January 30, 2005

Modal haplotype of Tehran, Iran

The modal haplotype of Tehran, Iran in YHRD is 14-13-29-23-10-11-12-13,16 and according to the haplogroup predictor is indicative of haplogroup J2 (*). It occurs in 35 individuals in the current release, including 12 from Europe and 19 from Asia.

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(*) It could also be J1 which is not included in the haplogroup predictor.

Modal haplotype of Zagreb, Croatia

The modal haplotype of Zagreb, Croatia in YHRD is 16-13-31-24-11-11-13-14,15 and according to the haplogroup predictor is indicative of haplogroup I1b. This haplotype occurs in 94 samples of the current release, including 89 from Europe:

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It's interesting (and surprising) that this modal haplotype is not detected in Greece, even though Greece has about 10% of haplogroup I1b.

January 29, 2005

Distribution of Moscow, Kiev and Warsaw modal haplotypes

Moscow, Kiev and Warsaw are the respective capitals of the three great Eastern European Slavic nations of Russia, Ukraine and Poland. Using YHRD I attempted to see the distribution of the modal Y-chromosomal haplotypes from these three locations.

In Moscow, the modal haplotype is 16-13-30-25-11-11-13-11,14. As expected, according to Whit Athey's haplogroup predictor, this haplotype is most indicative of haplogroup R1a. It is found in 116 individuals in the current release, including 91 from Europe and 21 from Asia:

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The Kiev modal haplotype is 17-13-30-25-10-11-13-10,14 and seems to indicate haplogroup R1a as well. It is found in 130 individuals, including 126 from Europe and 2 from Asia, and in general seems to be more geographically constrained than that of Moscow, being (mostly or wholly) absent e.g., from Scandinavia, the British Isles and the Caucasus:

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The Warsaw modal haplotype is the same as that of Kiev. Interestingly -as far as I can tell- the Kiev-Warsaw modal haplotype does not seem to be found in Moscow, while the Moscow modal haplotype is found in both Kiev and Warsaw.

UPDATE: The modal haplotype of the Baltic capitals of Riga, Latvia and Vilnius Lithuania seems to be the same as that of Moscow.

January 28, 2005

Western Norwegian modal haplotype

Western Norway, being relatively remote from the European continent and the known source of Viking migrations is of special anthropological interest. It may represent a relatively untainted North Germanic gene pool, and is usually thought to be a good representative of the Norsemen of the Viking age.

The modal haplotype of W. Norway is 14-12-28-23-10-11-13-14,14 and according to Whit Athey's haplogroup predictor it is suggestive of Y-haplogroup I1a which has a well-known Northwestern European main distribution. Its prevalence in Europe (129 matches) is shown below:

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The distribution of a one-step neighbor of the above (14-12-28-23-10-11-13-13,14) with 105 occurrences in Europe has the following distribution:

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Global prevalence of Mongolian and Kazakh modal haplotypes

Three Mongolian groups are included in the latest release of the YHRD Y-chromosomal database: Mongolia, Mongolia [Buryat], and Mongolia [Khalkh].

A search for the Mongolian modal haplotype (16-13-29-25-10-11-13-12,13) returned the following 62 matches, which seem to be confined to Altaic-speaking populations:

Ankara, Turkey: 1 / 39

Mongolia: 10 / 60

Mongolia [Khalkh]: 4 / 39

Taraz, Kazakhstan: 47 / 175

A search for the Buryat modal haplotype (16-14-30-23-10-14-14-11,13) returned the following 4 matches:

Gdansk, Poland: 1 / 543

Mongolia [Buryat] 3 / 42

The Mongolian [Khalkh] modal haplotype is the same as that of the Mongolian group, not surprising given the predominance of the Khalkh group in Mongolia.

The modal haplotype of the population from Taraz Kazakhstan is also the same as that of the Mongolian group. The Kazakhs are Altaic-speaking and exhibit the Turanid (mixed Caucasoid-Mongoloid) racial type.

Stand up to lose weight

A new article in Science comes to the conclusion that lean individuals differ from obese ones in the amount of time they spent standing up. For a non-technical summary see The Fit Tend to Fidget, and Biology May Be Why, a Study Says and Why fidgeters tend to be leaner.

Science, Vol 307, Issue 5709, 584-586 , 28 January 2005

Interindividual Variation in Posture Allocation: Possible Role in Human Obesity

James A. Levine et al.

Obesity occurs when energy intake exceeds energy expenditure. Humans expend energy through purposeful exercise and through changes in posture and movement that are associated with the routines of daily life [called nonexercise activity thermogenesis (NEAT)]. To examine NEAT's role in obesity, we recruited 10 lean and 10 mildly obese sedentary volunteers and measured their body postures and movements every half-second for 10 days. Obese individuals were seated, on average, 2 hours longer per day than lean individuals. Posture allocation did not change when the obese individuals lost weight or when lean individuals gained weight, suggesting that it is biologically determined. If obese individuals adopted the NEAT-enhanced behaviors of their lean counterparts, they might expend an additional 350 calories (kcal) per day.


January 27, 2005

Distribution of Eastern European haplotype in Europe

According to the recent article on Y-STR variation in Europe, a particular haplotype, 16-13-17-25-10-11-13 (over DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393) seems to be ancestral for haplogroup R1a and occurs (together with its one-step neighbors) in a frequency of 30.6% in "Eastern Europe" vs. only 0.6% in "Western Europe". This haplotype is highly suggestive of Eastern European origin.

A search of this haplotype in YHRD gave the following result:

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Note that red color indicates presence of the haplotype, while blue indicates its absence. It appears that there is core Eastern European area where the haplotype is present, and this includes most (all?) Slavo-Baltic countries. In Scandinavia, the Netherlands, Belgium and the British Isles the haplotype is mostly lacking(*), which seems to indicate its likely absence in the Proto-Germanic gene pool; this is not true for Germany, Austria and Switzerland, reflecting historical contacts with Slavic and Baltic peoples. The haplotype is also mostly lacking in the Italo-Celtic world, and in the Southern Balkans, again illustrating its essentially Balto-Slavic likely origin (in most cases).

The omnipresence of the Eastern European haplotype in Balto-Slavic lands make it likely that it was part of the Proto-Balto-Slavs, and its geographical extent on the map is a rough approximation for the genetic influence of the representatives of that branch of the Indo-European family.(**)

(*) Note that two of the sites of the British Isles are of Indo-Pakistani populations where R1a achieves a high frequency and a third one is cosmopolitan London.
(**) Or possible of Indo-Iranians as the presence of the marker in the Indian subcontinent, as well as in Iran demonstrates. This influence was, however, probably minimal in Europe until recently.

Herculaneum and the Lost Works of Epicurus

A recent article from the Sunday Times gives an update on the current status of the uncovered library in Herculaneum where numerous Greek and Latin texts have been preserved under the ashes of Vesuvius and are being read with the use of modern technology. Worth reading in its entirety, but what struck me in particular was this sentence:
Apart from the texts of Philodemus, hundreds of other lost works of Greek philosophy — including half of Epicurus’s entire opus, missing for 2,300 years — have been rediscovered.
Epicurus, a 4th c. BC Athenian philosopher was reputed to have written more than 300 books (more properly scrolls, each of our own books being contained in several scrolls) none of which survive in its entirety. Scraps of the Epicurean corpus are available online and give tantalizing hints about the philosophy of the man who more than anyone else symbolized the culmination of the naturalistic tradition of Greek philosophy. This new discovery and eventual publication of the lost works of Epicurus will eventually help us appreciate a tradition which stood opposed to that of Plato and Aristotle for centuries after the death of its founder.

January 26, 2005

January 25, 2005

Ecological dominance, social competition

This paper examines Richard Alexander's model of "ecological dominance, social competition" as the explanation for the develoment of human intelligence. According to this model, our ancestors' mastery of the "forces of nature", or ecological dominance triggered a process of social competition. Unlike other animals whose fitness is determined by whether they can survive in nature, humans tamed their environment, and thus their fitness started being determined by how well they could socially compete with other humans. This transfer of emphasis from nature to society is the distinguishing feature of our lineage, and it can explain the complete departure of human cognitive ability from that of our hominin ancestors.

Evolution and Human Behavior
Volume 26, Issue 1 , January 2005, Pages 10-46

Ecological dominance, social competition, and coalitionary arms races
Why humans evolved extraordinary intelligence

Mark V. Flinn et al.


Human cognitive abilities are extraordinary. Our large brains are significantly modified from those of our closest relatives, suggesting a history of intense natural selection. The conditions favoring the evolution of human cognitive adaptations, however, remain an enigma. Hypotheses based on traditional ecological demands, such as hunting or climatic variability, have not provided satisfying explanations. Recent models based on social problem solving linked with ecological conditions offer more convincing scenarios. But it has proven difficult to identify a set of selective pressures that would have been sufficiently unique to the hominin lineage. What was so special about the evolutionary environments of our ancestors that caused them, and them alone, to diverge in such astonishing ways from their close relatives and all other life forms? Richard Alexander proposed a comprehensive integrated explanation. He argued that as our hominin ancestors became increasing able to master the traditional “hostile forces of nature,” selective pressures resulting from competition among conspecifics became increasingly important, particularly in regard to social competencies. Given the precondition of competition among kin- and reciprocity-based coalitions (shared with chimpanzees), an autocatalytic social arms race was initiated, which eventually resulted in the unusual collection of traits characteristic of the human species, such as concealed ovulation, extensive biparental care, complex sociality, and an extraordinary collection of cognitive abilities. We term this scenario the “ecological dominance–social competition” (EDSC) model and assess the feasibility of this model in light of recent developments in paleoanthropology, cognitive psychology, and neurobiology. We conclude that although strong or direct tests are difficult with current data, Alexander's model provides a far-reaching and integrative explanation for the evolution of human cognitive abilities that is consistent with evidence from a wide range of disciplines.


Linkage disequilibrium varies among populations

Linkage disequilibrium (LD) is said to occur when knowledge of the allele in a particular locus (gene) gives us information about the state of the allele in a different locus. That is, in a sense, these two genes are co-inherited, and this is often the case when genes are very close to each other on a chromosome (and thus the probability of them being split during meiosis is limited), or when they "work well together", making their co-occurrence more likely.

A new paper in European Journal of Human Genetics studies the extent to which LD varies among different human populations. This is an important finding since LD is often used to determine how many polymorphisms to examine. For example, if a long sequence of DNA is in LD, then typing a single SNP somewhere on it implicitly reveals the state of the entire sequence. But this may lead to mistakes if applied to a different population X for which whole sequence information is not available, as the sequence in question might not be in LD in X.

The paper confirms the lower LD in Africans than in non-Africans, which may be used to support an African origin for humans. However, an important finding is that LD is not the same in different loci, with e.g., Europeans showing higher LD in a particular locus than Asians and vice versa.

European Journal of Human Genetics (advance online publication)

Linkage disequilibrium patterns vary substantially among populations

Sarah L Sawyer et al.

A major initiative to create a global human haplotype map has recently been launched as a tool to improve the efficiency of disease gene mapping. The 'HapMap' project will study common variants in depth in four (and to a lesser degree in up to 12) populations to catalogue haplotypes that are expected to be common to all populations. A hope of the 'HapMap' project is that much of the genome occurs in regions of limited diversity such that only a few of the SNPs in each region will capture the diversity and be relevant around the world. In order to explore the implications of studying only a limited number of populations, we have analyzed linkage disequilibrium (LD) patterns of three 175-320 kb genomic regions in 16 diverse populations with an emphasis on African and European populations. Analyses of these three genomic regions provide empiric demonstration of marked differences in frequencies of the same few haplotypes, resulting in differences in the amount of LD and very different sets of haplotype frequencies. These results highlight the distinction between the statistical concept of LD and the biological reality of haplotypes and their frequencies. The significant quantitative and qualitative variation in LD among populations, even for populations within a geographic region, emphasizes the importance of studying diverse populations in the HapMap project to assure broad applicability of the results.


More on Frank Salter

David B. has written the second part of his criticism of Frank Salter. Some comments of my own on the first part here. And some numbered comments on the second part here:

1. I see this as a minor point and one that can ultimately be defeated by either the "correlated alleles" approach or the "how small a difference is too small" approach.

2. Well, only in the case of polymorphic genes does it make sense to speak of competition between alleles, so I'm not sure I understand this criticism.

3. I agree with Salter on this one. Adaptive to an environment X = increasing in frequency when found in X. If an allele for a disease finds itself in an environment which favors it, even if it's an "irrational" environment which wants to perpetuate the disease, the allele is still adaptive.

4. I agree with David B. here. The human genome has mutations which are either neutral, adaptive or maladaptive. From an evolutionary perspective, an ethnic group ought to value adaptive mutations, because these are its strength. From a psychological perspective, an ethnic group might value its distinctive mutations even if they are neutral and maladaptive, e.g., mutations for a particular distinctive physical trait, e.g., the convex nose which was highly valued by Ancient Persians (*), or the freckled skin of many NW Europeans (**)

5. Related to the previous point. It is certainly the case that from an evolutionary perspective maladaptive alleles should not be preserved. For something like sickle-cell disease, an ethnic group removed from the malarial environment would probably feel no attachment for the trait, but this may not be the case for other traits mentioned in #4.

In conclusion, Frank Salter's work is one extreme in the spectrum of ideas, proposing the "objective" value of the ethnic preservationist strategy. At the other end is the older ideas of the more "tolerant" representatives of Nazi Rassenkunde, who did not ephasize the value of the Nordic race on the basis of its superiority, but rather of its distinctiveness. Richard McCulloch is the most prolific modern representative of this school of thought.

We could in fact break down ethnic preservationists based on whether they approach the issue of ethnic preservation on the basis of the distinctiveness or the superiority of their own ethnic group. Traditional racism maintains both distinctiveness and superiority. Eugenically-oriented preservationists emphasize the "deterioration" that would result by admixture rather than the loss of distinctiveness. Someone of McCulloch's ideology emphasizes ethnic distinctiveness and the need for preservation of distinct human forms, much as we seek to preserve endangered species. And, finally those who are neither interested in genetic distinctiveness nor in genetic superiority can be termed as cultural preservationists, emphasizing the non-genetic aspects of ethnicity. This ideology is dominant, or at least traditional in many modern nations (e.g., France) although it is increasingly challenged by the adherents of multi-culturalism who generally maintain that neither the genetic nor the cultural aspect of an ethnic group needs be preserved, but rather that countries should evolve in the direction of co-existence of racial stocks and cultures within the state.

(*) The convex nose may have had an adaptive origin in the distant past, but was hardly in more recent historical years.
(**) Freckled skin is associated with various skin diseases. It too might have had an adaptive, or at least neutral origin in the distant past, but not today.

January 24, 2005

Y-STRs in Europe

A very important new paper uses short tandem repeat (STR) markers on the human Y-chromosome over a set of 12,700 European individuals. STRs are fast mutating, making them unsuitable for the inference of phylogeny, but conversely suitable for detecting more recent population movements.

The main finding of this study is the detection of a strong differentiation between an "eastern" and a "western" cluster of haplotypes. In Central Europe where these two clusters meet, the gradient of change is sharper on an east-west axis than on a north-south axis. These two main population groupings are placed in boxes in the following dendrogram.

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In the next figure, the first three dimensions of an MDS on ΦST is shown:

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Inspection of Fig. 1 suggests that the similarity of Y-STR haplotypes decays much more rapidly along an east-west than a north-south gradient, at least in central Europe. This notion was formally corroborated by a MDS analysis of all pair-wise FST values. The first dimension, accounting for almost 89% of the variance (Table 1), clearly shows a decomposition of the European Y-STR genetic structure into three major components (Fig. 4a), closely corresponding to the "Western", "Central" and "Eastern" sub-clusters of Fig. 2. The first dimension also highlights the genetic peculiarity of metropolitan Paris and Vienna, Finland, and the two Balkan-Slavic samples of Slovenia and Croatia in relation to their respective surroundings. The degree of east-west stratification of the European Y-STR haplotype spectrum was quantified by Spearman rank correlation analysis between the latitudinal and longitudinal distances, respectively, and pair-wise PHgrST (Fig. 5). For 81 samples, the correlation was stronger with longitude than with latitude, and the few populations showing a notably reversed effect were from the fringe of the continent (Fig. 5). Furthermore, whilst only five samples showed a negative correlation with longitude, namely Emilia Romagna (I), Vaesterbotten (S), Finland, Estonia and Northern Norway, the same was true for 12 samples with latitude. The second dimension of the MDS analysis revealed more subtle structural features, such as, for example, the distinction between the Turkish and non-Turkish samples in "Southern Europe" and the divide between the two Dutch meta-samples. The third dimension eventually depicted an underlying north-south gradient that is usually seen in Y-SNP studies of European populations (Rosser et al. 2000; Semino et al. 2000). However, since the second and third dimensions of the Y-STR MDS accounted for less than 10% of the variance (Table 1), the major geographic structuring associated with the two types of markers must be substantially different.

Now, with respects to the Greeks, the following observations can be made. Greeks belong to a cluster (see dendrogram above) which stretches from parts of Italy and Sicily to the west to Turkey and from Hungary in the north to Greece in the south. This area corresponds quite closely to that of Gimbutas' Old Europe and the Eastern Roman ("Byzantine") Empire. I am also reminded of what I wrote about 1.5 years ago:
The Aegean-Mediterranean racial element does not seem to have penetrated much to the north of Hungary along the continental route. Interestingly, Hungarians appear to have a significant frequency of Y chromosome haplogroup E -which has a peri-Mediterranean distribution- and were found to be more similar to Greeks than the Greeks' more immediate northern neighbors according to Cavalli-Sforza.
It is also interesting that the Balkan Slavs are not allied with the "Eastern European" cluster. This may indicate a limited extent of Proto-Slavic intrusion across the Danube, or the well-known Finno-Ugrian admixture in Eastern Slavs, or both.

In Table 2, the authors perform a pseudo-admixture analysis of the studied populations into Western, Eastern, and Other clusters. It is noteworthy that Greeks have 44% of the Western and 27% of the Eastern cluster. By contrast, Bulgarians have 53% of the Eastern cluster and 28% of the Western one, and Romanians 57/24% respectively, and Albanians 53/34%. Hence, it seems that Greeks are differentiated from their Balkan neighbors in being less "Eastern". In fact the fraction of the Eastern cluster in Greeks is similar to that in West Italians (20%) and Sicilians (18%). This underscores the limited influence of demographic processes taking part north of Greece on the Greek population.

The differentiation of Turks from Turkey and the Balkans from other Balkan populations on the second dimension of the MDS plot most likely indicates the presence of unique Anatolian or Central Asian haplotypes among the former, as the Turks were formed by an amalgamation of West Asian Caucasoids with Central Asians of mixed Caucasoid-Mongoloid background.

There is much more interesting information in the paper, e.g., "The area covered by the former German Democratic Republic significantly overlaps with the homeland of Slavic (i.e. Wendish) people from the Middle Ages, including the Sorbes, Pomeranes, Wagriens, Obodrites, and Ranes. This geographical coincidence would explain the obvious preservation of "Slavic" haplotypes in eastern Germany far better than, for example, the settlement of eastern European World War II refugees, since the latter were mostly Germans anyway." which confirms a recent study which arrived at the same conclusions.

Human Genetics (Published Online)

Signature of recent historical events in the European Y-chromosomal STR haplotype distribution

Lutz Roewer et al.

Abstract Previous studies of human Y-chromosomal single-nucleotide polymorphisms (Y-SNPs) established a link between the extant Y-SNP haplogroup distribution and the prehistoric demography of Europe. By contrast, our analysis of seven rapidly evolving Y-chromosomal short tandem repeat loci (Y-STRs) in over 12,700 samples from 91 different locations in Europe reveals a signature of more recent historic events, not previously detected by other genetic markers. Cluster analysis based upon molecular variance yields two clearly identifiable sub-clusters of Western and Eastern European Y-STR haplotypes, and a diverse transition zone in central Europe, where haplotype spectra change more rapidly with longitude than with latitude. This and other observed patterns of Y-STR similarity may plausibly be related to particular historical incidents, including, for example, the expansion of the Franconian and Ottoman Empires. We conclude that Y-STRs may be capable of resolving male genealogies to an unparalleled degree and could therefore provide a useful means to study local population structure and recent demographic history.


Ethnic genetic interests: do they exist, and did they evolve?

The debate over Frank Salter's work on ethnic genetic interests is flaring up over at Gene Expression in response to a post by David B. criticizing Salter's work. Here is a small contribution to put the debate in its proper perspective:

There are two components to the 'ethnic genetic interests' problem.

#1: Is it adaptive to prefer co-ethnics to foreigners?
#2: Did we evolve to prefer co-ethnics to foreigners?

The answer to #1 is probably yes, provided that we don't sacrifice too much of our personal and close family fitness in the process.

If, for example there are two ethnic groups A, B each of which controls equal amounts of equal-quality land. If A allows immigration from B, but B does not allow immigration from A, then the distinctive genes of A may end up having a percentage of only e.g., 30% in the joint population, since the members of B will fill their own land to its carrying capacity, and also use some of the resources of the land of A by migrating there.

Therefore, a politician from B who enacted such a policy would do a great benefit to his 'distinctive genes'

The answer to #2 is probably no, because unlike members of our own family which are both close to us and highly valuable, members of our ethnic group are much less valuable and distant from us. The opportunity for any 'ethnic nepotism' gene to evolve would thus be miniscule, since it could only evolve by providing dramatic benefits to many co-ethnics, and the opportunity for such dramatic actions would be lacking for the vast majority of the population.

January 20, 2005

Genetic admixture and Cardiovascular health in African Americans

A new paper demonstrates that the percentage of genetic admixture in African Americans is related to cardiovascular health, but so are socioeconomic factors.

Am. J. Hum. Genet., 76:000, 2005

Population Structure, Admixture, and Aging-Related Phenotypes in African American Adults: The Cardiovascular Health Study

Alexander P. Reiner et al.

U.S. populations are genetically admixed, but surprisingly little empirical data exists documenting the impact of such heterogeneity on type I and type II error in genetic-association studies of unrelated individuals. By applying several complementary analytical techniques, we characterize genetic background heterogeneity among 810 self-identified African American subjects sampled as part of a multisite cohort study of cardiovascular disease in older adults. On the basis of the typing of 24 ancestry-informative biallelic single-nucleotide–polymorphism markers, there was evidence of substantial population substructure and admixture. We used an allele-sharing–based clustering algorithm to infer evidence for four genetically distinct subpopulations. Using multivariable regression models, we demonstrate the complex interplay of genetic and socioeconomic factors on quantitative phenotypes related to cardiovascular disease and aging. Blood glucose level correlated with individual African ancestry, whereas body mass index was associated more strongly with genetic similarity. Blood pressure, HDL cholesterol level, C-reactive protein level, and carotid wall thickness were not associated with genetic background. Blood pressure and HDL cholesterol level varied by geographic site, whereas C-reactive protein level differed by occupation. Both ancestry and genetic similarity predicted the number and quality of years lived during follow-up, but socioeconomic factors largely accounted for these associations. When the 24 genetic markers were tested individually, there were an excess number of marker-trait associations, most of which were attenuated by adjustment for genetic ancestry. We conclude that the genetic demography underlying older individuals who self identify as African American is complex, and that controlling for both genetic admixture and socioeconomic characteristics will be required in assessing genetic associations with chronic-disease–related traits in African Americans. Complementary methods that identify discrete subgroups on the basis of genetic similarity may help to further characterize the complex biodemographic structure of human populations.


January 19, 2005

Y-chromosome variation in Azores (II)

Following a very recent paper on Y-chromosomal variation in the Azores, a new study deals with the subject of difference in different islands of the Azores, reflecting different patterns of settlement. Unfortunately, as the authors acknowledge, the level of phylogenetic resolution used by this study is insuficient to resolve the fraction of origin of the population from Portugal, other European countries, Jews, North and Sub-Saharan Africans.

Ann Hum Genet (Online Early)

Analysis of Y-chromosome Variability and its Comparison with mtDNA Variability Reveals Different Demographic Histories Between Islands in the Azores Archipelago (Portugal)

R. Montiel et al.


We determined the Y-chromosomal composition of the population of the Azores Islands (Portugal), by analyzing 20 binary polymorphisms located in the non-recombining portion of the Y-chromosome (NRY), in 185 unrelated individuals from the three groups of islands forming the Archipelago (Eastern, Central and Western). Similar to that described for other Portuguese samples, the most frequent haplogroups were R1(xR1b3f) (55.1%), E(xE3a) (13%) and J (8.6%). Principal components analysis revealed a Western European profile for the Azorean population. No significant differences between Azores and mainland Portugal were observed. However, the haplogroup distribution across the three groups of islands was not similar (P<0.003). The Western group presented differences in the frequencies of haplogroups R1, E(xE3a) and I1b2 (27.3%, 22.7% and 13.6%, respectively) when compared to the other two groups. An assessment of the NRY variability, and its comparison with mitochondrial DNA (mtDNA) variability, was further evidence of the differential composition of males during the settlement of the three groups of islands, contrary to what has been previously deduced for the female settlers using mtDNA data.


January 18, 2005

To Read

I'll use this entry to list some books that come to my attention.

Not By Genes Alone : How Culture Transformed Human Evolution
Collapse: How Societies Choose to Fail or Succeed
Coevolution: Genes, Culture, and Human Diversity
No Place to Hide: Behind the Scenes of Our Emerging Surveillance Society
Where Do We Come From?: The Molecular Evidence for Human Descent

Ancient DNA review paper

Proceedings: Biological Sciences (Online)

Review Paper
Ancient DNA

Eske Willerslev et al.


In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets.


Late reproduction coupled with female longevity

Proceedings: Biological Sciences (Online)

Are reproductive and somatic senescence coupled in humans? Late, but not early, reproduction correlated with longevity in historical Sami women

Samuli Helle et al.


Evolutionary theory of senescence emphasizes the importance of intense selection on early reproduction owing to the declining force of natural selection with age that constrains lifespan. In humans, recent studies have, however, suggested that late-life mortality might be more closely related to late rather than early reproduction, although the role of late reproduction on fitness remains unclear. We examined the association between early and late reproduction with longevity in historical post-reproductive Sami women. We also estimated the strength of natural selection on early and late reproduction using path analysis, and the effect of reproductive timing on offspring survival to adulthood and maternal risk of dying at childbirth. We found that natural selection favoured both earlier start and later cessation of reproduction, and higher total fe cundity. Maternal age at childbirth was not related to offspring or maternal survival. Interestingly, females who produced their last offspring at advanced age also lived longest, while age at first reproduction and total fecundity were unrelated to female longevity. Our results thus suggest that reproductive and somatic senescence may have been coupled in these human populations, and that selection could have favoured late reproduction. We discuss alternative hypotheses for the mechanisms which might have promoted the association between late reproduction and longevity.


January 17, 2005

3-million year old polymorphism in Europeans

A new study in Nature Genetics by a group of Icelandic scientists has found a 900kbp inversion whose origin appears to be 3 million years before present, i.e., during the time that Homo erectus existed on earth, or even before that time. The mutation is found in Caucasoids (~20%) almost absent in Mongoloids, and rare in Negroids. The authors also discovered that the presence of the mutation has an effect on women having more children and higher recombination rates [the two have been found to be related].

The presence of such an ancient mutation is still a mystery, but two alternative explanations are proposed. The first one is that the polymorphism has been maintained in the human gene pool through balancing selection, which would indicate that its fitness benefits in heterozygotes might have corresponding fitness costs in homozygotes, which remain to be discovered. Since the polymorphism is more frequent in Europeans, it may be the case that there is something in the European environment which allows the fitness benefit to manifest itself, similar to the malarial environments in many places of the world which allow sickle-cell alleles to persist.

The second explanation -which is more likely in my opinion- is that ancestral Caucasoids underwent admixture with a different type of hominin which survived in Western Eurasia and which partially interbred with incoming modern sapiens humans. The mutation subsequently may have spread in the Caucasoid population by balancing selection (since it has not been fixed), and its absence in other populations may indicate simply that they did not interbreed with the different type of hominin.

As far as we know, during the radiation of anatomically modern Homo sapiens, the only candidate species for hybridization with it would be Homo neandertalensis. It's possible then that this was the source of the mutation in question, but since Neanderthals are also a relatively young species (less than 1 million years old) it may be the case that they also received it from a previous hominin species.

After the contested Flores hominin and the recent discovery of possible hybridization of Mongoloids with Homo erectus, this new study presents a new mystery about the origin of modern humans. It remains to be seen how these developments will eventually affect the current picture about human origins which insists on a recent African origin for our species. mtDNA research on humans and Neanderthals suggests no significant hybridization between the two species, and the arguments of the multiregionalists have been severely criticized, but I suspect that in the end the Out-of-Africa theory will have to accommodate the presence of (at least limited) admixture from older forms of Homo in the origins of modern humankind.

For more info Genes Promoting Fertility Are Found in Europeans, Scientists Find Effect of Natural Selection on Human Genome, Gene Arrangement Makes Some Europeans More Fertile.

Nature Genetics (published online)

A common inversion under selection in Europeans

Hreinn Stefansson et al.

A refined physical map of chromosome 17q21.31 uncovered a 900-kb inversion polymorphism. Chromosomes with the inverted segment in different orientations represent two distinct lineages, H1 and H2, that have diverged for as much as 3 million years and show no evidence of having recombined. The H2 lineage is rare in Africans, almost absent in East Asians but found at a frequency of 20% in Europeans, in whom the haplotype structure is indicative of a history of positive selection. Here we show that the H2 lineage is undergoing positive selection in the Icelandic population, such that carrier females have more children and have higher recombination rates than noncarriers.


January 16, 2005

Salter revisited

David B at Gene Expression criticizes Frank Salter's contention that intra-ethnic marriage raises the fitness of a person's genes. Here is a small commentary on this matter:

Intra- or inter-racial marriage does nothing for the fitness of individual genes in itself, so anyone who chooses one or the other with the hope of promoting his ethnic genes is misguided.

If immigration is to be resisted it is because it shifts the resource/population ratio for different ethnic groups. An ethnic group which maximizes its resource/population ratio (e.g., handful of Mongols controlling the greater part of Eurasia) will eventually raise its fitness.

Additionally, widespread practice of inter-racial marriage may not (in itself) say much about shifts in gene frequencies, but it does say something about the potential for such shifts.

If the world consisted of 50% of group A and 50% of group B, then group A can hope to outplay group B and grow to e.g., 75% vs. 25%, and this would be beneficial for its specific alleles.

By incorporating these alleles in inter-racial offspring, the potential that these alleles will become more (or less) frequent diminishes.

If, for example China and India remain distinctive gene pools, then it is possible that sometime in the future China might nuke India or vice versa, and thus give a big frequency gain for the specific Mongoloid genes in the Chinese population. If, on the other hand there was widespread intermarriage between Indians and Chinese, the potential for such a change would diminish, since e.g., future warfare between the two countries would not affect the frequency of these genes to the same extent, as they would be present at appreciable frequencies in both territories.

So, ethnic groups who hope to propagate their distinctive genes should better maintain some level of genetic individuality - knowing of course that in this way they also risk the fate of countless extinct peoples. Historically, many peoples have taken this gamble, and some (like Europeans in North America) have succeeded, while others (like the Samaritans) have failed.

January 15, 2005

The doctrine of the Trinity

Post moved to a Dienekes' Theology Blog, a place where I will occasionally discuss philosophical and theological issues, as well as issues of religion and its impact in the world.

Racial (and non-racial) differences

A recent protracted discussion over at Gene Expression gives me the opportunity to discuss an important issue in thinking about racial differences. We were discussing whether or not Mongoloids have a spatial genetic endowment for visuospatial (V/S) ability, or whether their high performance in V/S tests may be due to their use of the logographic system from an early age. During this discussion, the V/S performance of Eskimos was cited in support of the genetic explanation, to which I replied that Eskimos are hardly typical for Mongoloids, and we should not base conclusions for Mongoloids based on Eskimos, just as we would not base conclusions for Caucasoids based on Swedes. After many twists and turns, my counterpart in the debate came up with this illustrating quote, which will serve as the starting point in our discussion:
As Swedes are typical of Caucasoids broadly considered in terms of prognathism, so Eskimoes are typical of Mongoloids broadly considered in terms of visuospatial ability.
Any two populations will almost invariably differ in their distributions for almost any physical attribute (+), and this includes degree of prognathism, IQ scores, scores on tests of V/S ability, height etc. Many of these differences may be shown to be statistically significant based on sample sizes, and this will usually indicate differences in causal factors (genetic or environmental) between them. Some of them may also be shown to be "large" allowing us to differentiate between the populations, as in e.g., several measures of facial flatness would differentiate Swedes from several Mongoloid groups. It may also be that several attributes may not show large differences in themselves, but their correlated differences would.

Races, which as I have stated elsewhere exist as clusters of phenetic similarity, are special cases of populations which are (1) sufficiently differentiated and which show a relative persistence (2) in time to make them useful concepts. In this sense, Caucasoids and Mongoloids are races, and Swedes/Eskimos are identified as Caucasoid and Mongoloid.

The Swedish population differs from the Caucasoid population as does the Eskimo population from the Mongoloid one. This is a consequence of our observation (+) above. In some attributes, e.g., prognathism, Swedes may not be much different than Caucasoids in general, and this may also the case for e.g., frequency of epicanthic fold in Eskimos compared to Mongoloids. Hence, Swedes and Eskimos are typical for their respected races for this attribute.

If we take other attributes, e.g., the very low cranial index of Eskimos or the very light pigmentation of Swedes we see that these deviate from those of their respected races. Indeed, Swedes might resemble some Uralic groups in terms of pigmentation more than they do Armenians, and Eskimos resemble Negroids in terms of cranial index more than they do the Chinese.

The above discussion illustrates the distinction that needs to be made between racial differences such as the naso-dacryal subtense, a measure of nasal flatness, and non-racial differences such as the cranial index. The former differentiates Caucasoids from Mongoloids while the latter does not.

One must exercize caution when generalizing from the features of populations within races to the races themselves. This mistake was made in the past, when e.g., it was believed that Caucasoids and Mongoloids were differentiated on the basis of the cranial index, yet now we know that this is not the case.

There are two reasons why this mistake persists. Practically, one is rarely exposed to the full range of variation within a race, and thus tends to generalize from the subset to the whole. For example, many people tended to identify light skin pigmentation as a main feature of Caucasoids which led to naming them as "whites", and yellowish pigmentation as a main feature of Mongoloids, yet there are millions of yellowish or dark Caucasoids and many northern Mongoloids who are paler than southern Caucasoid groups.

The second reason is more sinister, as people often want the identified differences to be racial in character, since this allows them to practice the sort of politically-motivated racial essentialism that has been out of vogue in anthropology for several decades. Nasal flatness, the presence of epicanthus, or the presence of Y-haplogroups have a racial significance, yet they are value-free, and hence cannot be politicized, unlike things like V/S ability or other useful features.

Getting back to the original quote, we know that Swedes are orthognathic and that this is typical Caucasoid feature. We do not know that Eskimos have a genetic endowment for a high V/S ability, and we should not infer that their high V/S performance reflects a Mongoloid specialty. Such a generalization would be akin to a group of Polynesians being exposed to a group of blond English soldiers and concluding that Europeans are generally blond.

Once many Mongoloid groups have been sampled, especially those who have not been exposed to the logographic systems and are reasonably thought to be representative of Mongoloid populations, we will be able to conclude whether high V/S performance is a racial feature of the Mongoloids.

Until enough evidence points in that direction, we must not add to Rushton-like laundry lists of differences, which have been shown to be suspect. A much healthier (and honest) attitude is to differentiate among features known to be of racial significance, like nasal projection, features known to be of no racial significance, like the cranial index, and features whose racial significance is uncertain, such as V/S ability.

(1) There is no a priori definition of "sufficiently"; sufficiently with present-day technology will suffice as a working definition.
(2) Since gene flow occurs between races, these are not necessary permanent; on the other hand it makes little practical sense to name recently admixed groups of varying ancestral proportions such as African Americans or Latin Americans as races.

January 14, 2005

Hominins represent a single lineage

A very important new paper deals with the problem of the taxonomic validity of various postulated species of hominins, i.e., of species of Hominidae related to humans, including our own genus, Homo, and its species, including Homo sapiens, the only extant hominin species.

Hominins have evolved from short, small-brained ancestors to tall, large-brained ones, and it is clear that humans of today are quite different from human-like creatures of millions of years ago. But, do these differences represent different lineages, or stages of a single evolving lineage?

The controversy between lumpers, who group different specimens into few species and splitters who name new species even on minute differences -considered of taxonomic significance, is nothing new, and the new paper supports an extreme "lumper" position, namely that all hominins represent a single evolving lineage, and hence its various "species" should not be acknowledged.

The authors test discover a clear temporal and geographical trend in the evolution of hominins, but they realize that the various specimens are not differentiated enough from each other to merit designation as distinct species. They could simply be stages of the evolution of a single lineage, snapshots separated in space and time of the evolution of a single species.

Of course this does not prove that hominins are a single species. But, it does show that statistically there does not exist enough evidence for postulating multiple different species; such species cannot be rejected, but the most parsimonious explanation at present is the single-lineage one.

HOMO - Journal of Comparative Human Biology
Volume 55, Issues 1-2 , 18 October 2004, Pages 21-37

Hominins are a single lineage: brain and body size variability does not reflect postulated taxonomic diversity of previous termhomininsnext term

M. Henneberg and C. de Miguel


Fossil previous termhomininnext term taxonomy is still debated, chiefly due to the fragmentary nature of fossils and the use of qualitative (subjective) morphological traits. A quantitative analysis of a complete database of previous termhomininnext term cranial capacities (CC, n=207) and body weight estimates (Wt, n=285), covering a period from 5.1 ma (millions of years) to 10 ka (thousands of years) shows no discontinuities through time or geographic latitude. Distributions of residuals of CC and Wt around regressions on date and latitude are continuous and do not differ significantly from normal. Thus, with respect to these characteristics, all previous termhomininsnext term appear to be a single gradually evolving lineage.


The rate of human evolutionary change

A commonly stated assumption about our genetic heritage is that we humans are basically quasi-identical to the hunter-gatherers of the Old Stone Age, and our differentiation from those is due to the acquisition of culture at an increasing rate since the beginning of the Neolithic.

This assumption is used to explain many of the ills of modern man, and to propose solutions, such as the Paleolithic diet. According to its adherents, human beings must adjust their environment and lifestyle to mimic aspects of the Paleolithic.

The main argument in favor of this idea is that the Paleolithic has lasted a lot longer than more recent geological ages. In other words, there has not been enough time to shake up our hunter-gatherer genes.

In some cases, e.g., those of as hunter-gatherer tribes who have recently made the transition to agriculture and settled life, there can be no doubt that this assumption is correct. However, the majority of human beings are descended from ancestors who adopted food producing subsistence methods thousands of years ago; a short time in geological terms, but measuring in hundreds of generations.

The rate of evolutionary change is not a constant. It is a function of the rate of mutation, which creates new genetic variants (1) and of selection intensity which shifts allele frequencies around. The latter is a function of the rate at which the environment changes, and this depends on both the rate of cultural and ecological change (2), but also on the rate of migration, since migration brings people into new environments for which they are not yet adapted.

Clearly, the rate of cultural change has been significant since the Paleolithic, and so must have been the rate of migration, judging and extrapolating from the historical period. Hence, it is not unlikely that we may have evolved quite a bit since our hunter-gatherer ancestors, and indeed, changes in body and head form, documented for recent as well as older human groups should find parallels in the evolution of other human attributes, both behavioral and physical.

A case in point is the issue of racial differences, where it is often claimed that human races differ from each other due to their exposure to "hard winters" or "tropical climates" during the Paleolithic age. This can of course be substantiated for some primary racial characters which survive in the record, but as Vincent Sarich points out, human racial variation may be of much more recent origin, and is certainly not as marked in older periods. And, of course, in many cases it may not be genetic in origin, especially in behavior qualities which are much more malleable than physical ones.

A case can be made that human beings are maladapted for modern living conditions, and that this results in selection, e.g., on the road, or in the bedroom. But, this should lead us into thinking that perhaps the modern lifestyle -as opposed to the premodern, not the Paleolithic one- is to blame.

This idea is also supported by a review of the paleoanthropological record which does indeed show an increase in disease, decrease in stature, etc. after the Neolithic transition, but also shows a marked in this and other attributes after the initial cultural shock, which continued -with fluctuations- until present times, with modern humans in developed nations being taller than all preceding ones (3).

It is not now that our Paleolithic genomes find themselves in a strange new world for which they are poorly designed; that crisis had already occurred thousands of years in the past. We would be better off thinking about the easing the ills of our present transformation into industrial and post-industrial beings, instead of idealizing the Paleolithic past, or joining chimerical battles against civilization.

(1) And which can be expected to be a constant in most cases, but see this post on the evolution of evolvability for exceptions to this rule.
(2) Until the modern age, man was probably not able to effect planetary scale ecological change, but he did create significant local changes, by e.g., clearing forests or building edifices; it is the immediate environment, which is most man-made and which most affects man.
(3) I have dealt with the arguments of those bemoaning the rise of degenerative disease rates elsewhere.

mtDNA in Southeastern Europe

Coll Antropol. 2004 Jun;28(1):193-8.

Frequencies of mtDNA haplogroups in southeastern Europe--Croatians, Bosnians and Herzegovinians, Serbians, Macedonians and Macedonian Romani.

Cvjetan S et al.

Mitochondrial DNA polymorphisms were analyzed in of 1,610 randomly chosen adult men from 11 different regions from southeastern Europe (Croatians, Bosnians and Herzegovinians, Serbians, Macedonians and Macedonian Romani). MtDNA HVS-I region together with RFLP sites diagnostic for main Euroasian and African mtDNA haplogroups were typed to determine haplogroup frequency distribution. The most frequent haplogroup in studied populations was H with the exception of Macedonian Romani among whom the most frequent were South Asian (Indian) specific variants of haplogroup M. The multidimensional scaling plot showed two clusters of populations and two outliers (Macedonian Romani and the most distant from mainland Croatian island of Korcula). The first cluster was formed by populations from three Croatian islands (Hvar, Krk and Brac) and the second cluster was formed by Macedonians, Serbians, Croatians from mainland and coast, Herzegovinians, Bosnians, Slovenians, Poles and Russians. The present analysis does not address a precise evaluation of phylogenetic relations of studied populations although some conclusions about historical migrations could be noticed. More extended conclusions will be possible after deeper phylogenetic and statistical analyses.


Siberian mtDNA and Native American Origins

Ann Hum Genet. 2005 Jan;69(Pt 1):67-89.

Mitochondrial DNA diversity in indigenous populations of the southern extent of siberia, and the origins of native american haplogroups.

Starikovskaya EB et al.

Summary In search of the ancestors of Native American mitochondrial DNA (mtDNA) haplogroups, we analyzed the mtDNA of 531 individuals from nine indigenous populations in Siberia. All mtDNAs were subjected to high-resolution RFLP analysis, sequencing of the control-region hypervariable segment I (HVS-I), and surveyed for additional polymorphic markers in the coding region. Furthermore, the mtDNAs selected according to haplogroup/subhaplogroup status were completely sequenced. Phylogenetic analyses of the resulting data, combined with those from previously published Siberian arctic and sub-arctic populations, revealed that remnants of the ancient Siberian gene pool are still evident in Siberian populations, suggesting that the founding haplotypes of the Native American A-D branches originated in different parts of Siberia. Thus, lineage A complete sequences revealed in the Mansi of the Lower Ob and the Ket of the Lower Yenisei belong to A1, suggesting that A1 mtDNAs occasionally found in the remnants of hunting-gathering populations of northwestern and northern Siberia belonged to a common gene pool of the Siberian progenitors of Paleoindians. Moreover, lineage B1, which is the most closely related to the American B2, occurred in the Tubalar and Tuvan inhabiting the territory between the upper reaches of the Ob River in the west, to the Upper Yenisei region in the east. Finally, the sequence variants of haplogroups C and D, which are most similar to Native American C1 and D1, were detected in the Ulchi of the Lower Amur. Overall, our data suggest that the immediate ancestors of the Siberian/Beringian migrants who gave rise to ancient (pre-Clovis) Paleoindians have a common origin with aboriginal people of the area now designated the Altai-Sayan Upland, as well as the Lower Amur/Sea of Okhotsk region.


January 08, 2005

Ancient Mesopotamian Accounting and Human Cognitive Evolution

Abstract: Recent archaeological evidence supports the claim that the first system of writing and the first use of abstract numerical representation evolved from the clay token accounting system of ancient Mesopotamia. Writing and other abstract symbol systems have subsequently transformed human cognitive capacities within only few millennia, a time period too short for any substantial changes in our biologically-evolved brains. This paper uses Merlin Donald's theory of human cognitive and cultural evolution [in Origins of the Modern Mind; 1991] to identify the role played by ancient accounting in these evolutionary processes. Specifically, it is argued that this early accounting system paved the way for writing by instigating revolutionary cognitive structures for processing visual/ symbolic artifacts and establishing a primitive but very powerful form of external memory (external to the brain). The paper also explores the role that accounting systems continue to play in the provision of "cognitive scaffolding" with respect to our organizational and institutional environments, and provides a cursory overview of the pioneering developments of ancient Mesopotamien accounting in this regard.


January 03, 2005

Out-of-town shopping malls 'were pioneered by rich Romans'

By Richard Savill
(Filed: 28/12/2004)

The luxury housing estate and out-of-town shopping centre may need to be added to the long list of what the Romans did for Britain.

Work in Bath suggests that rich Romans were so keen to live close to city centre attractions that they abandoned the empire's traditional habit of building lavish villas in the countryside, well away from the neighbours and commerce within the city walls.

Full Story (Telegraph)

Forgers 'tried to rewrite biblical history'

Conal Urquhart in Jerusalem
Friday December 31, 2004
The Guardian

Hundreds of biblical artefacts in museums all over the world could be fakes, it has emerged after Israeli investigators uncovered what they claim is a sophisticated forgery ring.

Full Story (Guardian)

Ancient tsunamis

In an older post (Thera Eruption Revisited) I linked to some information about ancient tsunamis in the Aegean and their role in shaping historical events in the region.

January 02, 2005

The World of Alexander Was Rich and Beautiful Even Before the Movies

Glaring misinformation in an otherwise informative NY Times article about Alexander the Great.
"Philip II hired Aristotle to tutor Alexander at age 14 in Greek, Hebrew, Babylonian and Latin, rhetoric and justice."

Of course, Aristotle did not tutor Alexander in foreign languages, nor were foreign languages ever part of a Greek education, let alone Latin and Hebrew which were almost completely unknown, together with the respective peoples, the Romans and the Hebrews, for centuries after Alexander's time.