Thursday, 28 March 2013

Morphological and mtDNA analysis of Mezzena mandible


I've written about late Neandertals becoming more AMH-like, and a new study on an Italian specimen that postdates the arrival of AMH in Europe lends some further support to that idea.
The Mezzena jaw has Neandertal mtDNA and shares a number of morphological traits with other Neandertals, but its overall shape places it within the cluster of modern humans  (triangles; figure on the left). Notice also that Qafzeh 9 (Q9) and Shkul V (SV) are also within the cluster of modern humans, and Spy 1 (a Neandertal) is actually closer to modern humans than to other Neandertals.
From the paper:

The position on the scatter plot of our specimen of interest, Mezzena, has been calculated a posteriori. Unsurprisingly, the Mezzena mandible does not present any particular affinities with mid-Pleistocene specimens. It is most similar to AMHs being positioned within the H. sapiens cloud of points and the DFA classifies the specimen with modern humans (Table S7). Especially its shape is similar to that of Ohalo II and to a lesser extent to the recent modern human specimen China5. However, it should be noted that its position also indicates affinities with some Neanderthal specimens: the late Neanderthal Spy 1 and Saint-Césaire, the Near-East specimens Tabūn II and Amud 1, and to a lesser extent the classic Neanderthals La Ferrassie 1 and Guattari III (Figure 2).
According to the authors:
In this light, we can interpret the position of the Mezzena mandible which stands within the modern human shape space, while presenting strong shape similarities with some Neanderthal specimens. Such a conflicting taxonomical position is not surprising, considering the geological age of the mandible [30]. Indeed, numerous late Neanderthals such as Spy 1, Saint Césaire and the Near-East mandibles Amud 1 and Tabun II possess hints of a chin (i.e. tuber symphyseo) though not a true modern human morphology [37], [51]. Late Neanderthals lived in area where AMHs might have been already present [2], [23], [52], while the Levantine fossils are displaying a less derived Neanderthal morphology [35], [36]. 
Therefore, in our view, this change in morphology of the mandibular chin among the fossils of Mezzena and other late Neanderthals could have been the result of a small degree of interbreeding with AMHs.
It would be interesting to sequence Mezzena to confirm the existence of AMH admixture.
PLoS ONE 8(3): e59781. doi:10.1371/journal.pone.0059781
Possible Interbreeding in Late Italian Neanderthals? New Data from the Mezzena Jaw (Monti Lessini, Verona, Italy)
Silvana Condemi et al.
In this article we examine the mandible of Riparo Mezzena a Middle Paleolithic rockshelter in the Monti Lessini (NE Italy, Verona) found in 1957 in association with Charentian Mousterian lithic assemblages. Mitochondrial DNA analysis performed on this jaw and on other cranial fragments found at the same stratigraphic level has led to the identification of the only genetically typed Neanderthal of the Italian peninsula and has confirmed through direct dating that it belongs to a late Neanderthal. Our aim here is to re-evaluate the taxonomic affinities of the Mezzena mandible in a wide comparative framework using both comparative morphology and geometric morphometrics. The comparative sample includes mid-Pleistocene fossils, Neanderthals and anatomically modern humans. This study of the Mezzena jaw shows that the chin region is similar to that of other late Neanderthals which display a much more modern morphology with an incipient mental trigone (e.g. Spy 1, La Ferrassie, Saint-Césaire). In our view, this change in morphology among late Neanderthals supports the hypothesis of anatomical change of late Neanderthals and the hypothesis of a certain degree of interbreeding with AMHs that, as the dating shows, was already present in the European territory. Our observations on the chin of the Mezzena mandible lead us to support a non abrupt phylogenetic transition for this period in Europe.

Refined IBD in Beagle 4


The Beagle page doesn't show version 4 yet, but I'm sure it will eventually turn up there since this paper has just been published.
Genetics doi: 10.1534/genetics.113.150029

Improving the Accuracy and Efficiency of Identity by Descent Detection in Population Data
Brian L. Browning and Sharon R. Browning
Segments of identity by descent (IBD) detected from high-density genetic data are useful for many applications, including long-range phase determination, phasing family data, imputation, IBD mapping and heritability analysis in founder populations. We present Refined IBD, a new method for IBD segment detection. Refined IBD achieves both computational efficiency and highly accurate IBD segment reporting by searching for IBD in two steps. The first step (identification) uses the GERMLINE algorithm to find shared haplotypes exceeding a length threshold. The second step (refinement), evaluates candidate segments with a probabilistic approach to assess the evidence for IBD. Like GERMLINE, Refined IBD allows for IBD reporting on a haplotype level, which facilitates determination of multi-individual IBD and allows for haplotype-based downstream analyses. To investigate the properties of Refined IBD, we simulate SNP data from a model with recent super-exponential population growth that is designed to match UK data. The simulation results show that Refined IBD achieves a better power/accuracy profile than fastIBD or GERMLINE. We find that a single run of Refined IBD achieves greater power than 10 runs of fastIBD. We also apply Refined IBD to SNP data for samples from the UK and from Northern Finland, and describe the IBD sharing in these data sets. Refined IBD is powerful, highly accurate, easy to use, and is implemented in Beagle version 4.

Wednesday, 27 March 2013

Was Homo floresiensis a cretin?


From the paper:

We are therefore disturbed that Brown (2012), though selecting those features that imply to him that LB1 could not be a cretin, does not also cite the many features in those same publications that imply cretinism, nor does he cite the many more features, both observational and quantitative implying cretinism, in Oxnard (2008), Oxnard et al. (2011), and Dennison et al. (2012). What is sorely needed is an independent review of, and free access to, the Liang Bua material.

HOMO - Journal of Comparative Human Biology
Volume 63, Issue 6, December 2012, Pages 407–412
More on the Liang Bua finds and modern human cretins
Charles Oxnard et al.
Brown (2012: LB1 and LB6 Homo floresiensis are not modern human (Homo sapiens) cretins, Journal of Human Evolution) makes errors of fact, omission and interpretation. Brown's comments refer, among others, to (1) delayed growth and development indicated by unfused epiphyses, (2) postcranial limb proportions: limbs to trunk, between limbs, and within limbs, (3) postcranial bone torsions and angles, (4) postcranial robusticity, real and apparent, (5) skull features, and (6) cretinism on Flores. In each of these areas, much information about cretins is incorrect and much information (Oxnard et al., 2010) comparing the Liang Bua remains with cretins is ignored.


Population structure in the Netherlands


The three PCs are color-coded in panels b,c,d.
European Journal of Human Genetics , (27 March 2013) | doi:10.1038/ejhg.2013.48
Population structure, migration, and diversifying selection in the Netherlands
Abdel Abdellaoui et al.
Genetic variation in a population can be summarized through principal component analysis (PCA) on genome-wide data. PCs derived from such analyses are valuable for genetic association studies, where they can correct for population stratification. We investigated how to capture the genetic population structure in a well-characterized sample from the Netherlands and in a worldwide data set and examined whether (1) removing long-range linkage disequilibrium (LD) regions and LD-based SNP pruning significantly improves correlations between PCs and geography and (2) whether genetic differentiation may have been influenced by migration and/or selection. In the Netherlands, three PCs showed significant correlations with geography, distinguishing between: (1) North and South; (2) East and West; and (3) the middle-band and the rest of the country. The third PC only emerged with minimized LD, which also significantly increased correlations with geography for the other two PCs. In addition to geography, the Dutch North–South PC showed correlations with genome-wide homozygosity (r=0.245), which may reflect a serial-founder effect due to northwards migration, and also with height (♂: r=0.142, ♀: r=0.153). The divergence between subpopulations identified by PCs is partly driven by selection pressures. The first three PCs showed significant signals for diversifying selection (545 SNPs - the majority within 184 genes). The strongest signal was observed between North and South for the functional SNP in HERC2 that determines human blue/brown eye color. Thus, this study demonstrates how to increase ancestry signals in a relatively homogeneous population and how those signals can reveal evolutionary history.


Monday, 25 March 2013

Admixture and pigmentation in Cape Verde


The interesting thing about this paper is that it shows that one can explain skin color in people from Cape Verde better if one uses their proportion of African/European admixture, rather than by looking at individuals' genotypes at loci associated with the trait. This probably means that many loci of minor effect on the trait differentiate Europeans from Africans.
Prediction of skin color based on ancestry is much better than prediction of eye color from the same, which is not surprising since skin color is a highly polygenic trait.
PLoS Genet 9(3): e1003372. doi:10.1371/journal.pgen.1003372
Genetic Architecture of Skin and Eye Color in an African-European Admixed Population
Sandra Beleza et al.
Variation in human skin and eye color is substantial and especially apparent in admixed populations, yet the underlying genetic architecture is poorly understood because most genome-wide studies are based on individuals of European ancestry. We study pigmentary variation in 699 individuals from Cape Verde, where extensive West African/European admixture has given rise to a broad range in trait values and genomic ancestry proportions. We develop and apply a new approach for measuring eye color, and identify two major loci (HERC2[OCA2] P = 2.3×10−62, SLC24A5 P = 9.6×10−9) that account for both blue versus brown eye color and varying intensities of brown eye color. We identify four major loci (SLC24A5 P = 5.4×10−27, TYR P = 1.1×10−9, APBA2[OCA2] P = 1.5×10−8, SLC45A2 P = 6×10−9) for skin color that together account for 35% of the total variance, but the genetic component with the largest effect (~44%) is average genomic ancestry. Our results suggest that adjacent cis-acting regulatory loci for OCA2 explain the relationship between skin and eye color, and point to an underlying genetic architecture in which several genes of moderate effect act together with many genes of small effect to explain ~70% of the estimated heritability.


Long live the 25th March 1821