after all

I can understand people searching for Atlantis, or Shangri-La, El Dorado or whatever is one's favorite lost city/continent/civilization, but, c'mon Ithaca? Why search for something whose location already exists, and it is, (surprise), Ithaca.

I remember reading about the book coming out of the project to identify Homeric Ithaca with Cephalonia. The main argument for denying Ithaca's claim to be itself was that the Homeric account can't be reconciled well with the reality of the island, e.g., the idea that Ithaca is the westmost of the Ionian islands, which doesn't correspond to its real location. I always thought this was a shoddy argument. Greece has thousands of islands, and I'd bet that with the exception of locals, geography wizards or career seamen, very few people know the exact location on the map of most of them. Why would Homer, or whoever composed the Odyssey, who, most likely live in the west coast of Asia Minor, know the relative position of Ithaca or the details of its geography?

‘Ithaca was Homeric land of Odysseus’
Greeks yesterday hailed a new study showing the modern-day island of Ithaca is the same as that of Homer's legendary hero Odysseus, rejecting a recent British theory that pointed to a nearby island.

British researchers last year claimed they had solved an intriguing classical puzzle, saying the kingdom of Ithaca was located on another Ionian island, further west.

«This new study shows how wrong and inaccurate the British theory is,» Ithaca councilor and former island Mayor Spyros Arsenis told Reuters of the study conducted by Greek geology professors and other scientists over eight months.

Arsenis also heads the island's Friends of Homer society.

The British study - which suggested that Homer's Ithaca was actually part of what is modern-day Cephalonia - had enraged islanders who are fiercely proud of their renowned ancestor, the wiliest of the ancient Greek writer's epic heroes.

The British team suggested that drilling showed the Paliki peninsula on Cephalonia may have once been an island and that it better matched Homer's description of the homeland which Odysseus left behind to fight in the Trojan War.

«The new Greek study shows... the geological formations could not have been formed in just 3,000 years and there is no evidence of any sea channel,» Arsenis said.

The study will be officially presented next week. The island's local council also welcomed the results.

«This study rules out once and for all the theory that the Paliki peninsula was once a separate island. It is a slap in the face for the British researchers,» it said in a statement.

Finding ancient Ithaca could rival the discoveries in the 1870s of ancient Troy on Turkey's Aegean coast and the mask of Agamemnon, who led the Greek forces against the Trojans. No one knows for certain whether Odysseus or his city really existed.

The discovery of the ruins of Troy, where Odysseus, Achilles, Paris, Menelaus and other Greek heroes did battle, has led scholars to believe there is more to Homer's tales than just legend.

March 15, 2008

Perhaps beautiful people are not more intelligent after all

The author is criticizing Kanazawa and Kovar (2004) Why beautiful people are more intelligent. The paper's conclusion:
Measuring intelligence and its correlates is a fundamental research endeavour in psychology which has attracted huge interest and no little controversy amongst scholars. It is vital therefore that claims about the relationship between intelligence and other variables are carefully established. This paper argues that KK's claim is theoretically suspect and that the evidence that is claimed to support it is, in fact, weak and inconclusive.
What struck me when reading the recent paper is how little direct and strong evidence for a relationship between beauty and intelligence in adults exists. It is known, for example, that beautiful people make more money, that intelligent people make more money, but one can't conclude on the basis of these two facts that beauty and intelligence go together in the same individuals. Hopefully someone will study the issue of cognitive ability and beauty directly.

Intelligence doi:10.1016/j.intell.2008.01.003

Beauty and intelligence may – or may not – be related

Kevin Denny


In a recent paper, [Kanazawa S. & Kovar J.L. (2004). Why beautiful people are more intelligent, Intelligence, 32, 227–243] assert that given certain empirical regularities about assortative mating and the heritability of intelligence and beauty, that it logically follows that more intelligent people are more beautiful. It is argued here that this “theorem” is false and that the evidence does not support it.


Archaeology magazine interview with John Hawks

Archaeology magazine has a nice interview with John Hawks. where he talks about, among other things, his recent work on accelerated recent human evolution. Here are some interesting parts from the interview:
It means that there was a time when everybody in the human population had that allele and its been reducing in frequency over time because the other alleles have some advantage. So when we look today at things that make you susceptible to long-term chronic diseases like Alzheimers and Type 2 diabetes a lot of those alleles are the ancestral forms. Ancient people just were not well adapted to today's circumstances. And the alleles aren't gone, they have been reducing but they are still here and they are causing what we consider to be problems although 50,000 years ago they weren't problems, people lived a different lifestyle.
This is a great point to make, and actually represents the flip side of usual way of thinking. Instead of viewing a novel alleles that is increasing in frequency as advantageous, we can think of the old (ancestral) allele as disadvantageous in the new circumstances.

Sometimes people think that our ancestral forms "work just fine", until some new mutation comes along that works better, somewhat like a new car model replacing an old but effective one. In this view, humans are "perfecting themselves" by acquiring new and better abilities.

But, evolution doesn't work that way. Some of the new alleles favored by recent evolution could have arisen several times in the past in earlier Homo or even more distant ancestors. But, selection did not favor them then because the circumstances weren't right.

John also talks about why Neanderthals may have been the source for FOXP2 in humans:
It seems to me we've got a 50/50 chance that it originated in modern humans and was passed to Neanderthals.


If it came from Neanderthals we would have to propose that FOXP2 arose about 100,000 years ago when modern humans and Neanderthals were in contact in the Near East. The key is that if FOXP2 is more recently fixed than the common ancestor of humans and Neanderthals who lived 300,000 or 400,000 years ago, then it had to be transferred in one direction or the other. Given that it's there in several Neanderthal specimens and it's globally dispersed in humans, this transfer, if it happened, had to happen early enough for FOXP2 to get to where it was. So I'm thinking in the time frame of 100,000 years ago, but I'm waiting to see a date.
If I were to meet somebody who lived 50,000 years ago, how would that person be different from me?

Well number one, somebody from 50,000 years ago who was transported to today in a time machine would probably be dead within two years from some infectious disease. That's the number one difference, we have resistance to all kinds of diseases that have emerged during the process of civilization that never existed before. The smallpox that killed many of the Native Americans, the susceptibility was there for genetic reasons. There would be some digestive changes. When we look at the diversity among people in the world to day in terms of Type 2 diabetes, and obesity susceptibility, some of those differences are going to be explained by recently selected genes that have to do with diet. I suspect there would be some behavioral changes. We're looking at a large category of genes that effect the central nervous system, we don't know what they do but I can expect there must be some behavioral differences that have influenced human populations across the last 50,000 years.

March 14, 2008

Cattle, sheep, and goats as endangered species

Why is genetic diversity in animals worthy of preservation? After all, if one has selected a super-breed of sheep that e.g., produces the best wool/expenditure ratio, why would one raise animals with suboptimal ratios? On the face of it, that doesn't make economic sense.

There is nothing wrong with doing that - in the short term. But, over time, you can expect that animals will be exposed to novel environmental challenges, e.g., changing climate, or food types, or newly evolved pathogens. Natural populations face these challenges by exploiting their existing genetic variation, changing in subtle ways to adapt to changing environmental conditions. By reducing genetic variation in a population, one is effectively reducing its ability to adapt to its environment.

Mol Ecol. 2008 Jan;17(1):275-84. Epub 2007 Oct 8.

Are cattle, sheep, and goats endangered species?

Taberlet P, Valentini A, Rezaei HR, Naderi S, Pompanon F, Negrini R, Ajmone-Marsan P.

For about 10 000 years, farmers have been managing cattle, sheep, and goats in a sustainable way, leading to animals that are well adapted to the local conditions. About 200 years ago, the situation started to change dramatically, with the rise of the concept of breed. All animals from the same breed began to be selected for the same phenotypic characteristics, and reproduction among breeds was seriously reduced. This corresponded to a strong fragmentation of the initial populations. A few decades ago, the selection pressures were increased again in order to further improve productivity, without enough emphasis on the preservation of the overall genetic diversity. The efficiency of modern selection methods successfully increased the production, but with a dramatic loss of genetic variability. Many industrial breeds now suffer from inbreeding, with effective population sizes falling below 50. With the development of these industrial breeds came economic pressure on farmers to abandon their traditional breeds, and many of these have recently become extinct as a result. This means that genetic resources in cattle, sheep, and goats are highly endangered, particularly in developed countries. It is therefore important to take measures that promote a sustainable management of these genetic resources; first, by in situ preservation of endangered breeds; second, by using selection programmes to restore the genetic diversity of industrial breeds; and finally, by protecting the wild relatives that might provide useful genetic resources.


March 13, 2008

Ancient mtDNA from Late Bronze and Iron Age Sardinia

From the paper:
In the multidimensional scaling of Fig. 3, Nuragic Sardinians cluster with the majority of the European populations. Given the small sample size, inevitable in ancient DNA studies, it is at present impossible to infer their evolutionary relationships from mtDNA aYnities. Nevertheless, in relation with ancient samples, Nuragic Sardinians appear more related to the Iberians than to the Etruscans, whose position in the graph is eccentric. Three data points are not enough for a robust generalisation. However, one can at least conclude that Sardinians and Iberians show a greater genealogical continuity with the Bronze-Age inhabitants of the same regions than the Tuscans.
Human Genetics Volume 122, Numbers 3-4 / November, 2007. DOI: 10.1007/s00439-007-0403-6

Genetic variation in prehistoric Sardinia

David Caramelli et al.

Abstract We sampled teeth from 53 ancient Sardinian (Nuragic) individuals who lived in the Late Bronze Age and Iron Age, between 3,430 and 2,700 years ago. After eliminating the samples that, in preliminary biochemical tests, did not show a high probability to yield reproducible results, we obtained 23 sequences of the mitochondrial DNA control region, which were associated to haplogroups by comparison with a dataset of modern sequences. The Nuragic samples show a remarkably low genetic diversity, comparable to that observed in ancient Iberians, but much lower than among the Etruscans. Most of these sequences have exact matches in two modern Sardinian populations, supporting a clear genealogical continuity from the Late Bronze Age up to current times. The Nuragic populations appear to be part of a large and geographically unstructured cluster of modern European populations, thus making it difficult to infer their evolutionary relationships. However, the low levels of genetic diversity, both within and among ancient samples, as opposed to the sharp differences among modern Sardinian samples, support the hypothesis of the expansion of a small group of maternally related individuals, and of comparatively recent differentiation of the Sardinian gene pools.


The phylogeny of Native American mtDNA haplogroups


Associated Press has a story:
Nearly all of today's Native Americans in North, Central, and South America can trace part of their ancestry to six women whose descendants immigrated around 20,000 years ago, a DNA study suggests.

Those women left a particular DNA legacy that persists to today in about about 95 percent of Native Americans, researchers said.


The six "founding mothers" apparently did not live in Asia because the DNA signatures they left behind aren't found there, Perego said. They probably lived in Beringia, the now-submerged land bridge that stretched to North America, he said.

PLoS ONE. 2008 Mar 12;3(3):e1764.

The Phylogeny of the Four Pan-American MtDNA Haplogroups: Implications for Evolutionary and Disease Studies.

Achilli A, Perego UA, Bravi CM, Coble MD, Kong QP, Woodward SR, Salas A, Torroni A, Bandelt HJ.

Only a limited number of complete mitochondrial genome sequences belonging to Native American haplogroups were available until recently, which left America as the continent with the least amount of information about sequence variation of entire mitochondrial DNAs. In this study, a comprehensive overview of all available complete mitochondrial DNA (mtDNA) genomes of the four pan-American haplogroups A2, B2, C1, and D1 is provided by revising the information scattered throughout GenBank and the literature, and adding 14 novel mtDNA sequences. The phylogenies of haplogroups A2, B2, C1, and D1 reveal a large number of sub-haplogroups but suggest that the ancestral Beringian population(s) contributed only six (successful) founder haplotypes to these haplogroups. The derived clades are overall starlike with coalescence times ranging from 18,000 to 21,000 years (with one exception) using the conventional calibration. The average of about 19,000 years somewhat contrasts with the corresponding lower age of about 13,500 years that was recently proposed by employing a different calibration and estimation approach. Our estimate indicates a human entry and spread of the pan-American haplogroups into the Americas right after the peak of the Last Glacial Maximum and comfortably agrees with the undisputed ages of the earliest Paleoindians in South America. In addition, the phylogenetic approach also indicates that the pathogenic status proposed for various mtDNA mutations, which actually define branches of Native American haplogroups, was based on insufficient grounds.


Pathogens and Collectivism

From the article:
Infectious diseases have been agents of morbidity and mortality throughout human history (Anderson & May 1991; Ewald 1994; Dobson & Carper 1996; Wolfe et al. 2007), and a growing body of empirical research indicates that people possess psychological mechanisms that serve the function of antipathogen defence. For instance, ethnocentrism, xenophobia and other specific forms of interpersonal prejudice appear to result, in part, from the operation of these mechanisms (e.g. Faulkner et al. 2004; Navarrete & Fessler 2006; Park et al. 2007).
Proc. R. Soc. B doi: 10.1098/rspb.2008.0094

Pathogen prevalence predicts human cross-cultural variability in individualism/collectivism

Corey L. Fincher, Randy Thornhill, Damian R. Murray, Mark Schaller


Pathogenic diseases impose selection pressures on the social behaviour of host populations. In humans (Homo sapiens), many psychological phenomena appear to serve an antipathogen defence function. One broad implication is the existence of cross-cultural differences in human cognition and behaviour contingent upon the relative presence of pathogens in the local ecology. We focus specifically on one fundamental cultural variable: differences in individualistic versus collectivist values. We suggest that specific behavioural manifestations of collectivism (e.g. ethnocentrism, conformity) can inhibit the transmission of pathogens; and so we hypothesize that collectivism (compared with individualism) will more often characterize cultures in regions that have historically had higher prevalence of pathogens. Drawing on epidemiological data and the findings of worldwide cross-national surveys of individualism/collectivism, our results support this hypothesis: the regional prevalence of pathogens has a strong positive correlation with cultural indicators of collectivism and a strong negative correlation with individualism. The correlations remain significant even when controlling for potential confounding variables. These results help to explain the origin of a paradigmatic cross-cultural difference, and reveal previously undocumented consequences of pathogenic diseases on the variable nature of human societies.


March 11, 2008

1,000 ancient graves from Thessaloniki

Ancient Graves Found in Greece

ATHENS, Greece (AP) — Greek workers discovered around 1,000 graves, some filled with ancient treasures, while excavating for a subway system in the historic city of Thessaloniki, the state archaeological authority said Monday.

Some of the graves, which dated from the first century B.C. to the 5th century A.D., contained jewelry, coins and various pieces of art, the Greek archaeological service said in a statement.

Thessaloniki was founded around 315 B.C. and flourished during the Roman and Byzantine eras. Today it is the Mediterranean country's second largest city.

Most of the graves — 886 — were just east of the city center in what was the eastern cemetery during Roman and Byzantine times. Those graves ranged from traces of wooden coffins left in simple holes in the ground, to marble enclosures in five-room family mausoleums.

A separate group of 94 graves were found near the city's train station, in what was once part of the city's western cemetery.

More findings were expected as digging for the Thessaloniki metro continues. Digging started in 2006 and the first 13 stations are expected to be done by the end of 2012. A 10-station extension to the west and east has been announced.

Domestication of the donkey

The EurekAlert press release:
An international group of researchers has found evidence for the earliest transport use of the donkey and the early phases of donkey domestication, suggesting the process of domestication may have been slower and less linear than previously thought.

Based on a study of 10 donkey skeletons from three graves dedicated to donkeys in the funerary complex of one of the first Pharaoh's at Abydos, Egypt, the team, led by Fiona Marshall, Ph.D., professor of Anthropology at Washington University in St. Louis, and Stine Rossel of the University of Copenhagen, found that donkeys around 5,000 years ago were in an early phase of domestication. They looked like wild animals but displayed joint wear that showed that they were used as domestic animals.

“Genetic research has suggested African origins for the donkey,” said Marshall. “But coming up with an exact time and location for domestication is difficult because signs of early domestication can be hard to see. Our findings show that traces of human management can indicate domestication before skeletal or even genetic changes."

The previously unpublished research was presented in “Domestication of the Donkey: New Data on Timing, Process and Indicators” in the March 10 online edition of the Proceedings of the National Academy of Sciences.

Domestication of the donkey from the African wild ass was a pivotal point in human history. It transformed ancient transport systems in Africa and Asia and the organization of early cities and pastoral societies.

The research team examined the 5,000-year-old Abydos skeletons along with 53 modern donkey and African wild ass skeletons. Analysis showed that the Abydos metacarpals were similar in overall proportions to those of wild ass, but individual measurements varied. Mid-shaft breadths resembled wild ass, but mid-shaft depths and distal breadths were intermediate between wild ass and domestic donkey.

Despite this, all the Abydos skeletons exhibited a range of wear and other pathologies on their bones consistent with load carrying. Morphological similarities to wild ass show that despite their use as beasts of burden, donkeys were still undergoing considerable phenotypic change during the early dynastic period in Egypt. This pattern is consistent with recent studies of other domestic animals that suggest that the process of domestication is slower and more complicated than had been previously thought.

Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0709692105

Domestication of the donkey: Timing, processes, and indicators

Stine Rossel et al.


Domestication of the donkey from the African wild ass transformed ancient transport systems in Africa and Asia and the organization of early cities and pastoral societies. Genetic research suggests an African origin for the donkey, but pinpointing the timing and location of domestication has been challenging because donkeys are uncommon in the archaeological record and markers for early phases of animal domestication are hard to determine. We present previously undescribed evidence for the earliest transport use of the donkey and new paleopathological indicators for early phases of donkey domestication. Findings are based on skeletal data from 10 {approx}5,000-year-old ass skeletons recently discovered entombed in an early pharaonic mortuary complex at Abydos, Middle Egypt, and a concurrent study of 53 modern donkey and African wild ass skeletons. Morphometric studies showed that Abydos metacarpals were similar in overall proportions to those of wild ass, but individual measurements varied. Midshaft breadths resembled wild ass, but midshaft depths and distal breadths were intermediate between wild ass and domestic donkey. Despite this, all of the Abydos skeletons exhibited a range of osteopathologies consistent with load carrying. Morphological similarities to wild ass show that, despite their use as beasts of burden, donkeys were still undergoing considerable phenotypic change during the early Dynastic period in Egypt. This pattern is consistent with recent studies of other domestic animals that suggest that the process of domestication is slower and less linear than previously thought.


Earliest human footwear (Tianyuan and Sunghir)

Journal of Archaeological Science (Article in Press)

See also Earliest shoe wearers and 40,000 year old human from China.

Anatomical evidence for the antiquity of human footwear: Tianyuan and Sunghir

Erik Trinkaus and Hong Shang

Trinkaus [Trinkaus, E., 2005. Anatomical evidence for the antiquity of human footwear use. J. Archaeol. Sci. 32, 1515–1526] provided a comparative biomechanical analysis of the proximal pedal phalanges of western Eurasian Middle Paleolithic and Middle Upper Paleolithic humans, in the context of those of variably shod recent humans. The anatomical evidence indicated that supportive footwear was rare in the Middle Paleolithic but became frequent by the Middle Upper Paleolithic. Based on that analysis, additional data are provided for the Middle Upper Paleolithic (not, vert, similar27,500 cal BP) Sunghir 1 and the earlier (not, vert, similar40,000 cal BP) Tianyuan 1 modern humans. Both specimens exhibit relatively gracile middle proximal phalanges in the context of otherwise robust lower limbs. The former specimen reinforces the association of footwear with pedal phalangeal gracility in the Middle Upper Paleolithic. Tianyuan 1 indicates a greater antiquity for the habitual use of footwear than previously inferred, predating the emergence of the Middle Upper Paleolithic.


365AD Tsunami in the Mediterranean

From the New Scientist article:
The survivors of a tsunami that killed thousands living on the shores of the Mediterranean in AD 365 called it the "day of horror". Worryingly, history may be due to repeat itself, say geologists who have located the source of the wave.

No one had been able to find evidence pinpointing the earthquake that caused the tsunami, which struck the Egyptian city of Alexandria and the Nile Delta in AD 365. The mainstream view was that a series of quakes had struck the region – cumulatively thrusting a section of western Crete upwards by 10 metres.

Beth Shaw and colleagues at the University of Cambridge carbon-dated a section of corals on the coast of Crete that were lifted clear of the water during the upheavals.

The corals' distribution and identical age revealed that one giant quake must have lifted all of them by 10 metres in one massive push – revealing the tsunami's source.

The only thing that could have generated such a large uplift at that location is an earthquake in a steep fault in the Hellenic trench, near Crete, says Shaw.
Nature Geoscience doi:10.1038/ngeo151

Eastern Mediterranean tectonics and tsunami hazard inferred from the AD 365 earthquake

B. Shaw et al.

Historical accounts describe an earthquake and tsunami on 21 July AD 365 that destroyed cities and drowned thousands of people in coastal regions from the Nile Delta to modern-day Dubrovnik. The location and tectonic setting of this earthquake have been uncertain until now. Here, we present evidence from radiocarbon data and field observations that western Crete was lifted above sea level, by up to 10 m, synchronously with the AD 365 earthquake. The distribution of uplift, combined with observations of present-day seismicity, suggest that this earthquake occurred not on the subduction interface beneath Crete, but on a fault dipping at about 30° within the overriding plate. Calculations of tsunami propagation show that the uplift of the sea floor associated with such an earthquake would have generated a damaging tsunami through much of the eastern Mediterranean. Measurement of the present rate of crustal shortening near Crete yields an estimate of approx5,000 yr for the repeat time of tsunamigenic events on this single fault in western Crete, but if the same process takes place along the entire Hellenic subduction zone, such events may occur approximately once every 800 yr.


Ancient lineage of modern humans

Journal of Human Evolution (Article in Press) doi:10.1016/j.jhevol.2007.10.010

Human cranial diversity and evidence for an ancient lineage of modern humans

Michael A. Schillaci


This study examines the genetic affinities of various modern human groupings using a multivariate analysis of morphometric data. Phylogenetic relationships among these groupings are also explored using neighbor-joining analysis of the metric data. Results indicate that the terminal Pleistocene/early Holocene fossils from Australasia exhibit a close genetic affinity with early modern humans from the Levant. Furthermore, recent human populations and Upper Paleolithic Europeans share a most recent common ancestor not shared with either the early Australasians or the early Levantine humans. This pattern of genetic and phylogenetic relationships suggests that the early modern humans from the Levant either contributed directly to the ancestry of an early lineage of Australasians, or that they share a recent common ancestor with them. The principal findings of the study, therefore, lend support to the notion of an early dispersal from Africa by a more ancient lineage of modern human prior to 50 ka, perhaps as early as OIS 5 times (76–100 ka).


Y chromosome haplogroup Q5 in India

BMC Evol Biol. 2007 Nov 19;7:232.

A novel subgroup Q5 of human Y-chromosomal haplogroup Q in India.

Sharma S, Rai E, Bhat AK, Bhanwer AS, Bamezai RN.

BACKGROUND: Y-chromosomal haplogroup (Y-HG) Q is suggested to originate in Asia and represent recent founder paternal Native American radiation into the Americas. This group is delineated into Q1, Q2 and Q3 subgroups defined by biallelic markers M120, M25/M143 and M3, respectively. Recently, a novel subgroup Q4 has been identified which is defined by bi-allelic marker M346, representing HG Q (0.41%, 3/728) in Indian population. With scanty details of HG Q in Asia, especially India, it was pertinent to explore the status of the Y-HG Q in Indian population to gather an insight to determine the extent of diversity within this region. RESULTS: We observed 15/630 (2.38%) Y-HG Q individuals in India with an ancestral state at M120, M25, M3 and M346 markers, indicating an absence of already known Q1, Q2, Q3 and Q4 sub-haplogroups. Interestingly, we further observed a novel 4 bp deletion/insertion polymorphism (ss4 bp, rs41352448) at 72,314 position of human arylsulfatase D pseudogene, defining a novel sub-lineage Q5 (in 5/15 individuals, i.e., 33.3 % of the observed Y-HG Q) with distributions independent of the social, cultural, linguistic and geographical affiliations in India. CONCLUSION: The study adds another sublineage Q5 in the already existing arrangement of Y-HG Q in literature. It was quite interesting to observe an ancestral state Q* and a novel sub-branch Q5, not reported elsewhere, in Indian subcontinent, though in low frequency. A novel subgroup Q4 was identified recently which is also restricted to Indian subcontinent. The most plausible explanation for these observations could be an ancestral migration of individuals bearing ancestral lineage Q* to Indian subcontinent followed by an autochthonous differentiation to Q4 and Q5 sublineages later on. However, other explanations of, either the presence of both the sub haplogroups (Q4 and Q5) in ancestral migrants or recent migrations from central Asia, cannot be ruled out till the distribution and diversity of these subgroups is explored extensively in Central Asia and other regions.


March 08, 2008

ISABS 2007 abstracts

Quite a few interesting abstracts from last year's ISABS Conference (book of abstracts).


Khusnutdinova E. et al.

Turkic-speaking Bashkirs are dispersed throughout the southern Ural region. They are considered by historians as descendants of Turkic- speaking nomadic communities that arrived in southern Urals at Early Medieval ages and assimilated indigenous population. We performed phylogenetic analysis of Y-chromosome lineages in a sample of 587 Bashkirs drawn from different parts of the southern Ural region and neighbouring areas: Abzelilovskiy (N=152), Sterlibashevskiy (N=54), Baimakskiy (N=95), and Burzyanskiy (N=82) districts of Bashkortostan republic, Orenburg (N=79), Perm (N=72), Samara and Saratov (N=51) Oblasts of Russia. Obtained samples of Y-chromosomes were analyzed using 24 biallelic markers of the Y chromosome non-recombining region. A total of 17 haplogroups were identified among which R1b3-M269, R1a1- SRY 1532, and N3-M46 lineages were predominant. Since N3-M46 lineage is prevalent among neighbouring Finno- Ugric populations and is rarely found in Central Asia, where numerous Turkicspeaking confederations dominated over a long period ancestors of Finno-Ugric groups are probable source population that contributed N3 lineage into Bashkirs. Y- Chromosome lineages specific to Central and East Asian populations (C3c- M48, O-M175) were absent or found with very low overall frequency (less than 10%). The only exception is R1b2 lineage which was found with very high frequency among Transural Bashkirs. Overall prevalence of typical West Eurasian (R1a-SRY 1532 and R1b3- M269) and North Eurasian (N3) lineages imply that Turkic-speaking newcomers were either admixed or genetic input associated with their arrival was limited.


Balanovsky O et al.

To reveal degree of the regional Y chromosomal variation in Europe we compared our data on Russians (14 regional populations), Ukrainians (4 populations) and Belorussians (2 populations, and 2 populations from Behar et al., 2003) with the published regional data on other European countries. For reliable calculations neighbour populations were pooled to reach sample sizes above 70. To measure the intra-ethnic variation we calculated (i) the average genetic distance between regional populations of every group and (ii) Gst (Fst) variation. Gst value was considered as preferable measure, as it was found to be less sensitive to level of phylogenetic resolution in the data. Croatians, Finns, Russians and Italians were proved to be the most diverse (genetically subdivided) groups; Swedes and Germans demonstrated moderate variation; Greeks, Turks, Poles, Belorussians and Ukrainians were more genetically homogenous, showing lower geographic variation of the paternal lineages inside their countries. However, even lower variation of the Y chromosome is significantly higher as compared with analogous values calculated from mitochondrial DNA and autosomal data. This finding stresses that forensic studies may demand not only country-specific, but provincespecific databases (at least for listed above highly genetically subdivided countries), since haplogroup profiles differ significantly from one province to another, inside the same country. Despite the high intra-ethnic variation (Gst=0.03 on average), the inter-ethnic differences were five times higher (Gst=0.15), revealing dominance of inter-ethnic variation in structuring the paternal gene pool in Europe.


Stepanov V et al.

Aim of the study was to reconstruct the evolution of paternal lineages in populations of Siberia, Central Asia and Eastern Europe. Forty population samples from 22 ethnic groups were studied. Totally 1600 Y chromosomes were genotyped for 40 biallelic markers according to Y chromosome consortium (YCC) classification. The microsatellite haplotypes within HG were constructed using 7 STR loci. Thirty one haplogroups were observed, but frequencies of only 7 of them (N3a, R1a1, Q*, C3xC3c, N2, C3c, O3) were higher than 3 percent. In sum these 7 haplogroups comprise 86% of Y-chromosomal gene pool in North Eurasia. The proportion of inter- population differences in the total genetic variability of region's population according to the analysis of molecular variance is 19%. Analysis of genetic relationships between populations reveals three main clusters of populations in space of two first PCs reflecting the differential presence of ancient West-Eurasian Caucasoid, Proto-Uralic and Paleoasiatic components. Based on analysis of microsatellite haplotypes within main Y- chromosomal haplogroups, molecular diversity within monophyletic lineages were calculated and phylogenetic trees for most common haplogroups were reconstructed. Western-Eurasian lineages (R1a1, R1b) are characterized by the maximal diversity in Eastern European populations. Eastern-Eurasian lineages have the high level of diversity in populations of Eastern Siberia and North-East Asia. The age of genetic diversity generation and time of population differentiation (Td) shows that most lineages which are common in North Eurasian populations dated back to Upper Paleolithic period before the last glacial maximum.


Grechanina EY et al.

Study of mtDNA polymorphism for estimation genetic diversity of Ukrainian population. There are 239 samples of Ukrainians from different regions of Ukraine. There are sequention of hypervariable segment HVS I in combination with RFLPanalysis of coding sites of mtDNA and phylogeographical analysis. This research was in Estonian Biocenter. Length of sequencing fragment was 377 bp 102 positions from 377 were polymorphic. From these 91 nucleotide substitutions are transitions, with prevalence pyrimidine under purine (69:22). Transversions were in 11 sites. Were determined 157 haplotypes. The most common haplotype (10.0%) corresponds to CRS. Indexes of genetic diversity for Ukrainian population are H=0.986 and Di=5.19. Screening of polymorphic sites established following haplogroups of mtDNA, which have all-European spreading: H-33.5%, V-5.4%, HV-3.7%, J- 11.7%, T-6.7%, U-20.9% (U2, U3, U4, U5, U7, U8), K-2.9%, I-2.1%, W- 2.1%, X-2.5%. Subhaplogroup U3 (2.5%) may testify the presence Iranian component. Subhaplogroup U4 was detected with frequency 3.7%. Subhaplogroup U5 has maximal frequency in Scandinavian people also was detected in Ukrainian population with high frequency 10.8%. Haplogroup V, as marker of Finnish-Hungarian people, has high frequency in Ukrainian population. There were found Asian lines (A, B, C, D, Z) with frequency 2.0%. Data indicate on complicated ethnical formation of modern Ukrainian population, where assimilation processes and inter-ethnic interactions played considerable role. They will be important additions in context about polymorphism of European populations mtDNA.


Pennarun E et al.

In the coverage of the genetic pool of Europe, some major cavities were left, hence to fill one of them, namely the French mtDNA pool we collected 868 samples from twelve different locations of France. Those samples were sequenced for the hypervariable segment I (HVS-I) and then typed for SNPs in the coding region, either by RFLP or 5' nuclease allelic discrimination, in order to assign them to the right haplogroup. Then the mtDNA gene pools of French Basques and Bretons were compared in terms of frequency and composition with relevant neighbouring populations. The French Basques’ mtDNA pool shares some common cardinal features with that of the Spanish Basques, represented in the high prevalence of haplogroup H. However, the French Basques do show a number of distinct features, most notably expressed in the much higher frequency of haplogroups linked with the Neolithic diffusion in Europe. In Brittany, Finistère shows closer affinities with Britain and Scandinavia than the two other departments of Brittany. The mtDNA haplogroup composition of the French does not differ significantly from the surrounding European genetic landscape. In a finer grain, microgeographical differentiation can be revealed as shown for the French Basque country and for Brittany.


Gokcumen O et al.

Anatolia has been an important crossroads for numerous populations since the Neolithic. Among these, the Hattis, Urartians, Lydians, Phyrigians and Ottomans emerged in Anatolia proper. In addition, although non-Anatolian in origin, the Hittites, Greeks, Romans and Byzantines influenced and were influenced by local Anatolian cultures. These dynamics, as well as more recent events, such as the Turco-Ottoman War of late 19th century, the reconfiguration of the populations of the Ottoman Empire and the Greek- Turkish population exchange of 1920s, have made Anatolia a culturally and genetically complex region. Despite this complex history, Anatolia has been often been viewed as a uniform cultural landscape. Working from this perspective, previous studies of genetic variation in Anatolia analyzed samples from Turkish populations obtained from mostly urban hospitals or universities. Such studies not only overlooked the regional variation within Anatolia, but also treated contemporary Turkish populations as the direct representatives of Medieval and Neolithic Anatolian populations. To address these problems, we collected ~125 samples and extensive ethnographic data from a location in Central Anatolia southeast of Ankara. The samples were analyzed for mtDNA and NRY diversity, and the resulting data compared with those from previous genetic analyses of Turkish populations. We observed that several ethnic and cultural groups having different population histories co-existed in this location. This pattern likely represents the typical picture of Anatolian variation. We are using our genetic data to help us clarify these distinct population histories in greater detail.

March 07, 2008

Genetic traces of east-to-west human expansion waves in Eurasia

American Journal of Physical Anthropology (early view)

Genetic traces of east-to-west human expansion waves in Eurasia

Raphaëlle Chaix et al.

In this study, we describe the landscape of human demographic expansions in Eurasia using a large continental Y chromosome and mitochondrial DNA dataset. Variation at these two uniparentally-inherited genetic systems retraces expansions that occurred in the past 60 ky, and shows a clear decrease of expansion ages from east to west Eurasia. To investigate the demographic events at the origin of this westward decrease of expansion ages, the estimated divergence ages between Eurasian populations are compared with the estimated expansion ages within each population. Both markers suggest that the demographic expansion diffused from east to west in Eurasia in a demic way, i.e., through migrations of individuals (and not just through diffusion of new technologies), highlighting the prominent role of eastern regions within Eurasia during Palaeolithic times.


mtDNA of Altaian Kazakhs from Russia

From the paper:
In this study, we also find that all Turkic and Mongolic groups possess a common set of maternal haplogroups (C, D, G2a, H), and a minimal number of haplotypes from these lineages at appreciable frequencies. However, the overall patterns of haplotype sharing amongst these groups vary considerably. This finding is not necessarily incompatible with the cultural diffusion model per se, but implies that present day Turkic-Mongolic ethnic groups emerged from a common mtDNA pool that was widely distributed in Central and East Asia.
This suggests that the movements of Turkic-Mongolic people did not consist only of males but also had a female component to them. Also of interest from the paper:
Haplogroup N1a was also present in the Altaian Kazakhs. Seeing as how there were no occurrences of this lineage in other Kazakh populations or neighboring populations (Kolman et al., 1996; Comas et al., 1998; Yao et al., 2004), this finding was intriguing (Table 3). The haplotypic variation within the seven N1a samples was relatively high (Table 2), with these haplotypes belonging to both the European and Central Asian branches of this haplogroup, as recently defined by Haak et al. (2005). Thus, the source of N1a haplotypes in Altaian Kazakhs was unclear, although they seemed to have originated west of this part of Central Asia (Gokcumen et al., 2007).
Interestingly, mtDNA haplogroup N1a also pops up in Havik Brahmins from India, ancient high status Hungarians, as well as Iron Age Kazakhstan, and Neolithic Central Europeans.

American Journal of Physical Anthropology (early view)

Genetic variation in the enigmatic Altaian Kazakhs of South-Central Russia: Insights into Turkic population history

Omer Gokcumen et al.

The Altaian Kazakhs, a Turkic speaking group, now reside in the southern part of the Altai Republic in south-central Russia. According to historical accounts, they are one of several ethnic and geographical subdivisions of the Kazakh nomadic group that migrated from China and Western Mongolia into the Altai region during the 19th Century. However, their population history of the Altaian Kazakhs and the genetic relationships with other Kazakh groups and neighboring Turkic-speaking populations is not well understood. To begin elucidating their genetic history, we analyzed the mtDNAs from 237 Altaian Kazakhs through a combination of SNP analysis and HVS1 sequencing. This analysis revealed that their mtDNA gene pool was comprised of roughly equal proportions of East (A-G, M7, M13, Y and Z) and West (H, HV, pre-HV, R, IK, JT, X, U) Eurasian haplogroups, with the haplotypic diversity within haplogroups C, D, H, and U being particularly high. This pattern of diversity likely reflects the complex interactions of the Kazakhs with other Turkic groups, Mongolians, and indigenous Altaians. Overall, these data have important implications for Kazakh population history, the genetic prehistory of the Altai-Sayan region, and the phylogeography of major mitochondrial lineages in Eurasia.


Grandmothers' longevity negatively affects daughters' fertility

American Journal of Physical Anthropology (early view)

Grandmothers' longevity negatively affects daughters' fertility

Lorena Madrigal, Mauricio Meléndez-Obando


The evolution of postmenopausal longevity in human females has been the subject of debate. Specifically, there is disagreement about whether the evolution of the trait should be understood as an adaptive or a neutral process, and if the former, what the selective mechanism is. There are two main adaptive proposals to explain the evolution of postreproductive longevity: the grandmother and the mother hypotheses. The grandmother hypothesis proposes that postreproductive longevity evolved because it is selectively advantageous for females to stop reproducing and to help raise their grandchildren. The mother hypothesis states that postmenopausal longevity evolved because it is advantageous for women to cease reproduction and concentrate their resources and energy in raising the children already produced. In this article, we test the mother and the grandmother hypotheses with a historical data set from which we bootstrapped random samples of women from different families who lived from the 1500s to the 1900s in the central valley of Costa Rica. We also compute the heritability of longevity, which allows us to determine if genes involved in longevity are nearly fixed in this population. Here we show that although longevity positively affects a woman's fertility, it negatively affects her daughter's fertility; for this reason, the heritability of longevity is unexpectedly high. Our data provide strong grounds for questioning the universality of the grandmother hypothesis and for supporting the mother hypothesis as a likely explanation for the evolution of human postreproductive longevity.


Using pedigree information to infer ancestral proportions

This is a nice paper, which would be potentially very useful to genetic genealogists. Roughly speaking, existing methods for inferring ancestry rely either on pedigrees (one's ancestry is inferred from the ancestry of one's known ancestors), or on comparisons between the genotype of the unknown individual and those of reference populations. The novelty is this work is that it shows how genotypes and pedigree data can be combined to provide a better estimate of a person's ancestral proportions.

Am J Hum Genet. 2008 Mar;82(3):748-55.

Estimating ethnic admixture from pedigree data.

Sinsheimer JS, Plaisier CL, Huertas-Vazquez A, Aguilar-Salinas C, Tusie-Luna T, Pajukanta P, Lange K.

This paper introduces a likelihood method of estimating ethnic admixture that uses individuals, pedigrees, or a combination of individuals and pedigrees. For each founder of a pedigree, admixture proportions are calculated by conditioning on the pedigree-wide genotypes at all ancestry-informative markers. These estimates are then propagated down the pedigree to the nonfounders by a simple averaging process. The large-sample standard errors of the founders' proportions can be similarly transformed into standard errors for the admixture proportions of the descendants. These standard errors are smaller than the corresponding standard errors when each individual is treated independently. Both hard and soft information on a founder's ancestry can be accommodated in this scheme, which has been implemented in the genetic software package Mendel. The utility of the method is demonstrated on simulated data and a real data example involving Mexican families of mixed Amerindian and Spanish ancestry.


March 06, 2008

Discovery of Mycenaean tomb in Lefkada

Ancient Tomb Discovered on Greek Island
ATHENS, Greece (March 5) - Road construction on the western Greek island of Lefkada has uncovered and partially destroyed an important tomb with artifacts dating back more than 3,000 years, officials said on Wednesday.

The find is a miniature version of the large, opulent tombs built by the rulers of Greece during the Mycenaean era, which ended around 1100 B.C. Although dozens have been found in the mainland and on Crete, the underground, beehive-shaped monuments are very rare in the western Ionian Sea islands, and previously unknown on Lefkada.


She said the tomb contained several human skeletons, as well as smashed pottery, two seal stones, beads made of semiprecious stones, copper implements and clay loom weights. It appeared to have been plundered during antiquity.

With a nine-foot diameter, the tomb is very small compared to others, such as the Tomb of Atreus in Mycenae, which was more than 46 feet across and built of stones weighing up to 120 tons.

March 05, 2008

Adaptations to Climate in Candidate Genes for Common Metabolic Disorders

This is an open access article, so you can read it all for yourselves; the main conclusion is easy enough to grasp:
  • Genes related to metabolic disorders influence the body's energy management
  • Energy management is crucial for adapting to different climates, e.g., managing cold (example the higher basal metabolic rate of the Siberian Yakut).
  • It is expected theoretically that such genes would have been subjected to natural selection as humans spread around the world and found themselves in different climates
Indeed, this theoretical prediction is supported by the data. What this means, practically, is that for many genes involved in metabolism, similarity of climate implies to some extent similar allele distributions, due to similar selective pressures; spatial proximity or population history do not suffice. Indeed, Natural selection has driven population differentiation in modern humans.

It is noteworthy how much research into the evolution of humans has been based on the 52 populations of the Human Genome Diversity Project. It is precisely by looking at how human populations differ from each other genetically, and correlating this with their different environments and cultures that we will be able to derive a more complete history of our species.

(Yann also blogged about this)

PLoS Genetics

Adaptations to Climate in Candidate Genes for Common Metabolic Disorders

Angela M. Hancock et al.

Evolutionary pressures due to variation in climate play an important role in shaping phenotypic variation among and within species and have been shown to influence variation in phenotypes such as body shape and size among humans. Genes involved in energy metabolism are likely to be central to heat and cold tolerance. To test the hypothesis that climate shaped variation in metabolism genes in humans, we used a bioinformatics approach based on network theory to select 82 candidate genes for common metabolic disorders. We genotyped 873 tag SNPs in these genes in 54 worldwide populations (including the 52 in the Human Genome Diversity Project panel) and found correlations with climate variables using rank correlation analysis and a newly developed method termed Bayesian geographic analysis. In addition, we genotyped 210 carefully matched control SNPs to provide an empirical null distribution for spatial patterns of allele frequency due to population history alone. For nearly all climate variables, we found an excess of genic SNPs in the tail of the distributions of the test statistics compared to the control SNPs, implying that metabolic genes as a group show signals of spatially varying selection. Among our strongest signals were several SNPs (e.g., LEPR R109K, FABP2 A54T) that had previously been associated with phenotypes directly related to cold tolerance. Since variation in climate may be correlated with other aspects of environmental variation, it is possible that some of the signals that we detected reflect selective pressures other than climate. Nevertheless, our results are consistent with the idea that climate has been an important selective pressure acting on candidate genes for common metabolic disorders.


Early Bronze Age cemetary in Pella

Kathimerini has a news story about the discovery of an ancient cemetary dating from the early Bronze Age in Pella, the historical Macedonian capital. Excerpt:
Exciting new finds at the archaeological site of Pella have opened a new chapter in Macedonian history. Beneath the ruins of the ancient capital of the Macedonian kingdom is a large prehistoric burial ground that has yielded the first evidence of organized life in Pella during the third millennium BC.

It was while they were engaged in conservation, repairs and other work to highlight the site that the excavation team from Aristotle University came across more than 100 Early Bronze Age burials in large jars, accompanied by marble works of art from the Cyclades, local ceramics and metalware.

The finds are so recent that experts at the Demokritos Center have not yet completed the analysis of bones that will yield precise dates. However, the initial evidence supplements what is already known about Pella in the Early Bronze Age (2100-2000 BC), when it was the most important city in Bottiaea, long before it was made capital of the Macedonian realm. What became known as “the greatest of Macedonian cities” was apparently built on top of the prehistoric graveyard when Archelaus moved his capital there from Aiges, excavation director Professor Ioannis Akamatis told Kathimerini.

March 04, 2008

Single origin of Native Americans based on full mtDNA sequencing

You might also want to read East-West cranial differentiation in Central and Northern America and New synthesis on the first arrivals into the New World. The latter study gives a 15kya age for the expansion into the Americas which is comparable to the 18-15kya figure given by the current mtDNA-based study.

Am J Hum Genet. 2008 Feb 27 [Epub ahead of print]

Mitochondrial Population Genomics Supports a Single Pre-Clovis Origin with a Coastal Route for the Peopling of the Americas.

Fagundes NJ, Kanitz R, Eckert R, Valls AC, Bogo MR, Salzano FM, Smith DG, Silva WA Jr, Zago MA, Ribeiro-Dos-Santos AK, Santos SE, Petzl-Erler ML, Bonatto SL.

It is well accepted that the Americas were the last continents reached by modern humans, most likely through Beringia. However, the precise time and mode of the colonization of the New World remain hotly disputed issues. Native American populations exhibit almost exclusively five mitochondrial DNA (mtDNA) haplogroups (A-D and X). Haplogroups A-D are also frequent in Asia, suggesting a northeastern Asian origin of these lineages. However, the differential pattern of distribution and frequency of haplogroup X led some to suggest that it may represent an independent migration to the Americas. Here we show, by using 86 complete mitochondrial genomes, that all Native American haplogroups, including haplogroup X, were part of a single founding population, thereby refuting multiple-migration models. A detailed demographic history of the mtDNA sequences estimated with a Bayesian coalescent method indicates a complex model for the peopling of the Americas, in which the initial differentiation from Asian populations ended with a moderate bottleneck in Beringia during the last glacial maximum (LGM), around approximately 23,000 to approximately 19,000 years ago. Toward the end of the LGM, a strong population expansion started approximately 18,000 and finished approximately 15,000 years ago. These results support a pre-Clovis occupation of the New World, suggesting a rapid settlement of the continent along a Pacific coastal route.


AAPA 2008 abstracts

The 2008 meeting of the American Association of Physical Anthropologists will take place this April, and the book of abstracts for the conference is online in pdf format. As usual, there is a great variety of exciting research to be announced in the meeting; here is my sampling thereof:

A seemingly very important new piece of work on Central Anatolia:

O. Gokcumen et al., The Land of the Tired Ox: Ethnogenetic Insights into Rural Central Anatolian Population History
Excerpt: "For example, in one study area in the vicinity of Ankara, we have observed at least four distinct groups based on historical and ethnographic observations. Their self-claimed ancestries trace back to Afsar, Kurdish, Caucasian Cherkess, and Karaman groups. These groups came into the same area from different source regions and at different moments in history. Indeed, our data indicate that there were significant disparities between the paternal and maternal genetic diversity among these groups. These data also allow us to more accurately reconstruct the population history of the study area, as well as begin to provide new perspectives on the regional history of Central Anatolia in relation to historical Turkic invasions and perhaps the Neolithic transition. Finally, we discuss the utility of a more focal and detailed sampling approach for elucidating Anatolian population history."

I can only hope that more researchers will look into historical processes that have shaped modern populations. Too often I see research published which tries to infer human prehistory from modern populations, seemingly oblivious to the complex set of events in historical time that have shaped these populations. Anatolia, so often discussed in the context of the origin of the Neolithic is a prime example of this, as it contains multiple layers of population settlement and ethnic change.

M. C. Dulik et al. Y-chromosome variation in Altaian ethnic groups
Excerpt: "A large portion of all Altaian haplotypes belonged to haplogroup R. Differences in haplogroup frequency between the northern and southern Altaian populations were also observed, with more individuals from northern groups belonging to haplogroups N and Q, and haplogroup C being more prevalent in southern populations. In addition, there were village level patterns of NRY variation, while the overall diversity of NRY haplotypes suggested a significant cultural influence on the partitioning of genetic variation (i.e., patrilocality)."
The three elements involved in Siberian prehistory are indeed haplogroup R, in particular R1a1 which (in my opinion) represents the Western-derived Caucasoid element of likely Iranic affiliation, haplogroups N and Q which represent the Palaeo-Mongoloid element indigenous to Siberia and which has radiated from Siberia to the west (in the case of N) and to the east and into the Americas (in the case of Q), and the Mongoloid proper element which is associated with haplogroup C in this region, and which reflects the Eastern-derived movements of Mongoloid(-influenced) Altaic speakers such as the Mongols.

L. Pipes et al. Analysis of mtDNA in Mongolian Populations

J. Hawks. "Adaptive evolution of human hearing and the appearance of language"
Language requires not only a detailed anatomical and neurological system of language production, but also a highly adapted system of reception. Considering the frequency and amplitude range of human speech, the necessity of perceiving a large number of distinct speakers, the extended life history of humans, the need for children to learn phonemic distinctions at an early age, and the spatial distances covered by vocal communication in humans compared to other primates, it is likely that humans have distinctive auditory adaptations to language. This study tests the hypothesis of selection on the human auditory system, by interspecific genomic comparisons and genome-wide selection scans in living people. A set of hearing-related human genes shows clear signs of recurrent selected substitutions in humans compared to chimpanzees and macaques. These recurrent substitutions may have occurred at any time during human evolutionary history, but they were repeated with several selected variants for each gene. A smaller set of genes shows signs of significant population differentiation within the past 50,000 years, due to recent strong selection. Further, a relatively large set of hearing-related genes have segregating variants under recent strong selection in one or more human populations. These genes reflect continuing selection on hearing within the last 2000—3000 years. Together, these results suggest that human vocal communication exerted repeated selection pressures on the auditory system, that the system of human language continued to evolve during the Late Pleistocene, and that humans may still be adapting to language.
It seems that Hawks et al. paper on accelerated recent human evolution was just the beginning...

B.E. Hemphill. Are the inhabitants of Madaklasht an emigrant Persian population in northern Pakistan?: a dental morphometric investigation.
The answer: "Madaklasters share closest affinities to prehistoric Central Asians and more distant affinities to prehistoric inhabitants of the Iranian Plateau. Such results support the claim that the inhabitants of Madaklast are an intrusive population into Pakistan whose origins most likely may be found in northeastern Afghanistan and Tajikistan."

Someone should look at their genes. Human history is a giant jigsaw puzzle and it is populations that differ from their neighbors and came from somewhere else that allow us to catch a glimpse of the past (in this case prehistoric Central Asia).

N. Seguchi. "Re-analysis of the ainu-samurai hypothesis using population genetic analysis."
The conclusion: "The result shows that the Kamakura ties to the Ainu first, before it ties to the other ethnic Japanese. In addition, the Kamakura group shows more variability,indicating that the Kamakura group may have experienced significantly more gene flow. This indicates the Ainu-derived people who lived in East Japan at that time made a genetic contribution to the warrior class of Kamakura."
J. K. Rilling et al. "Abdominal depth as a principal determinant of human female attractiveness."
Excerpt: "Multiple linear regression analysis revealed that the depth of the lower torso at the umbilicus, or abdominal depth, was the strongest predictor of attractiveness, stronger than either BMI or WHR, and that its impact was significantly greater for video and side view stimuli in which it was clearly visible compared with front and back view stimuli. Women with shallow abdominal depth are more likely to be healthy, fertile and non-pregnant, suggesting that this may be an adaptive male preference that has been shaped by natural selection."