Ancient subclades of mtDNA haplogroup M in northern island Melanesia

Proc Natl Acad Sci USA (published online)

Ancient mitochondrial M haplogroups identified in the Southwest Pacific

D. Andrew Merriwether et al.

Based on whole mtDNA sequencing of 14 samples from Northern Island Melanesia, we characterize three formerly unresolved branches of macrohaplogroup M that we call haplogroups M27, M28, and M29. Our 1,399 mtDNA control region sequences and a literature search indicate these haplogroups have extremely limited geographical distributions. Their coding region variation suggests diversification times older than the estimated date for the initial settlement of Northern Island Melanesia. This finding indicates that they were among the earliest mtDNA variants to appear in these islands or in the ancient continent of Sahul. These haplogroups from Northern Island Melanesia extend the existing schema for macrohaplogroup M, with many independent branches distributed across Asia, East Africa, Australia, and Near Oceania.

Link

Famous DNA

A compendium of published DNA results for famous people.

Serendipity

I had to take a picture...

Calabrians as Greek descenants

Before the Roman conquest, and for a long time afterwards, Calabria was Greek speaking. Greek speakers were descended from the Ancient Greek colonists, but also from medieval Greek settlements during the Byzantine era. Greek was widely spoken in very recent times, and even today there are few Greek-speaking survivors, speaking Griko, an Italian dialect of the Greek language.

Most of the Greeks of Calabrians are now Italianized, but it is very likely that due to the mostly rural conditions of the region, the absence of significant foreign settlements and the late survival of Greek, that they may be largely descended from the medieval Greeks of the region, and even before that, the Greeks of mainland Greece. Moreover, since Greek settlement in Calabria largely pre-dates the descents of Slavs and Albanians in Greece, we may be able to (roughly) determine the extent of the impact of these elements in the modern Greek population.

Two papers in the literature [1, 2] report on the frequency of Y-chromosome haplogroups in the population of Calabira. [1] reports data labeled as "Calabrians", and [2] reports data on the population of Reggio and Paola. The cumulative sample has a size of N=87. Frequency data are shown below, with Greek frequency data also shown for comparison from [3]



Of course, frequencies may be modified by random genetic drift, and Calabrians are not descended from all Greek regions, but we can still make some general observations about their commonalities and differences.

In both Calabrians and Greeks, haplogroup J2 appears to be very frequent, and haplogroup E3b is also very frequent. It appears very likely that these two haplogroups were represented in ancient populations.

Calabrians have a higher frequency of haplogroup R1b. This haplogroup originated in Asia, but its most recent expansions mark the movements of people from Iberia and Anatolia after the Last Glacial Maximum. Italians have a generally higher frequency of this haplogroup, and hence it appears likely that R1b in Calabrians may partially represent the contribution of native Italians to their gene pool.

Calabrians also have a higher frequency of haplogroup J1. This haplogroup originated in the southern part of the Fertile Crescent, and is often (but not exclusively) found in modern Semitic speakers such as Jews and Arabs. This may represent remnants of Near Eastern people during post-Roman times, even though its earlier arrival cannot be entirely excluded.

Finally, a striking feature of the frequency table is the paucity of R1a and I lineages in Calabrians. R1a originated in the Ukraine and spread after the Last Glacial Maximum, but more recently with Slavic speakers. I1b originated in the Balkans and spread during late Paleolithic and early Neolithic and subsequent times.

It is fairly interesting that in a study which included a Cypriot sample [4], only 2% of Cypriots carried haplogroup R1a chromosomes. Cypriots are also a population which separated from mainland Greeks before the medieval period. The frequency of haplogroup I chromosomes is not available for Cypriots.

Also, of interest is the fact that in regions of Anatolia [5] inhabited by Greek speakers until recently, and in which the native population may be assumed to be descended partially from Islamized Greeks, the frequencies of haplogroups R1a and I are also low. In the Aegean region (8) they are 3.3% and 6.7%, and in the eastern Black Sea region (3) where Muslim Greek speakers still exist, they are 4.8% and 2.4%. Moreover in Anatolia R1a1 frequency is correlated with longitude, declining towards Greece. R1a frequency also decreases from north to south in the Balkans [6].

In conclusion, this small survey provides some evidence against the notion that Y-haplogroups I and especially R1a were substantially represented in ancient Greeks. The relative absence of these haplogroups in populations thought to be partially descended from Greeks, in addition to the decrease in frequency of R1a both north-to-south in the Balkans and east-to-west in Anatolia are the main reasons for this observation.

Naturally, I doubt that we can statistically exclude the presence of either haplogroup -at some low frequency- in ancient Greeks using these relatively small samples, but at least we have some indication that they probably did not form a substantial part of their patrilineal descent.

Update

In a larger sample of Calabrians, the haplogroup I frequency is 5.4%, and that in Sicilians is 8.8% [7]. Haplogroup I lineages in the Balkans and Italy are divided mainly into I1a, I1b, and I*(xI1a, I1b).

Update 2

I also came across this interesting paper (Coll Antropol. 2001 Jun;25(1):189-93.) which further substantiates the idea of the genetic isolation of Reggio Calabria, listed as REG above:

Surnames of grandparents were collected from children in the primary schools of the Albanian-Italian, Croat-Italian, and Greek-Italian villages. The coefficients of relationships by isonymy show almost no relationship with ethnicity. Ethnolinguistic minorities of Southern Italy and Sicily are geographically subdivided in two main clusters: the first cluster comprises the Albanian, Croat, and Greek communities of the Adriatic area; and the second cluster comprises the Albanian communities of the Ionian, Thirrenian and Sicilian area. The Greeks of Reggio Calabria Province are completely separated from the other communities.

It would be extremely interesting to see a study that focused only on Greek speakers of Reggio Calabria.

References

[1] O. Semino et al., "The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective", Science, 290(5494): 1155-1159.
[2] F. Di Giacomo et al., "Clinal patterns of human Y chromosomal diversity in continental Italy and Greece are dominated by drift and founder effects." Molecular Phylogenetics and Evolution, 28(3): 387-395.
[3] C. Flores et al., "Isolates in a corridor of migrations: a high-resolution analysis of Y-chromosome variation in Jordan", Journal of Human Genetics (in press).
[4] Z. Rosser et al., "Y-Chromosomal Diversity in Europe Is Clinal and Influenced Primarily by Geography, Rather than by Language", American Journal of Human Genetics, 67(6): 1526-1543.
[5] C. Cinnioglu et al., "Excavating Y-chromosome haplotype strata in Anatolia", Human Genetics 114(2): 127–148.
[6] M. Pericic et al., "High-Resolution Phylogenetic Analysis of Southeastern Europe (SEE) Traces Major Episodes of Paternal Gene Flow Among Slavic Populations", Molecular Biology and Evolution (in press).
[7] S. Rootsi et al., "Phylogeography of Y-chromosome haplogroup I reveals distinct domains of prehistoric gene flow in europe", American Journal of Human Genetics 75(1): 128-37.

Jordanian Y chromosomes

New paper on Y chromosomes in Jordan, showing how the smoothness of macro-scale genetic variation often finds significant deviations at the more micro-scale level. It is imperative that such studies be conducted in more Near Eastern populations so that we can understand better the origin and evolution of Caucasoids in the region.

The Y-haplogroup frequency table is also interesting because it lists frequency of haplogroups in several populations. Greek frequency data are compiled from the literature and appear in the final column, and allow us to quantify the non-Caucasoid admixture in Greeks (0.2% Sub-Saharan haplogroup A and 1.3% Asian haplogroup C; total 1.5%). Haplogroup B (0.2%) reported in Greeks in the table is an error (see update below).



Update:

I contacted the authors of the study, pointing out that haplogroup B did not occur in the studies used to obtain results for the Greek population, and they have confirmed that this is the case:

Thank you for your careful revision of our article about Y chromosome in Jordan. Yes, you are right. There is a mistake in table 1. The greek B haplotypes are in fact indeterminated Y*.
We apologize for this error.
Sincerely yours,

A.M. González
e-mail: amglez@ull.es

Journal of Human Genetics (Online early)

Isolates in a corridor of migrations: a high-resolution analysis of Y-chromosome variation in Jordan

Carlos Flores et al.

Abstract A high-resolution, Y-chromosome analysis using 46 binary markers has been carried out in two Jordan populations, one from the metropolitan area of Amman and the other from the Dead Sea, an area geographically isolated. Comparisons with neighboring populations showed that whereas the sample from Amman did not significantly differ from their Levantine neighbors, the Dead Sea sample clearly behaved as a genetic outlier in the region. Its high R1*-M173 frequency (40%) has until now only been found in northern Cameroonian samples. This contrasts with the comparatively low presence of J representatives (9%), which is the modal clade in Middle Eastern populations, including Amman. The Dead Sea sample also showed a high presence of E3b3a-M34 lineages (31%), which is only comparable to that found in Ethiopians. Although ancient and recent ties with sub-Saharan and eastern Africans cannot be discarded, it seems that isolation, strong drift, and/or founder effects are responsible for the anomalous Y-chromosome pool of this population. These results demonstrate that, at a fine scale, the smooth, continental clines detected for several Y-chromosome markers are often disrupted by genetically divergent populations.

Link

Population growth or selective sweep (Part II)

In Population growth or selective sweep I reported on a recent Current Anthropology article which addressed the issue of whether current human mtDNA variation is best interpreted as a signal of a population expansion from a small founder population or the successful remainder of a selective sweep.

John Hawks, who advocates the selection hypothesis has responded to the article with a blog post titled Selection, nuclear genetic variation, and mtDNA. This should highlight the controversial nature of the subject, and the fact that we are far from reaching a consensus.

Personally, I have always been somewhat skeptical of the idea that much can be learned about our most ancient past from genetic variation in modern populations. Modern populations are the result of so many evolutionary processes involving selection, drift, and intermixture, both in Paleolithic and most recent (and more tumultuous) Neolithic-historical times.

Genetic models seem to be fairly inadequate to capture the richness of human prehistory, as they more often than not tend to be fairly simple, with a lot of "best guesses" given to critical parameters. This has led to at least one palaeoanthropologist (Erik Trinkaus) proposing that we should do away with them altogether:

The analyses of extant human molecular data generally have little biologically relevant statistical power (whatever probability values their statistical computations may generate); most analyses use analytical algorithms whose biological assumptions and appropriateness are unstated, untested, and frequently untestable; many assume demographic stability over the past 50,000–200,000 years (see above); most consider the human populational dynamics of the past 30 millennia to have been trivial; many use distance statistics and graphic techniques (such as dendrograms), which deny the reticulate nature of human population evolution (hence assuming replacement); a number of them invoke molecular clocks whose reliability and precision within the time period of concern is undemonstrated and/or whose calibration (based on the fossil record) is simply wrong; and many employ living human samples of opportunity when those samples have biases relative
to the issue of modern human origins. And finally, all of them have a real-time depth of perhaps a century, and the interpretations based on those data are dependent on their analytical assumptions. This last point is evident in the large number of articles concerned more with the analytical techniques and their assumptions than with interpreting the available data.

It would be heartening to think that things are better in palaeoanthropology, but non-genetic factors affecting morphology, significant dating uncertainties, unavailability of key fossils for study, as well as the largely spotty record (a few skulls over tens of thousands of years) probably make that field as unreliable as genetics.

Perhaps we don't yet have either the data or the tools to make authoritative inferences about our origins quite yet, but the process is certainly interesting!

Portuguese Y chromosomes

A new paper in Annals of Human Genetics studies Portuguese Y chromosomal distribution from several locations around the country, demonstrating relative homogeneity, with an exception of a single outlier population.

Annals of Human Genetics (online early)

Micro-Phylogeographic and Demographic History of Portuguese Male Lineages

Sandra Beleza et al.

Abstract

The clinal pattern observed for the distribution of Y-chromosome lineages in Europe is not always reflected at a geographically smaller scale. Six hundred and sixty-three male samples from the 18 administrative districts of Portugal were typed for 25 Y-chromosome biallelic and 15 microsatellite markers, in order to assess the degree of substructuring of male lineage distribution. Haplogroup frequency distributions, Analysis of Molecular Variance (AMOVA) and genetic distance analyses at both Y-SNP and Y-STR levels revealed a general genetic homogeneity of Portuguese sub-populations. The traditional division of the country in north, central and south, which is usually considered in studies addressing questions of the genetic variation distribution in Portugal, was not reflected in the Y-haplotype distribution. Instead, just one sub-region (Alentejo) stood out due to the presence of high diversity levels and a higher number of different lineages, at higher frequencies than in other regions. These results are reconciled with the historical evidence available, assuming that from prehistorical times down to the end of the medieval period this region harboured the most diverse groups of people and, because of economic depression, remained relatively isolated from recent homogenisation movements. The finding of a broadly homogeneous background for the Portuguese population has vast repercussions in forensic, epidemiological and association studies.

Link

Heath-Carter somatotyping method

Somatotyping, pioneered by William Sheldon in the 1940s is the description of body type based on three components of endomorphy ("fatness"), mesomorphy ("muscularity"), and ectomorphy ("thinness"). A somatotype is usually given as a composite of three numbers, e.g., 711, where each number demonstrates the strength of one of the three components. The most widely used somatotyping method today is that of Heath and Carter. You can read an instruction manual for somatotyping online in pdf form.

Black Indians

Great article from Wired on the descendants of black freedmen who seek membership in Native American tribes, in part due to the economic gain of membership, with an emphasis on genetic testing to determine whether or not they have Native American ancestry. Of course, as stated in the article by Dr. Tony Frudakis, it is possible for a Greek or Pakistani to show a high proportion of Native American "heritage". Anomalous results such as these would render this avenue of testing almost useless for the purpose of establishing Amerindian descent.

Population growth or selective sweep?

A new article in Current Anthropology revisits the issue of the contribution of Neandertals to the modern human gene pool. Two issues are considered: first, is Neandertal mtDNA really that distinctive from modern human mtDNA? second, is the relative homogeneity of modern human DNA the result of a selective sweep or of rapid population growth. With regard to the first question, the authors have this to say:

Is Neandertal mtDNA actually so distinctive? One basic assumption of our simulations is that Neandertal mtDNA lineages are distinct relative to the variation found in living humans. The initial studies by the Neandertal mtDNA sequencing groups found that living human and Neandertal sequences differed substantially from each other (Krings et al. 1997, 2000; Ovchinnikov et al. 2000; Schmitz et al. 2002). A reanalysis by Gutiérrez, Sánchez, and Marín (2002) did conclude that Neandertal mtDNA was within the range of living human variation, but this result may have been an artifact of bootstrapping sequences to generate neighbor-joining trees with a rapidly evolving genetic system such as mtDNA, in which the ratio of noisy (i.e., highly inconsistent or homoplastic) to stable sites is high. This approach may create many neighbor-joining trees whose topology is determined primarily by inconsistent sites, so by chance some living humans and Neandertals sometimes group together to the exclusion of other living humans (A. Knight, personal communication). In contrast, Caramelli et al. (2003) found no overlap between modern human and Neandertal mtDNA sequences using multidimensional scaling, and along with living human sequences this analysis included possible (because contamination cannot be ruled out) ancient modern human sequences from Paglicci 12 and 25, Italy (P12 and P25), and Lake Mungo 3, Australia (LM3). Knight (2003) used a phylogenetic approach to Neandertal mtDNA and found four highly consistent synapomorphies that unite Neandertals to the exclusion of all living humans and four highly consistent synapomorphies that unite all living humans to the exclusion of Neandertals (a total of eight highly consistent sites that define the two clades, including an insertion, which is a very rare event). These eight sites are consistent across thousands of living humans and are known to have low mutation rates. Additionally, for preserved sites, the mtDNA sequences from P12 and P25, LM3, and the nuclear mitochondrial insert (thought to have diverged shortly before the oldest coalescence of living human mtDNA sequences [Zischler et al. 1995]) have none of the Neandertal synapomorphies while possessing all of the diagnostic derived sites of living human sequences (A. Knight, personal communication). Recently, mtDNA fragments were extracted from four additional Neandertal and five early modern human fossils that had similar biomolecular preservation. All the Neandertals and none of the ancient modern humans yielded sequences similar to previous Neandertal sequences (Cooper, Drummond, and Willerslev 2004, Serre et al. 2004). It appears, therefore, that the assumption that Neandertal mtDNA is distinct from that of living humans is reasonable.

The second question is quite interesting. The fact that modern human mtDNA is similar to each other and differs from Neandertal mtDNA can be explained in either of two ways: (i) modern humans and Neandertals were two separate lineages evolving on their own, or (ii) modern human mtDNA is the product of selection, i.e., modern humans possess only those mtDNA types that have survived a selective sweep. The implication of this is that formerly, humans had much different mtDNA types which no longer exist because they were culled by natural selection.

The "rapid population growth" model suggests that the relative homogeneity of human mtDNA is the result of the fact that until a few tens of thousands years ago, humans formed a small population, with relatively little mtDNA diversity. Hence, our current mtDNA diversity is due to the fact that even though we now number in the billions, we are still ultimately descended from a small group of individuals in the not-so-distant past. This model contrasts with the "selective sweep" model, in which our genetic diversity is a remnant of past genetic diversity over a long period of time, the remnant that has survived the selective sweep. The authors review the evidence, and suggest that the "rapid population growth" model explains the data better than the alternative:

The significance of ancient Neandertal mtDNA for resolving the fate of Neandertals increases greatly when considered in light of models for modern human origins derived from archaeology. On the basis of mtDNA, if Neandertals survived late in Europe, their per generation contribution to early modern human populations must have been fairly small (<0.2%).Archaeology tends to support the rapid population growth model (Klein et al. 2004, Stiner et al. 1999), as does living human mtDNA (Excoffier and Schneider 1999, Ingman et al. 2000). Other genetic regions are more equivocal about the timing and magnitude of population growth (Harpending and Rogers 2000, Ptak and Przeworski 2002, Wall and Przeworski 2000), but recent studies of SNPs and microsatellites appear to be reaching a consensus consistent with the results for mtDNA (Marth et al. 2004, Zhivotovsky, Rosenberg, and Feldman 2003). Our results stress the importance of fully integrating archaeological, fossil, and genetic evidence in investigations of modern human origins.

This earlier post on human-Neanderthal admixture, estimated at less than 0.1% is also of interest.

CURRENT ANTHROPOLOGY Volume 46, Number 4, August-October 2005

Ancient DNA, Late Neandertal Survival, and Modern-Human Neandertal Genetic Admixture

Timothy D. Weaver and Charles C. Roseman

(No abstract)

Link

Racial analysis calculator (female version)

I have created a female version of the Racial Analysis Calculator which can be found here. This works by first converting raw measurements into "male-equivalents" and then checking these against the previously identified metric types. The accuracy will depend on (i) the goodness of the conversion process which was based on regression on male-female population data that was available to me, and also of course (ii) the accuracy of the raw measurements. As before, this works only for Caucasoids. If you are male, then you can still access the male version here.

I'm always interested in hearing comments from people who've used the various calculator tools which can be found at the Anthropological Research Page, so leave a comment here or post at the Dodona forum. In many cases errors in measurement technique render the results meaningless, but if you persevere and obtain correct measurements, then (unless you have a particularly oddly shaped head) you should get some interesting results.

Haplogroup frequency correlations in Southeastern Europe

I have decided to investigate the correlations between haplogroup frequencies in southeastern Europe and some neighboring populations. Currently, I have collected frequency data for the main haplogroups found in the region (E3b, J2, I, R1a, R1b) for 16 populations. Most 3-letter codes should be recognizable, but KAL=Kosovo Albanians, SMA=Slav Macedonians, CAL=Calabrians. I should also note that the frequency of haplogroup I in Bulgarians is interpolated from frequencies in Romanians, Greeks, Slav Macedonians and Serbians, as it was missing in the original article. Conclusions about Bulgarians are especially weak, due to this reason, and also the small original sample (N=24).

I began by calculating the correlation matrix in my sample.



A few features strike the eye:

• The negative correlation between haplogroup R1 and haplogroups E3b, J2, and R1b
• The negative correlation between haplogroup I and haplogroups J2 and R1b
• The positive correlation between haplogroup J2 and haplogroup R1b
• The absence of a substantial correlation between "Neolithic" haplogroups J2 and E3b

As the next analysis will make clear, variation is explained by the presence of two main groupings: a "continental" group comprising of Slavic speakers and a "coastal" group comprising of all others.

The absence of a correlation between J2 and E3b is significant, because it hints that these haplogroups did not diffuse as a result of a single process. The eastern-most populations of our sample, but also the two Italian populations show a higher J2/E3b ratio compared to the "continental" populations.

The second analysis is a dendrogram using Euclidean distance of the normalized haplogroup frequencies. As is apparent, this way of representing the frequency data results in a separation of the two main clusters.



Finally, a principal components analysis is shown in the following plot. The first two components summarize about 77% of the variance.



We observe the two main "contrasts" in the data between "coastal" J2/R1b and "continental" I1b and between "Neolithic" E3b and "Slavic" R1a (*)

Several conclusions can be drawn.

• The spread of the Neolithic economy into continental Europe involved E3b bearers in a riverine expansion whose northern expression is associated with the Linearbandkeramik. This does not mean that E3b was the only haplogroup associated with these early European farmers, only that it definitely seems to correlate better with this movement compared to the other Neolithic haplogroup (J2).
• The early diffusion of E3b occurred over a haplogroup I Paleolithic background. It is likely that as groups moved northward the frequency of haplogroup E3b abated, and this is in fact shown in the frequency distribution. This movement is probably associated with the narrow-faced Danubian Mediterranean racial types.
• This native European population later received an influx of R1a speakers; the frequency of R1a is correlated with latitude. This led to a decrease of the native component in favor of the foreign R1a component (*)
• The frequency of haplogroup J2 was established by three movements: (i) the initial arrival of J2 from Asia Minor; this did not significantly penetrate into the Western Balkans; (ii) the initial dispersal of J2 into Italy and further west, and around the Black Sea in pre-Greek times, which may be associated with the arrival of gracile Mediterranean racial types into the Ukraine; (iii) the latter dispersal of additional J2 as a result of Greek colonization.

It is imperative that the fine-level phylogeography of haplogroup J2 be resolved. The high frequency of this haplogroup around the Black Sea compared to the western Balkans is highly suggestive of Greek colonization, as it is well known that Greek colonization of the Black Sea was much more intensive than Greek activity in the Adriatic. However, archaeological evidence also shows the northward diffusion of agriculturalists in Thrace to Romania, culminating in the Tripoljie culture and its steppe offshoots. We must be able to distinguish between this earlier movement and the later maritime arrival of the Greeks.

The critical question would be: what fraction of J2 lineages in the Ukraine can be explained as the result of ancient and recent Greek settlement in the Crimea, and what fraction predates the Greeks?

(*) We should note that these are rough correspondences. If the theory of riverine diffusion of haplogroup E3b into Central and Northern Europe is correct, then it is likely that E3b existed in a small frequency in Proto-Slavs; conversely, R1a diffused after the LGM before its most recent diffusion associated perhaps with Slavic languages.

Update: A reader alerts me to a different study which listed the Hungarian R1a frequency as substantially lower than the one used here (Semino et al. 2000). Unfortunately, that study did not list frequencies of all haplogroups needed for comparison, so it could not be used directly. If the frequency of R1a=20.4% is used, then a slightly different clustering is obtained.

Affinities of Early Upper Paleolithic Europeans

Some interesting information about the affinities of Early Upper Paleolithic (EUP) European crania. EUP Europeans were generalized Caucasoids, and are remarkably similar to modern Europeans despite the tens of thousands of years that have intervened and the substantial replacement of the original EUP population by later migrations evidenced in European mtDNA.

Some of the discordance Van Vark et al. see between genetic and morphometric results may be attributable to their methodological choices. It is clear that the affiliation expressed by a given skull is not independent of the number of measurements taken from it. From their Table 3, it is evident that those skulls expressing Norse affinity are the most complete and have the highest number of measurements ( = 50.8), while those expressing affinity to African populations (Bushman or Zulu) are the most incomplete, averaging just 16.8 measurements per skull. Use of highly incomplete or reconstructed crania may not yield a good estimate of their morphometric affinities. When one considers only those crania with 40 or more measurements, a majority express European affinity.

To examine this idea further, we use the eight Upper Paleolithic crania available from the test series of Howells ([1995]), all of which are complete. Our analysis of these eight, based on 55 measurements, is presented in Table 1. Using raw measurements, 6 of 8 express an affinity to Norse, and with the shape variables of Darroch and Mosimann ([1985]), 5 of 8 express a similarity to Norse. Using shape variables reduces the Mahalanobis distance, substantially in some cases. Typicality probabilities (Wilson, [1981]), particularly for the shape variables, show the crania to be fairly typical of recent populations. The results presented in Table 1 are consistent with the idea that Upper Paleolithic crania are, for the most part, larger and more generalized versions of recent Europeans. Howells ([1995]) reached a similar conclusion with respect to European Mesolithic crania.



...

Next, let us examine the issue of whether the EUP situation can be regarded as parallel to the Native American one. There are some obvious differences, principal among them the time frame. The European crania used by Van Vark et al. span 26,000 years, as against our North American sample that spans about 2,400 years. Their EUP series dates from 37,000 BP to about 9,000 BP, as against a maximum time frame for our North American sample of 9,400-7,000 BP (Jantz and Owsley, [2001]). The Upper Paleolithic time span is significantly older and more than 10 times longer than the American one, yet the EUP crania are not correspondingly further removed from the contemporary population. Given that European fossil crania are separated from their supposed descendants by greater temporal distance than is the case in America, one could easily accept that European fossil crania might be more loosely connected to the modern population. Yet, we observe just the opposite. The data in Van Vark et al. demonstrate a higher degree of affiliation with the supposed descendent modern population (16/35 = 46%) than we found in the American situation (1/11 = 9%).

American Journal of Physical Anthropology
Volume 121, Issue 2, Pages 185-188

Reply to Van Vark et al.: Is European Upper Paleolithic cranial morphology a useful analogy for early Americans?

Richard L. Jantz, Douglas W. Owsley

No abstract

Link

The Indian Genome Variation database

Indian scientists have announced in Human Genetics the launch of a new program to understand genetic variation within the diverse and fragmented Indian population. This exciting new project should help us understand the origin of about 1/6 of modern humanity, in addition to important medical applications.

The following two maps of the distribution of morphological types and linguistic groups in India are a broad reflection of the cultural and biological diversity of the country.




The Indian Genome Variation database (IGVdb): a project overview

The Indian Genome Variation Consortium

Abstract

Indian population, comprising of more than a billion people, consists of 4693 communities with several thousands of endogamous groups, 325 functioning languages and 25 scripts. To address the questions related to ethnic diversity, migrations, founder populations, predisposition to complex disorders or pharmacogenomics, one needs to understand the diversity and relatedness at the genetic level in such a diverse population. In this backdrop, six constituent laboratories of the Council of Scientific and Industrial Research (CSIR), with funding from the Government of India, initiated a network program on predictive medicine using repeats and single nucleotide polymorphisms. The Indian Genome Variation (IGV) consortium aims to provide data on validated SNPs and repeats, both novel and reported, along with gene duplications, in over a thousand genes, in 15,000 individuals drawn from Indian subpopulations. These genes have been selected on the basis of their relevance as functional and positional candidates in many common diseases including genes relevant to pharmacogenomics. This is the first large-scale comprehensive study of the structure of the Indian population with wide-reaching implications. A comprehensive platform for Indian Genome Variation (IGV) data management, analysis and creation of IGVdb portal has also been developed. The samples are being collected following ethical guidelines of Indian Council of Medical Research (ICMR) and Department of Biotechnology (DBT), India. This paper reveals the structure of the IGV project highlighting its various aspects like genesis, objectives, strategies for selection of genes, identification of the Indian subpopulations, collection of samples and discovery and validation of genetic markers, data analysis and monitoring as well as the project’s data release policy.

Link

Sex differences in progressive matrices

A new article by Paul Irwing and Richard Lynn suggests that men score approximately 4.6 IQ points higher than women in the Progressive Matrices test. From the article:

It has frequently been asserted that there is no sex difference in average general intelligence but that the variance is greater in males. In this paper we examine these two propositions by a meta-analysis of studies of sex differences on the Progressive Matrices among university students. We find that both are incorrect.

...

There are five points of interest in the results. First, the present meta-analysis of sex differences on the Progressive Matrices among university students showing that men obtain significantly higher means than females confirms the results of our meta-analysis of sex differences on this test among general population samples (Lynn & Irwing, 2004). The magnitude of the male advantage found in the present study lies between 3.3 and 5 IQ points, depending on various assumptions. Arguably the best estimate of the advantage of men to be derived from the present study is .31d, based on all the studies and shown in the first row of Table 2. This is the equivalent of 4.6 IQ points and is closely similar to the 5 IQ points found in the meta-analyses of general population samples previously reported.

...

Second, the Progressive Matrices is widely regarded as one of the best tests of Spearman’s g, the general factor underlying all cognitive abilities... Now that we have established that men obtain higher means than women on the Progressive Matrices, it follows that men have higher general intelligence or g.

...

Third, the finding that males have a higher mean reasoning ability than females raises the question of how this can be explained... Hence, the larger average brain size of men may theoretically give men an advantage in intelligence arising from a larger average brain size of 0.78 multiplied by 0.40, giving a theoretical male advantage of .31d = 4.7 IQ points. This is a close fit to the sex difference obtained empirically in our previous meta-analysis of the sex difference of 5 IQ points on the Progressive Matrices in general population samples, and of 4.6 IQ points on the Progressive Matrices, in the present meta-analysis of the sex difference in college student samples.

...

Fourth, a number of those who have asserted that there is no sex difference in intelligence have qualified their position by writing that there is no sex difference ‘worth speaking of’ Mackintosh (1996, p. 567), ‘only a very small advantage of boys and men’ (Geary, 1998, p. 310), ‘ no practical differences in the scores obtained by males and females’ (Halpern, 2000, p. 90), ‘no meaningful sex differences’ (Lippa, 2002), and ‘negligible differences’ (Jorm et al., 2004, p. 7)... These different proportions of men and women with high IQs are clearly ‘worth speaking of’ and may go some way to explaining the greater numbers of men achieving distinctions of various kinds for which a high IQ is required, such as chess grandmasters, Fields medallists for mathematics, Nobel prize winners and the like.

...

Fifth, the finding in this meta-analysis that there is no sex difference in variance on the Advanced Progressive Matrices and that females show greater variance on the Standard Progressive Matrices is also contrary to the frequently made contention, documented in the introduction, that the variance of intelligence is greater among males. This result should be generalizable to the general population of normal intelligence. The greater male variance theory may, however, be correct for general population samples that include the mentally retarded... The issue of whether there is greater male variance for intelligence in general population samples needs to be addressed by meta-analysis.

British Journal of Psychology (preprint)

Sex differences in means and variability on the
progressive matrices in university students: A meta-analysis

Paul Irwing and Richard Lynn

(no abstract)

Link

More on Ancient Alaskan mtDNA

I had previously posted about ancient DNA extracted from a prehistoric Alaskan sample (On Yourk Knees Cava Man, or OYKCM). In this news article, Brian Kemp, the scientist responsible for this research elaborates about the work which has been submitted to Nature for publication. Interestingly, by comparing the ancient DNA with that of modern humans with the same haplotype, and taking into account the 10,300 years separating the two, he was able to measure the mutation rate, finding it to be faster than what was previously thought:

In the late 1990s, scientists used DNA studies to propose that people first advanced upon the continent from Asia as much as 40,000 years ago. But data from numerous archaeological sites across the Americas have placed the migration at closer to 10,000 to 12,000 years ago.

Kemp has used OYKCM as a measuring stick to come up with dates much closer to the archaeological record. "Because we know that this guy represents the oldest known example of this lineage, that places a minimum date on the emergence of the lineage," he explains.

In other words, OYKCM represents one end of the measuring stick. At the other end are the 47 people who belong to his haplotype. According to the rules of the molecular clock, this makes it possible to measure the genetic changes between OYKCM and the modern samples and calculate the time it would have required for those changes to occur.

"My calibration shows that the changes were occurring two to four times faster than previously thought," Kemp says. "It means some people have overestimated the time. It wasn't so long ago."

Of course ancient DNA is susceptible to so-called phantom mutations occurring after the subject's death. So, even if OYKCM's mtDNA was exactly similar to that of living humans, damage in the intervening 10,300 years may have caused it to appear different. Thus, the mutation rate may be overestimated due to this problem. It will be interesting to see whether this problem is addressed in the published paper, since there are ways to distinguish between genuine and post-mortem mutations in ancient DNA.