Gene-environment interaction for human fertility

Mega-analysis of 31,396 individuals from 6 countries uncovers strong gene-environment interaction for human fertility
Family and twin studies suggest that up to 50% of individual differences in human fertility within a population might be heritable. However, it remains unclear whether the genes associated with fertility outcomes such as number of children ever born (NEB) or age at first birth (AFB) are the same across geographical and historical environments. By not taking this into account, previous genetic studies implicitly assumed that the genetic effects are constant across time and space. We conduct a mega-analysis applying whole genome methods on 31,396 unrelated men and women from six Western countries. Across all individuals and environments, common single-nucleotide polymorphisms (SNPs) explained only ~4% of the variance in NEB and AFB. We then extend these models to test whether genetic effects are shared across different environments or unique to them. For individuals belonging to the same population and demographic cohort (born before or after the 20th century fertility decline), SNP-based heritability was almost five times higher at 22% for NEB and 19% for AFB. We also found no evidence suggesting that genetic effects on fertility are shared across time and space. Our findings imply that the environment strongly modifies genetic effects on the tempo and quantum of fertility, that currently ongoing natural selection is heterogeneous across environments, and that gene-environment interactions may partly account for missing heritability in fertility. Future research needs to combine efforts from genetic research and from the social sciences to better understand human fertility.

Testosterone-related abstracts from AAPA 2016

Facial width-to-height ratio (fWHR) is not associated with pubertal testosterone
Several researchers have proposed that facial width-to-height ratio (fWHR) is a sexually dimorphic signal that develops under the influence of pubertal testosterone (T); however, this hypothesis is currently under supported. Here we examine the association between fWHR and T during the period of the life span when facial growth is canalized--adolescence. To do so, we examine the association between T, known T-derived traits (i.e. strength and voice pitch), and craniofacial measurements in a sample of adolescent Tsimane males. If fWHR variation derives from pubertal T’s influence on craniofacial growth, several predictions can be made: 1) fWHR should increase with age as T increases, 2) fWHR should reflect adolescent T (rather than adult T per se), 3) fWHR should exhibit a growth spurt in parallel with T, 4) fWHR and T should correlate after controlling for potential confounds, and 5) fWHR should show a strong relationship to other T-derived traits. These effects were not observed. We also examined three additional facial masculinity ratios: facial width/lower face height, cheekbone prominence, and facial width/full face height. In contrast to fWHR, each of the three additional measures exhibit a strong age-related pattern of change and are associated with both T and T-dependent traits. In summary, our results challenge the status of fWHR as a sexually-selected signal of pubertal T and T-linked traits.
The relationship between social status, body size, and salivary hormone levels among Garisakang forager-horticulturalist men of lowland Papua New Guinea
Social hierarchy is a robust phenomenon that exists within all human societies. Over the past several decades, a growing body of evidence from industrialized Western populations has suggested that social status is closely related to individual measures of stress, health, and many other fitness-related traits. Data regarding such relationships, however, remain rare among small-scale subsistence societies, preventing a clear understanding of the importance of social position for fitness cross-culturally. Here we contribute to this area of research by exploring the relationship between adult male social status, BMI, and levels of salivary testosterone and diurnal cortisol among Garisakang small-scale forager-horticulturalists of lowland Papua New Guinea (N = 32). Three measures of individual social status – Respect, Dominance and Prosociality – were extracted from principal components analysis of photo-rank data for locally valued male traits (e.g., sociability, hunting ability, community influence). Preliminary results from multiple regression models controlling for age suggest complex relationships between social status, body size, and salivary hormone levels among the Garisakang. Male Dominance is positively related to BMI (p < 0.05) but not with salivary hormone measures, while greater male Respect is associated with reduced salivary cortisol (p = 0.06) but not testosterone or BMI. Prosociality, conversely, is not significantly related to any evaluated measure. We discuss the evolutionary implications of our findings, with a focus on future directions for investigating the biocultural interface of health in this population.
Men’s reproductive ecology and diminished hormonal regulation of skeletal muscle phenotype: An analysis of between- and within-individual variation among rural Polish men
Human life history is characterized by several distinctive features—sexual division of labor, prolonged care of altricial young, multiple dependents of different ages, and male provisioning. Testosterone has been suggested to mediate a trade-off between men’s reproduction and survival, through the regulation of sexually dimorphic musculature. This hypothesis predicts a relationship between testosterone and musculature in which mating effort, elevated testosterone, and dimorphic musculature covary positively. Testosterone is also posited to mediate a trade-off between mating and parenting effort, and accordingly, investing fathers show decreased testosterone production. Because men use their musculature not only in mating competition but also to support work demands, an important component of parenting effort, a relatively fixed relationship between testosterone and muscularity would seem maladaptive. We hypothesize that men’s parenting effort, specifically provisioning and subsistence activities, becomes a primary determinant of muscularity. Life history, anthropometric, and hormonal data were collected from 122 rural Polish men (at the Mogielica Human Ecology Study Site) during the summer harvest and for 103 of these participants in the winter. We found that fatherhood jointly predicted heavier workload and decreased testosterone, but positively predicted muscle mass and strength measures. Furthermore, within-individuals, men experienced intensified workload and suppressed testosterone during summer, along with a concomitant increase in muscularity and strength. These findings provide preliminary support for our model, termed the ‘Paternal Provisioning Hypothesis’. Between and within individuals, men’s provisioning and subsistence activities were robust predictors of muscular development and performance, whereas their testosterone levels had no appreciable effect on skeletal muscle phenotype.
Testosterone, musculature, and development in Kanyawara chimpanzees and Tsimane forager-horticulturalists
Considerable evidence suggests that the steroid hormone testosterone mediates major life-history trade-offs in primates, promoting mating effort at the expense of parenting effort or survival. In many species, chronic shifts in testosterone production over the life course correlate with investment in male-male competition. Chimpanzees and humans represent interesting test cases, because although closely related, they maintain divergent mating systems. Chimpanzee males do not invest in pair bonds or paternal care. Consequently, across the lifespan, their testosterone levels are expected to track changes in (1) behavioral investment in dominance striving, and (2) investment in sexually dimorphic musculature employed in male-male competition. Humans, by contrast, are expected to show weaker associations between testosterone and musculature, because the latter is important not only for male competition, but for men’s work provisioning wives and children. We assayed >7000 chimpanzee and >3350 Tsimane urine samples for testosterone, creatinine, and specific gravity, in the same laboratory using the same assay methods. Male chimpanzees showed peak acceleration in testosterone increase at age 6, peak velocity at age 10, and peak deceleration at age 14, reaching adult levels by 15-16, when they began to challenge other adult males. Adult levels of testosterone were achieved 3 years later than in captivity, likely reflecting energetic constraints in the wild. Indirect measures of muscle mass followed a similar pattern, and were highly correlated with testosterone. As predicted, Tsimane men exhibited a weaker correlation, with testosterone accounting for half as much variance in the muscle mass measure as in the chimpanzee sample.
Dads and cads? Male reproductive success, androgen profiles, and male-infant social bonds in wild mountain gorillas (Gorilla beringei beringei)
Male reproductive strategies are often reduced to a ‘dad versus cad’ dichotomy. When paternity certainty is high and mating opportunities scarce, theory predicts high levels of paternal investment; if paternity certainty is low and/or access to mating opportunities plentiful, male parenting is expected to be scarce. However, conflict between mating and parenting behavior is not equally strong across ecologies and social structures. Wild mountain gorillas (Gorilla beringei) have variable paternity certainty and a morphology suggestive of intense male contest competition. Despite this, relationships between males and infants are an important component of group structure, likely because males protect infants from infanticide and predation. Using data from gorilla groups monitored by the Dian Fossey Gorilla Fund’s Karisoke Research Center, we evaluated 1) the relationship between male-infant social bond strength and males’ reproductive success, and 2) the relationship between male-infant social bonds and males’ fecal androgen metabolite levels. Higher testosterone levels are generally correlated with increased aggression and mating activity, which are typically considered incompatible with parenting behavior. After controlling for male age and rank, males who had the strongest social bonds with infants were also the males with the highest reproductive success. There was no relationship between strength of male-infant social bonds and fecal androgen metabolite levels. Results demonstrate that reductive descriptions of male reproductive strategies may obscure important connections between mating and parenting effort, and highlight the need for additional data on the relationship between androgen activity, mating, and parenting in multimale/multifemale social systems.

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Race Is a Social Construct, Scientists Argue:

In an article published today (Feb. 4) in the journal Science, four scholars say racial categories are weak proxies for genetic diversity and need to be phased out. [Unraveling the Human Genome: 6 Molecular Milestones]

They've called on the U.S. National Academies of Sciences, Engineering and Medicine to put together a panel of experts across the biological and social sciences to come up with ways for researchers to shift away from the racial concept in genetics research.

"It's a concept we think is too crude to provide useful information, it's a concept that has social meaning that interferes in the scientific understanding of human genetic diversity and it's a concept that we are not the first to call upon moving away from," said Michael Yudell, a professor of public health at Drexel University in Philadelphia.

Yudell said that modern genetics research is operating in a paradox, which is that race is understood to be a useful tool to elucidate human genetic diversity, but on the other hand, race is also understood to be a poorly defined marker of that diversity and an imprecise proxy for the relationship between ancestry and genetics.

"Essentially, I could not agree more with the authors," said Svante Pääbo, a biologist and director of the Max Planck Institute for Evolutionary Anthropology in Germany, who worked on the Neanderthal genome but was not involved with the new paper. [. . .]

So what other variables could be used if the racial concept is thrown out? Pääbo said geography might be a better substitute in regions such as Europe to define "populations" from a genetic perspective. However, he added that, in North America, where the majority of the population has come from different parts of the world during the past 300 years, distinctions like "African Americans" or "European Americans" might still work as a proxy to suggest where a person's major ancestry originated.

Update: A commenter points to this previous contribution from Michael Yudell:
Rooting human variation in blood or in kinship was a relatively new way to categorize humans. The idea gained strength towards the end of the Middle Ages as anti-Jewish feelings, which were rooted in an antagonism towards Jewish religious beliefs, began to evolve into anti-Semitism. These blood kinship beliefs rationalized anti-Jewish hatred instead as the hatred of a people. For example, Marranos, Spanish Jews who had been baptized, were considered a threat to Christendom by virtue of their ancestry because they could not prove purity of blood to the Inquisition.
But it's hard to imagine Yudell's ethnic neuroses could have anything to do with his totally non-tendentious (not to mention fresh, novel) advocacy for "Taking race out of human genetics". Who could disagree with his "simple goal", as stated in the concluding paragraph of his current paper: "to improve the scientific study of human difference and commonality" and "strengthen research by thinking more carefully about human genetic diversity". Please suppress any cognitive dissonance engendered by the second to last paragraph:
Phasing out racial terminology in biological sciences would send an important message to scientists and the public alike: Historical racial categories that are treated as natural and infused with notions of superiority and inferiority have no place in biology. We acknowledge that using race as a political or social category to study racism and its biological effects, although fraught with challenges, remains necessary. Such research is important to understand how structural inequities and discrimination produce health disparities in socioculturally defined groups.
Who would argue impartial, objective science is not synonymous with the promotion of minority grievance politics?

Paleolithic European mtDNA

Pleistocene Mitochondrial Genomes Suggest a Single Major Dispersal of Non-Africans and a Late Glacial Population Turnover in Europe (free full text):
How modern humans dispersed into Eurasia and Australasia, including the number of separate expansions and their timings, is highly debated [ 1, 2 ]. Two categories of models are proposed for the dispersal of non-Africans: (1) single dispersal, i.e., a single major diffusion of modern humans across Eurasia and Australasia [ 3–5 ]; and (2) multiple dispersal, i.e., additional earlier population expansions that may have contributed to the genetic diversity of some present-day humans outside of Africa [ 6–9 ]. Many variants of these models focus largely on Asia and Australasia, neglecting human dispersal into Europe, thus explaining only a subset of the entire colonization process outside of Africa [ 3–5, 8, 9 ]. The genetic diversity of the first modern humans who spread into Europe during the Late Pleistocene and the impact of subsequent climatic events on their demography are largely unknown. Here we analyze 55 complete human mitochondrial genomes (mtDNAs) of hunter-gatherers spanning ∼35,000 years of European prehistory. We unexpectedly find mtDNA lineage M in individuals prior to the Last Glacial Maximum (LGM). This lineage is absent in contemporary Europeans, although it is found at high frequency in modern Asians, Australasians, and Native Americans. Dating the most recent common ancestor of each of the modern non-African mtDNA clades reveals their single, late, and rapid dispersal less than 55,000 years ago. Demographic modeling not only indicates an LGM genetic bottleneck, but also provides surprising evidence of a major population turnover in Europe around 14,500 years ago during the Late Glacial, a period of climatic instability at the end of the Pleistocene.

Visscher's commentary on "Limitations of GCTA as a solution to the missing heritability problem"

Commentary on "Limitations of GCTA as a solution to the missing heritability problem" (abstract; pdf):
In a recent publication entitled "Limitations of GCTA as a solution to the missing heritability problem" Krishna Kumar et al. (2015 PNAS) claim that "GCTA applied to current SNP data cannot produce reliable or stable estimates of heritability". Here we show that those claims are false and that results presented by Krishna Kumar et al. are in fact entirely consistent with and can be predicted from the theory underlying GCTA.

More ancient DNA from Britain supporting significant later Anglo-Saxon genomic impact

Genomic signals of migration and continuity in Britain before the Anglo-Saxons:

The purported migrations that have formed the peoples of Britain have been the focus of generations of scholarly controversy. However, this has not benefited from direct analyses of ancient genomes. Here we report nine ancient genomes (~1 ×) of individuals from northern Britain: seven from a Roman era York cemetery, bookended by earlier Iron-Age and later Anglo-Saxon burials. Six of the Roman genomes show affinity with modern British Celtic populations, particularly Welsh, but significantly diverge from populations from Yorkshire and other eastern English samples. They also show similarity with the earlier Iron-Age genome, suggesting population continuity, but differ from the later Anglo-Saxon genome. This pattern concords with profound impact of migrations in the Anglo-Saxon period. Strikingly, one Roman skeleton shows a clear signal of exogenous origin, with affinities pointing towards the Middle East, confirming the cosmopolitan character of the Empire, even at its northernmost fringes.
The full text is freely accessible. More:
Ancient sample ancestry within Britain

To place our ancient genomes within a detailed British context, we next plotted these in a background PCA using 3,075 published genotypes from British3, Irish23 and southern Netherlands samples24. The modern samples were analysed using SNP genotypes at ~250,000 loci and projected into a single plot using smartpca (Fig. 3a). As in Burton et al.3 the first component of the variation was informative for the structure within Britain. Given the close ancestral relationships between these populations and their well-known history of migrational exchange, a substantial overlap between regional groups was both expected and observed. However, by considering median values, one can see a clear progression from Irish samples at one pole through Scottish, Welsh, English to the Dutch cohort at the other extreme. In this plot the York Romans cluster centrally close to the modern Welsh median value, along with the Iron-Age genome. The local Anglo-Saxon is placed differently, closest to modern East Anglians between the English and Dutch medians.

This first component also offers an opportunity to compare within the English sample. Figure 3b shows a boxplot of PC1 values for each subsample and structure is evident, with higher median values in Eastern regions such as East Anglia, East Midlands, intermediate values in the southern and western parts and lower values in the north and northwest. This pattern is more clearly seen in a geographical plot of interpolated values (Fig. 5a). When the York Romans are compared together with each modern cohort, they are most similar to the Welsh distribution of PC1 values and differ significantly from all other regional groups, apart from those from North and Northwest England (Mann–Whitney test; Fig. 3b, Supplementary Note 2 and Supplementary Table 13). An interesting difference is the marked one between the Driffield Terrace ancient and contemporary Yorkshire samples (P=0.003), implying regional discontinuity. It is also worth noting that the PC1 coordinate of the Anglo-Saxon individual is closer to the median PC1 value of East Anglians, possibly reflecting a more pronounced contribution of Germanic immigrants to eastern British populations. However, we note the inherent uncertainty in drawing inference from a single sample.

Ancient Irish genomes confirm Bronze Age steppe incursion

Press release: First ancient Irish human genomes sequenced.

BBC: Ancient DNA sheds light on Irish origins.

Guardian: Origins of the Irish down to mass migration, ancient DNA confirms.

These settlers were followed by people, initially from the Pontic steppe of southern Russia, who knew how to mine for copper and work with gold, and who carried the genetic variant for a blood disorder called haemochromatosis, a hereditary genetic condition so common in Ireland that it is sometimes called Celtic disease.

These people also brought with them the inherited variation that permits the digestion of milk in maturity – much of the world becomes intolerant to the milk sugar lactose after infancy – and they may even have brought the language that became what is now Irish. Some of them, too, had blue eyes.

“There was a great wave of genome change that swept into Europe from above the Black Sea into Bronze Age Europe and we now know it washed all the way to the shores of its most westerly island,” said Dan Bradley, professor of population genetics at Trinity College Dublin.

“And this degree of genetic change invites the possibility of other associated changes, perhaps even the introduction of language ancestral to western Celtic tongues.”

The Dublin team and colleagues from Queens University Belfast report in the Proceedings of the National Academy of Sciences that the two great changes in European prehistory – the emergence of agriculture and the advance of metallurgy – were not just culture shifts: they came with new blood. An earlier population of hunter gatherers was successively overwhelmed by new arrivals. And in Ireland, these new settlers began to define a nation.

But the latest study throws more light on the birth of a nation. All three dead men from Rathlin Island carried what is now the most common type of Irish Y chromosome, inherited only from male forebears. [. . .]

And Lara Cassidy, a researcher in genetics at Trinity College Dublin and another co-author, said “Genetic affinity is strongest between Bronze Age genomes and modern Irish, Scottish and Welsh, suggesting establishment of central attributes of the insular Celtic genome 4,000 years ago.”

The PNAS paper: Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome
The Neolithic and Bronze Age transitions were profound cultural shifts catalyzed in parts of Europe by migrations, first of early farmers from the Near East and then Bronze Age herders from the Pontic Steppe. However, a decades-long, unresolved controversy is whether population change or cultural adoption occurred at the Atlantic edge, within the British Isles. We address this issue by using the first whole genome data from prehistoric Irish individuals. A Neolithic woman (3343–3020 cal BC) from a megalithic burial (10.3× coverage) possessed a genome of predominantly Near Eastern origin. She had some hunter–gatherer ancestry but belonged to a population of large effective size, suggesting a substantial influx of early farmers to the island. Three Bronze Age individuals from Rathlin Island (2026–1534 cal BC), including one high coverage (10.5×) genome, showed substantial Steppe genetic heritage indicating that the European population upheavals of the third millennium manifested all of the way from southern Siberia to the western ocean. This turnover invites the possibility of accompanying introduction of Indo-European, perhaps early Celtic, language. Irish Bronze Age haplotypic similarity is strongest within modern Irish, Scottish, and Welsh populations, and several important genetic variants that today show maximal or very high frequencies in Ireland appear at this horizon. These include those coding for lactase persistence, blue eye color, Y chromosome R1b haplotypes, and the hemochromatosis C282Y allele; to our knowledge, the first detection of a known Mendelian disease variant in prehistory. These findings together suggest the establishment of central attributes of the Irish genome 4,000 y ago.

Ancient DNA: Late Upper Paleolithic Swiss and Caucasus hunter-gatherers sequenced

Upper Palaeolithic genomes reveal deep roots of modern Eurasians (open access):
We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic–Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ~45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ~25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ~3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.
Press release: 'Fourth strand' of European ancestry originated with hunter-gatherers isolated by Ice Age

Selection against Neanderthal introgression (two biorxiv preprints)

The Strength of Selection Against Neanderthal Introgression

Ivan Juric, Simon Aeschbacher, Graham Coop
doi: http://dx.doi.org/10.1101/030148

Hybridization between humans and Neanderthals has resulted in a low level of Neanderthal ancestry scattered across the genomes of many modern-day humans. After hybridization, on average, selection appears to have removed Neanderthal alleles from the human population. Quantifying the strength and causes of this selection against Neanderthal ancestry is key to understanding our relationship to Neanderthals and, more broadly, how populations remain distinct after secondary contact. Here, we develop a novel method for estimating the genome-wide average strength of selection and the density of selected sites using estimates of Neanderthal allele frequency along the genomes of modern-day humans. We confirm that East Asians had somewhat higher initial levels of Neanderthal ancestry than Europeans even after accounting for selection. We find that there are systematically lower levels of initial introgression on the X chromosome, a finding consistent with a strong sex bias in the initial matings between the populations. We find that the bulk of purifying selection against Neanderthal ancestry is best understood as acting on many weakly deleterious alleles. We propose that the majority of these alleles were effectively neutral-and segregating at high frequency-in Neanderthals, but became selected against after entering human populations of much larger effective size. While individually of small effect, these alleles potentially imposed a heavy genetic load on the early-generation human-Neanderthal hybrids. This work suggests that differences in effective population size may play a far more important role in shaping levels of introgression than previously thought.

The Genetic Cost of Neanderthal Introgression

Kelley Harris, Rasmus Nielsen
doi: http://dx.doi.org/10.1101/030387
Approximately 2-4% of the human genome is in non-Africans comprised of DNA intro- gressed from Neanderthals. Recent studies have shown that there is a paucity of introgressed DNA around functional regions, presumably caused by selection after introgression. This observation has been suggested to be a possible consequence of the accumulation of a large amount of Dobzhansky-Muller incompatibilities, i.e. epistatic effects between human and Neanderthal specific mutations, since the divergence of humans and Neanderthals approx. 400-600 kya. However, using previously published estimates of inbreeding in Neanderthals, and of the distribution of fitness effects from human protein coding genes, we show that the average Neanderthal would have had at least 40% lower fitness than the average human due to higher levels of inbreeding and an increased mutational load, regardless of the dominance coefficients of new mutations. Using simulations, we show that under the assumption of additive dominance effects, early Neanderthal/human hybrids would have experienced strong negative selection, though not so strong that it would prevent Neanderthal DNA from entering the human population. In fact, the increased mutational load in Neanderthals predicts the observed reduction in Neanderthal introgressed segments around protein coding genes, without any need to invoke epistasis. The simulations also predict that there is a residual Neanderthal derived mutational load in non-African humans, leading to an average fitness reduction of at least 0.5%. Although there has been much previous debate about the effects of the out-of-Africa bottleneck on mutational loads in non-Africans, the significant deleterious effects of Neanderthal introgression have hitherto been left out of this discussion, but might be just as important for understanding fitness differences among human populations. We also show that if deleterious mutations are recessive, the Neanderthal admixture fraction would gradually increase over time due to selection for Neanderthal haplotypes that mask human deleterious mutations in the heterozygous state. This effect of dominance heterosis might partially explain why adaptive introgression appears to be widespread in nature.

"Eight thousand years of natural selection in Europe" preprint - updated with Anatolian Neolithic and other data

Eight thousand years of natural selection in Europe

The arrival of farming in Europe around 8,500 years ago necessitated adaptation to new environments, pathogens, diets, and social organizations. While indirect evidence of adaptation can be detected in patterns of genetic variation in present-day people, ancient DNA makes it possible to witness selection directly by analyzing samples from populations before, during and after adaptation events. Here we report the first genome-wide scan for selection using ancient DNA, capitalizing on the largest genome-wide dataset yet assembled: 230 West Eurasians dating to between 6500 and 1000 BCE, including 163 with newly reported data. The new samples include the first genome-wide data from the Anatolian Neolithic culture, who we show were members of the population that was the source of Europe's first farmers, and whose genetic material we extracted by focusing on the DNA-rich petrous bone. We identify genome-wide significant signatures of selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height. [. . .]

Our sample of 26 Anatolian Neolithic individuals represents the first genome-wide ancient DNA data from the eastern Mediterranean. Our success at analyzing such a large number of samples is likely due to the fact that at the Barcin site–the source of 21 of the working samples–we sampled from the cochlea of the petrous bone 9 , which has been shown to increase the amount of DNA obtained by up to two orders of magnitude relative to teeth (the next-most-promising tissue) 3 . Principal component (PCA) and ADMIXTURE 10 analysis, shows that the Anatolian Neolithic samples do not resemble any present-day Near Eastern populations but are shifted towards Europe, clustering with Neolithic European farmers (EEF) from Germany, Hungary, and Spain 7 (Fig. 1b, Extended Data Fig. 2). Further evidence that the Anatolian Neolithic and EEF were related comes from the high frequency (47%; n=15) of Y-chromosome haplogroup G2a typical of ancient EEF samples 7 (Supplementary Data Table 1), and the low F ST (0.005-0.016) between Neolithic Anatolians and EEF (Supplementary Data Table 2). These results support the hypothesis 7 of a common ancestral population of EEF prior to their dispersal along distinct inland/central European and coastal/Mediterranean routes. The EEF are slightly more shifted to Europe in the PCA than are the Anatolian Neolithic (Fig. 1b) and have significantly more admixture from Western hunter-gatherers (WHG), shown by f 4 -statistics (|Z|>6 standard errors from 0) and negative f 3 -statistics (|Z|>4) 11 (Extended Data Table 3). We estimate that the EEF have 7- 11% more WHG admixture than their Anatolian relatives (Extended Data Fig. 2, Supplementary Information section 2).

On the presence of the "East Asian" EDAR variant in Scandinavian hunter-gatherers:
We find a surprise in six Scandinavian hunter-gatherers (SHG) from the Motala site in southern Sweden. In three out of six samples, we observe the haplotype carrying the derived allele of rs3827760 in the EDAR gene (Extended Data Fig. 5), which affects tooth morphology and hair thickness and has been the subject of a selective sweep in East Asia 24 , and today is at high frequency in East Asians and Native Americans. The EDAR derived allele is largely absent in present-day Europe except in Scandinavia, plausibly due to Siberian movements into the region millennia after the date of the Motala samples. The SHG have no evidence of East Asian ancestry 4,7 , suggesting that the EDAR derived allele may not have originated not in East Asians as previously suggested 24 . A second surprise is that, unlike closely related western hunter-gatherers, the Motala samples have predominantly derived pigmentation alleles at SLC45A2 and SLC24A5.
Polygenic selection on height in Europe:

We also tested for selection on complex traits. The best-documented example of this process in humans is height, for which the differences between Northern and Southern Europe have driven by selection 25 . To test for this signal in our data, we used a statistic that tests whether trait-affecting alleles are both highly correlated and more differentiated, compared to randomly sampled alleles 26 . We predicted genetic heights for each population and applied the test to all populations together, as well as to pairs of populations (Fig. 4). Using 180 height-associated SNPs 27 (restricted to 169 where we successfully targeted at least two chromosomes in each population), we detect a significant signal of directional selection on height (p=0.002). Applying this to pairs of populations allows us to detect two independent signals. First, the Iberian Neolithic and Chalcolithic samples show selection for reduced height relative to both the Anatolian Neolithic (p=0.042) and the Central European Early and Middle Neolithic (p=0.003). Second, we detect a signal for increased height in the steppe populations (p=0.030 relative to the Central European Early and Middle Neolithic). These results suggest that the modern South-North gradient in height across Europe is due to both increased steppe ancestry in northern populations, and selection for decreased height in Early Neolithic migrants to southern Europe. We do not observe any other significant signals of polygenetic selection in five other complex traits we tested: body mass index 28 (p=0.20), waist-to-hip ratio 29 (p=0.51), type 2 diabetes 30 (p=0.37), inflammatory bowel disease 21 (p=0.17) and lipid levels 16 (p=0.50).

Political background and identification of US professors circa 1969

Previously, we've seen that upper income Jews in Boston voted much further left than Protestant Bostonians in the middle of the 20th century; that "Boston Brahmins" were a relatively conservative group; that Jewish billionaires are further left than non-Jewish billionaires; etc.

It should not come as much of a surprise to anyone passingly familiar with non-Moldbuggist American history that in a 1969 survey of professors, Jews reported themselves more leftist in parental background, personal identification, voting behavior, and their children's activism than Protestants.

In "Jewish academics in the United States", Lipset reports:

The extent to which the political background of Jewish academics differs from that of others may be seen in the responses to the Carnegie survey question: "What were your father's politics while you were grow- ing up?" Forty-six per cent of the Jews, as contrasted to 19 per cent of the Catholics and but 14 per cent of the Protestant majority, reported fathers who were "left" or "liberal" in their views. Conversely, less than 20 per cent of the Jewish professors had "conservative" fathers, while 63 per cent of the Protestant academics indicated such a background (Table 19).

Family political-intellectual tradition affects the behavior of the chil- dren of academics. Among those faculty with children of college age, a majority (56 per cent) of the Jews report that their children have "been active in civil rights, anti-Vietnam, or other demonstrations," as con- trasted with little more than one-fifth (22 per cent) of the Gentile pro- fessors. The reason, of course, is that the children of liberal academics participate much, much more in demonstrations than children of con- servative academics, and Jewish faculty are disproportionately liberal. That the correlation is between parental politics and participation is made clear by Table 20, which shows that 68 per cent of the left faculty having children of the right age—regardless of religion—said their children had been active in demonstrations, compared to just 4 per cent of the strongly conservative professors.

The contribution of faculty of Jewish background to liberal and left political groups has been stressed in a number of surveys preceding our own. Almost all earlier studies found that close to 90 per cent of Jewish academics regularly voted Democratic in presidential elections. 45 Jewish faculty also were found to contribute heavily to the backing of leftist third parties. Thus, according to a 1948 study, fully 30 per cent of the Jewish professors voted for Henry Wallace. 46 The same proclivity can be seen in Britain, where a faculty opinion study reported that the Jews were "the most left-wing of all." 47 Recent studies of American college professors conclude that Jews have been much more heavily opposed to the Vietnam war, and stronger supporters of student activism, than their Gentile colleagues. 48

The Carnegie Commission's national survey yielded the same strong relationships. The Jewish faculty were much more inclined to identify their politics as "left" or "liberal" than Protestants and Catholics (Table 21 ). 49 Jews contributed disproportionately to the small group who backed left-wing third party presidential candidates in 1968; they were much more likely to have been for the nomination of Eugene McCarthy than of Hubert Humphrey at the Democratic convention, and gave Richard Nixon an exceptionally low vote in the election. In 1964 only 2 per cent of the Jewish faculty voted for Barry Goldwater, compared to 24 per cent of those of Protestant parentage (Tables 22, 23, and 24).

The Jews, as a group, took much more liberal positions on such issues as the use of force at the Chicago Democratic convention in 1968, the Vietnam war, student activism, the treatment of blacks in both the university and the larger society, and the legalization of marijuana (Tables 25, 26 and 27). The gap between Jews and Christians on these issues is very large, while among Christians, Protestants are usually slightly more conservative than Catholics. For example, 59 per cent of the Jews gave general approval to "the emergence of radical student activism in recent years," compared to 44 per cent of the Catholics and 40 per cent of the Protestants. The proportion of Jews favoring immediate United States withdrawal from Vietnam is twice that of non-Jews. Three- fifths of the Jews favored the legalization of marijuana (59 per cent), compared to 33 per cent of the Catholics and 29 per cent of the Protestants.

Religious backgrounds of US professors circa 1969

This data comes from "a large national sample (60,000) of faculty who filled out questionnaires for the Carnegie Commission on Higher Education in 1969", as reported in "JEWISH ACADEMICS IN THE UNITED STATES: THEIR ACHIEVEMENTS, CULTURE AND POLITICS" by Seymour Martin Lipset and a co-author (pdf).

Jewish overrepresentation was even greater among faculty of elite colleges and universities, and Protestants were reduced to a bare-majority of under-30 professors at elite schools by this time.

Lipset:

The considerable presence of Jews in social science departments (and schools of social work), in comparison to most of the humanities and natural sciences, may be related to the disposition of secularized Western Jews for reform-oriented politics, to be discussed later. A variety of studies of undergraduate career choices indicate that the more left- disposed students are more inclined than others to an academic career, particularly in the politically relevant social sciences. 14 As the newest group of disciplines, the social sciences have been less discriminatory, more committed to universalistic principles than the humanities. The latter, as the oldest and least "practical" fields, have tended to be identified with high status, and hence were more restrictive in their admission policies.

The underrepresentation of Jews in the humanities and history may reflect the continuation of a distinction frequently made in Wilhelminian and even Weimar Germany. Some who supported the appointment of Jews to professorships in the sciences and social sciences argued that they could not be professors of German literature or history. These subjects were at the heart of the Volkswesen, the national essence, while the Jews (obviously) were wesenfremd, alien to the national essence. Suspicions about the Volkswesen suitability of Jews in English and history have not completely vanished in the U.S. In his presidential address to the American Historical Association, in 1962, Carl Bridenbaugh lamented that "many of the younger practitioners of our craft . . . are products of lower middle-class or foreign origins and . . . find themselves in a real sense outsiders to our past and feel themselves shut out. This is certainly not their fault, but it is true." By "products of . . . foreign origins," we would hazard the guess, Professor Bridenbaugh was not thinking primarily of Albanians. 15

Moldbug's sources: Forrest McDonald, "Celtic Southernism", and the Lew Rockwell school of late 20th C. PC anti-Yankeeism

As he himself eventually confirmed, moldbug's ideology was formed by mashing up a variety of vaguely rightist and libertarian ideas and filtering them through the lens of what he perceived to be "good for the Jews".

Similarly, moldbug's school of pseudo-history arose from moldbug latching on to a convenient thread and running with it to outlandish extremes, the overriding goal not being to promote understanding but to absolve Jews (and moldbug's Communist grandparents, in particular) of any agency in their radical political activity.

Moldbug picked up the initial inspiration for moldbuggist history from the anti-Yankeeism of lewrockwell.com contributors like Clyde Wilson, Jimmy Cantrell, and Thomas "Abraham Lincoln was the real racist" DiLorenzo, some of which was outlandish enough to begin with. They, in turn, were influenced by Forrest McDonald.

Linguistics, Archaeology & Genetics conference abstracts

This conference, aimed at "integrating new evidence for the origin and spread of the Indo-European languages", will take place next week. Some abstracts (pdf):

Close genetic relationship of Neolithic Anatolians to early European farmers

Iosif Lazaridis 1,2 , Songül Alpaslan 3 , Daniel Fernandes 4 , Mario Nowak 4 , Kendra Sirak 4 , Nadin Rohland 1,2 , Swapan Mallick 1,2,5 , Kristin Stewardson 1,5 , Fokke Gerritsen 6 , Nick Patterson 2 , Ron Pinhasi 4, *, David Reich 1,2,5, *

We study 1.2 million genome-wide single nucleotide polymorphisms on a sample of 26 Neolithic individuals (~6,300 years BCE) from northwestern Anatolia. Our analysis reveals a homogeneous population that was genetically similar to early farmers from Europe (F ST =0.004±0.0003 and frequency of 60% of Y-chromosome haplogroup G2a). We model Early Neolithic farmers from central Europe and Iberia as a genetic mixture of ~90% Anatolians and ~10% European hunter-gatherers, suggesting little influence by Mesolithic Europeans prior to the dispersal of European farmers into the interior of the continent. Neolithic Anatolians differ from all present-day populations of western Asia, suggesting genetic changes have occurred in parts of this region since the Neolithic period. We suggest that the language spoken by the homogeneous Anatolian-European Neolithic farmers is unlikely to have been the same as that spoken by the Yamnaya steppe pastoralists whose ancestry was derived from eastern Europe and a different population from the Caucasus/Near East [Haak et al. 2015], and discuss implications for alternative models of Indo-European dispersals.

The Genetic History and Structure of Britain

Nick Patterson, Broad Institute, Boston and David Reich, Harvard Medical School and Broad Institute, Boston

The recently published paper on the genetic structure of Britain (Leslie et al. Nature 2015) has shown subtle genetic variation correlating with geography. Here we reexamine the evidence in the light of our understanding of the genetics of Ancient Europe and comment on some implications for how Indo-Europeans spread into Europe.

In search for initial Indo-European gene pool from genome-wide data on IE popula- tions as compared with their non-IE neighbors

Oleg Balanovsky, Vavilow Institue of General Genetics, Russian Academy of Sci- ences, Moscow

From Yamnaya to Bell Beakers: Mechanisms of Transmission in an Interconnected Europe, 3500–2000 BC

Volker Heyd, Universtiy Bristol, Bistol and University of Helsinki, Helsinki

Yamnaya Peoples in the East and Bell Beakers Users in the West are rightly seen as the apogees in a long-term process of individualisation, gender differentiation, warrior display and internationalisation/unification that fundamentally change the face of the European Continent from the mid fourth and throughout the third millennium BC. We can only approach the reasons why prehistoric peoples and cultures from regions across Europe, which were no more than marginally in touch before, join in the same emblematic pottery, new drinking habits, similar burial customs, anthropomorphic stelae, ostentatious display of weapons and other paraphernalia, and thus common values. However rather than seeing this development as an internal European progress I want to point to the importance of the Pontic-Caspian steppes, and a 2000 years lasting interaction scenario of infiltrating Suvorovo-Novodanilovka, Nizhnemikhailovka-Kvityana and Yamnaya peoples and populations with their more sedentary contemporaries in southeast Europe, the Carpathian basin and northeast of the Carpathian bow. A crucial part of this interaction –besides migrations and the exchange of genes and goods as recently highlighted in several publications not only in Nature and Science– is the forwarding of innovations in the sphere of subsistence economy. We see this archaeologically in a further importance of animal husbandry, with larger herds, specialised breeding and new forms of herding management in particular for cattle. This obviously sets in motion a substantial shift in general mobility patterns and of communication networks.

It is easily conceivable that this interaction must also have had a profound impact on the whole settlement organisation and people’s way-of-life, in consequence probably fundamentally affecting the basics of societies and thus challenging the whole system of ideas, imaginations, morale, symbols and terms – a new world-view and ultimately the base for a new language.

Pre-Indo-European speech carrying a Neolithic signature emanating from the Aegean

Guus Kroonen, Institute for Nordic Studies and Linguistics, Copenhagen University, Copenhagen

When different Indo-European speaking groups settled Europe, they did not arrive in terra nullius. Both from the perspective of the Anatolian hypothesis 1,2,3 and the Steppe hypothesis, 4,5,6 the carriers of Indo-European speech likely encountered existing populations that spoke dissimilar, unrelated languages. Relatively little is known about the Pre-Indo-European linguistic landscape of Europe, as the Indo-Europeanization of the continent caused a largely unrecorded, massive linguistic extinction event. However, when the different Indo-European groups entered Europe, they incorporated lexical material from Europe’s original languages into their own vocabularies. 7 By integrating these “natural samples” of Pre-Indo-European speech, the original European linguistic and cultural landscape can partly be reconstructed and matched against the Anatolia and the Steppe hypotheses. My results reveal that Pre-Indo-European speech contains a clear Neolithic signature emanating from the Aegean, 8 and thus patterns with the prehistoric migration of Europe’s first farming populations. 9,10,11 These results also imply that Indo-European speech came to Europe following a later migration wave, and therefore favor the Steppe Hypothesis as a likely scenario for the spread of the Proto-Indo-Europeans. 12

More carriers of deeply diverged Y lineage (haplogroup A00) found in Cameroon

This possibly archaic African Y lineage was discovered a few years ago by hobbyists, and a project run and funded by hobbyists to collect and test additional A00 samples has started to report results:
There are some striking patterns in the results already. 85% of the A00 so far are from the Bangwa (Nweh) people, and 15% from the Nkongho-Mbo. This is despite the fact that nearly 57% of the samples collected were from Mbo, and only 37% were from Bangwa. Once all the results have been fully tabulated, we can provide more complete statistics. It will take a while to transcribe all the rich data from those handwritten sheets into electronic spreadsheets. [. . .]

What's next? Matthew would like to head back to the field quite soon, in the second half of October, when the school where he teaches has a break. Our current plan is for him to visit the region of the Bamileke people. Matthew, an ethno-historian, has said "The similarity in names, language, dancing style and all other aspects of life suggest that the Bangwa are 90 percent Bamileke." By testing a good number of Bamileke, we'll be able to see whether the heritage they share includes A00, or not. It is possible that the A00 among the Bangwa comes from the indigenous people who originally inhabited the hills, before they arrived several centuries ago, or it could also have been present among the Bamileke earlier. Our results should give strong evidence to answer that question.

The next field trips should be even more exciting. One of our goals is to collect the most diverse samples of A00 possible, to uncover its internal structure. By sequencing the Y-DNA of A00 lines that have diverged and settled in different parts of Cameroon, we should be able to get a good idea of when those different lineages had a common ancestor, and understand better how the peoples among whom it's found are related.

One trip will take Matthew westward into the lowland regions close to Nigeria, where the Banyangi and Ejagham peoples live, toward the Cross River, home of the endangered Cross River Gorilla. These villages are also on the roads that led to the old Nigerian port of Calabar, where captives from Cameroon's highlands, including some Bangwa, were sold into slavery in the past. He has never before sampled in the western regions, and only 16 Banyangi have been tested in his past research, but there are versions of Bangwa history which say that these peoples make up a significant element of their founders. Members of the A0 haplogroup have been found in Nigeria, but we have no idea yet whether A00 are also found in that direction. The famed Iwo Eleru cave is in southern Nigeria, where a skull with archaic features has been found that dates to only 13,000 years ago, suggesting long survival of diverse humans in that region.

In his other trip, he'll seek to sample members of several of the different Pygmy communities of Cameroon, who live to the South and East. Among the Pygmy peoples, Matthew collected 53 samples in 2006, and two of them belonged to A00! These communities are far from the highlands where the Bangwa and Mbo live, so we can expect that their A00 will be quite distinct. This should be extremely interesting!

1000 Genomes phase 3 papers

Both papers are freely accessible:

A global reference for human genetic variation

An integrated map of structural variation in 2,504 human genomes

"Male Homosexual Preference" and social stratification

I don't necessarily buy positive selection for genes predisposing to male homosexuality in stratified societies via pleiotropic effects in females. But I could easily believe that evolutionary mismatch leads to higher levels of homosexuality in denser (though population density is apparently not a significant predictor in their analysis) and/or more stratified societies, and that sexually antagonistic selection plays some role in slowing down selection against homosexuality.

Male Homosexual Preference: Where, When, Why? (PLoS ONE):

Male homosexual preference (MHP) has long been of interest to scholars studying the evolution of human sexuality. Indeed, MHP is partially heritable, induces a reproductive cost and is common. MHP has thus been considered a Darwinian paradox. Several questions arise when MHP is considered in an evolutionary context. At what point did MHP appear in the human evolutionary history? Is MHP present in all human groups? How has MHP evolved, given that MHP is a reproductively costly trait? These questions were addressed here, using data from the anthropological and archaeological literature. Our detailed analysis of the available data challenges the common view of MHP being a “virtually universal” trait present in humans since prehistory. The conditions under which it is possible to affirm that MHP was present in past societies are discussed. Furthermore, using anthropological reports, the presence or absence of MHP was documented for 107 societies, allowing us to conclude that evidence of the absence of MHP is available for some societies. A recent evolutionary hypothesis has argued that social stratification together with hypergyny (the hypergyny hypothesis) are necessary conditions for the evolution of MHP. Here, the link between the level of stratification and the probability of observing MHP was tested using an unprecedented large dataset. Furthermore, the test was performed for the first time by controlling for the phylogenetic non-independence between societies. A positive relationship was observed between the level of social stratification and the probability of observing MHP, supporting the hypergyny hypothesis. [. . .]

Minor sub-Saharan and substantial Levantine admixture in Southern Europe

According to "The Role of Recent Admixture in Forming the Contemporary West Eurasian Genomic Landscape", something like a third of Southern Italian and Tuscan genetic ancestry appears to derive from the Levant in Roman times:

Moorjani et al [S?], who use a method based on allele frequency comparisons, and not haplotypes (ROLLOFF), found evidence for sub-Saharan African admixture in Sardinia 71±28 generations ago, at a proportion of 3%. These are the same Sardinians included in our analysis. In the largest Sardinian (sardi13) cluster in our analysis we infer West African admixture 66 (53-82) generations ago at a proportion of 2%.

S5.2 Continuous low level African admixture in the Mediterranean and Anatolia

We infer West African admixture across broad date ranges, but at low admixture proportions (admixture α < 0.07; Figs. 2 and S3) in several Mediterranean groups, consistent with a long term movement be- tween sub-Saharan Africa and southern Europe [S?,S?]. Specific West African admixture dating to the Arabic conquest of the Mediterranean [S?] is seen in Spanish (spani27: 1042 (740-1201CE)), Southern Italian and Sicilian (sicil30: 1105 (882-1250CE)), and Basque (basqu24: 886 (283-1162CE)) clusters. Earlier African admixture at low admixture proportion is inferred in the Cypriots (cypri12: 427(107- 734CE)), and a Sardinian cluster (sardi13: 36 (458BCE-430CE); α = 0.02). This latter event is con- sistent with the occurrence of A3b2-M13 (0.6%) and E1a-M44 (0.4%) African Y chromosome lineages in Sardinia [S?]. and the dating is more compatible with documented exchanges between the island and Mauretania Cesariensis in Roman times (2 nd century BCE to 2 nd century CE) than later displacements of northern-African males to Sardinia at the time of the Vandals rule (5 th century CE) [S?]. [. . .]

S5.3 A key role for the Levant in the genetic history of the Mediterranean

Early admixture involving source groups most similar to contemporary populations from in and around the Levant (which we define as the World Region containing individuals from Syria, Palestine, Lebanon, Jordan, Saudi, Yemen and Egypt) is seen at high proportions in several clusters from Italy dating to the first half of the first millennium CE, from Southern Italy (itali8: 295CE (72BCE-604CE); α = 0.34), Tuscany (tsi23: 400CE(30BCE-686); α = 0.29), and Sardinia, as well as in a large cluster from Armenia at an early date (armen27: 363BCE(1085BCE-383CE)). [. . .] these events loosely coincide with the formation of the pan-Mediterranean Roman Empire [S?], which may also have allowed increased gene flow from east to west Mediterranean. [. . .] We infer more recent Levant admixture in the French (frenc24: 728(424-1011CE)) and in a complex multiway event in a Spanish cluster (spani9: 668 (286-876CE)). The dates and sources of admixture in these cases are consistent with movements of Middle Eastern and North African individuals during the Islamic Conquest of Spain [S?], and suggest a legacy of this key moment in southern European history in the genomes of French as well as Spanish populations.

Autosomal DNA from Atapuerca pre- or proto-Neanderthals

DNA from Neandertal relative may shake up human family tree

The Sima people, who lived before Neandertals, were thought to have emerged in Europe. Yet their teeth, jaws, and large nasal cavities were among the traits that closely resembled those of Neandertals, according to a team led by paleontologist Juan-Luis Arsuaga of the Complutense University of Madrid. As a result, his team classified the fossils as members of Homo heidelbergensis, a species that lived about 600,000 to 250,000 years ago in Europe, Africa, and Asia. Many researchers have thought H. heidelbergensis gave rise to Neandertals and perhaps also to our species, H. sapiens, in the past 400,000 years or so. [. . .]

After 2 years of intense effort, paleogeneticist Matthias Meyer of the Max Planck Institute for Evolutionary Anthropology has finally sequenced enough nuclear DNA from fossils of a tooth and a leg bone from the pit to solve the mystery. [. . .] They scanned this DNA for unique markers found only in Neandertals or Denisovans or modern humans, and found that the two Sima fossils shared far more alleles—different nucleotides at the same address in the genome—with Neandertals than Denisovans or modern humans. “Indeed, the Sima de los Huesos specimens are early Neandertals or related to early Neandertals,” suggesting that the split of Denisovans and Neandertals should be moved back in time, Meyer reported at the meeting. [. . .]

“It resolves one controversy—that they’re in the Neandertal clade,” says paleoanthropologist Chris Stringer of the Natural History Museum in London. “But it’s not all good news: From my point of view, it pushes back the origin of H. sapiens from the Neandertals and Denisovans.” The possibility that humans were a distinct group so early shakes up the human family tree, promising to lead to new debate about when and where the branches belong.

Darren Curnoe points out:
What are the broader implications of the research for understanding the evolution of living humans?

First, the finding pushes the age of the shared human-Neanderthal ancestor well beyond 400,000 years ago, suggesting our species, H. sapiens, might also be at least this old.

Also, with the Atapuerca group living in Europe, it’s even possible that our species evolved in this or an adjacent region of Eurasia, and later migrated back into Africa.

And being close to the common ancestor, the Atapuerca fossils give us real insights into what it must have looked like and the ancestral body form of our own species.

The fossils from Europe, Asia and Africa from around this time are physically very diverse, with some researchers thinking they represent multiple species, only one of which could be the ancestor of living humans.

Question is, which one?

This new research suggests the European branch is closest among them all and deserves much more attention in this regard.

In contrast, we don’t know, and will doubtless ever know, whether Homo naledi had anything to do with the evolution of living humans, least of all whether its brain, mind or behaviour were anything like our own.

ASHG 2015: growth rate estimates from whole Y chromosome sequences

Estimation of growth rates for populations and haplogroups using full Y chromosome sequences.

F. L. Mendez; G. D. Poznik; C. D. Bustamante; 1000 Genomes Project Consortium

Department of Genetics, Stanford University, Stanford, CA.

Evolutionary processes affecting a population influence gene genealogies across the genome. Coalescent theory provides the mathematical framework to connect realized genealogies to the underlying evolutionary processes. However, in most cases, information about the genealogies is obtained only indirectly through the observation of genetic variation. Therefore, in general, very limited information about any individual locus is available. As the longest non-recombining portion of the human genome, the Y chromosome accumulates mutations relatively quickly. When large amounts of sequence are used, the Y chromosome provides an unparalleled ability to resolve the structure and coalescence times of its genealogy. Because patterns of variation in the Y chromosome are only influenced by processes affecting men, they can be used to study both demographic and social phenomena. The 1000 Genomes Project includes whole Y-chromosome data from more than 1000 men and has an extensive representation of most lineages that have experienced recent massive expansions in size. Though the dynamics of population growth have likely changed over time, we are more interested in the growth rates at the times of these rapid expansions than on an average effect. To study this, we have developed a new method that takes advantage of the temporal resolution provided by Y-chromosome data and of historical data, while accounting for the uncertainties associated with the coalescent and mutational processes. We estimate the growth rates for several branches of the Y-chromosome tree, including those in Europe, sub-Saharan Africa and South Asia. We estimate that several lineages within the European R1b, sub-Saharan African E1b, and South Asian R1a haplogroups experienced growth rates of at least 20-60% per generation at the onset of their massive expansions, some 3-5 thousand years ago. These high growth rates are comparable to those experienced by human populations during the 20th century. However, we find that most observed genealogies are unlikely to be the result of whole population expansion or of natural selection.