July 31, 2014

Wine cup of Pericles found

Wine cup used by Pericles found in grave north of Athens
Experts are "99 per cent" sure that the cup was used by the Athenian statesman, as one of the other names listed, Ariphron, is that of Pericles' elder brother.

"The name Ariphron is extremely rare," Angelos Matthaiou, secretary of the Greek Epigraphic Society, told the newspaper.

"Having it listed above that of Pericles makes us 99 per cent sure that these are the two brothers," he said.
Finding the cup of Pericles is cool, but finding his actual tomb would be even cooler. Thanks to Pausanias and other ancient observers, the location and identity of many of the tombs of ancient prominent Athenians is known.

July 29, 2014

Lethal mutations quantified

A very interesting new preprint on the arXiv (so it can be freely read). The founder population is the Hutterites. The key sentence:
Our approach indicates that on average, one in every two humans carries a recessive lethal allele on the autosomes that lead to lethality after birth and before reproductive age or to complete sterility.

arXiv:1407.7518 [q-bio.PE]

An estimate of the average number of recessive lethal mutations carried by humans

Ziyue Gao, Darrel Waggoner, Matthew Stephens, Carole Ober, Molly Przeworski

The effects of inbreeding on human health depend critically on the number and severity of recessive, deleterious mutations carried by individuals. In humans, existing estimates of these quantities are based on comparisons between consanguineous and non-consanguineous couples, an approach that confounds socioeconomic and genetic effects of inbreeding. To circumvent this limitation, we focused on a founder population with almost complete Mendelian disease ascertainment and a known pedigree. By considering all recessive lethal diseases reported in the pedigree and simulating allele transmissions, we estimated that each haploid set of human autosomes carries on average 0.29 (95% credible interval [0.10, 0.83]) autosomal, recessive alleles that lead to complete sterility or severe disorders at birth or before reproductive age when homozygous. Comparison to existing estimates of the deleterious effects of all recessive alleles suggests that a substantial fraction of the burden of autosomal, recessive variants is due to single mutations that lead to death between birth and reproductive age. In turn, the comparison to estimates from other eukaryotes points to a surprising constancy of the average number of recessive lethal mutations across organisms with markedly different genome sizes.

Link

July 26, 2014

Ancestry of Cubans

PLoS Genet 10(7): e1004488. doi:10.1371/journal.pgen.1004488

Cuba: Exploring the History of Admixture and the Genetic Basis of Pigmentation Using Autosomal and Uniparental Markers

Beatriz Marcheco-Teruel et al.

We carried out an admixture analysis of a sample comprising 1,019 individuals from all the provinces of Cuba. We used a panel of 128 autosomal Ancestry Informative Markers (AIMs) to estimate the admixture proportions. We also characterized a number of haplogroup diagnostic markers in the mtDNA and Y-chromosome in order to evaluate admixture using uniparental markers. Finally, we analyzed the association of 16 single nucleotide polymorphisms (SNPs) with quantitative estimates of skin pigmentation. In the total sample, the average European, African and Native American contributions as estimated from autosomal AIMs were 72%, 20% and 8%, respectively. The Eastern provinces of Cuba showed relatively higher African and Native American contributions than the Western provinces. In particular, the highest proportion of African ancestry was observed in the provinces of Guantánamo (40%) and Santiago de Cuba (39%), and the highest proportion of Native American ancestry in Granma (15%), Holguín (12%) and Las Tunas (12%). We found evidence of substantial population stratification in the current Cuban population, emphasizing the need to control for the effects of population stratification in association studies including individuals from Cuba. The results of the analyses of uniparental markers were concordant with those observed in the autosomes. These geographic patterns in admixture proportions are fully consistent with historical and archaeological information. Additionally, we identified a sex-biased pattern in the process of gene flow, with a substantially higher European contribution from the paternal side, and higher Native American and African contributions from the maternal side. This sex-biased contribution was particularly evident for Native American ancestry. Finally, we observed that SNPs located in the genes SLC24A5 and SLC45A2 are strongly associated with melanin levels in the sample.

Link

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.

Link

Craniofacial feminization and the origin of behavioral modernity

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

Robert L. Cieri et al.

Abstract:

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.

Link

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.

Link

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.

Link

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.

Link

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.

Link

June 26, 2014

4,000-year old chariot burial from Georgia

This would make it roughly contemporaneous to the chariot burials of the Sintashta-Petrovka culture of the European steppe.

4,000-Year-Old Burial with Chariots Discovered in South Caucasus
An ancient burial containing chariots, gold artifacts and possible human sacrifices has been discovered by archaeologists in the country of Georgia, in the south Caucasus.

The burial site, which would've been intended for a chief, dates back over 4,000 years to a time archaeologists call the Early Bronze Age, said Zurab Makharadze, head of the Centre of Archaeology at the Georgian National Museum.

Archaeologists discoveredthe timber burial chamber within a 39-foot-high (12 meters) mound called a kurgan. When the archaeologists reached the chamber they found an assortment of treasures, including two chariots, each with four wooden wheels. [See Images of the Burial Chamber & Chariots]

...

The burial dates back to a time before domesticated horses appeared in the area, Makharadze said. While no animals were found buried with the chariots, he said, oxen would have pulled them.

Neandertals ate their veggies

PLoS ONE 9(6): e101045. doi:10.1371/journal.pone.0101045

The Neanderthal Meal: A New Perspective Using Faecal Biomarkers

Ainara Sistiaga et al.

Neanderthal dietary reconstructions have, to date, been based on indirect evidence and may underestimate the significance of plants as a food source. While zooarchaeological and stable isotope data have conveyed an image of Neanderthals as largely carnivorous, studies on dental calculus and scattered palaeobotanical evidence suggest some degree of contribution of plants to their diet. However, both views remain plausible and there is no categorical indication of an omnivorous diet. Here we present direct evidence of Neanderthal diet using faecal biomarkers, a valuable analytical tool for identifying dietary provenance. Our gas chromatography-mass spectrometry results from El Salt (Spain), a Middle Palaeolithic site dating to ca. 50,000 yr. BP, represents the oldest positive identification of human faecal matter. We show that Neanderthals, like anatomically modern humans, have a high rate of conversion of cholesterol to coprostanol related to the presence of required bacteria in their guts. Analysis of five sediment samples from different occupation floors suggests that Neanderthals predominantly consumed meat, as indicated by high coprostanol proportions, but also had significant plant intake, as shown by the presence of 5β-stigmastanol. This study highlights the applicability of the biomarker approach in Pleistocene contexts as a provider of direct palaeodietary information and supports the opportunity for further research into cholesterol metabolism throughout human evolution.

Link

June 21, 2014

Nonmetric dental traits and the origin of East Asians

AJPA DOI: 10.1002/ajpa.22537

Demographic transitions and migration in prehistoric East/Southeast Asiathrough the lens of nonmetric dental traits

Hirofumi Matsumura1,and Marc F. Oxenham

The aim of this study is to examine and assess the nonmetric dental trait evidence for the population history of East and Southeast Asia and, more specifically, to test the two-layer hypothesis for the peopling of Southeast Asia. Using a battery of 21 nonmetric dental traits we examine 7,247 individuals representing 58 samples drawn from East and Southeast Asian populations inhabiting the region from the late Pleistocene, through the Neolithic, Bronze Age, Iron Age, and into the historic and modern periods. The chief data reduction technique is a neighbor-joining tree generated from the triangular matrix of mean measure of divergence values. Principal findings indicated a major dichotomization of the dataset into (1) an early Southeast Asian sample with close affinities to modern Australian and Melanesian populations and (2) a very distinct grouping of ancient and modern Northeast Asians. Distinct patterns of clinal variation among Neolithic and post-Neolithic Mainland Southeast Asian samples suggest a center to periphery spread of genes into the region from Northeast Asia. This pattern is consistent with archaeological and linguistic evidence for demic diffusion that accompanied agriculturally driven population expansion in the Neolithic. Later Metal Age affinities between Island and Mainland coastal populations with Northeast Asian series is likely a consequence of a South China Sea interaction sphere operating from at least 500 BCE, if not from the Neolithic. Such results provide extensive support for the two-layer hypothesis to account for the population history of the region. Am J Phys Anthropol, 2014. © 2014 Wiley Periodicals, Inc.

Link

Sima de los Huesos hominins: ~430 thousand years old and on the Neandertal lineage

Science 20 June 2014: Vol. 344 no. 6190 pp. 1358-1363 DOI: 10.1126/science.1253958

Neandertal roots: Cranial and chronological evidence from Sima de los Huesos

J. L. Arsuaga et al.

Seventeen Middle Pleistocene crania from the Sima de los Huesos site (Atapuerca, Spain) are analyzed, including seven new specimens. This sample makes it possible to thoroughly characterize a Middle Pleistocene hominin paleodeme and to address hypotheses about the origin and evolution of the Neandertals. Using a variety of techniques, the hominin-bearing layer could be reassigned to a period around 430,000 years ago. The sample shows a consistent morphological pattern with derived Neandertal features present in the face and anterior vault, many of which are related to the masticatory apparatus. This suggests that facial modification was the first step in the evolution of the Neandertal lineage, pointing to a mosaic pattern of evolution, with different anatomical and functional modules evolving at different rates.

Link

June 15, 2014

Chimp mutation rate is equal to human mutation rate but driven more by males

This is important because (a) it shows evidence for the "slow" mutation rate in a species related to humans, (b) it shows that chimp and human mutation rates are equal and so using the human mutation rate in studies of divergence with chimps is justified, and (c) it is driven differently by males/females than in humans.

Science 13 June 2014: Vol. 344 no. 6189 pp. 1272-1275
DOI: 10.1126/science.344.6189.1272

Strong male bias drives germline mutation in chimpanzees

Oliver Venn

ABSTRACT

Germline mutation determines rates of molecular evolution, genetic diversity, and fitness load. In humans, the average point mutation rate is 1.2 × 10−8 per base pair per generation, with every additional year of father’s age contributing two mutations across the genome and males contributing three to four times as many mutations as females. To assess whether such patterns are shared with our closest living relatives, we sequenced the genomes of a nine-member pedigree of Western chimpanzees, Pan troglodytes verus. Our results indicate a mutation rate of 1.2 × 10−8 per base pair per generation, but a male contribution seven to eight times that of females and a paternal age effect of three mutations per year of father’s age. Thus, mutation rates and patterns differ between closely related species.

Link