Dual origins of the Japanese

Very interesting paper on Y-chromosomal variation in Japan and neighboring regions. Haplogroup frequencies:


Japan 259; northeast Asia (NEA) 441; Southeast Asia (SEA) 683; central Asia (CAS) 419; south Asia (SAS) 496; Oceania (OCE) 209.

Interesting quote, which again confirms the East Asian origin of the NO clade:

Haplogroup N is the fourth most common haplogroup in Japan (1.5%) and is found only among mainland Japanese (Table 1). Clades N and O share a common node in the Y chromosome tree that is defined by marker M214. While NO* chromosomes are extremely rare, they are found in Japan at higher frequency than elsewhere in our survey, albeit only at 2.3%.

Also of interest is the detection of Caucasoid haplogroups I,J,G,R in some of the studied populations. In some cases these may represent recent admixture, but they may also represent older events, especially in the case of haplogroups J,G which are rare in most former European colonial powers.

J Hum Genet. 2005 Nov 18; [Epub ahead of print]

Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes.

Hammer MF, Karafet TM, Park H, Omoto K, Harihara S, Stoneking M, Horai S.

Historic Japanese culture evolved from at least two distinct migrations that originated on the Asian continent. Hunter-gatherers arrived before land bridges were submerged after the last glacial maximum (>12,000 years ago) and gave rise to the Jomon culture, and the Yayoi migration brought wet rice agriculture from Korea beginning ~2,300 years ago. A set of 81 Y chromosome single nucleotide polymorphisms (SNPs) was used to trace the origins of Paleolithic and Neolithic components of the Japanese paternal gene pool, and to determine the relative contribution of Jomon and Yayoi Y chromosome lineages to modern Japanese. Our global sample consisted of >2,500 males from 39 Asian populations, including six populations sampled from across the Japanese archipelago. Japanese populations were characterized by the presence of two major (D and O) and two minor (C and N) clades of Y chromosomes, each with several sub-lineages. Haplogroup D chromosomes were present at 34.7% and were distributed in a U-shaped pattern with the highest frequency in the northern Ainu and southern Ryukyuans. In contrast, haplogroup O lineages (51.8%) were distributed in an inverted U-shaped pattern with a maximum frequency on Kyushu. Coalescent analyses of Y chromosome short tandem repeat diversity indicated that haplogroups D and C began their expansions in Japan ~20,000 and ~12,000 years ago, respectively, while haplogroup O-47z began its expansion only ~4,000 years ago. We infer that these patterns result from separate and distinct genetic contributions from both the Jomon and the Yayoi cultures to modern Japanese, with varying levels of admixture between these two populations across the archipelago. The results also support the hypothesis of a Central Asian origin of Jomonese ancestors, and a Southeast Asian origin of the ancestors of the Yayoi, contra previous models based on morphological and genetic evidence.

Link

The hubris of the humanities

Worth reproducing in its entirety:

The hubris of the humanities

The New York Times
December 6, 2005
The Hubris of the Humanities
By NICHOLAS D. KRISTOF

The best argument against "intelligent design" has always been humanity itself. At a time when only 40 percent of Americans believe in evolution, and only 13 percent know what a molecule is, we're an argument at best for "mediocre design."

But put aside the evolution debate for a moment. It's only a symptom of something much deeper and more serious: a profound illiteracy about science and math as a whole.

One-fifth of Americans still believe that the Sun goes around the Earth, instead of the other way around. And only about half know that humans did not live at the same time as dinosaurs.

The problem isn't just inadequate science (and math) teaching in the schools, however. A larger problem is the arrogance of the liberal arts, the cultural snootiness of, of ... well, of people like me - and probably you.

What do I mean by that? In the U.S. and most of the Western world, it's considered barbaric in educated circles to be unfamiliar with Plato or Monet or Dickens, but quite natural to be oblivious of quarks and chi-squares. A century ago, Einstein published his first paper on relativity - making 1905 as important a milestone for world history as 1066 or 1789 - but relativity has yet to filter into the consciousness of otherwise educated people.

"The great edifice of modern physics goes up, and the majority of the cleverest people in the Western world have about as much insight into it as their neolithic ancestors would have had," C. P. Snow wrote in his classic essay, "The Two Cultures."

The counterargument is that we can always hire technicians in Bangalore, while it's Shakespeare and Goethe who teach us the values we need to harness science for humanity. There's something to that. If President Bush were about to attack Iraq all over again, he would be better off reading Sophocles - to appreciate the dangers of hubris - than studying the
science of explosives.

But don't pin too much faith on the civilizing influence of a liberal education: the officers of the Third Reich were steeped in Kant and Goethe. And similar arguments were used in past centuries to assert that all a student needed was Greek, Latin and familiarity with the Bible - or,
in China, to argue that all the elites needed were the Confucian classics.

Without some fluency in science and math, we'll simply be left behind in the same way that Ming Dynasty Chinese scholars were. Increasingly, we face public policy issues - avian flu, stem cells - that require some knowledge of scientific methods, yet the present Congress contains 218
lawyers, and just 12 doctors and 3 biologists. In terms of the skills we need for the 21st century, we're Shakespeare-quoting Philistines.

A year ago, I wanted to ornament a column with a complex equation, so, as a math ninny myself, I looked around the Times newsroom for anyone who could verify that it was correct. Now, you can't turn around in the Times newsroom without bumping into polyglots who come and go talking of Michelangelo. But it took forever to turn up someone confident in his calculus - in the science section.

So Pogo was right.

This disregard for science already hurts us. The U.S. has bungled research on stem cells, perhaps partly because Mr. Bush didn't realize how restrictive his curb on research funds would be. And we're risking our planet's future because our leaders are frozen in the headlights of
climate change.

In this century, one of the most complex choices we will make will be what tinkering to allow with human genes, to "improve" the human species. How can our leaders decide that issue if they barely know what DNA is?

Intellectuals have focused on the challenge from the right, which has led to a drop in the public acceptance of evolution in the U.S. over the last 20 years, to 40 percent from 45 percent. Jon Miller, a professor at the Northwestern University medical school who has tracked attitudes toward evolution in 34 countries, says Turkey is the only one with less support for evolution than the U.S.

It's true that antagonism to science seems peculiarly American. The European right, for example, frets about taxes and immigration, but not about evolution.

But there's an even larger challenge than anti-intellectualism. And that's the skewed intellectualism of those who believe that a person can become sophisticated on a diet of poetry, philosophy and history, unleavened by statistics or chromosomes. That's the hubris of the humanities.

Waterways and the Neolithic

The authors of this paper present a model which considers the effect of waterways (rivers) in the spread of the Neolithic. According to their model, the farmers from Southeastern Europe did not simply diffusion in all directions into Europe, but were constrained to move closely to rivers. Interestingly, these findings seem to agree with some modern population genetic data, according to which:

A lower frequency of E3b1 significantly distinguishes populations of the Adriatic-Dinaric complex, i.e. mainland Croatians, Bosnians and Herzegovinians (7.9%; 95% CI 0.054-0.114) from their neighboring populations of the Vardar-Morava-Danube river system, i.e. Serbians and Macedonians (21.9%; 95% CI 0.166-0.283). These observations hint a mosaic of different E3b1 dispersal modes over a short geographic distance and point to the Vardar-Morava-
Danube river system as one of major routes for E3b1, in fact E3b1α, expansion from south and southeastern to continental Europe. In fact, dispersals of farmers throughout the Vardar-Morava-Danube catchments basin are also evidenced in archeological record (Taringham, 2000).

Journal of Archaeological Science (Article in Press)

The role of waterways in the spread of the Neolithic

Kate Davison et al.

Abstract

The causes and implications of the regional variations in the spread of the incipient agriculture in Europe remain poorly understood. We use population dynamics models to study the dispersal of the Neolithic in Europe from a localised area in the Near East, solving the two-dimensional reaction-diffusion equation on a spherical surface. We focus on the role of major river paths and coastlines in the advance of farming, to model the rapid advances of the Linear Pottery (LBK) and the Impressed Ware traditions along the Danube–Rhine corridor and the Mediterranean coastline, respectively. We argue that the random walk of individuals, which results in diffusion of the population, can be anisotropic in those areas and hence lead to an effective advection. The standard reaction-diffusion equation is thus supplemented with an advection term, confined to the proximity of major rivers and coastlines. The model allows for the spatial variation in both the human mobility (diffusivity) and the carrying capacity, reflecting the local altitude and latitude. This approach can easily be generalised to include other environmental factors, such as the bioproductivity of landscapes. Our model successfully accounts for the regional variations in the spread of the Neolithic, consistent with the radiocarbon data, and reproduces a time delay in the spread of farming to the Eastern Europe, Britain and Scandinavia.

Link

Y-chromosome diversity in East Asia and Oceania

This chapter is a comprehensive review of Y-chromosomal diversity in East Asia and Oceania. It should come in useful to those (like me) who don't have a deep knowledge of the diverse populations of that part of the world.

Peter A. Underhill, A Synopsis of Extant Y chromosome Diversity in East Asia and Oceania (pdf).

An interesting excerpt:

Conversely, the LLY22g and TAT frequency and distribution data from Karafet et al. (2001) and unpublished data regarding M214* indicate that these chromosomes are informative in East Asian and Siberian populations. The low microsatellite diversity reported for TAT defined chromosomes indicates the occurrence of a bottleneck and subsequent demographic and range expansion (Zerjal et al. 1997). The presence of M214* lineages in East Asia suggest that they may have originated here and then dispersed northward on trajectories reaching the Baltic region. An East Asian origin of M214 is reinforced by the fact that it is a sister clade of the M175 clade that comprises the majority of East Asian lineages.

The link between haplogroup N and M175 is further reinforced by the discovery that M214 is also found in O-M175 chromosomes.

PS: You might want to read Inferring Human History: Clues from Y-chromosome haplotypes first to get an overview of human Y chromosome phylogeny.

mtDNA of Neolithic Siberians from Lake Baikal

A new article for the Ancient DNA Compendium. Geneticists have studied the genetic structure of Neolithic Mongoloids from the Lake Baikal region. It was previously thought that there was an 800-year "gap" in the occupation of the studied region, and the mtDNA data supports this theory, because populations before, and after this gap were quite different in their mtDNA profiles. Here are the haplogroup frequencies:



Interesting quote about the continuity of population from the Neolithic to the Hun period:

Russian scholars generally believe that the Xiongnu were immigrants who did not interact with the indigenous groups in the region (Okladnikov, 1964). However, the similarity of Serovo-Glazkovo and Xiongnu mtDNA haplogroup distributions suggests that gene flow may have occurred between matrilineal descendents of the Serovo-Glazkovo and groups representing the northern extent of the Huns. This association is compelling, as it suggests that temporal stability was maintained in the regional matrilineal gene pool of Lake Baikal for over four millennia (i.e., from 4200 BC–200 AD).

And on possible non-Mongoloid elements in the population:

The only definitive non-East Eurasian haplogroup identified in either population is haplogroup U5a. The geographic origins of haplogroup U5a are ambiguous, as it has been observed in both West and East Eurasian populations (Richards et al., 1998; Sykes, 1999; Derenko et al., 2002b, 2003), but it has great temporal depth. This haplogroup was detected both in many modern Siberian groups (e.g., Derbeneva et al., 2002a,b; Derenko et al., 2003; Pakendorf et al., 2003; Schurr et al., 2004) and in other prehistoric Asian cemetery populations (e.g., Oota et al., 1999; Keyser-Tracqui et al., 2003). By exploring the geographic origins of haplogroup U5a, it may be possible to reveal another facet of Siberian population history.

Am J Phys Anthropol. 2005 Dec 1; [Epub ahead of print]

Population affinities of Neolithic Siberians: A snapshot from prehistoric Lake Baikal.

Mooder KP, Schurr TG, Bamforth FJ, Bazaliiski VI, Savel'ev NA.

Archaeological evidence supports the inhabitation of the Lake Baikal region since the Paleolithic. Both metric and nonmetric osteological studies suggest that Neolithic Cis-Baikal populations are the ancestors of contemporary inhabitants of the region. To date, ancient DNA data have not been used to corroborate this biological continuity hypothesis. This study presents a temporal snapshot of the Cis-Baikal Neolithic by examining mtDNA diversity in two cemetery populations situated on the Angara River downstream of Lake Baikal. The 800 years separating the use of the two cemeteries is thought to represent a biocultural hiatus in the Cis-Baikal region, one that ended when a new group migrated into the area. To assess the likelihood that genetic continuity exists between these two Neolithic groups, we examined both mtDNA coding region and hypervariable region I (HVI) polymorphisms from skeletal remains excavated from both cemeteries (Lokomotiv and Ust'-Ida). The mtDNA haplogroup distributions of the two cemetery populations differ significantly, suggesting that they were biologically distinct groups. When the biological distance between these Neolithic groups is compared with modern Siberian and other East Eurasian groups, the posthiatus group (Serovo-Glazkovo) generally aligns with contemporary Siberians, while the prehiatus (Kitoi) individuals are significantly different from all but modern Kets and Shorians living in the Yenisey and Ob River basins to the west of Lake Baikal. These results suggest that the Lake Baikal region experienced a significant depopulation event during the sixth millennium BP, and was reoccupied by a new immigrant population some 800 years later.

Link

Differentiation of Indian Proto-Australoids

Am J Phys Anthropol. 2005 Dec 1; [Epub ahead of print]

Microsatellite diversity reveals the interplay of language and geography in shaping genetic differentiation of diverse Proto-Australoid populations of west-central India.

Gaikwad S, Vasulu TS, Kashyap VK.

Microsatellite diversity was analyzed in four Proto-Australoid tribes, including Indo-European (Marathi)-speaking Katkari, Pawara, Mahadeo-Koli, and Dravidian (Gondi)-speaking groups of Maharashtra, west-central India, to understand their genetic structure and to identify the congruence between language and gene pool. Allele frequency data at 15 short tandem repeat (STR) loci in studied tribes was compared with data of 22 Indo-European- and Dravidian-speaking caste and tribal populations using heterozygosity, allele size variance, analysis of molecular variance (AMOVA), G(ST) estimate, PC plot, and Mantel correlation test. Our results demonstrate that "Gondi" tribes comprising the Madia-Gond, a hunter-gatherer population, and the agriculturist Dheria-Gond harbor lower diversity than "Marathi" tribal groups, which are culturally and genetically distinct. Katkari, a hunter-gatherer tribe, showed greater diversity and the presence of a large number of unique alleles, genetically distinct from all others except the Pawara, supporting their old cultural links. The agriculturist Pawara tribe represents a splinter subgroup of the Bhil tribe and has experienced gene flow. The Mahadeo-Koli, an agriculturally oriented tribe, displayed significant heterozygote deficiency, attributable to the practice of high endogamy. The Proto-Australoid tribal populations were genetically differentiated from castes of similar morphology, suggesting different evolutionary mechanisms operating upon the populations. The populations showed genetic and linguistic similarity, barring a few groups with varied migratory histories. The microsatellite variation clearly demonstrates the interplay of sociocultural factors including linguistic, geographical contiguity, and microevolutionary processes in shaping the genetic diversity of populations in contemporary India. This study supports the ethno-historical relationships of Indian populations.

Link

mtDNA and Y chromosomes of Ibiza

Am J Phys Anthropol. 2005 Dec 1; [Epub ahead of print]

Differential maternal and paternal contributions to the genetic pool of Ibiza Island, Balearic Archipelago.

Tomas C, Jimenez G, Picornell A, Castro JA, Ramon MM.

We report on a comparison of the genetic diversity between Ibiza and the population of the other Balearic islands and also between the archipelago with respect to circum-Mediterranean populations. For such a comparison, autosomal and Y-chromosome STRs, as well as mtDNA sequence data analyzed from the same individuals, were studied. Analysis of 14 autosomal STRs showed that Ibiza had significant differentiation with respect to other Balearic populations and also with respect to insular and continental populations from the Mediterranean area. Nevertheless, the results obtained from the analysis of eight Y-STRs showed a high level of genetic homogeneity for eight western Mediterranean populations. On the other hand, these populations did not show a compacted group when mtDNA diversity was analyzed, since they showed genetic differentiation among them. The analyses of haplotypes shared between populations indicated that mtDNA haplotypes have drifted to higher frequencies than the Y chromosome. This fact could be due to a shared recent history between Ibiza and other western Mediterranean populations, with numerous male displacements originated by wars and, especially, commercial relations. The results of mtDNA from the Ibiza population could be due to a maternal Carthaginian/Phoenician founder effect, together with genetic drift, in accordance with the historical and demographic data of the area.

Link

mtDNA of Aleuts and Circumpolar populations

Am J Phys Anthropol. 2005 Dec 1; [Epub ahead of print]

Genetic structure of the Aleuts and Circumpolar populations based on mitochondrial DNA sequences: A synthesis.

Zlojutro M, Rubicz R, Devor EJ, Spitsyn VA, Makarov SV, Wilson K, Crawford MH.

The mtDNA variation of 198 Aleuts, as well as North American and Asian populations drawn from the literature, were analyzed to reconstruct the Aleuts' genetic prehistory and to investigate their role in the peopling of the Circumarctic region. From median-joining network analysis, three star-like clusters were identified in the Aleuts within the following subhaplogroups: A3, A7 (an Aleut-specific subclade of A3), and D2. Mismatch analyses, neutrality test scores, and coalescent time estimates for these three components provided evidence of two expansion events, one occurring at approximately 19,900 B.P. and the other at 5,400 B.P. Based on these findings and evidence from the archaeological data, four general models for the genetic prehistory of the Aleutian Island chain are proposed: 1) biological continuity involving a kin-structured peopling of the archipelago; 2) intrusion and expansion of a non-native biface-producing population dominated by subhaplogroup D2; 3) amalgamation of Arctic Small Tool tradition peoples characterized by D2 with an older Anangula substratum; and 4) biological continuity with significant gene flow from neighboring populations of the Alaskan mainland and Kodiak Island. The Aleut mtDNAs are consistent with the Circumarctic pattern by the fixation of A3 and D2, and the exhibition of depressed diversity levels relative to Amerind and Siberian groups. The results of this study indicate a broad postglacial reexpansion of Na-Dene and Esko-Aleuts from reduced populations within northern North America, with D2 representing a later infusion of Siberian mtDNAs into the Beringian gene pool.

Link

Ages of R1a1

(in kya)

Balkans: 15.8
India: 14.0
Oman: 11.4
Eastern Europe: 11.4
South Siberia: 11.3
Anatolia: 8.9

Sperm motility in mtDNA haplogroup U

From the article:

Comparison of the sperm motility and vitality between the different U sublineages revealed statistically significant differences in both motility (F = 3.37, P = 0.013) and vitality (F = 3.75, P = 0.011; ANOVA)

...

European haplogroup U subdivided into two major subhaplogroups, U5 and U1811.

...

To further investigate the genotypic basis for the phenotypic differences between U5 and U1811 spermatozoa, we characterized the potentially functional variants in subbranches of U5 and U1811. U5 subdivides into two primary branches: U5a and U5b (Achilli et al., 2005) (Fig. 1). U5a was founded by one cytb missense mutation: nt 14793G/H16R (CI = 54%) and the most abundant U5a sublineage, U5a1 has another cytb mutation nt 15218G/T158A (CI = 79%). The remaining U5 mtDNAs occupy a separate branch, U5b defined by two synonymous variants.

The U1811 lineage divides into several sublineages, including U4, Uk [previously defined as K haplogroup, (Torroni et al., 1996) and U1811rest, the later incorporating several small lineages. The U4 sublineage is founded by four synonymous variants and a cytb missense mutation at nt 15693C/M316T (CI = 74%). The Uk sublineage is founded by four synonymous variants and two non-synonymous mutations: a cytb mutation at nt 14798C/F18L (CI = 77%) and an ATP6 mutation at nt 9055A/A177T (CI = 85%). The U1811rest sublineages lack highly conserved nodal missense mutations.

...

The sublineages of U1811 were all lower than the U5 lineages, again confirming that the COIII nt 9477G mutation has a positive effect on ATP production. Within the U1811 sublineages, the rank order of sperm motility and vitality and therefore probable mitochondrial ATP production was Uk, U1811rest, and U4. U4 which harbours the cytb nt 15693C mutation had the lowest sperm motility and vitality, between 4% and 10% below those of Uk and U1811rest (Fig. 3).

...

Data from the literature was compiled on the European distribution of 1802 individuals harbouring haplogroup U mtDNAs (Table 2). This revealed a highly significant north–south geographic distribution of different haplogroup U sublineages (χ2 = 109.6, df = 5, P ≤ 0.001). For the U5 subhaplogroup, the U5a sublineage with cytb mutations was more prevalent in northern Europe (ratio = 1.9), while the U5b sublineage without cytb mutations was more common in southern Europe (ratio = 0.7). Of the U1811 subhaplogroup, Uk and U1811rest were equally distributed in both latitudes (ratio = 0.9 and 1.0, respectively), but the U4 sublineage was enriched in the north (ratio = 1.9). Moreover, the frequency of this subhaplogroup, as well as its proportion in the haplogroup U, increased eastwards, reaching maximum values in the populations of Northwest Siberia (Malyarchuk, 2004). Thus the combination of the cytb mutation-containing sublineages U4, Uk and U5a was in substantial excess in northern Europe.

Gene (Article in press)

Differences of sperm motility in mitochondrial DNA haplogroupnext term U sublineages

Francisco Montiel-Sosa et al.

Abstract

We had previously shown that sperm from men harbouring haplogroup T mtDNAs swim less vigorously than those from haplogroup H. However, the biochemical basis of this motility was difficult to investigate because of the multiple mutations, the most important of which affected respiratory complex I for which there is no crystal structure. To more thoroughly study the relationship between mtDNA variation and differences in mitochondrial energy metabolism, we turned to the analysis of sperm baring haplogroup U mtDNAs. Haplogroup U is a monophyletic ancient and thus heterogeneous maternal lineage that is broadly distributed among European individuals. Several sublineages of haplogroup U were found to be associated with differences in sperm motility and vitality. These differences could be related to a highly conserved missense mutation in the mtDNA COIII gene (V91) and several equally conserved mutations in the cytochrome b (cytb) gene. Moreover, the lineages with the cytb mutations were substantially enriched in northern Europe, while those lacking these mutations were more prevalent in southern Europe. We suggest that some of these ancient conserved cytb missense mutations permitted our ancestors to adapt to cold by partially uncoupling mitochondrial oxidative phosphorylation (OXPHOS).

Link

Evolutionary psychology of Facial beauty

A comprehensive review of the literature; should be useful for anyone interested in this subject.

Annual Reviews of Psychology Vol. 57: 199-226

THE EVOLUTIONARY PSYCHOLOGY OF FACIAL BEAUTY

Gillian Rhodes

Abstract

What makes a face attractive and why do we have the preferences we do? Emergence of preferences early in development and cross-cultural agreement on attractiveness challenge a long-held view that our preferences reflect arbitrary standards of beauty set by cultures. Averageness, symmetry, and sexual dimorphism are good candidates for biologically based standards of beauty. A critical review and meta-analyses indicate that all three are attractive in both male and female faces and across cultures. Theorists have proposed that face preferences may be adaptations for mate choice because attractive traits signal important aspects of mate quality, such as health. Others have argued that they may simply be by-products of the way brains process information. Although often presented as alternatives, I argue that both kinds of selection pressures may have shaped our perceptions of facial beauty.

Link

More on the Cohen modal haplotype

A few days after my previous post on the Cohen modal haplotype, here is an abstract from the October ASHG meeting which essentially confirms my main points, that the CMH is not indicative of Hebrew ancestry and is split between J1 and J2 lineages.

An Updated World-Wide Characterization of the Cohen Modal Haplotype.

J.E. Ekins et al.

Since the definition of the Cohen Modal Haplotype (CMH) in 1998, the 6 SNP-6 STR genetic motif has been utilized to infer connections of contemporary individuals and communities to the ancient Hebrew population. The elucidation of the YCC SNP Phylogeny has allowed cataloguing of chromosomes compatible with the original CMH definition into several different Y-SNP subclades. Haplogroup membership was determined for 266 samples matching at ≥5 of the CMH STR alleles, defined as the Cohen Modal Haplogroup (CMHg). The bulk of the CMHg chromosomes were observed in J1 (53.0%) and J2 (43.2%), with a small portion falling outside of haplogroup J (3.8%). Members of the CMHg were observed throughout the world, with significant frequencies in various Arab populations: Oman (20.1%), Iraq (15.2%), Palestine (9.5%). Coalescent simulations were performed for CMH chromosomes within each SNP haplogroup using 24 STR loci. Estimates within J1 [6.5kybp(4K-12K)] and J2 [13kybp(7K-27K)] were substantially deeper than previous figures obtained from a heavily weighted Jewish sampling, indicating a likely origin of the compound haplotype prior to the establishment of the Hebrew population. The significant presence of CMH chromosomes in deeply divergent clades J1 and J2 (>20kybp), indicates the present CMH definition is not sufficient to distinguish lineages that likely arose by parallel IBS mutations. An expanded STR definition is proposed which allows differentiation between CMH-compatible chromosomes in J1 and J2. The inference of Jewish ancestry based on the original CMH definition should be performed with caution as subjects may be falsely categorized into the eponymous CMH lineage when the true origin is in the deeply divergent IBS branch. These observations underscore the importance of using updated SNP classifications when utilizing the CMH to infer ancestry in Jewish populations, or the use of the expanded STR definition.

Link

Annual Meeting of the AAPA 2006

The annual meeting of the AAPA is still months away, but the list of titles of posters and papers is available online. Here are some interesting titles:

The complex genetic landscape of Africa: a Y chromosome perspective. ELIZABETH T. WOOD, DARYN A. STOVER, VERONICA CHAMBERLAIN, CHRISTOPHER EHRET, GIOVANNI DESTRO-BISOL, MICHAEL F. HAMMER.

Whole mtDNA genome analysis of ancient African lineages. MARY K. GONDER, HOLLY M. MORTENSEN, FLOYD A. REED, ALEXANDRA DE SOUSA, SARAH A. TISHKOFF.

Mitochondrial DNA variation in Old Believer and ethnic Russian populations of northern Siberia. SAMARA RUBINSTEIN, NISHI MEHTA, MAGGIE COCCA, SERGEY ZHADANOV, L. OSIPOVA, THEODORE G. SCHURR.

MtDNA story of Turkic-speaking Altai populations: implication for the prehistory of Siberia. SERGEY I. ZHADANOV, LUDMILA P. OSIPOVA, MATT C. DULIK, MARINA GUBINA, THEODORE G. SCHURR.

Timing of the peopling of the Americas: genetic analysis early Holocene skeletal remains. BRIAN M. KEMP.

The distribution of a Native American-specific allele. KARI B. SCHROEDER, DAVID G. SMITH.

Who was buried in the Old Frankfort Cemetery? Using ancient DNA to leverage anthropometrics. CHRISTOPHER R. TILLQUIST, PETER KILLORAN, FABIAN CRESPO, MINDI KING, BRANDY SCHWALLIE, CHANDLER GATENBEE, A. HOWARD, A. HELM, DAVID POLLACK.

Variation in the upper-midface of modern ‘Hispanic’ samples compared to Caucasoid and Amerindian samples. ELIGIO J. RAMIREZ.

Fordisc 2.0 the ultimate test: What is the truth? NICOLE A. NAAR, DANA HILGENBERG, GEORGE J. ARMELAGOS.

Mitochondrial DNA variation of Yuman speaking populations. CARA R. MONROE.

Mitochondrial DNA Variation in Northern Altaian Ethnic Groups. MATTHEW C. DULIK, SERGEY I. ZHADANOV, L.P. OSIPOVA, THEODORE G. SCHURR.

Mitochondrial DNA analysis of the Jomon and Epi-Jomon individuals in Hokkaido, Japan. NOBORU ADACHI.

A study of the L1c haplogroup of the mitochondrial DNA. CHIARA BATINI, VALENTINA COIA, MAYA METNI PILKINGTON, CINZIA BATTAGGIA, JORGE ROCHA, GABRIELA SPEDINI, GIOVANNI DESTRO-BISOL, DAVID COMAS, FRANCESC CALAFELL.

Identifying the most informative regions of the mitochondrial genome using phylogenetic analysis. AMY L. NON, ANDREW KITCHEN, CONNIE J. MULLIGAN.

South American population genetic structure and history: the Y perspective. GRACIELA S. CABANA, PAUL W. LÓPEZ, ANGELA CÁCERES, BEATRIZ LIZÁRRAGA, ANNE C. STONE.

Distributions of newly defined Y-chromosome haplogroups K6 and K7 in Island Melanesia. KRISTA E. LATHAM, JONATHAN S. FRIEDLAENDER, FRANCOISE R. FRIEDLAENDER, MICHAEL F. HAMMER, TANYA M. KARAFET, GEORGE KOKI, JOESEPH G. LORENZ.

Genetic variation of Alu insertions in Easter Island supports “Slow Boats” hypothesis for the peopling of Polynesia. EMILI GONZALEZ-PEREZ, ESTHER ESTEBAN, MARC VIA, CLARA GARCIA-MORO, MIQUEL HERNANDEZ, PEDRO MORAL.

The origin of syphilis: a phylogenetic approach suggesting New World origin. KRISTIN N. HARPER.

An investigation of secular change in the craniofacial morphology of White and Black males and females in the United States. SANDRA CRIDLIN.

Ecogeographic variation in human nasal passages. TODD R. YOKLEY.

Can Khoi San cranial morphology be explained by paedomorphism? KATRIN SCHAEFER, PHILIPP GUNZ, CAROLINE FENES, PHILIPP MITTEROECKER, FRED L. BOOKSTEIN.

Are there two human ontogenies? an investigation of growth trajectories among tropical foragers and farmers. ROBERT S. WALKER.

Population structure analysis from prehistoric skeletal material. LYLE W. KONIGSBERG, JANE E. BUIKSTRA.

Serial coalescent simulations suggest weak genealogical relationships between Etruscans and modern Tuscans. ELISE M. S. BELLE, UMA RAMAKRISHNAN, JOANNA MOUNTAIN, GUIDO BARBUJANI.

Migrations across the Red Sea: Mitochondrial DNA analysis of populations from the Horn of Africa and Arabia. CONNIE J. MULLIGAN, AMY NON, ANDREW KITCHEN.

Out of Africa with admixture. ALAN R. ROGERS.

Revisiting Neanderthal mitochondrial DNA sequence variation. DAVID ILTIS.

mtDNA analysis of human remains from the Danish Iron and Viking ages. LINEA C. MELCHIOR, JØRGEN DISSING, NIELS LYNNERUP.

Prehistoric peoples and ancient migrations: Exploring population affinities in East Eurasia. KAREN P. MOODER, TIA THOMSON, FIONA J. BAMFORTH.

The genetic structure of the Aleuts and circumarctic populations and its implications for the peopling of North American. MARK ZLOJUTRO, ROHINA RUBICZ, MICHAEL H. CRAWFORD.

Historical peopling of the New World: Y chromosome roots. TATIANA M. KARAFET, STEPHEN L. ZEGURA, MICHAEL F. HAMMER.

Inferring population continuity versus replacement with aDNA: a cautionary tale in the Aleutians. SILVIA E. SMITH, M.GEOFFREY HAYES, JOAN BRENNER COLTRAIN, DENNIS H. O'ROURKE.

Anomalies of dental development in modern humans and Homo floresiensis. JOHN R. LUKACS, GREG C. NELSON, CAM WALKER.

The place of Jebel Moya in northeast African prehistory: A dental perspective. JOEL D. IRISH.

Wealth, status and gender at Bronze Age Tepe Hissar: An investigation of intracemetery variation in dental pathology prevalence in prehistoric Iran. BRIAN E. HEMPHILL.

Do early South Americans show biological similarity to Australians?: Lagoa Santa in odontometric and craniometric perspective. NORIKO SEGUCHI, HIDEYUKI UMEDA, A. RUSSELL NELSON, C. LORING BRACE.

Early human skeletal remains from Sabana de Bogotá, Colombia, South America: Implications for the settlement of the New World. WALTER NEVES, MARK HUBBE, GONZALEZ CORREAL, DANUSA MUNFORD.

Sequence variation in mtDNA hypervariable segment l indicates within haplogroup continuity between contemporary and prehistoric Aleut populations. JACQUEL L. ARISMENDI, DENNIS H. O'ROURKE.

Origins of Aleut populations: Molecular perspectives. MICHAEL H. CRAWFORD, ROHINA C. RUBICZ, MARK ZLOJUTRO.

Maternal and paternal lineages of African Americans. RICK A. KITTLES.

Genetic admixture, phenotype, and perception of admixture in Hispanics and Native Americans in New Mexico. YANN C. KLIMENTIDIS.

The phylogeography of mtDNA variation in Altaian Kazakh populations. OMER GOKCUMEN, LUDMILLA OSIPOVA, SERGEY I. ZHADANOV, O. ANDREENKOV, L. TABIKHANOVA, M. GUBINA, THEODORE G. SCHURR.

Not footprints after all...

The 40,000-year-old footprints from Mexico that I had blogged about earlier turn out to be >1 million year old and hence, are probably not footprints at all:

"The evidence (the British team) has provided in their arguments that these are footprints is not sufficient to convince me they are footprints," said White, who did not contribute to the new work that Renne's group is reporting in Nature. "The evidence Paul has produced by dating basically means that this argument is over, unless indisputable footprints can be found sealed within the ash."

Renne determined the new date using the argon/argon dating technique, which reliably dates rock as young as 2,000 years or as old as 4 billion years. The British-led researchers, however, relied mainly on carbon-14 dates of overlying sediments. Carbon-14 cannot reliably date materials older than about 50,000 years.

Academic catfight in the pages of Intelligence

Read also: How to settle the question of the racial IQ gap and Richard Lynn's Massaged IQ Data

Editorial note on controversial papers

Douglas K. Detterman

As anyone who reads Intelligence on a regular basis knows, from time to time we publish what might be considered controversial articles. It has always been my policy that differences of opinion are best resolved in print. For this reason, neither I nor the reviewers have backed away from controversy.

At the same time, we have been cautious and deliberate. Whenever an article evokes strong contrasting opinions from reviewers, the article is very carefully reviewed and in all cases a majority of the reviewers feel that the paper should be published. Some reviewers vote for publication even when they disagree with the content.

In cases where strong differences exist among reviewers, commentary on the original article from the reviewers or others is sometimes solicited (as in the present case). The purpose of these commentaries is to fairly present the broad range of opinion that exists in the field. Since commentaries are not as stringently reviewed as the original article, the author is given a chance to respond to the commentators. It goes without saying that we expect all parties involved to respect the rules of civil debate.

I believe that it is important that controversial ideas have access to the pages of this journal. Without a forum for the resolution of controversy, controversy will not be resolved and science will not advance. If a journal does not advance science, then what good is it? All it can do is fortify the status quo.

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Temperature, skin color, per capita income, and IQ: An international perspective

Donald I. Templer and Hiroko Arikawa

The impetus for our study was the contention of both Lynn [Lynn, R. (1991). Race differences in intelligence: A global perspective. Mankind Quarterly, 31, 255–296] and Rushton [Rushton, J. P. (1995). Race, evolution and behavior: A life history perspective. New Brunswick, NJ: Transaction; Rushton, J. P. (1997). Race, intelligence, and the brain: The errors and omissions of the revised edition of S.J. Gould's the mismeasure of man. Personality and Individual Differences, 23, 169–180; Rushton, J. P. (2000). Race, evolution, and behavior. A life history perspective (3rd edition). Port Huron: Charles Darwin Research Institute] that persons in colder climates tend to have higher IQs than persons in warmer climates. We correlated mean IQ of 129 countries with per capita income, skin color, and winter and summer temperatures, conceptualizing skin color as a multigenerational reflection of climate. The highest correlations were − 0.92 (rho = − 0.91) for skin color, − 0.71 (rho = − 0.75) for mean high winter temperature, − 0.61 (rho = − 0.68) for mean low winter temperature, and 0.63 (rho = 0.74) for real gross domestic product per capita. The correlations with population of country controlled for are almost identical. Our findings provide strong support for the observation of Lynn and of Rushton that persons in colder climates tend to have higher IQs. These findings could also be viewed as congruent with, although not providing unequivocal evidence for, the contention that higher intelligence evolves in colder climates. The finding of higher IQ in Eurasians than Africans could also be viewed as congruent with the position of Diamond (1997) that knowledge and resources are transmitted more readily on the Eurasian west–east axis.

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Sorry, wrong numbers: An analysis of a study of a correlation between skin color and IQ

Earl Hunt and Robert J. Sternberg

We argue that the report by Templer and Arikawa contains misleading conclusions and is based upon faulty collection and analysis of data. The report fails to hold up for quality of data, statistical analysis, and the logic of science.

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The Jensen and the Hunt and Sternberg comments: From penetrating to absurd

Donald I. Templer and Hiroko Arikawa

We praised the comments of Jensen and regard most of the contentions of Hunt and Sternberg as absurd. It is ridiculous to question the validity of the skin color map and its application since meaningful group differences and meaningful correlations between temperature and skin color were found. It was inappropriate for Hunt and Sternberg to attribute prejudices and erroneous preconceptions to our raters who were assigned a task that inherently permits very minimal subjective interpretation. The suggestion of Hunt and Sternberg that higher intelligence evolves in equatorial people is incongruent with the correlation or − 0.62 between cranial capacity and distance from the equator reported by Beals et al. Hunt and Sternberg failed to provide a balanced perspective in their critique of the Lynn and Vanhanen international presentation of IQs.

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Autosomal analysis of Japanese and neighboring Mongoloids

Human Genetics (Online early)

Phylogenetic relationship of the populations within and around Japan using 105 short tandem repeat polymorphic loci

Shi-Lin Li et al.

Abstract We have analyzed 105 autosomal polymorphic short tandem repeat (STR) loci for nine East and South-eastern Asian populations (two Japanese, five Han Chinese, Thai, and Burmese populations) and a Caucasian population using a multiplex PCR typing system. All the STR loci are genomewide tetranucleotide repeat markers of which the total number of observed alleles and the observed heterozygosity were 756 and 0.743, respectively, for Japanese populations. Phylogenetic analysis for these allele frequency data suggested that the Japanese populations are more closely related with southern Chinese populations than central and/or northern ones. STRUCTURE program analysis revealed the almost clearly divided and accountable population structure at K=2–6, that the two Japanese populations always formed one group separated from the other populations and never belong to different groups at K≥3. Furthermore, our new allele frequency data for 91 loci were analyzed with those for 52 worldwide populations published by previous studies. Phylogenetic and multidimensional scaling (MDS) analyses indicated that Asian populations with large population size (six Han Chinese, three Japanese, two Southeast Asia) formed one distinct cluster and are closer to each other than other ethnic minorities in east and Southeast Asia. This pattern may be the caviar of comparing populations with greatly differing population sizes when STR loci were analyzed.

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