Global Admixture Analysis at K=6

December 31, 2013

This new study has one of the biggest global admixture analyses ever done (185 populations at 293,832 SNPs), but it's a little hard to view so I made a more user friendly version of one of the runs. I chose K=6 because it shows clearly the divisions and admixture between the six main racial groups: Capoid (red), Negroid (orange), Caucasoid (blue), Americoid (green), Mongoloid (yellow) and Australoid (purple). Click the image below to enlarge it and scroll down for examples of the racial types.

K=2 separates African from non-African populations.

K=3 reveals a West Eurasian ancestry component [Blue].

K=4 breaks the African component into an African hunter-gatherer ancestry maximized in Bushmen such as the Ju_hoan_North [Red] and an African farmer component maximized in the Yoruba [Orange].

K=5 breaks the ENA [eastern non-African] component down into one maximized in the Karitiana from the Americas [Green] and one maximized in the Ami from Taiwan [Yellow].

K=6 reveals a south Eurasian component maximized in Papuans [Purple], which is also represented in South Asians.

Ju'hoan (Namibia)
Yoruba (Nigeria)
Sardinian (Italy)

Karitiana (Brazil)
Ami (Taiwan)
Papuan (PNG)

Calling Out JayMan

November 28, 2013

JayMan is an HBd blogger obsessed with IQ, heredity and achievement, and probably Richard Lynn's #1 fan. He claims to be Jamaican, which makes him either the most insanely self-hating black person on earth, or a white Nordicist pretending to be black so he can get away with insulting blacks and everyone else who isn't Northwestern European. Either way, he's an idiot.

Recently he "called me out" on his blog re: my stance on environmental factors in global IQ disparities. I had debated him there about a year and a half ago and easily won, and I guess he's been traumatized by it ever since. He links to that post in his new one, and I wondered why he would want to remind people of his defeat, but when I checked it again I noticed that he'd deleted my final reply to try and make himself look like the winner (you can read the unedited discussion here; the deleted comment is "Mar 27 2012 9:57 AM"). Then when I attempted to reply to his latest "challenge" the other day, he refused to approve that comment too. Just thought you'd want to know what a pathetic, dishonest, chickenshit loser he is...if you couldn't already tell.

Anyway, my response to his nonsense was this study showing that poverty leads to a significant drop in IQ points, and this new one which concludes similarly that the wealth of nations determines "national IQs" (not the other way around).

Haplogroups L3 and E are Asian, not African

October 28, 2013

The latest evidence suggests that two major haplogroups long considered African actually arose in Asia and then back-migrated to Africa.

The presence of the L haplogroup common in Africa was unexpected given the clustering of the Saudis with Europeans in the phylogenetic tree and suggests some recent African admixture. To examine this further, we performed formal tests for a history of admixture and found no evidence of African admixture in the Saudi after the split. Taken together, these analyses suggest that the L3 haplogroup found in the Saudi were present before the bottleneck 50,000 YBP. Given the TMRCA estimates for the L3 haplogroup of approximately 70,000 YBP and the timing of the Out-of-Africa split, these analyses suggest that L3 haplogroup arose in the Middle East with a subsequent back migration and expansion into Africa over the Horn-of-Africa during the lower sea levels found during the glacial period bottleneck.

Farrell et al. "The Saudi Arabian Genome Reveals a Two Step Out-of-Africa Migration". Am Soc Hum Genet, 2013.

It remained mysterious that how many times the anatomically modern human migrated out of Africa, since that among the three superhaplogrous C, DE and F, Haplogroup F distributes in whole Eurasia, C in Asia and Austronesia, D exclusively in Asia, while D's brother clade E distribute mainly in Africa, so there are two hypotheses, 1) haplogroups D and CF migrated out of Africa separately; 2) the single common ancestor of CF and DE migrated out of Africa followed by a back-migration of E to Africa. From this study, the short interval between CF/DE and C/F divergences weakens the possibility of multiple independent migrations (CF, D, and DE*) out of Africa, and thus supports the latter hypothesis (Fig. S2 a).

Shi Yan et al. "Y Chromosomes of 40% Chinese Are Descendants of Three Neolithic Super-grandfathers". arXiv:1310.3897 [q-bio.PE], 2013.

Poverty Lowers IQ

September 4, 2013

Poverty and all its related concerns require so much mental energy that the poor have less remaining brainpower to devote to other areas of life, according to research based at Princeton University. As a result, people of limited means are more likely to make mistakes and bad decisions that may be amplified by — and perpetuate — their financial woes.

Published in the journal Science, the study presents a unique perspective regarding the causes of persistent poverty. The researchers suggest that being poor may keep a person from concentrating on the very avenues that would lead them out of poverty. A person's cognitive function is diminished by the constant and all-consuming effort of coping with the immediate effects of having little money, such as scrounging to pay bills and cut costs. Thusly, a person is left with fewer "mental resources" to focus on complicated, indirectly related matters such as education, job training and even managing their time.

In a series of experiments, the researchers found that pressing financial concerns had an immediate impact on the ability of low-income individuals to perform on common cognitive and logic tests. On average, a person preoccupied with money problems exhibited a drop in cognitive function similar to a 13-point dip in IQ, or the loss of an entire night's sleep. But when their concerns were benign, low-income individuals performed competently, at a similar level to people who were well off, said corresponding author Jiaying Zhao, who conducted the study as a doctoral student in the lab of co-author Eldar Shafir, Princeton's William Stewart Tod Professor of Psychology and Public Affairs.


The cognitive effect of poverty the researchers found relates to the more general influence of "scarcity" on cognition, which is the larger focus of Shafir's research group. Scarcity in this case relates to any deficit — be it in money, time, social ties or even calories — that people experience in trying to meet their needs. Scarcity consumes "mental bandwidth" that would otherwise go to other concerns in life, Zhao said.

"These findings fit in with our story of how scarcity captures attention. It consumes your mental bandwidth," Zhao said. "Just asking a poor person to think about hypothetical financial problems reduces mental bandwidth. This is an acute, immediate impact, and has implications for scarcity of resources of any kind."

Morgan Kelly. "Poor concentration: Poverty reduces brainpower needed for navigating other areas of life". News at Princeton, August 29, 2013.

The poor often behave in less capable ways, which can further perpetuate poverty. We hypothesize that poverty directly impedes cognitive function and present two studies that test this hypothesis. First, we experimentally induced thoughts about finances and found that this reduces cognitive performance among poor but not in well-off participants. Second, we examined the cognitive function of farmers over the planting cycle. We found that the same farmer shows diminished cognitive performance before harvest, when poor, as compared with after harvest, when rich. This cannot be explained by differences in time available, nutrition, or work effort. Nor can it be explained with stress: Although farmers do show more stress before harvest, that does not account for diminished cognitive performance. Instead, it appears that poverty itself reduces cognitive capacity. We suggest that this is because poverty-related concerns consume mental resources, leaving less for other tasks. These data provide a previously unexamined perspective and help explain a spectrum of behaviors among the poor. We discuss some implications for poverty policy.

Mani et al. "Poverty Impedes Cognitive Function". Science, 2013.

Related: Parasite prevalence and cognitive development

Ancestry of Latinos

June 12, 2013

As they say, Hispanic is not a race. Latin Americans are a three-way mix of Europeans (from Spain), Native American Indians, and Sub-Saharan Africans, but proportions of these genetic components vary a lot both between and within different groups.

We find that the most likely source of the indigenous ancestry in Caribbean islanders is a Native South American component shared among coastal tribes from Venezuela, Central America, and the Yucatan peninsula, suggesting extensive gene flow across the Caribbean in pre-Columbian times. We find evidence of two pulses of African migration. The first pulse — which today is reflected by shorter, older ancestry tracts — consists of a genetic component more similar to coastal West African regions involved in early stages of the trans-Atlantic slave trade. The second pulse — reflected by longer, younger tracts — is more similar to present-day West-Central African populations, supporting historical records of later transatlantic deportation. Surprisingly, we also identify a Latino-specific European component that has significantly diverged from its parental Iberian source populations, presumably as a result of small European founder population size.


Figure 1B shows the distribution in PCA space of each individual, recapitulating clustering patterns previously observed in Hispanic/Latino populations: Mexicans cluster largely between European and Native American components, Colombians and Puerto Ricans show three-way admixture, and Dominicans principally cluster between the African and European components. Ours is the first study to characterize genomic patterns of variation from (1) Hondurans, which we show have a higher proportion of African ancestry than Mexicans, (2) Cubans, which show extreme variation in ancestry proportions ranging from 2% to 78% West African ancestry, and (3) Haitians, which showed the largest average proportion of West African ancestry (84%).

Assuming a K=3 admixture model, population admixture patterns are driven by continental reference samples with no continental subdivision (Figure 1C, top panel). However, higher Ks show substantial substructure in all three continental components. [...] At K=8, when the clinal gradient of differentiation between Southern and Northern Europeans appears, the Latino European component is seen only in low proportions in individuals from Portugal and Spain, whereas it is the major European component among Latinos (Figure 1C, bottom panel).

ADMIXTURE clustering analysis using the high-density dataset containing approximately 390K autosomal SNP loci in common across admixed and reference panel populations. Unsupervised models assuming K=3 and K=8 ancestral clusters are shown. At K=3, Caribbean admixed populations show extensive variation in continental ancestry proportions among and within groups. At K=8, sub-continental components show differential proportions in recently admixed individuals. A Latino-specific European component accounts for the majority of the European ancestry among Caribbean Latinos and is exclusively shared with Iberian populations within Europe. Notably, this component is different from the two main gradients of ancestry differentiating southern from northern Europeans. Native Venezuelan components are present in higher proportions in admixed Colombians, Hondurans, and native Mayans.

Moreno-Estrada et al. "Reconstructing the Population Genetic History of the Caribbean". PLOS Genetics, 2013.