July 17, 2014

More selection on the X than in autosomes in humans

Mol Biol Evol (2014) doi: 10.1093/molbev/msu166

Evidence for Increased Levels of Positive and Negative Selection on the X Chromosome versus Autosomes in Humans

Krishna R. Veeramah et al.

Partially recessive variants under positive selection are expected to go to fixation more quickly on the X chromosome as a result of hemizygosity, an effect known as faster-X. Conversely, purifying selection is expected to reduce substitution rates more effectively on the X chromosome. Previous work in humans contrasted divergence on the autosomes and X chromosome, with results tending to support the faster-X effect. However, no study has yet incorporated both divergence and polymorphism to quantify the effects of both purifying and positive selection, which are opposing forces with respect to divergence. In this study, we develop a framework that integrates previously developed theory addressing differential rates of X and autosomal evolution with methods that jointly estimate the level of purifying and positive selection via modeling of the distribution of fitness effects (DFE). We then utilize this framework to estimate the proportion of nonsynonymous substitutions fixed by positive selection (α) using exome sequence data from a West African population. We find that varying the female to male breeding ratio (β) has minimal impact on the DFE for the X chromosome, especially when compared with the effect of varying the dominance coefficient of deleterious alleles (h). Estimates of α range from 46% to 51% and from 4% to 24% for the X chromosome and autosomes, respectively. While dependent on h, the magnitude of the difference between α values estimated for these two systems is highly statistically significant over a range of biologically realistic parameter values, suggesting faster-X has been operating in humans.


Craniofacial feminization and the origin of behavioral modernity

Current Anthropology Vol. 55, No. 4, August 2014

Robert L. Cieri et al.


The past 200,000 years of human cultural evolution have witnessed the persistent establishment of behaviors involving innovation, planning depth, and abstract and symbolic thought, or what has been called “behavioral modernity.” Demographic models based on increased human population density from the late Pleistocene onward have been increasingly invoked to understand the emergence of behavioral modernity. However, high levels of social tolerance, as seen among living humans, are a necessary prerequisite to life at higher population densities and to the kinds of cooperative cultural behaviors essential to these demographic models. Here we provide data on craniofacial feminization (reduction in average brow ridge projection and shortening of the upper facial skeleton) in Homo sapiens from the Middle Pleistocene to recent times. We argue that temporal changes in human craniofacial morphology reflect reductions in average androgen reactivity (lower levels of adult circulating testosterone or reduced androgen receptor densities), which in turn reflect the evolution of enhanced social tolerance since the Middle Pleistocene.


Early Neandertal disappearance in Iberia

Journal of Human Evolution DOI: 10.1016/j.jhevol.2014.06.002

New evidence of early Neanderthal disappearance in the Iberian Peninsula

Bertila Galván et al.

The timing of the end of the Middle Palaeolithic and the disappearance of Neanderthals continue to be strongly debated. Current chronometric evidence from different European sites pushes the end of the Middle Palaeolithic throughout the continent back to around 42 thousand years ago (ka). This has called into question some of the dates from the Iberian Peninsula, previously considered as one of the last refuge zones of the Neanderthals. Evidence of Neanderthal occupation in Iberia after 42 ka is now very scarce and open to debate on chronological and technological grounds. Here we report thermoluminescence (TL) and optically stimulated luminescence (OSL) dates from El Salt, a Middle Palaeolithic site in Alicante, Spain, the archaeological sequence of which shows a transition from recurrent to sporadic human occupation culminating in the abandonment of the site. The new dates place this sequence within MIS 3, between ca. 60 and 45 ka. An abrupt sedimentary change towards the top of the sequence suggests a strong aridification episode coinciding with the last Neanderthal occupation of the site. These results are in agreement with current chronometric data from other sites in the Iberian Peninsula and point towards possible breakdown and disappearance of the Neanderthal local population around the time of the Heinrich 5 event. Iberian sites with recent dates (less than 40 ka) attributed to the Middle Palaeolithic should be revised in the light of these data.


July 15, 2014

k-means and structure

I was reading one of the many negative reviews of Nicholas Wade's new book when I came across this statement:
"The problem is that Structure, which uses an algorithm called “k-means,”"
I pointed out that Structure does not use k-means and a small discussion ensued on twitter. I see that the above statement has now been removed from the article, but an endnote on the topic remains:
*Originally, I wrote that STRUCTURE uses the k-means algorithm. Some population geneticists thought that I oversimplified what STRUCTURE does. Different clustering algorithms make different assumptions. STRUCTURE is indeed very similar to k-means, but with a particular error structure – binomial instead of gaussian. This is a fine technical detail compared with the principal point, which is that k is picked by the user, and does not emerge from the data automatically. To learn more, see this Twitter chain and this and this. Thanks to Graham Coop at UC Davis.
I did not intend to spend more time on this, but since the author of the article invited me to comment at more than 140 characters on the topic, I thought it was a good idea to do so.

k-means is completely unrelated to the structure algorithm of Pritchard and Stephens. Remember that structure can be run in either a no-mixture or a mixture mode. In both modes, the input is a set of N individuals and K, the number of ancestral populations. In the no-mixture mode, individuals are assigned to one of K populations, while in the mixture mode, their ancestry proportions from K populations are inferred. (Incidentally, allele frequencies in the K ancestral populations are also inferred, although usually not reported).

k-means has no mixture mode, but rather it is a clustering algorithm which assigns individuals to K populations. Thus, it can be used to solve the same problem as the no-mixture mode of structure. The two algorithms solve this problem in entirely different ways. Saying that structure uses k-means is equivalent to saying that any partitioning method into k groups uses k-means.

More importantly, structure is commonly used in mixture mode, including in the landmark paper by Rosenberg et al. (2002) that both Wade and the author of the review refer to. In this mode, structure does not even solve the same problem as k-means. Rather than find some partitioning of N individuals into K disjoint clusters, it estimates the mixture proportions of each of N individuals into all K populations. In practice (including the paper by Rosenberg et al. 2002), many individuals often have most (or all) of their ancestry from one or a few of the K populations. If humans had no structure at a particular K, the algorithm could very well produce a jumbled mess of different colors. Instead it produces neat ancestral populations that correspond well to what may be instantly recognizable as major human groups.

The reader is invited to look at any standard implementation of k-means, such as the one in R to be convinced that k-means does not even produce the same output as structure. The point is a trivial one, but k-means estimates N parameters (the cluster label for each of N individuals), whereas structure estimates N(K-1) parameters (the mixture proportions of N individuals in K populations; only K-1 numbers are needed as they have to add up to unity).

The only thing these algorithms have in common is that they require that the user input K. This point has been used by the plethora of negative reviews of Wade's book to argue that the classification of humans into biological races is arbitrary as it is subjective (it relies on user input of K).

This is a rather weak objection, for at least a couple of reasons: first, K can also be estimated from data and there are indeed clustering algorithms (such as fineStructure) that do not require user input of K and identify a value of K and organize the K ancestral populations into a hierarchical tree whose deep splits correspond exactly to the continental human races. Another popular algorithm, ADMIXTURE, proposes a cross-validation procedure to choose K. So, the choice of K can be automated and need not be subjective.

The more important reason against the "subjective K" objection is that it does not in any way invalidate the partitioning of humans into different K at different levels of granularity. This is reasonably easy to understand: the whole field of taxonomy divides living things into a hierarchical structure. In some cases it is useful to speak of vertebrates, and in others it's useful to speak of mammals, or primates, etc. In humans it's sometimes useful to speak of the entire species H. sapiens in contradistinction to other species, when studying what is common to humans, and sometimes it is useful to speak of major populations of H. sapiens (such as Europeans or East Asians), or minor ones (e.g., Mongols and Vietnamese), when studying how human groups differ from one another. These groupings are not arbitrary, but appear when biological traits (e.g., SNPs) are subjected to various types of analysis (including structure and similar algorithms).

July 14, 2014

Armed conflict in the Sahara, ~13 thousand years ago

An interesting story from the Independent:
Scientists are investigating what may be the oldest identified race war 13,000 years after it raged on the fringes of the Sahara. French scientists working in collaboration with the British Museum have been examining dozens of skeletons, a majority of whom appear to have been killed by archers using flint-tipped arrows.


Parallel research over recent years has also been shedding new light as to who, in ethnic and racial terms, these victims were.

Work carried out at Liverpool John Moores University, the University of Alaska and New Orleans’ Tulane University indicates that they were part of the general sub-Saharan originating population – the ancestors of modern Black Africans.

The identity of their killers is however less easy to determine. But it is conceivable that they were people from a totally different racial and ethnic group – part of a North African/ Levantine/European people who lived around much of the Mediterranean Basin.

The two groups – although both part of our species, Homo sapiens – would have looked quite different from each other and were also almost certainly different culturally and linguistically. The sub-Saharan originating group had long limbs, relatively short torsos and projecting upper and lower jaws along with rounded foreheads and broad noses, while the North African/Levantine/European originating group had shorter limbs, longer torsos and flatter faces. Both groups were very muscular and strongly built.

July 08, 2014

Generalist Genes influence both reading and math ability

Nature Communications 5, Article number: 4204 doi:10.1038/ncomms5204

The correlation between reading and mathematics ability at age twelve has a substantial genetic component

Oliver S. P. Davis

Dissecting how genetic and environmental influences impact on learning is helpful for maximizing numeracy and literacy. Here we show, using twin and genome-wide analysis, that there is a substantial genetic component to children’s ability in reading and mathematics, and estimate that around one half of the observed correlation in these traits is due to shared genetic effects (so-called Generalist Genes). Thus, our results highlight the potential role of the learning environment in contributing to differences in a child’s cognitive abilities at age twelve.


Neandertal-like temporal labyrinth of Xujiayao 15

From the press release:
While it's tempting to use the finding of a Neandertal-shaped labyrinth in an otherwise distinctly "non-Neandertal" sample as evidence of population contact (gene flow) between central and western Eurasian Neandertals and eastern archaic humans in China, Trinkaus and colleagues argue that broader implications of the Xujiayao discovery remain unclear.  
"The study of human evolution has always been messy, and these findings just make it all the messier," Trinkaus said. "It shows that human populations in the real world don't act in nice simple patterns.  
"Eastern Asia and Western Europe are a long way apart, and these migration patterns took thousands of years to play out," he said. "This study shows that you can't rely on one anatomical feature or one piece of DNA as the basis for sweeping assumptions about the migrations of hominid species from one place to another."
I think this study highlights the possibility that some of the traits thought to be characteristic of Neandertals may in fact be part of Eurasian hominins in general, and the fact that they have been associated with Neandertals is a consequence of the much greater attention paid to that species until recently. As East Eurasian Pleistocene Homo becomes better described, it may become clear what are indeed the traits that were specific to H. neanderthalensis.

PNAS doi: 10.1073/pnas.1410735111

Temporal labyrinths of eastern Eurasian Pleistocene humans

Xiu-Jie Wu et al.

One of the morphological features that has been identified as uniquely derived for the western Eurasian Neandertals concerns the relative sizes and positions of their semicircular canals. In particular, they exhibit a relatively small anterior canal, a relatively larger lateral one, and a more inferior position of the posterior one relative to the lateral one. These discussions have not included full paleontological data on eastern Eurasian Pleistocene human temporal labyrinths, which have the potential to provide a broader context for assessing Pleistocene Homo trait polarities. We present the temporal labyrinths of four eastern Eurasian Pleistocene Homo, one each of Early (Lantian 1), Middle (Hexian 1), and Late (Xujiayao 15) Pleistocene archaic humans and one early modern human (Liujiang 1). The labyrinths of the two earlier specimens and the most recent one conform to the proportions seen among western early and recent modern humans, reinforcing the modern human pattern as generally ancestral for the genus Homo. The labyrinth of Xujiayao 15 is in the middle of the Neandertal variation and separate from the other samples. This eastern Eurasian labyrinthine dichotomy occurs in the context of none of the distinctive Neandertal external temporal or other cranial features. As such, it raises questions regarding possible cranial and postcranial morphological correlates of Homo labyrinthine variation, the use of individual “Neandertal” features for documenting population affinities, and the nature of late archaic human variation across Eurasia.


July 02, 2014

Altitude adaptation in Tibetans came from Denisovans

This is somewhat strange given that Denisova cave is not at high altitude.

Nature (2014) doi:10.1038/nature13408

Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA

Emilia Huerta-Sánchez et al.

As modern humans migrated out of Africa, they encountered many new environmental conditions, including greater temperature extremes, different pathogens and higher altitudes. These diverse environments are likely to have acted as agents of natural selection and to have led to local adaptations. One of the most celebrated examples in humans is the adaptation of Tibetans to the hypoxic environment of the high-altitude Tibetan plateau1, 2, 3. A hypoxia pathway gene, EPAS1, was previously identified as having the most extreme signature of positive selection in Tibetans4, 5, 6, 7, 8, 9, 10, and was shown to be associated with differences in haemoglobin concentration at high altitude. Re-sequencing the region around EPAS1 in 40 Tibetan and 40 Han individuals, we find that this gene has a highly unusual haplotype structure that can only be convincingly explained by introgression of DNA from Denisovan or Denisovan-related individuals into humans. Scanning a larger set of worldwide populations, we find that the selected haplotype is only found in Denisovans and in Tibetans, and at very low frequency among Han Chinese. Furthermore, the length of the haplotype, and the fact that it is not found in any other populations, makes it unlikely that the haplotype sharing between Tibetans and Denisovans was caused by incomplete ancestral lineage sorting rather than introgression. Our findings illustrate that admixture with other hominin species has provided genetic variation that helped humans to adapt to new environments.