October 31, 2008

60,000-year-old Y-chromosome haplogroup D? Not really

I am probably sounding like a broken record, but here comes another study which uses the wholly inappropriate "evolutionary" mutation rate of 0.00069/locus/generation. This rate is suitable for a haplogroup that grows due to drift alone and which is expected in 60,000 years (or 2,400 generations) to have grown to the grand number of ~1,200 men.

Not only is this the case, but the authors give "confidence intervals" on their age estimates of 61-71kya which is almost certainly an underestimate of the truth based on an incomplete assessment of the factors affecting uncertainty about the haplogroup's age. This nice and tight estimate is accomplished using the grand total of eight STRs!

Based on using the wrong mutation rate, and artificially narrow confidence intervals, the authors joyously proclaim:
The estimated ages of the D-M174 lineages are older than those previously reported
based on both Y chromosome and mtDNA variations in East Asia [8, 9, 21]. To see
whether it is over-estimated, using the same method, we calculated the divergence
time between DE* and E-M40. The estimated age is 27,176 years, which is much younger than the D-M174 lineage, but consistent with the previous estimation (27,800-37,000 years ago) [3]. Hence, the antiquity of D-M174 likely reflects the true prehistory of human populations in East Asia. The age estimation model developed by Zhivotovsky (2001) is not sensitive to effective population size and recent population expansion though the effect of population substructure cannot be totally ruled out. The antiquity of D-M174 was also supported by a previous study in which the origin of D-M174 was estimated more than 50,000 years ago [5].
Study [5] by Underhill et al., which supposedly supports the origin of haplogroup D 50,000 years ago, actually doesn't derive this estimate on the basis of any genetic data, but rather from theory about the "Southern Coastal Route":
The early human groups that used this route around 50000 years ago (taking the earliest occupation of Australia as the endpoint of this dispersal) were not restricted to coastal areas, and must have successfully colonized the Asian mainland, as shown by the distribution of surviving Group IV and V lineages.
I am constantly amazed by how the tremendous amount of effort required to identify, sample, catalogue, process, and genotype great numbers of people from around the world is accompanied by an apparently complete lack of interest in checking the basic premises on which interpretation of this data is based.

This paper and its supplementary data is a wonderful resource for Y-chromosome haplogroup D, but if you want to know more about the origins of this haplogroup, the sister clade of the common haplogroup E, you'll have to look elsewhere.

BMC Biology doi: 10.1186/1741-7007-6-45

Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations

Hong Shi et al.

Abstract

Background

The phylogeography of the Y chromosome in Asia previously suggested that modern humans of African origin initially settled in mainland southern East Asia, and about 25,000-30,000 years ago, migrated northward, spreading throughout East Asia. However, the fragmented distribution of one East Asian specific Y chromosome lineage (D-M174), which is found at high frequencies only in Tibet, Japan and the Andaman Islands, is inconsistent with this scenario.

Results

In this study, we collected more than 5,000 male samples from 73 East Asian populations and reconstructed the phylogeography of the D-M174 lineage. Our results suggest that D-M174 represents an extremely ancient lineage of modern humans in East Asia, and a deep divergence was observed between northern and southern populations.

Conclusions

We proposed that D-M174 has a southern origin and its northward expansion occurred about 60,000 years ago, predating the northward migration of other major East Asian lineages. The Neolithic expansion of Han culture and the last glacial maximum are likely the key factors leading to the current relic distribution of D-M174 in East Asia. The Tibetan and Japanese populations are the admixture of two ancient populations represented by two major East Asian specific Y chromosome lineages, the O and D haplogroups.

Link

Time-dependent evolutionary mutation rate? Adélie Penguins say no

I have been a vocal critic of the applicability of the evolutionary mutation rate for human Y-chromosomes. Now, a new ancient mtDNA study on Antarctic penguins shows that the evolutionary and germline mutation rates over a period of 37,000 years are not significantly different.

This is an important discovery, since the mutation rate is a basic component of the molecular clock method. A molecular clock infers the amount of time necessary to accumulate the observed present-day variation if this variation accumulates according to a particular rate.

A "slow" evolutionary rate, allegedly supported by fossils in some species, or motivated by the presence of bottlenecks in humans, leads to an overestimation of ages.

From the paper:
Therefore, in order to compare molecular rates accurately over different time periods and within a single species, the following are required: extant natural populations from which large numbers of pedigree samples can be collected, along with large numbers of ancient samples of the same species from an undisturbed environment. Adélie penguins meet these requirements and therefore represent an ideal model for resolving disparate views about the time dependency of molecular rates. Using this species, it is possible to estimate both mutation and evolutionary rates for the same region of the genome precisely.

PLoS Genetics doi: 10.1371/journal.pgen.1000209

Mutation and Evolutionary Rates in Adélie Penguins from the Antarctic

Craig D. Millar et al.

Abstract

Precise estimations of molecular rates are fundamental to our understanding of the processes of evolution. In principle, mutation and evolutionary rates for neutral regions of the same species are expected to be equal. However, a number of recent studies have shown that mutation rates estimated from pedigree material are much faster than evolutionary rates measured over longer time periods. To resolve this apparent contradiction, we have examined the hypervariable region (HVR I) of the mitochondrial genome using families of Adélie penguins (Pygoscelis adeliae) from the Antarctic. We sequenced 344 bps of the HVR I from penguins comprising 508 families with 915 chicks, together with both their parents. All of the 62 germline heteroplasmies that we detected in mothers were also detected in their offspring, consistent with maternal inheritance. These data give an estimated mutation rate (μ) of 0.55 mutations/site/Myrs (HPD 95% confidence interval of 0.29–0.88 mutations/site/Myrs) after accounting for the persistence of these heteroplasmies and the sensitivity of current detection methods. In comparison, the rate of evolution (k) of the same HVR I region, determined using DNA sequences from 162 known age sub-fossil bones spanning a 37,000-year period, was 0.86 substitutions/site/Myrs (HPD 95% confidence interval of 0.53 and 1.17). Importantly, the latter rate is not statistically different from our estimate of the mutation rate. These results are in contrast to the view that molecular rates are time dependent.

Link

October 30, 2008

Complete mtDNA sequence of Tyrolean Iceman

It remains to be seen whether or not the mtDNA branch of the Iceman's sequence will turn up in modern Europeans. Quite a lot of people are ordering full-mtDNA sequences these days, and this is probably going to continue and intensify (unless the global economy completely implodes).

Still, the finding that the Iceman had such a unique genetic sequence is consistent with the idea that selection has had an effect on human mtDNA diversity, effectively causing the mtDNA gene pool to be dominated by a few successful lineages, with many older lineages not persisting to the present. This is not unique to humans but may be shared with our oldest animal friend.

UPDATE (31 Oct): Blaine Bettinger informs me that there may be a second independent attempt at sequencing the Iceman's mtDNA that did find a modern relative:
According to the article, Alan Cooper - head of the University of Adelaide’s Australian Center for Ancient DNA - has also sequenced Otzi’s mtDNA and stated that "We have found someone very, very closely related." I’m looking forward to comparing the mtDNA genome obtained by the two research groups. Will they be the same?
John Hawks suggests selection for the disappearance of the "Iceman clade" from the modern mtDNA gene pool, but also quotes Antonio Torroni to the effect that his idiosyncratic mtDNA may be due to a reversal:
It’s possible but unlikely that Ötzi belonged to a fourth branch of K1 that is now extinct or rare, Torroni says. He considers it more probable that a random mutation in the Iceman’s mitochondrial DNA erased the only genetic marker currently used to identify members of the most common K1 branch.

Current Biology doi: 10.1016/j.cub.2008.09.028

Complete Mitochondrial Genome Sequence of the Tyrolean Iceman

Luca Ermini et al.

Abstract

The Tyrolean Iceman was a witness to the Neolithic–Copper Age transition in Central Europe 5350–5100 years ago, and his mummified corpse was recovered from an Alpine glacier on the Austro-Italian border in 1991 [1]. Using a mixed sequencing procedure based on PCR amplification and 454 sequencing of pooled amplification products, we have retrieved the first complete mitochondrial-genome sequence of a prehistoric European. We have then compared it with 115 related extant lineages from mitochondrial haplogroup K. We found that the Iceman belonged to a branch of mitochondrial haplogroup K1 that has not yet been identified in modern European populations. This is the oldest complete Homo sapiens mtDNA genome generated to date. The results point to the potential significance of complete-ancient-mtDNA studies in addressing questions concerning the genetic history of human populations that the phylogeography of modern lineages is unable to tackle.

Link

"Phoenician" Y-chromosomes

It has been several years since the inception of the Genographic project, and to say that the quantity and quality of the work produced by it is underwhelming would be charitable.

The newest bit of Genographic wisdom is that haplogroup J2 in the Mediterranean is associated not with the Neolithic, Greek, or other population movements, but with the sea-faring Phoenicians. They achieve this feat by (allegedly) comparing areas of Phoenician with those of no (or low) such influence.

I have intentionally limited myself to five major weak points of the study: to cover more would be too time-consuming and unnecessary.



1. The Hellenistic age did not happen

A central assumption of this work is that the conquest and occupation of the Middle East by Alexander the Great does not count as Greek influence, despite centuries of Greek domination that followed, both during Hellenistic, and later in Roman times.

The authors write that their method could be further used to:
include systematic investigations of military expansions, such as the Greek signal, from the time of Alexander the Great in central and south Asia
Apparently they didn't think of applying it to West Asia itself, which was also conquered by Alexander the Great, and in which the Greek-speaking element persisted far longer than in "south Asia".

Thus, the population of Phoenicia and its "periphery" is implicitly assumed to be free of Greek influence. That is a bizarre contention, given that Greek was spoken in "Phoenicia" long after the Phoenician language became extinct.

2. Crete was influenced by the Phoenicians

This totally unsupported claim is necessary for the authors' thesis, since Crete has the world maximum of haplogroup J2. I have no doubt that Phoenicians traded with Cretans, just as Cretans traded with Phoenicians. But, that is no excuse to think of Crete as an area of Phoenician influence.

Indeed, settlement of the Levant by Aegean peoples is archaeologically supported, while Phoenician settlement of Crete is not.

But, speaking of Phoenician settlement, the only area of Greece where such settlement is believed to have taken place is in mainland Greece, in Thebes, where Cadmus and his Phoenicians founded Cadmeis. I doubt that this had any substantial effect, but if the authors wanted to be intellectually honest, they would list this as an area of Phoenician influence, rather than Crete.

3. West Asia Minor (or the Pontus) was not colonized by Greeks

The most laughable claim of the authors (see map) is the absence of blue (Greek) dots on West Asia Minor, and the Pontus (Northeast Turkey). Apparently the Greek colonies of the far West (such as Marseilles) count as areas of Greek influence, while the countless Greek cities on the Asian side of the Aegean, or in northeast Turkey do not.

The motivation of this is obvious, since Asia Minor is a J2-heavy area and asserting the Greek influence there would upset the paper's thesis. But, it is absurd to place blue dots in Paphlagonia and Caria and not in Ionia or the Pontus.

4. Modern Lebanese are descendants of Phoenicians

This central assumption of the paper has no actual support, except for a vague geographical congruence. Modern Lebanese are a hybrid people, divided into Christians and Muslims. Both are Arabs, with Muslims being more influenced by the original Arabians, and Christians more influenced by the pre-Arab (Greco-Syrian) and post-Arab (West European) migrations. Perhaps, there is a trace of Phoenician genes in them, but this is really not a self-evident claim.

5. R1b in Greece and Turkey is due to the Celts

R1b in Greece and Turkey belongs primarily into the "eastern" variety, and not the "western" variety. It is in Italy and north of Greece where the two varieties begin to blend with each other. No care to distinguish between these varieties is taken.

Certainly, some R1b in this region may be due to Western Europeans (e.g. from the period of the Frankokratia), but to assign its totality to this factor is nonsensical. Apparently, the geniuses of the Genographic project have decreed that the brief foray of the Celts into Greece introduced massive amounts of R1b, but a thousand years of Greco-Roman domination of the Levant did nothing of the kind.

6 (bonus). Haplogroup J2 is more frequent in East than in West Sicily

Sicily is an island which had well-documented and not insignificant settlements by both Greeks and Phoenicians. Moreover, these settlements were geographically divided: Greeks in the East, Phoenicians in the West. It is in the East that J2 has its highest frequency, and not in the Phoenician West.

Conclusion

Is there anything of value in this paper? Well, it's a good idea to try to correlate Y-chromosome distribution with historical rather than pre-historical events. Too bad the authors botched the job, but their paper can at least serve as a reference point for how not to go about doing it.

UPDATE: Take a look at the "haplotype groups" suggested by the authors as signals of Phoenician and Greek colonization.



Not only are haplotype groups not clades (they do not designate common ancestry), but 7-marker haplotypes don't even designate anything that can be remotely tied to the time period in question, given the huge confidence intervals associated with even larger numbers of markers. Feel free to plug these haplotypes to yhrd or ysearch to find plenty of long-lost "Phoenicians" all over the planet.

UPDATE II: The "evolutionary" mutation rate rears its ugly head

From the paper:
Because there is a significant chance that a haplotype existing 3000 years ago has accumulated a one-step difference in an STR (we expect 0.6 mutations per seven-STR haplotype when a rate of 6.9x10-4 per locus per 25 yr is used), these one-step neighbors have been included in each set, producing what we have labeled STR+s. STR-s can contain both haplotypes deriving from mutations, which should have been included, and independent haplotypes unconnected with the migrations that we are trying to detect.
UPDDATE III: What of the Arabs?

The modern Lebanese are Arabs, as are most modern North Africans where Phoenician colonies were founded. The Arabs also affected several Mediterranean islands, as well as Iberia. One would think that the most salient feature of modern Mediterranean populations would be mentioned in a paper which attempted to trace patterns of Y-chromosome variation in the Mediterranean.

Certainly, the Neolithic, Greek, and Phoenician migrations, as well as the Jewish Diaspora moved people around. But the Phoenicians have been extinct for 2,000 years. The Jews had (and have) communities around the Mediterranean, but did not amount to a significant population element anywhere. It is the Arabs who are the elephant in the room, and yet they are ignored. Are similarities between the Levant, North Africa and Spain due to Phoenicians or due to this later Arab movement? By failing to trace the distribution of their "Phoenician colonization signals" among Arabians, the authors have overstated their case.


American Journal of Human Genetics doi: :10.1016/j.ajhg.2008.10.012

Identifying Genetic Traces of Historical Expansions: Phoenician Footprints in the Mediterranean

Pierre A. Zalloua et al.

Abstract

The Phoenicians were the dominant traders in the Mediterranean Sea two thousand to three thousand years ago and expanded from their homeland in the Levant to establish colonies and trading posts throughout the Mediterranean, but then they disappeared from history. We wished to identify their male genetic traces in modern populations. Therefore, we chose Phoenician-influenced sites on the basis of well-documented historical records and collected new Y-chromosomal data from 1330 men from six such sites, as well as comparative data from the literature. We then developed an analytical strategy to distinguish between lineages specifically associated with the Phoenicians and those spread by geographically similar but historically distinct events, such as the Neolithic, Greek, and Jewish expansions. This involved comparing historically documented Phoenician sites with neighboring non-Phoenician sites for the identification of weak but systematic signatures shared by the Phoenician sites that could not readily be explained by chance or by other expansions. From these comparisons, we found that haplogroup J2, in general, and six Y-STR haplotypes, in particular, exhibited a Phoenician signature that contributed > 6% to the modern Phoenician-influenced populations examined. Our methodology can be applied to any historically documented expansion in which contact and noncontact sites can be identified.

Link

Flat tummy, narrow waist, long legs make a woman attractive

Not very surprising, but an interesting methodology that examined video of actual women rather than static photos or unrealistic line drawings. Abdominal depth and waist circumference are, of course, correlated with the more widely used waist-hip ratio and body-mass index which have been used in previous attractiveness research, but they appear to be even stronger predictors of attractiveness.

Evolution and Human Behavior doi: 10.1016/j.evolhumbehav.2008.08.007

Abdominal depth and waist circumference as influential determinants of human female attractiveness

James K. Rilling et al.

Abstract

Previous research based largely on two-dimensional (2D) line drawings and picture stimuli has established that both body mass index (BMI) and waist-to-hip ratio (WHR) influence the perceived attractiveness of human female bodies. Here, we extend these studies by (1) creating a more ecologically valid stimulus set consisting of 3D videos and 2D still shots from real female “models” rotating in space, and (2) measuring and examining the influence of several additional anthropometric variables that previously have not been considered. Multiple linear regression analysis revealed that the depth of the lower torso at the umbilicus, or abdominal depth, and waist circumference were the strongest predictors of attractiveness, stronger than either BMI or WHR. Women with shallow abdominal depth and small waist circumference are more likely to be healthy and nonpregnant, suggesting that this may be an adaptive male preference that has been shaped by natural selection. Leg length was a consistent positive predictor of attractiveness, perhaps because it has been correlated with biomechanical efficacy or healthy prepubertal growth that is unhindered by nutritional or energetic deficiency. Our results show that conclusions regarding anthropometric predictors of attractiveness are influenced by the visual perspective of the perceiver, as well as the anthropometric variables considered for analysis.

Link

Balancing selection and homosexuality (revisited)

Genetic traits predisposing to homosexuality decrease their bearers' genetic fitness. Therefore, they should be weeded out of the gene pool. However, such traits could persist if their expression in homosexuals was balanced by a reproductive advantage when they are expressed in heterosexuals.

This paper looks at the heterosexual brothers of homosexuals (who share half their genes), to see if they have increased reproductive success -- and they don't.

This is consistent with my hypothesis that a factor contributing to homosexuality is an excess of feminine (or deficiency of masculine) traits expressed in the wrong (i.e. male) gender. According to this hypothesis, male homosexuality would be associated with greater reproductive success in female family members, who would possess an excess of feminine traits: what's bad for the males in the family would be good for the females. You can read more about this in Beautiful Wives and Gay Sons.

I think that an interesting aspect of the homosexual paradox stems from the common variant/common trait assumption, which states that a relatively common phenotype should be the result of a relatively common genotype. Thus the question: how is such a genotype maintained in the gene pool at a non-trivial frequency?

The idea of balancing selection is certainly a mechanism which may solve the paradox. But, on the other hand, it's also possible that the genetic basis of homosexuality is not a population-wide phenomenon, but rather multiple independent mutations arising all over the population in each generation, and quickly dying out after a few generations.

So, it is not a question of how the "gay gene" is maintained at a high-enough frequency in the gene pool despite its obvious reproductive shortcomings. Such common population-wide gene(s) probably do not exist.

In my opinion, homosexuality is maintained by several factors:
  1. The expression of feminizing (or masculinizing) genes in men (or women).
  2. Deleterious loss-of-function genes appearing de novo in each generation and quickly weeded out by selection
  3. Social pressures to produce offspring which limit the effects of selection.
An interesting consequence of #3 is that as social tolerance for this behavior increases, its genetic basis will decrease, as men who would -in previous generations- be involved in sham marriages are now free to engage in their preferred behavior, removing their genetic contribution to the gene pool. Of course, factors 1-2 in addition to environmental influences will suffice to reproduce the phenomenon in society.

Here is a previous post on balancing selection and homosexuality.

Evolution and Human Behavior doi:10.1016/j.evolhumbehav.2008.08.004

Testing Miller's theory of alleles preventing androgenization as an evolutionary explanation for the genetic predisposition for male homosexuality

Pekka Santtila et al.

Abstract

The genetic background of male homosexuality presents an evolutionary paradox, since homosexuality could be considered a reproductive disadvantage. We tested E.M. Miller's (2000) balanced polymorphism explanation, which states that alleles partially preventing androgenization in male fetuses during pregnancy would be associated with a homosexual orientation. Having all the alleles produces homosexuality, while heterosexual carriers with only a few of these alleles instead have a reproductive advantage; that is, they have more traits, which, by controlling for excessive aggressiveness and psychopathy, make them more attractive mates. Pairs of brothers were used to test these assumptions. If homosexuality is due to having all the androgenization-preventing alleles, then heterosexual men with homosexual brothers are more likely to also have some of the these alleles compared to heterosexual men with heterosexual brothers. These two categories were compared on variables related both directly and indirectly to reproductive success, with heterosexual men with a homosexual brother hypothesized to have an advantage on the variables. However, no statistically significant findings in support of the theory were detected. The results were discussed together with alternative explanations.

Link

Practicing a musical instrument and cognitive function

PLoS ONE doi: 10.1371/journal.pone.0003566

Practicing a Musical Instrument in Childhood is Associated with Enhanced Verbal Ability and Nonverbal Reasoning

Marie Forgeard et al.

Abstract

Background

In this study we investigated the association between instrumental music training in childhood and outcomes closely related to music training as well as those more distantly related.

Methodology/Principal Findings

Children who received at least three years (M = 4.6 years) of instrumental music training outperformed their control counterparts on two outcomes closely related to music (auditory discrimination abilities and fine motor skills) and on two outcomes distantly related to music (vocabulary and nonverbal reasoning skills). Duration of training also predicted these outcomes. Contrary to previous research, instrumental music training was not associated with heightened spatial skills, phonemic awareness, or mathematical abilities.

Conclusions/Significance

While these results are correlational only, the strong predictive effect of training duration suggests that instrumental music training may enhance auditory discrimination, fine motor skills, vocabulary, and nonverbal reasoning. Alternative explanations for these results are discussed.

Link

October 29, 2008

Sexual orientation and personal income

The results of this study are consistent with the hypothesis that "homosexuality is rooted in a side-effect of the expression of femininity-- or masculinity-enhancing traits in individuals of the wrong gender". Men generally make more money than women, so it is expected that men who are more feminine biologically will make less money, while women who are more masculine will make more money (on average).

Homosexual men have significantly lower personal incomes than heterosexual individuals
Homosexual women have higher incomes than straight women

Montreal, Canada – October 29, 2008 – A new study in the Canadian Journal of Economics provides the first evidence on sexual orientation and economic outcomes in Canada. The study found that gay men have 12 percent lower personal incomes and lesbians have 15 percent higher personal incomes than heterosexual men and women.

Christopher S. Carpenter of The Paul Merage School of Business at the University of California Irvine used data from the Canadian Community Health Survey which includes standard demographic questions as well as self-reports on sexual orientation.

Like previous patterns found in the U.S. and the U.K., results show that gay men have significantly lower personal incomes than similarly situated straight individuals, while lesbians have significantly higher personal incomes than straight women.

Also, similar to gay and straight differences in the U.S., gay men and lesbians in Canada are more likely to live in urban areas and more highly educated than heterosexuals in Canada.

"This is the first work to document statistically and economically meaningful differentials associated with sexual orientation in Canada," Carpenter concludes. "The long-term significance of the study will be to further the call for more research into the causes and consequences of gay/straight differences in Canada and elsewhere."
Canadian Journal of Economics doi: 10.1111/j.1540-5982.2008.00502.x

Sexual orientation, work, and income in Canada

Carpenter, Christopher S.

We provide the first evidence on sexual orientation and economic outcomes in Canada using confidential data that ask adults a direct question about their sexual orientation. Gay men have 12% lower personal incomes and lesbians have 15% higher personal incomes than otherwise similar heterosexual men and women, respectively. Different labour force patterns can account for some of the income differentials. We also document large differences in educational attainment, childrearing, and urbanicity that generally mirror patterns found in the US. Finally, we show that applying couples-based approaches common in this literature greatly overstates the magnitudes of gay/straight income gaps.

Link

October 28, 2008

Barack Obama or Barry Dunham? How names influence perception of ancestry

This paper shows that the same Asian-European multiracial faces are rated more "European" if they are associated with European names and more "Asian" if they are associated with Asian names.

This should come as no surprise to participants in various online anthropology boards, where the "Guess his origin/classify" kind of topic receives widely different responses depending on how much information is released about a given subject.

This result may seem "irrational" at first: why should the exact same stimulus be perceived differently depending on an associated name?

However, I would argue that people are acting like good Bayesians in this case:

Everyone has a mental model of P(appearance | European) and P(appearance | Asian), i.e., the distribution of phenotypes expected from persons of European or Asian ancestry. A person's P(European | appearance) opinion will not only depend on the above, but also on the P(European) and P(Asian) prior, and this will, of course, be influenced by knowledge that, e.g., a person is named Ng Yat Ho or David Smith.

Perception doi: 10.1068/p6255

Barack Obama or Barry Dunham? The appearance of multiracial faces is affected by the names assigned to them

Kirin F Hilliar, Richard I Kemp

Abstract

Does semantic information in the form of stereotypical names influence participants’ perceptions of the appearance of multiracial faces? Asian-Australian and European-Australian participants were asked to rate the appearance of Asian-Australian faces given typically Asian names, European-Australian faces given typically European names, multiracial faces given Asian names, and multiracial faces given European names. Participants rated the multiracial faces given European names as looking significantly ‘more European’ than the same multiracial faces given Asian names. This study demonstrates how socially derived expectations and stereotypes can influence face perception.

Link

October 27, 2008

Facial cues of upper-body strength

Proceedings of the Royal Society B doi: 10.1098/rspb.2008.1177

Human adaptations for the visual assessment of strength and fighting ability from the body and face

Aaron Sell et al.

Abstract

Selection in species with aggressive social interactions favours the evolution of cognitive mechanisms for assessing physical formidability (fighting ability or resource-holding potential). The ability to accurately assess formidability in conspecifics has been documented in a number of non-human species, but has not been demonstrated in humans. Here, we report tests supporting the hypothesis that the human cognitive architecture includes mechanisms that assess fighting ability—mechanisms that focus on correlates of upper-body strength. Across diverse samples of targets that included US college students, Bolivian horticulturalists and Andean pastoralists, subjects in the US were able to accurately estimate the physical strength of male targets from photos of their bodies and faces. Hierarchical linear modelling shows that subjects were extracting cues of strength that were largely independent of height, weight and age, and that corresponded most strongly to objective measures of upper-body strength—even when the face was all that was available for inspection. Estimates of women's strength were less accurate, but still significant. These studies are the first empirical demonstration that, for humans, judgements of strength and judgements of fighting ability not only track each other, but accurately track actual upper-body strength.

Link

October 26, 2008

Ancient mtDNA from Jomon skeletons

American Journal of Physical Anthropology doi: 10.1002/ajpa.20923

Mitochondrial DNA analysis of Jomon skeletons from the Funadomari site, Hokkaido, and its implication for the origins of Native American

Noburu Adachi et al.

Abstract

Ancient DNA recovered from 16 Jomon skeletons excavated from Funadomari site, Hokkaido, Japan was analyzed to elucidate the genealogy of the early settlers of the Japanese archipelago. Both the control and coding regions of their mitochondrial DNA were analyzed in detail, and we could securely assign 14 mtDNAs to relevant haplogroups. Haplogroups D1a, M7a, and N9b were observed in these individuals, and N9b was by far the most predominant. The fact that haplogroups N9b and M7a were observed in Hokkaido Jomons bore out the hypothesis that these haplogroups are the (pre-) Jomon contribution to the modern Japanese mtDNA pool. Moreover, the fact that Hokkaido Jomons shared haplogroup D1 with Native Americans validates the hypothesized genetic affinity of the Jomon people to Native Americans, providing direct evidence for the genetic relationships between these populations. However, probably due to the small sample size or close consanguinity among the members of the site, the frequencies of the haplogroups in Funadomari skeletons were quite different from any modern populations, including Hokkaido Ainu, who have been regarded as the direct descendant of the Hokkaido Jomon people. It appears that the genetic study of ancient populations in northern part of Japan brings important information to the understanding of human migration in northeast Asia and America.

Link

October 25, 2008

Admixture, ethnicity, and pigmentation of Hispanics and Native Americans

A very interesting new study co-authored by fellow blogger Yann Klimentidis, which tries to untangle many correlated but not equivalent concepts: genetic admixture from continental groups (in this case primarily Caucasoids and American Mongoloids), skin color, self-reported ethnicity, and self-assessed levels of admixture.

It was found that Native Americans tend to overestimate their genetic Native American-ness, while Hispanics tend to underestimate it. I don't find this surprising since Hispanics are descended from Spanish-influenced groups with Spanish as their language, and Catholicism as their religion, who viewed themselves in counterdistinction to the non-Spanish-influenced populations on the one hand, and English-speaking Americans to their north on the other. Thus, they may emphasize their "Spanish-ness" since it distinguishes them from both groups. Native Americans, on their other hand, view themselves in counterdistinction to Anglo-Americans, and identify with their native traditions, and hence tend to emphasize their "nativenesss".

Another interesting finding is that ethnicity among Hispanics (i.e. labels such as "half-white, half-Hispanic", "Spanish", "Mexican American" or "Mexican") is correlated with Native American genetic admixture in the expected order. 

Skin color was also associated with genetic admixture, although the correlation wasn't as strong, and skin color was a relatively weak predictor of ancestral proportions. That does not argue so much against physical anthropological determination of race, but rather against the use of a single trait. Mark Shriver's group had looked at the correlation between skin pigmentation and ancestry in a previous study.

American Journal of Physical Anthropology doi: 10.1002/ajpa.20945

Genetic admixture, self-reported ethnicity, self-estimated admixture, and skin pigmentation among Hispanics and Native Americans

Yann C. Klimentidis et al.

Abstract

The relationship between ethnicity and biology is of interest to anthropologists, biomedical scientists, and historians in understanding how human groups are constructed. Ethnic self-identification in recently admixed groups such as Hispanics, African Americans, and Native Americans (NA) is likely to be complex due to the heterogeneity in individual admixture proportions and social environments within these groups. This study examines the relationships between self-identified ethnicity, self-estimated admixture proportions, skin pigmentation, and genetic marker estimated admixture proportions. These measures were assessed using questionnaires, skin color measurements, and genotyping of a panel of 76 ancestry informative markers, among 170 Hispanics and NAs from New Mexico, a state known for its complex history of interactions between people of NA and European (EU) ancestry. Results reveal that NAs underestimate their degree of EU admixture, and that Hispanics underestimate their degree of NA admixture. Within Hispanics, genetic-marker estimated admixture is better predicted by forehead skin pigmentation than by self-estimated admixture. We also find that Hispanic individuals self-identified as half-White, half Hispanic and Spanish have lower levels of NA admixture than those self-identified as Mexican and Mexican American. Such results highlight the interplay between culture and biology in how individuals identify and view themselves, and have implications for how ethnicity and disease risk are assessed in a medical setting.

Link

October 24, 2008

Genetic structure in Northern Europe with 250K SNPs

A new study on genetic structure in Northern Europeans has appeared in PLoS ONE. Below is the STRUCTURE results for the Northern European populations. At K=2, the two clusters are centered on Eastern Finns and Germans-Brits, with Western Finns being intermediate and Swedes closer to the German-Brit (green) cluster). At K=3 Nordic populations are split into two clusters centering on Swedes and Eastern Finns. The pattern for K=4 is less distinct, except that the German-Brit cluster is split into blue and green components that don't appear to have any population specificity.


Interestingly, the researchers also carried out an analysis of the populations which included the HapMap populations:
When data from HapMap Han Chinese+Japanese and Yoruba individuals was included in the analysis, the MDS plot of IBS formed a triangle of the three continents in the first two dimensions, with the third dimension separating the European populations clinally from each other (Fig. S3). In the histograms of IBS between the five European populations and each HapMap population (Fig. 4a), the studied populations were most similar with the CEU and least similar with YRI. Interestingly, the similarity with the Asians varied between populations, being higher for Eastern Finns, Western Finns and Swedes than for the Germans and British (p less than 10−14 for all comparisons except for GER and BRI whose distributions did not differ). The same pattern was also observed when comparing the allele frequencies in the study populations and in CEU and CHB+JPT: the Eastern Finns had the largest proportion of SNPs deviating towards the Asian frequencies (Table S2; p less than 10−5), also when markers with smallest differences were excluded (data not shown).
They were able to differentiate between the effects of genetic drift and eastern influence by looking at the direction of the divergence:
To study the extent of eastern influence, we counted in each of the five European populations the number of markers where the population's allele frequency and the CHB+JPT allele frequency deviated from the CEU allele frequency to the same direction, and the number of markers where the allele frequencies deviated in opposite directions. We then compared the numbers to the null hypothesis that all the five populations stem from the same proto-European population (approximated by the CEU frequencies) from which they have subsequently diverged via genetic drift in the absence of admixture. In such a case, one would expect the number of markers drifting into a given direction (e.g. towards the Asian frequencies) to be similar across the populations, whereas a varying degree of eastern admixture in each population would result in disparate marker proportions. Using the number of deviating markers instead of the absolute size of the deviations should even out some of the effects of differing extent of drift in the populations.

This parallels my comment of an earlier study:
Under the theory of "drift due to isolation", the Finns might be distant from other Europeans, but not specifically at an East Eurasian direction.
The paper also discusses genetic structure within Finland:
The information about the grandparental birthplaces of the Finnish samples enabled a more detailed analysis of population structure within Finland. In the multidimensional scaling plot of IBS within Finland (Fig. 2c,d, Fig. S1b), the first dimension showed the division to Eastern and Western Finland; the Häme samples settled between the clusters. The second dimension showed a north-south gradient within Eastern and the third dimension within Western Finland. Here the Swedish-speaking Ostrobothnians showed no separation from their Finnish-speaking neighbours, whereas in the MDS plot of the European populations, the Finnish samples closest to the Swedes were almost exclusively Swedish-speakers (data not shown), and in the Structure analysis the Swedish-speaking Finns showed twice as large an admixture with the Sweden-dominated cluster as the other Western Finnish samples did (48.9% versus 24.6%, data not shown).


PLoS ONE doi: 10.1371/journal.pone.0003519

Genome-Wide Analysis of Single Nucleotide Polymorphisms Uncovers Population Structure in Northern Europe

Elina Salmela et al.

Abstract

Background
Genome-wide data provide a powerful tool for inferring patterns of genetic variation and structure of human populations.

Principal Findings
In this study, we analysed almost 250,000 SNPs from a total of 945 samples from Eastern and Western Finland, Sweden, Northern Germany and Great Britain complemented with HapMap data. Small but statistically significant differences were observed between the European populations (FST = 0.0040, p less than 10−4), also between Eastern and Western Finland (FST = 0.0032, p less than 10−3). The latter indicated the existence of a relatively strong autosomal substructure within the country, similar to that observed earlier with smaller numbers of markers. The Germans and British were less differentiated than the Swedes, Western Finns and especially the Eastern Finns who also showed other signs of genetic drift. This is likely caused by the later founding of the northern populations, together with subsequent founder and bottleneck effects, and a smaller population size. Furthermore, our data suggest a small eastern contribution among the Finns, consistent with the historical and linguistic background of the population.

Significance
Our results warn against a priori assumptions of homogeneity among Finns and other seemingly isolated populations. Thus, in association studies in such populations, additional caution for population structure may be necessary. Our results illustrate that population history is often important for patterns of genetic variation, and that the analysis of hundreds of thousands of SNPs provides high resolution also for population genetics.

Link

mtDNA from Neolithic European dogs

It is interesting that one out of three mtDNA haplotypes is not observed in modern dogs, just as all seven Paleolithic ones are not so observed. This, together with the apparently dramatic change in frequency of clade C since the Neolithic, is perfectly consistent with selection I hypothesized about earlier, which in the case of dogs may have been human-induced.

Journal of Archaeological Science doi:10.1016/j.jas.2008.10.011

Ancient DNA supports lineage replacement in European dog gene pool: insight into Neolithic South-East France

M.F. Deguilloux et al.

Abstract

We report palaeogenetic analysis of domesticated dog (Canis familiaris) remains excavated from three archaeological sites from South-East France and dating from Middle Neolithic. Ancient DNA analysis was attempted on teeth and bone samples taken from 11 dogs. Three 266-base-pair fragments of the mitochondrial genome hypervariable region I (HVR-I) could be retrieved and revealed two haplotypes belonging to HVR-I lineage C. These three sequences were compared to the sequences of Swedish and Italian Neolithic dogs and permitted to confirm that clade C was largely represented all over Western Europe during this period. One haplotype defined in Neolithic French dog was observed for the first time in Canis mtDNA, underlining the loss of mitochondrial diversity in Europe since the Neolithic. Finally, these results point out mitochondrial lineage replacement in Europe, since lineage C represents only 5% of extant European dogs. Altogether, these results support the proposition that palaeogenetic studies are essential for the reconstruction of the past demographic history and the domestication process of dogs.

Link

October 23, 2008

Y chromosomes and mtDNA of Sweden

It's interesting to see a study of the current population of a country. If one is interested in deep pre-historical origins, one must ensure that his sample has no known foreign ancestry among the lines of interest. But, if one is interested in the current and future course of the population, then the totality of the population must be sampled.

This is a good opportunity to track shifting gene frequencies due to immigration and/or differential fertility. It would be a good idea for countries to start spending some money on a genetic census of their population. This would not need to involve all the inhabitants, and could be carried out for the fraction of cost that governments pay to collect all sorts of other statistics. Such a census would provide an important source of data to future scientists investigating the demography of Europe during this transitional era.

From the paper:
Several haplogroups had interesting frequency patterns, but also wide confidence intervals, necessitating caution in the interpretations. The mtDNA haplogroup with the strongest geographical cline, U5b, is known to have high frequencies among the northern Saami population, consistent with our results (Tambets et al. 2004). The high frequency of the Y-chromosomal R1b in the south, observed also by Karlsson et al. 2006; is consistent with its abundance in Central Europe and Denmark (Semino et al. 2000; Brion et al. 2005). Haplogroup R1a1 is more common in Norway than in Sweden (Dupuy et al. 2006), and its high frequency in Värmland/Dalarna and Halland supports the historically plausible connection to Norway (Lindqvist, 2006). Y-chromosomal haplogroup N3 (Lappalainen et al. 2006) and mtDNA haplogroup H1f (Loogväli et al. 2004; Lappalainen et al. 2008) are common in Finland, and had increased frequencies in several Swedish counties with historical ties to Finland: Eastern Svealand was the most important destination of the Finnish immigration wave in the 1970's; in Norrland the Finnish influences date back to ancient times and in Dalarna to the 17th century (Pitkänen 1994).

When compared to previous knowledge of ethnic Swedes without immigration in their familial background (Lappalainen et al. 2008), the frequencies of several haplogroups showed effects of 20th century immigration from more distant countries. The Y-chromosomal I1a had decreased frequencies in Malmö and Gothenburg most probably due to replacement by haplogroups that are common among immigrants. African immigration contributes to the frequencies of mtDNA haplogroups L3*(xN,M) and L* (xL3) (Chen et al. 2000), and Y-chromosomal haplogroup A (Underhill et al. 2001; Jobling & Tyler-Smith 2003), while Near Eastern influence can be seen in mtDNA haplogroup U7 and possibly J (Richards et al. 2000; Abu-Amero et al. 2007; Achilli et al. 2007). Asian and American immigration can be observed in the slightly elevated frequencies of mtDNA haplogroups M, A, C, D and G (Quintana-Murci et al. 2004; Hill et al. 2007) and the Y-chromosomal O, K* and P* (Underhill et al. 2001; Jobling & Tyler-Smith 2003). The frequency of the Y-chromosomal haplogroup I1b may associate to immigrants from Balkan and Eastern Europe (Rootsi et al. 2004). In Malmö and Gothenburg immigration was the main contributor to their isolated positions in the Y-chromosomal PCA plot and probably also to the higher diversities compared to the surrounding populations. These phenomena were not observed in Stockholm, where most of the immigrants come from Finland (Statistics Sweden, http://www.scb.se).

Annals of Human Genetics doi: 10.1111/j.1469-1809.2008.00487.x

Population Structure in Contemporary Sweden—A Y-Chromosomal and Mitochondrial DNA Analysis

T. Lappalainen et al.

Abstract

A population sample representing the current Swedish population was analysed for maternally and paternally inherited markers with the aim of characterizing genetic variation and population structure. The sample set of 820 females and 883 males were extracted and amplified from Guthrie cards of all the children born in Sweden during one week in 2003. 14 Y-chromosomal and 34 mitochondrial DNA SNPs were genotyped. The haplogroup frequencies of the counties closest to Finland, Norway, Denmark and the Saami region in the north exhibited similarities to the neighbouring populations, resulting from the formation of the Swedish nation during the past millennium. Moreover, the recent immigration waves of the 20th century are visible in haplogroup frequencies, and have led to increased diversity and divergence of the major cities. Signs of genetic drift can be detected in several counties in northern as well as in southern Sweden. With the exception of the most drifted subpopulations, the population structure in Sweden appears mostly clinal. In conclusion, our study yielded valuable information of the structure of the Swedish population, and demonstrated the usefulness of biobanks as a source of population genetic research. Our sampling strategy, nonselective on the current population rather than stratified according to ancestry, is informative for capturing the contemporary variation in the increasingly panmictic populations of the world.

Link

Facial attractiveness predicted from average of attractive and unattractive faces

This paper seems quite interesting, and comes up with an attractiveness rating by comparing a face's relative distance to two averages: of attractive and of unattractive faces.

For some traits, the attractive and unattractive faces may have the same, or similar average. For example, very broad or very narrow mouths may be both considered unattractive. By averaging them out, the result may be an attractive mouth of intermediate proportions.

But, on other traits, the unattractiveness is asymmetrical, and hence will increase in a definite direction. So while very thin and very fat people are probably not very attractive, the weight of unattractiveness falls on the fatness side, and unattractive people tend to be systematically fatter-looking than attractive ones.

For traits of the first kind, the discriminating power will be low: at the limit, attractive and unattractive faces will have the same average, and all faces will be equidistant from the two prototypes. As attractive and unattractive faces become more differentiated -for traits of the second kind- the ability to distinguish between them will increase.

Neural Comput. 2008 Oct 17. [Epub ahead of print]

A Bi-Prototype Theory of Facial Attractiveness.

Chang F, Chou CH.

The attractiveness of human faces can be predicted with a high degree of accuracy if we represent the faces as feature vectors and compute their relative distances from two prototypes: the average of attractive faces and the average of unattractive faces. Moreover, the degree of attractiveness, defined in terms of the relative distance, exhibits a high degree of correlation with the average rating scores given by human assessors. These findings motivate a bi-prototype theory that relates facial attractiveness to the averages of attractive and unattractive faces rather than the average of all faces, as previously hypothesized by some researchers.

Link

October 21, 2008

Behavioral inhibition, gender, and left-handedness

Personality and Individual Differences doi: 10.1016/j.paid.2008.08.019

Handedness and behavioural inhibition: Left-handed females show most inhibition as measured by BIS/BAS self-report

Lynn Wright et al.

Abstract

This study investigated the relationship between handedness, gender and behavioural approach and inhibition using Carver and White’s (1994) BIS/BAS Scale. 112 participants took part: 46 left-handers and 66 right-handers. All participants completed Peters’ (1998) handedness questionnaire followed by the self-report BIS/BAS Scale. Significant effects of both handedness and gender on the BIS scores were found, with left-handers and females scoring significantly higher on inhibition. BIS scores were re-examined to include FFFS scores, which showed a significant effect of gender. Revised BIS scores replicated the original BIS findings. These findings are discussed in relation to handedness research.

Link

The Campanian Ignimbrite eruption

Some general info on this event can be found here.

Journal of Human Evolution doi: 10.1016/j.jhevol.2008.08.018

From the Bay of Naples to the River Don: the Campanian Ignimbrite eruption and the Middle to Upper Paleolithic transition in Eastern Europe

John F. Hoffecker et al.

Abstract

The Campanian Ignimbrite (CI) eruption, dated by 40Ar/39Ar and various stratigraphic methods to ca. 39,000 cal BP, generated a massive ash plume from its source in southern Italy across Southeastern and Eastern Europe. At the Kostenki-Borshchevo open-air sites on the Middle Don River in Russia, Upper Paleolithic artifact assemblages are buried below, within, and above the CI tephra (which is redeposited by slope action at most sites) on the second terrace. Luminescence and radiocarbon dating, paleomagnetism, and soil and pollen stratigraphy provide further basis for correlation with the Greenland and North Atlantic climate stratigraphy. The oldest Upper Paleolithic occupation layers at Kostenki-Borshchevo may be broadly correlated with warm intervals that preceded the CI event and Heinrich Event 4 (HE4; Greenland Interstadial: GI 12–GI 9) dating to ca. 45,000–41,000 cal BP. These layers contain an industry not currently recognized in other parts of Europe. Early Upper Paleolithic layers above the CI tephra are correlated with HE4 and warm intervals that occurred during 38,000–30,000 cal BP (GI 8–GI 5), and include an assemblage that is assigned to the Aurigancian industry, associated with skeletal remains of modern humans.

October 20, 2008

The Middle to Upper Paleolithic record of western Eurasia

Journal of Human Evolution doi:10.1016/j.jhevol.2008.04.002

At the end of the 14C time scale—the Middle to Upper Paleolithic record of western Eurasia

Olaf Jöris, and Martin Street

Abstract

The dynamics of change underlying the demographic processes that led to the replacement of Neandertals by Anatomically Modern Humans (AMH) and the emergence of what are recognized as Upper Paleolithic technologies and behavior can only be understood with reference to the underlying chronological framework. This paper examines the European chronometric (mainly radiocarbon-based) record for the period between ca. 40 and 30 ka 14C BP and proposes a relatively rapid transition within some 2,500 years. This can be summarized in the following falsifiable hypotheses: (1) final Middle Paleolithic (FMP) “transitional” industries (Uluzzian, Chatelperronian, leaf-point industries) were made by Neandertals and date predominantly to between ca. 41 and 38 ka 14C BP, but not younger than 35/34 ka 14C BP; (2) initial (IUP) and early (EUP) Upper Paleolithic “transitional” industries (Bachokirian, Bohunician, Protoaurignacian, Kostenki 14) will date to between ca. 39/38 and 35 ka 14C BP and document the appearance of AMH in Europe; (3) the earliest Aurignacian (I) appears throughout Europe quasi simultaneously at ca. 35 ka 14C BP. The earliest appearance of figurative art is documented only for a later phase ca. 33.0/32.529.2 ka 14C BP. Taken together, the Middle to Upper Paleolithic transition appears to be a cumulative process involving the acquisition of different elements of “behavioral modernity” through several “stages of innovation.”

Link

October 19, 2008

A common founder for the 35delG mutation

Am J Med Genet A. 2008 Oct 16. [Epub ahead of print]

Strong linkage disequilibrium for the frequent GJB2 35delG mutation in the Greek population.

Kokotas H, Van Laer L, Grigoriadou M, Iliadou V, Economides J, Pomoni S, Pampanos A, Eleftheriades N, Ferekidou E, Korres S, Giannoulia-Karantana A, Van Camp G, Petersen MB.

Department of Genetics, Institute of Child Health, Athens, Greece.

Approximately one in 1,000 children is affected by severe or profound hearing loss at birth or during early childhood (prelingual deafness). Up to 40% of congenital, autosomal recessive, severe to profound hearing impairment cases result from mutations in a single gene, GJB2, that encodes the connexin 26 protein. One specific mutation in this gene, 35delG, accounts for the majority of GJB2 mutations detected in Caucasian populations. Some previous studies have assumed that the high frequency of the 35delG mutation reflects the presence of a mutational hot spot, while other studies support the theory of a common founder. Greece is among the countries with the highest carrier frequency of the 35delG mutation (3.5%), and a recent study raised the hypothesis of the origin of this mutation in ancient Greece. We genotyped 60 Greek deafness patients homozygous for the 35delG mutation for six single nucleotide polymorphisms (SNPs) and two microsatellite markers inside or flanking the GJB2 gene. The allele distribution in the patients was compared to 60 Greek normal hearing controls. A strong linkage disequilibrium was found between the 35delG mutation and markers inside or flanking the GJB2 gene. Furthermore, we found a common haplotype with a previous study, suggesting a common founder for the 35delG mutation.

Link

October 18, 2008

Why Y-STR haplotype clusters are not clades

A Y-chromosome clade is the set of Y-chromosomes descended from a single Y-chromosome (the founder). In human terms, it consists of all the patrilineal descendants of a single man.

Clades are usually defined in terms of unique event polymorphisms (UEPs). Such polymorphisms occur rarely enough to be useful for cladistic analysis and determination of the human Y-chromosome phylogeny. A clade defined on the basis of UEPs is a haplogroup.

There is a misconception among some people that haplotypes, i.e. the alleles at several Y-STR loci can also define a clade. This is, however, impossible, for at least three reasons.

First, those who erroneously define clades based on Y-STR haplotypes do so by means of identification of a cluster of similar haplotypes.

But, this isn't enough. Suppose you identify a cluster of haplotypes, and every pair of them has a genetic distance of at most 3. First, it must be shown that the genetic distance between any haplotype in the cluster and any other haplotype (not in the cluster), must be greater than 3. Suppose you have identified a cluster of haplotypes {a, b, c} and dist(a, b)=3. Now, suppose that there is another haplotype d and dist(a, d) = 3. You are not justified to exclude d from the proposed "clade", since it may share a common ancestor with a that is more recent than the common ancestor of a and b.

Moreover, since age estimates are associated with very wide confidence intervals, it is not guaranteed that greater genetic distance implies an older MRCA. To ensure that a group of Y-chromosomes are part of a clade, you must ensure that other Y-chromosomes have an even greater genetic distance than 3, so great indeed, that it is extremely unlikely that they are closely related to any Y-chromosomes in the haplotype cluster.

Needless to say, none of the folks who propose various "clades" on the basis of Y-STR haplotypes have bothered to prove that their haplotype clusters share a common ancestor that is more recent than that between cluster members and non-cluster members.

Second, suppose that you have identified a very distinctive haplotype cluster that addresses the first concern. Suppose that every pair of haplotypes within this cluster is within a short genetic distance (e.g., 3) and very far from any other haplotype (e.g., more than 15). Is this sufficent to define a clade?

It is not, since you are not certain that you have sampled the relevant Y-chromosomes, i.e., those that bridge the gap between your cluster and other Y-chromosomes, revealing them to be part of a continuum, rather than distinct members of a particular clade.

There are several cases in which supposed clades were defined, e.g., if a marker has a value of 12 or 14 but no intermediate (13) values, only to be invalidated later on when chromosomes with intermediate values popped up.

So, while the first concern identifies the need for clusters to be tight and distinct, the second concern identifies the problem that tight and distinct clusters may be spurious due to incomplete sampling of the genetic continuum.

Third, suppose that you have identified a tight and distinct cluster, and that moreover you have extremely large and comprehensive samples that give you a strong degree of confidence in your cluster. Have you now identified a true clade of the Y-chromosome phylogeny?

The answer is still no, and the reason is the time symmetry of the mutation model of Y-STR loci. Consider the following Y-chromosome tree.


Nodes with capital letters are at most g=4 generations away from the clade founder. It is perhaps possible to devise a test that would be able to detect all these haplotypes as related. But, any test that would identify these haplotypes as descendants of the "founder" node, despite 4 generations of mutations, would also erroneously identify all the smallcase nodes, also at most 4 generations away from the "founder" as members of the clade.

A haplotype cluster centered on a presumed founder who lived g generations ago will invariably include a set of Y chromosomes that do not form a clade.

Whereas a clade includes all the descendants of a single founder, a haplotype cluster will invariably include many men who are g generations away from the founder, whether they are his descendants or not.

Why are Y-STRs qualitatively different from UEPs? While a UEP at the founder defines a watershed moment, separating the founder's descendants (who possess the UEP derived state) from his other relatives (who do not), Y-STRs do not define such a moment: node "m", a cousin of the founder, will possess a haplotype that is 4-generations removed from the "founder", just as node "Q" who is a great great grandson. By looking at haplotypes it is impossible to distinguish between the two.

There is a practical reason why the distinction between haplotype clusters and clades is important, and this has to do with ancient DNA.

Suppose that a very old archaeological sample (of age A years) is Y-STR tested and reveals an R1b-like haplotype. Can we make the inference that this was a member of the R1b clade? No, since many (non-descendant) patrilineal relatives of the R1b founder would have similar haplotypes.

Are we justified in claiming that the founder of haplogroup R1b was earlier than A years? The answer is again no, as haplotypes similar to current R1b ones existed before R1b was founded.

How is this compatible with the known fact that haplogroups can be predicted from sufficiently long Y-STR haplotypes?

First, such predictions don't rely only on the Y-STR haplotypes, but also on large number of haplotypes with known UEP results. Haplogroup prediction relies on UEPs and can't be made independent of UEPs.

Second, such predictions don't rely only on the Y-STR haplotypes, but also on the knowledge that they are present-day haplotypes (last row in the figure). Today, only the descendants of the clade founder survive in the haplotype cluster, but this is not necessarily the truth for earlier times.

Conclusion

Clades cannot be defined based on Y-STR haplotype clusters for several reasons, both practical and theoretical.

On the practical side, it is extremely difficult to define a clade using Y-STRs because haplotype clusters must be shown to be distinctive (clearly separated from other Y-chromosomes) and genuine (separated because of common descent, and not incomplete sampling).

But, even if a clear-cut genuine haplotype cluster is detected, it does not constitute a clade, since the time symmetry of Y-STR mutations necessitates that it will include (erroneously) non-descendant relatives of the founder.

There is nothing wrong with exploratory analysis of haplotype clusters, if one keeps in mind that such clusters are not and should not be thought of as clades of the Y-chromosome phylogeny.

Dog domestication in the Aurignacian (c. 32kyBP)

From the paper:
Interestingly, when compared to extant wolf and dog sequences available from GenBank, all seven haplotypes found in the Pleistocene samples were found to be unique and not described to date. This result is remarkable when considering the large number of wolf (~160) and particularly dog sequences (> 1,000 from almost all breeds known today) available in Genbank.

This may be consistent with selection affecting mtDNA since the Paleolithic, with recent dogs and wolves being descended from a small subset of the Paleolithic mtDNA diversity. Also from the paper:
Compared to wolves, ancient dogs exhibit a shorter and broader snout (Lawrence, 1967; Olsen, 1985; Sablin and Khlopachev, 2002). All Palaeolithic dogs in our study conform to this pattern.

...

As demonstrated above, the Palaeolithic dogs in our data set are very uniform in their skull shape. Even the Goyet dog, with an age of c. 31,700 BP, is not intermediate in form between the fossil wolves and the prehistoric dogs, but conforms to the configuration of the other Palaeolithic dogs, which are approximately 18,000 years younger. The abrupt appearance of a dog, much older than the Eliseevich I dogs, the oldest recognized dogs so far, suggest that the domestication process must have been quite rapid (cf. Crockford, 2000a).

Was the dog the very first animal to be domesticated by man, truly his "oldest friend"? I would not be surprised if our relationship with dogs stretches even further to the past. Dogs are such useful helpers in a hunting culture, that their value must have been recognized from early on.

Journal of Archaeological Science doi:10.1016/j.jas.2008.09.033

Fossil dogs and wolves from Palaeolithic sites in Belgium, the Ukraine and Russia: osteometry, ancient DNA and stable isotopes

Mietje Germonpré et al.

Abstract

Using multivariate techniques, several skulls of fossil large canids from sites in Belgium, Ukraine and Russia were examined to look for possible evidence of the presence of Palaeolithic dogs. Reference groups constituted of prehistoric dogs, and recent wolves and dogs. The fossil large canid from Goyet (Belgium), dated at c. 31,700 BP is clearly different from the recent wolves, resembling most closely the prehistoric dogs. Thus it is identified as a Palaeolithic dog, suggesting that dog domestication had already started during the Aurignacian. The Epigravettian Mezin 5490 (Russia) and Mezhirich (Ukraine) skulls are also identified as being Palaeolithic dogs. Select Belgian specimens were analysed for mtDNA and stable isotopes. All fossil samples yielded unique DNA sequences, indicating that the ancient Belgian large canids carried a substantial amount of genetic diversity. Furthermore, there is little evidence for phylogeographic structure in the Pleistocene large canids, as they do not form a homogenous genetic group. Although considerable variation occurs in the fossil canid isotope signatures between sites, the Belgian fossil large canids preyed in general on horse and large bovids.

Link

October 17, 2008

Epigenetic effects of slavery in African Americans (?)

I can't say I buy the thesis of these two papers, namely that inherited epigenetic effects from the days of slavery are responsible for birth-weight and cardiovascular disease (CVD) disparities between whites and blacks in the US.

Does anyone know of any studies of birth weight or CVD in biracial children with a white vs. a black mother, with otherwise similar admixture proportions? An expectation of this theory is that the former should have a higher birth weight.

American Journal of Human Biology doi: 10.1002/ajhb.20824

Low birth weight of contemporary African Americans: An intergenerational effect of slavery?

Grazyna Jasienska

Abstract

The average birth weight in the contemporary African-American population is about 250 g lower than the average birth weight of European Americans. Differences in genetic and socioeconomic factors present between these two groups can explain only part of birth weight variation. I propose a hypothesis that the low birth weight of contemporary African Americans not only results from the difference in present exposure to lifestyle factors known to affect fetal development but also from conditions experienced during the period of slavery. Slaves had poor nutritional status during all stages of life because of the inadequate dietary intake accompanied by high energetic costs of physical work and infectious diseases. The concept of fetal programming suggests that physiology and metabolism including growth and fat accumulation of the developing fetus, and, thus its birth weight, depend on intergenerational signal of environmental quality passed through generations of matrilinear ancestors. I suggest that several generations that have passed since the abolition of slavery in the United States (1865) has not been enough to obliterate the impact of slavery on the current biological and health condition of the African-American population.

Link

American Journal of Human Biology doi: 10.1002/ajhb.20822

Epigenetics and the embodiment of race: Developmental origins of US racial disparities in cardiovascular health

Christopher W. Kuzawa, Elizabeth Sweet

Abstract

The relative contribution of genetic and environmental influences to the US black-white disparity in cardiovascular disease (CVD) is hotly debated within the public health, anthropology, and medical communities. In this article, we review evidence for developmental and epigenetic pathways linking early life environments with CVD, and critically evaluate their possible role in the origins of these racial health disparities. African Americans not only suffer from a disproportionate burden of CVD relative to whites, but also have higher rates of the perinatal health disparities now known to be the antecedents of these conditions. There is extensive evidence for a social origin to prematurity and low birth weight in African Americans, reflecting pathways such as the effects of discrimination on maternal stress physiology. In light of the inverse relationship between birth weight and adult CVD, there is now a strong rationale to consider developmental and epigenetic mechanisms as links between early life environmental factors like maternal stress during pregnancy and adult race-based health disparities in diseases like hypertension, diabetes, stroke, and coronary heart disease. The model outlined here builds upon social constructivist perspectives to highlight an important set of mechanisms by which social influences can become embodied, having durable and even transgenerational influences on the most pressing US health disparities. We conclude that environmentally responsive phenotypic plasticity, in combination with the better-studied acute and chronic effects of social-environmental exposures, provides a more parsimonious explanation than genetics for the persistence of CVD disparities between members of socially imposed racial categories.

Link

October 16, 2008

iGENEA wins an award

... the newly instituted Anthropology Blog award for Outstanding Achievement in Misleading the Public about Human Population Genetics.

I don't usually post about specific genetic testing companies unless they do something innovative, but I got two e-mails recently about a particular company, and I have to make an exception.

First of all, let me state that I have no reason to doubt that their genetic testing results (i.e., the actual Y-STR values) are accurate. What I do have a problem with is the copious amount of misleading information provided in their website (as of Oct 16, 2008). 

You will learn for example that there is no haplogroup N in Finland, that there is 30% R1b in Russia, 5% of haplogroup J in Armenia, but 10% in Germany. You will also be pleased to know that Y-chromosome haplogroup J is associated with the  Jews and mtDNA haplogroup H with the Vikings. But, wait, haplogroup I1a is associated with the Scythians [absent in most of Siberia and Central Asia but who cares about details], while mtDNA haplogroup H with the Teutons.

If you have time to kill, browse around the site, it is priceless as entertainment, and don't forget to stop by this thread where the company not only asserts that Y-chromosomes of ancient Greeks and Macedonians have been tested, pointing to completely irrelevant bibliography, as "evidence", but also lists the percentages of various ancient tribes in modern nations. Apparently, Bulgarians are 49% Thracian, while Albanians 18%, whereas Greeks and "Macedonians" 0%. Those Thracians must have evacuated from Greek Thrace and flown over Macedonia to settle in Albania :)

If you have any understanding of population genetics, no more needs to be said. 

But, if you are a newbie researching the field, spend some time to educate yourself, and don't trust companies that offer you the sky. If it's too good to be true, it probably isn't.

ADRB2 allele associated with intelligence

The results of this study are entirely in synch with my recent thoughts on genes and intelligence. In this case, the same gene was found to have opposite effects on intelligence, indicating that it acts differently (positively) in the cohort of young related people and (negatively) in the cohort of older unrelated Scottish people. 

Behav Genet. 2008 Oct 15. [Epub ahead of print]

A Functional Polymorphism under Positive Evolutionary Selection in ADRB2 is Associated with Human Intelligence with Opposite Effects in the Young and the Elderly.

Bochdanovits Z, Gosso FM, van den Berg L, Rizzu P, Polderman TJ, Pardo LM, Houlihan LM, Luciano M, Starr JM, Harris SE, Deary IJ, de Geus EJ, Boomsma DI, Heutink P, Posthuma D.

Comparative genomics offers a novel approach to unravel the genetic basis of complex traits. We performed a two stage analysis where genes ascertained for enhanced protein evolution in primates are subsequently searched for the presence of non-synonymous coding SNPs in the current human population at amino acid sites that differ between humans and chimpanzee. Positively selected genes among primates are generally presumed to determine phenotypic differences between humans and chimpanzee, such as the enhanced cognitive ability of our species. Amino acid substitutions segregating in humans at positively selected amino acid sites are expected to affect phenotypic differences among humans. Therefore we conducted an association study in two family based cohorts and one population based cohort between cognitive ability and the most likely candidate gene among the five that harbored more than one such polymorphism. The derived, human-specific allele of the beta-2 adrenergic receptor Arg16Gly polymorphism was found to be the increaser allele for performance IQ in the young, family based cohort but the decreaser allele for two different measures of cognition in the large Scottish cohort of unrelated individuals. The polymorphism is known to affect signaling activity and modulation of beta-2 adrenergic signaling has been shown to adjust memory consolidation, a trait related to cognition. The opposite effect of the polymorphism on cognition in the two age classes observed in the different cohorts resembles the effect of ADRB2 on hypertension, which also has been reported to be age dependent. This result illustrates the relevance of comparative genomics to detect genes that are involved in human behavior.

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"James, brother of Jesus" ossuary a fraud

Exposing the 'Jesus' Brother' Fraud
The discovery of the ossuary was hailed in some quarters as a spectacular archeological find — solidly circumstantial proof, at last, of Christ's existence. For it would have held the remains of the Apostle James, who was killed in 62 A.D. and is described in the Bible as Jesus' brother.

When the James ossuary toured Canada in October 2002, it attracted thousands of the curious and faithful. Some visitors kneeled in quiet prayer. But back in Israel, police detectives, along with a growing posse of Biblical scholars, were growing skeptical of the ossuary's authenticity. After a two-year investigation, police in December 2004 charged the antiquities collector and four others of forgery, alleging that the James ossuary was a clever fake, and that Golan had masterminded an international ring of thieves that over the past 20 years had duped major museums and collectors out of millions. Put on trial, Golan denied the charges and some experts and the pious rallied to his side. Nevertheless, one of the detectives insisted: "Oded Golan played with our beliefs, the beliefs of Jews and Christians. That is why it's the fraud of the century."



Of course, this ossuary was never considered as proof of Jesus' existence by real Christians. According to the Antiquitates Judaicae, concerning the martyrdom of St. James:
But this younger Ananus, who, as we have told you already, took the high priesthood, was a bold man in his temper, and very insolent; he was also of the sect of the Sadducees, (23) who are very rigid in judging offenders, above all the rest of the Jews, as we have already observed; when, therefore, Ananus was of this disposition, he thought he had now a proper opportunity [to exercise his authority]. Festus was now dead, and Albinus was but upon the road; so he assembled the sanhedrim of judges, and brought before them the brother of Jesus, who was called Christ, whose name was James, and some others, [or, some of his companions]; and when he had formed an accusation against them as breakers of the law, he delivered them to be stoned.
and Hegesippus:
And, when many were fully convinced by these words, and offered praise for the testimony of James, and said, “Hosanna to the son of David,” then again the said Pharisees and scribes said to one another, “We have not done well in procuring this testimony to Jesus. But let us go up and throw him down, that they may be afraid, and not believe him.” And they cried aloud, and said: “Oh! oh! the just man himself is in error.” Thus they fulfilled the Scripture written in Isaiah: “Let us away with the just man, because he is troublesome to us: therefore shall they eat the fruit of their doings.” So they went up and threw down the just man, and said to one another: “Let us stone James the Just.” And they began to stone him: for he was not killed by the fall; but he turned, and kneeled down, and said: “I beseech Thee, Lord God our Father, forgive them; for they know not what they do.”

And, while they were thus stoning him to death, one of the priests, the sons of Rechab, the son of Rechabim, to whom testimony is borne by Jeremiah the prophet, began to cry aloud, saying: “Cease, what do ye? The just man is praying for us.” But one among them, one of the fullers, took the staff with which he was accustomed to wring out the garments he dyed, and hurled it at the head of the just man.
And so he suffered martyrdom; and they buried him on the spot, and the pillar erected to his memory still remains, close by the temple.
St. James the adelphotheos is celebrated on October 23.