Possible archaic African Y lineage

The paper has now been published: An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree
We report the discovery of an African American Y chromosome that carries the ancestral state of all SNPs that defined the basal portion of the Y chromosome phylogenetic tree. We sequenced ∼240 kb of this chromosome to identify private, derived mutations on this lineage, which we named A00. We then estimated the time to the most recent common ancestor (TMRCA) for the Y tree as 338 thousand years ago (kya) (95% confidence interval = 237–581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils. The extremely ancient age combined with the rarity of the A00 lineage, which we also find at very low frequency in central Africa, point to the importance of considering more complex models for the origin of Y chromosome diversity. These models include ancient population structure and the possibility of archaic introgression of Y chromosomes into anatomically modern humans. The A00 lineage was discovered in a large database of consumer samples of African Americans and has not been identified in traditional hunter-gatherer populations from sub-Saharan Africa. This underscores how the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during the interpretation of the geographic location of divergent branches of the Y chromosome phylogenetic tree for the elucidation of human origins.

Incomplete Y DNA results from two Corded Ware skeletons

The data:

The seemingly highly-confused interpretation offered by the authors:

Determining polymorphisms of SNP type from chromosome Y resulted in categorizing skeleton from grave no. 1 with very high probability into haplogroup G, whereas skeleton from grave no. 2 with very high probability into one of three haplogroups J, I or E*. Detailed results of determinations are included in the attached table 2. On the basis of the above mentioned expertise one can state that the skeletons are male individuals with no relationship between each other. [. . .]

An analysis of polymorphism of single nucleotide (SNP) of chromosome Y from genetic material derived from both burials has brought in different results than in the case of so far analyzed aDNA materials of burials of the Corded Ware culture or partly contemporary Beaker culture which revealed the presence of haplogroups R1a1 and R1b among them (Haak et al., 2008; Lee et al., 2012). In case of the dead from Wrocław-Jagodno genetic diversity of both individuals was observed. One of them does not have clearly determined haplogroup. We should reject his affiliation to paragroup E* characteristic mainly for Africa and identified among population of Bantu (Karafet et al., 2008). On the other hand, haplogroup J was probably formed about 30000 years ago in Arabian Peninsula and it is often identified as a indicator of the Neolithic demic diffusion associated with spreading agriculture (Semino et al., 2004, 1996). Its contemporary distribution covers mainly the area of Middle East and the Mediterranean Sea basin; it sporadically occurs in Central Europe. Latest analyses show that its spreading might be a marker of later migrations (Giacomo et al., 2004). Hence the most probable is acceptance of haplogroup I as a proper one for the examined individual. It is considered that it was developed between 15000 and 30000 years ago (Karafet et al., 2008) and its spreading is associated with the expansion of the Paleolithic Gravettian culture (Semino, 2000) or population from the beginning of Holocene (Rootsi et al., 2004). Thus we should think that this individual is most probably descendant of native hunting and gathering community. Haplogroup G, identified in the second individual, belongs to widespread multiethnic groups of Europe, Asia and northern Africa. This haplogroup is largely identified among analyzed aDNA materials from Europe including the early Neolithic in Spain and Germany and the late Neolithic in France. It is a serious factor supporting a conception of spreading of Neolithic from the area of Middle East (Haak et al., 2010; Lacan et al., 2011; Rootsi et al., 2012). It may indicate very complicated development processes of communities of the Corded Ware culture in which diverse populations participated – autochtonous deriving from hunting and gathering ancestors as well as Neolithic populations, genetically deriving from the Middle East areas but already living there since the beginning of Neolithic.

[Assessment of late Neolithic pastoralist's life conditions from the Wroclaw-Jagodno site (SW Poland) on the basis of physiological stress markers]

I see no basis whatsoever in the reported results for "categorizing skeleton from grave no. 1 with very high probability into haplogroup G". Possibly there is some miscommunication among the authors, or else a complete failure of logic. It appears the authors merely failed to exclude haplogroup G in sample 1 because of an unsuccessful test (and arbitrarily decided to make haplogroup G their "very highly probable" default assumption).

At the locations where both samples returned results, the only difference is at P25 (which we'll come back to). If I and J are possibilities for the haplogroup of sample 2, then possibilities for sample 1 include I, J, and G. [Edit: I originally wrote that among these choices haplogroup I would also be my guess, and it still is; but we shouldn't have to guess, and there are still other options not ruled out beyond I, J, and G.]. Note that if we ignore P25 (as the authors appear to have chosen to do), the Y haplotypes are identical at the available resolution and provide no basis for asserting the individuals are unrelated.

I'm not sure what to make of the fact that sample 1 shows CA and sample 2 shows C at P25. P25 exists in multiple copies in a palindromic region and is not the most reliable marker. But if in sample 1 any copy of P25 is A, it would suggest sample 1 is R1b.

Against this, the authors apparently take their results to indicate that sample 1 is ancestral for M207 (which would rule out R) and M45 (which would rule out P). [Update: removed speculation about errors due to strand issues. In this case, it should be safe to rule out R as a possibility for both samples, and to rule out P for skeleton 1 (though I'd still like to see comments from the authors about the "CA" at P25 for skeleton 1). The more fundamental point remains: more data will be needed to confidently assign haplogroups to these samples.]

Interesting-looking AAPA 2013 abstracts

Program here (pdf).
Natural selection acts to maintain diversity between Out of Africa and sub-Saharan African populations in genes related to neurological processes and brain development. JASON A. HODGSON1,5, ALI AL-MEERI2, CONNIE J. MULLIGAN3 and RYAN L. RAAUM4,5. 1Anthropology, New York University, 2Biochemistry and Molecular Biology, Sana'a University, Yemen, 3Anthropology, University of Florida, 4Anthropology, Lehman College and The Graduate Center CUNY, 5-, The New York Consortium in Evolutionary Primatology.

The Yemeni and Mozabite are closely related Out of Africa (OOA) populations from the Arabian Peninsula and North Africa respectively, while the Maasai are a sub-Saharan African (SSA) population. Using genome-wide SNP data (publicly available for the Mozabite and Maasai, and collected here for the Yemeni) we show the Yemeni to have ~7% and the Mozabite to have ~26% recent sub-Saharan admixture, while the Maasai have ~27% Middle Eastern admixture. We use an adaptation of the locus specific branch length method to look for the effects of natural selection on alleles introduced to the three populations through admixture. We specifically look for 1) the adaptive introgression of alleles from SSA into the Yemeni and Mozabite, 2) the adaptive introgression of alleles from OOA into the Maasai, 3) purifying selection of SSA alleles out of the Yemeni and Mozabite, and 4) purifying selection of OOA alleles out of the Maasai. We found correspondence in patterns of adaptive introgression and purifying selection between the populations for 18 genomic loci, all of which contain protein-coding genes. The correspondence in signatures of selection between three independent populations is strong evidence for natural selection, rather than the false positive signals common in genome-wide scans of selection. Strikingly, of the regions where purifying selection is acting to maintain diversity between the Out of Africa and sub-Saharan African populations, eight out of twelve genes with known ontologies are involved in neurological processes or brain development. A binomial test found this enrichment to be significant. This research was partially supported by NSF grant BCS-0518530.

Trivers-Willard effect in U.S. billionaires revisited

Revisiting a Sample of U.S. Billionaires: How Sample Selection and Timing of Maternal Condition Influence Findings on the Trivers-Willard Effect:
Based on evolutionary theory, Trivers & Willard (TW) predicted the existence of mechanisms that lead parents with high levels of resources to bias offspring sex composition to favor sons and parents with low levels of resources to favor daughters. This hypothesis has been tested in samples of wealthy individuals but with mixed results. Here, I argue that both sample selection due to a high number of missing cases and a lacking specification of the timing of wealth accumulation contribute to this equivocal pattern. This study improves on both issues: First, analyses are based on a data set of U.S. billionaires with near-complete information on the sex of offspring. Second, subgroups of billionaires are distinguished according to the timing when they acquired their wealth. Informed by recent insights on the timing of a potential TW effect in animal studies, I state two hypotheses. First, billionaires have a higher share of male offspring than the general population. Second, this effect is larger for heirs and heiresses who are wealthy at the time of conception of all of their children than for self-made billionaires who acquired their wealth during their adult lives, that is, after some or all of their children have already been conceived. Results do not support the first hypothesis for all subgroups of billionaires. But for males, results are weakly consistent with the second hypothesis: Heirs but not self-made billionaires have a higher share of male offspring than the U.S. population. Heiresses, on the other hand, have a much lower share of male offspring than the U.S. average. This hints to a possible interplay of at least two mechanisms affecting sex composition. Implications for future research that would allow disentangling the distinct mechanisms are discussed. [. . .]

A striking result of the current study, one implied by neither of the two initially stated variants of the TW hypothesis, is that heiresses have a considerably lower percentage of male offspring than heirs, self-made billionaires, and the general population. That is, for women, the observed effect is actually diametrical to the prediction made on the basis of the TW hypothesis. The difference in the proportion of male offspring between heiresses and heirs is, in fact, the highest difference observed in this study. Despite the large size of the effect and due to the low group size of 26 heiresses, however, it is only statistically significant when not controlling for multiple comparisons. Once this correction is applied, the difference remains only slightly above statistical significance in the logistic regression model. Future research should test whether this finding can be replicated with larger samples of elite women. [. . .]

These objections notwithstanding: What could drive this distinct finding for men and for women? A clue to an answer may be provided by the literature on the effect of various stressors on reducing the percentage of male offspring [13], [41]–[44], including occupational stress [38]. If stress and status both affect sex composition, at least two mechanisms may interact and confound each other in producing sex ratios in population subgroups. Could it be that heiresses, partners and spouses of self-made men, and those of male heirs have, on average, different work and career patterns and are thus exposed to various degrees of occupational stress? Specifically, heiresses may be more likely than the spouses of male billionaires to hold stressful leadership positions in companies they inherited from their parents.

Childhood intelligence is heritable, highly polygenic and associated with FNBP1L

New paper from Visscher, Deary, Plomin, and others, with results consistent with previous findings:
Intelligence in childhood, as measured by psychometric cognitive tests, is a strong predictor of many important life outcomes, including educational attainment, income, health and lifespan. Results from twin, family and adoption studies are consistent with general intelligence being highly heritable and genetically stable throughout the life course. No robustly associated genetic loci or variants for childhood intelligence have been reported. Here, we report the first genome-wide association study (GWAS) on childhood intelligence (age range 6-18 years) from 17 989 individuals in six discovery and three replication samples. Although no individual single-nucleotide polymorphisms (SNPs) were detected with genome-wide significance, we show that the aggregate effects of common SNPs explain 22-46% of phenotypic variation in childhood intelligence in the three largest cohorts (P=3.9 × 10(-15), 0.014 and 0.028). FNBP1L, previously reported to be the most significantly associated gene for adult intelligence, was also significantly associated with childhood intelligence (P=0.003). Polygenic prediction analyses resulted in a significant correlation between predictor and outcome in all replication cohorts. The proportion of childhood intelligence explained by the predictor reached 1.2% (P=6 × 10(-5)), 3.5% (P=10(-3)) and 0.5% (P=6 × 10(-5)) in three independent validation cohorts. Given the sample sizes, these genetic prediction results are consistent with expectations if the genetic architecture of childhood intelligence is like that of body mass index or height. Our study provides molecular support for the heritability and polygenic nature of childhood intelligence. Larger sample sizes will be required to detect individual variants with genome-wide significance. Molecular Psychiatry advance online publication, 29 January 2013; doi:10.1038/mp.2012.184.