Blue eyes, facial shape, and perceived trustworthiness

Blue eyes, facial shape, and perceived trustworthiness

A new paper suggests that Czechs tend to view brown-eyed people as more trustworthy than blue-eyed ones, although the difference seems to be due to differences in facial structure between brown- and blue-eyed people; an article in Scientific American covers this new paper fairly well.

I will add that the location of the sample (Czech Republic) is interesting, as it is intermediate between the Baltic area (where light eye pigmentation reaches quasi-fixation, and, hence, presumably, light eyes are not viewed with any suspicion) and southeastern Europe and Anatolia (where there is well-documented folklore about the association of eye pigmentation with the "evil eye").

I had encountered an explanation for this phenomenon in a work by P.G. Maxwell-Stuart on ancient color terminology, in which an argument was made that in predominantly dark-eyed peoples, light eyes -because of their rarity- may have an indirect association with glaucoma and viewed suspiciously for that reason -perceived chance of morbidity; the Wikipedia article suggests the phenomenon is explained on the basis of encounters with light-eyed foreigners who might be unaware of cultural norms against direct staring. But, the frequency of different eye colors in Czechs today is probably fairly balanced, making either explanation unsatisfactory.

Getting back to the article at hand, it appears that -at least in men- blue eyes are associated with a suite of other facial features. Razib offers the suggestion that the possible disadvantage conferred by reduced "trustworthiness" may be compensated in another way through pleiotropy, and the authors suggest:

The trade-off between a preference for colorful and visible physical features and the advantage of a trustworthy-looking face might have contributed to the high variability of European eye and hair color.

But, I'll get back to the possibility that the phenomenon may be driven by a historical process, i.e., the encounter between peoples who differed statistically in eye pigmentation and other facial features.

The picture on the left is from the Gospel Book of Otto III and is about 1,000 years old. Now, all eyes appear conventionally painted as brown dots here, but we can notice that the different provinces are painted with different hair color, with Sclavinia being darker than Germania and lighter than Gallia and Roma. This might make some sense, since Germanic peoples are thought to have originated in northern Germany/southern Scandinavia, and Slavs in C/E Europe (perhaps somewhere between Poland and Ukraine).

This raises the possibility that early Slavs were phenotypically somewhere in the middle of the European pigmentation continuum, although their exact position therein might only be determined with ancient DNA evidence. Today, the lighter-pigmented Slavs are probably those close to the Baltic (e.g., Russians and Poles), the darker ones from the Balkans, perhaps indicating different types of gene flow ("northern" Germanic/Baltic/Finno-Ugrian vs. "southern" Thraco-Illyrian-Greek).

If this is correct, then the slightly negative association of blue eyes in the present Czechs might be a culturally-transmitted vestige of inter-ethnic contact during the medieval period. A possible test would be to repeat the experiment with the Czechs' German neighbors, in which the process ought to operate in reverse -if my hypothesis is correct.

PLoS ONE 8(1): e53285. doi:10.1371/journal.pone.0053285

Trustworthy-Looking Face Meets Brown Eyes

Karel Kleisner et al.

We tested whether eye color influences perception of trustworthiness. Facial photographs of 40 female and 40 male students were rated for perceived trustworthiness. Eye color had a significant effect, the brown-eyed faces being perceived as more trustworthy than the blue-eyed ones. Geometric morphometrics, however, revealed significant correlations between eye color and face shape. Thus, face shape likewise had a significant effect on perceived trustworthiness but only for male faces, the effect for female faces not being significant. To determine whether perception of trustworthiness was being influenced primarily by eye color or by face shape, we recolored the eyes on the same male facial photos and repeated the test procedure. Eye color now had no effect on perceived trustworthiness. We concluded that although the brown-eyed faces were perceived as more trustworthy than the blue-eyed ones, it was not brown eye color per se that caused the stronger perception of trustworthiness but rather the facial features associated with brown eyes.

Link

Genetic variation in gorillas quantified (Scally et al. 2013)

Genetic variation in gorillas quantified (Scally et al. 2013)

The allele frequency spectrum (Figure 3) from the paper is shown on the left. From the paper:

Figure 3 shows the resulting mean conditional AFS for nine western lowland gorillas (excluding the three lowest-coverage samples as above), and comparable samples from three human populations whose ancestry derives from Africa, Asia and Europe [22]. In a population whose effective size has remained constant, the theoretical expectation for such a conditional AFS is a straight line of constant negative slope [23], shown by the dashed line in Figure 3. Compared to this, western lowland gorillas show a deficit of rare alleles, consistent with their having undergone genetic drift due to a bottleneck or other reduction in effective population size during their demographic history. The similar signal in non-African human populations has been attributed to population contraction associated with the out-of-Africa event [24]. By contrast to the gorillas and the non-African humans, the African YRI population in Figure 3 shows an excess of rare alleles, consistent with population expansion and again similar to the signal seen in other African human data [24]. 

A population bottleneck culls rare alleles, and thus leads to a "dip" in the AFS on the left. An allele that occurs at, say, 10% frequency in a very small population is more likely to go extinct "by accident" than one which occurs at exactly the same frequency in a large population. You can think of this by taking the two extreme cases:

1. if an allele exists in exactly one physical copy (i.e., 1 copy in 5 diploid individuals = 10% frequency), then its bearer must survive, must reproduce, and the allele must be inherited by one offspring in order for it survive.
2. if the population has infinite size, then 10% frequency is still = infinite number of physical copies, hence the allele will survive no matter what [unless it always kills its unlucky bearer, but then how did it end up at 10% frequency in the first place?]

On the other hand, low-frequency alleles become more prevalent when the population expands in the recent past, because there is an ever growing number of bodies, an ever growing number of mutated alleles, but not enough time for these new alleles to grow in frequency.

A different mechanism whereby low-frequency alleles appear in excess in a population is admixture. African Americans, for example, have ~20% European ancestry, so any alleles that are present in Europeans and absent in Sub-Saharan Africans would tend to appear as low-frequency alleles in African Americans.

It is an open question to what degree modern human differences in the presence of low-frequency alleles are due to bottlenecks (such as the Out-of-Africa event) and to what degree they are due to admixture with other non-modern groups. A recent paper discovered a signal of Neandertal admixture when one considered alleles with 10% or less frequency in Europeans.

In the case of African Americans, we can tell that some of their low-frequency alleles were acquired by admixture with Europeans, because we have European samples; and, in the case of Europeans, we can tell that some of their low-frequency alleles were acquired by admixture with Neandertals, because we have a Neandertal genome. But, we don't have many of the genomes of archaic human groups that may have contributed variants to modern humans (and in some cases, like the Denisovans, we did not even know they existed in the first place!), so we must always keep in mind the possibility that such alleles may lurk on the left side of the AFS.

arXiv:1301.1729 [q-bio.PE]

A genome-wide survey of genetic variation in gorillas using reduced representation sequencing

Aylwyn Scally et al.

All non-human great apes are endangered in the wild, and it is therefore important to gain an understanding of their demography and genetic diversity. To date, however, genetic studies within these species have largely been confined to mitochondrial DNA and a small number of other loci. Here, we present a genome-wide survey of genetic variation in gorillas using a reduced representation sequencing approach, focusing on the two lowland subspecies. We identify 3,274,491 polymorphic sites in 14 individuals: 12 western lowland gorillas (Gorilla gorilla gorilla) and 2 eastern lowland gorillas (Gorilla beringei graueri). We find that the two species are genetically distinct, based on levels of heterozygosity and patterns of allele sharing. Focusing on the western lowland population, we observe evidence for population substructure, and a deficit of rare genetic variants suggesting a recent episode of population contraction. In western lowland gorillas, there is an elevation of variation towards telomeres and centromeres on the chromosomal scale. On a finer scale, we find substantial variation in genetic diversity, including a marked reduction close to the major histocompatibility locus, perhaps indicative of recent strong selection there. These findings suggest that despite their maintaining an overall level of genetic diversity equal to or greater than that of humans, population decline, perhaps associated with disease, has been a significant factor in recent and long-term pressures on wild gorilla populations.

Link

Estonian Biocentre public data (corrected)

Estonian Biocentre public data (corrected)

There was apparently some ID reshuffling needed in the Estonian Biocentre data, so if any of you downloaded it before, make sure you get the corrected versions.

mtDNA variation in East Africa (Boattini et al. 2013)

mtDNA variation in East Africa (Boattini et al. 2013)

From the paper:

Language diversity in EA fits well with its complicated genetic history. In Fleming words, ‘‘Ethiopia by itself has more languages than all of Europe, even counting all the so-called dialects of the Romance family’’ (Fleming, 2006). All African linguistic phyla are found in EA: Afro-Asiatic (AA), Nilo-Saharan, Niger-Congo and Khoisan (however, the genealogical unit of Khoisan is no longer generally accepted). Among them, AA is the most differentiated, being represented by three (Omotic, Cushitic, Semitic) of its six major clades (the others being Chadic, Berber and Egyptian). Omotic and Cushitic are considered the deepest clades of AA, and both are found almost exclusively in the Horn of Africa, along with the linguistic relict Ongota that is traditionally assigned to the Cushitic family but whose classification is still widely debated (Fleming, 2006). These observations are in agreement with a North-Eastern African origin of the AA languages, most probably in pre-Neolithic times (Ehret, 1979, 1995; Kitchen et al., 2009).

and:

This study confirms the central role of EA and the Horn of Africa in the genetic and linguistic history of a wide area spanning from Central and Northern Africa to the Levant. Our results confirm high mtDNA diversity and strong genetic structuring in EA. We were indeed able to identify three population clusters (A, B1, B2) that are related both to geography and linguistics, and signaling different population events in the history of the region. The Horn of Africa (cluster A), in accordance with its role as a major gateway between sub-Saharan Africa and the Levant, shows widespread contacts with populations from CA (AA-Chadic speakers), the Arabian peninsula and the Nile Valley. Southwards, Kenya, and Tanzania (clusters B1 and B2), despite being both heavily involved in Bantu and Nilo-Saharan pastoralist expansions, reveal traces of a more ancient genetic stratum associated with Cushitic-speaking groups (cluster B2). Conversely, Berber- and Semitic-speaking populations of NA and the Levant show only marginal traces of admixture with sub-Saharan groups, as well as a different mtDNA genetic background, making the hypothesis of a Levantine origin of AA unlikely. In conclusion, EA genetic structure configures itself as a complicated palimpsest in which more ancient strata (AA-Cushiticspeaking groups) are largely overridden by recent different migration events. Further explorations of AA-Cushitic- speaking populations – both in terms of sampled groups and typed genetic markers – will be of great importance for the reconstruction of the genetic history of EA and AA-speakers. 

The African origin of Afroasiatic would agree with its linguistic separateness from Eurasian languages, and the fact that a single branch of the family (Semitic) is likely to have originated in Asia, and fairly recently at that.

Related:

• Disentangling the histories of mtDNA haplogroups M1 and U6
• Ethiopian origins (Pagani et al. 2012)
• mtDNA and ethnic differentiation in East Africa

Am J Phys Anthropol DOI: 10.1002/ajpa.22212

mtDNA variation in East Africa unravels the history of afro-asiatic groups

Alessio Boattini et al.

East Africa (EA) has witnessed pivotal steps in the history of human evolution. Due to its high environmental and cultural variability, and to the long-term human presence there, the genetic structure of modern EA populations is one of the most complicated puzzles in human diversity worldwide. Similarly, the widespread Afro-Asiatic (AA) linguistic phylum reaches its highest levels of internal differentiation in EA. To disentangle this complex ethno-linguistic pattern, we studied mtDNA variability in 1,671 individuals (452 of which were newly typed) from 30 EA populations and compared our data with those from 40 populations (2970 individuals) from Central and Northern Africa and the Levant, affiliated to the AA phylum. The genetic structure of the studied populations—explored using spatial Principal Component Analysis and Model-based clustering—turned out to be composed of four clusters, each with different geographic distribution and/or linguistic affiliation, and signaling different population events in the history of the region. One cluster is widespread in Ethiopia, where it is associated with different AA-speaking populations, and shows shared ancestry with Semitic-speaking groups from Yemen and Egypt and AA-Chadic-speaking groups from Central Africa. Two clusters included populations from Southern Ethiopia, Kenya and Tanzania. Despite high and recent gene-flow (Bantu, Nilo-Saharan pastoralists), one of them is associated with a more ancient AA-Cushitic stratum. Most North-African and Levantine populations (AA-Berber, AA-Semitic) were grouped in a fourth and more differentiated cluster. We therefore conclude that EA genetic variability, although heavily influenced by migration processes, conserves traces of more ancient strata.

Link

Y-haplogroup Q and Native American origins (Regueiro et al. 2013)

Y-haplogroup Q and Native American origins (Regueiro et al. 2013)

From the paper:

Table 2 provides coalescence time estimations based on 15 Y-STR loci for haplogroup Q-M242 and subhaplogroups Q1a3-M346, Q1a3a-L54 and Q1a3a1-M3. Due to the limitations and assumptions associated with the current calibrations of Y-STR mutation rates (Zhivotovsky et al., 2004; Goedbloed et al., 2009; Ravid-Amir and Rosset, 2010; Burgarella and Navascue/s, 2011), the dates generated in this study should only be taken as relative estimates. However, these relative values may be useful for comparisons among populations. Using the pedigree mutation rate (average mutation rate of 0.0025 per locus per generation; Goedbloed et al., 2009), we obtained coalescence estimates that were approximately three times younger than those calculated with the evolutionary rate (average mutation rate of 0.00069 per locus per generation; Zhivotovsky et al., 2004). In general, the genealogical estimates are more compatible with archeological data than the evolutionary rates 

According to Table 2, the oldest TMRCA for M242 chromosomes is ~11ky using the pedigree rate and ~29ky using the evolutionary rate. In a previous post, I argued that in order to account for the fact that modern-day haplogroups have millions of modern representatives, a fairly high growth rate must be assumed for them, with one estimate of the effective rate being 0.84μ, where μ is the genealogical rate. Ergo, the ~11ky time estimate must be updated to something like ~13ky, which corresponds reasonably well -within the confidence limits- to the first colonization of the Americas.

The paper's conclusion:

Overall, our data are best explained by invoking a single major pre-Holocene migration that proceeded eastward in a trans-continental trek across Beringia and then southward to transverse the length of Americas-a scenario that fits nicely with the South Altaian origin of Native Americans as proposed by Dulik et al. (2012). The subsequent winnowing of the Native American gene pool via repeated founder effects and bottleneck events could have produced the Y chromosome distribution illustrated on the pie map (Fig. 2). The Q haplogroup frequency pattern of the Native Americans features: 1) a dramatic reduction of the ancestral L54 and MEH2 lineages of Central Asia and/or northeast Siberia and 2) a concomitant increase in the derived M3 state, which exerts total domination of the Q landscape in nearly all of South American reference populations examined. We also see evidence of a dramatic Mesoamerican postmigration population growth in the ubiquitous and diverse Y-STR profiles of the Mayan and other Mesoamerican populations in the PCA (Fig. 4), and the M242 and M3 networks (Fig. 5A,D). In the case of the Mayans, this demographic population growth was most likely fueled by the agricultural- and trade-based subsistence adopted during the pre-Classic age of their empire. Our results indicate that the oldest dates for Q-M242 are found in Northeast Siberia followed by populations from Mesoamerica, which is most likely a consequence of demographic expansion as discussed above. The diversity levels observed in the Altaian and Tuvinian regions of Central Asia, the lowest of all populations examined may be the consequence of bottleneck events fostered by the spatial isolation and low effective population size characteristic of a nomadic lifestyle. 

It seems likely that the migration of Q-M242 descendants corresponds mainly to the "First Americans" sensu Reich et al. (2012) which makes up the bulk of Amerindian Y-chromosomes. Interestingly:

The recently sequenced genome of a Paleo-Eskimo _ 4,000 years old, belonging to the Saqqaq culture, provides evidence for a more recent migration from Siberia into the New World some 5.5 kya, independent of the pre-Holocene penetration that gave rise to the modern Native Americans and Inuit (Rasmussen et al., 2010). In addition, the Paleo-Eskimo individual is a member of the haplogroup Q1a*-MEH2 suggesting that this lineage likely traces a population migration originating in Northeast Siberia across the Bering Strait (Rasmussen et al., 2010). 

and:

In the MDS plot, we observe a segregation between Eskimo populations from northeast Siberia and the Native American populations, differentiation likely due to the northeast Siberian presence of the MEH2 mutation which defines the Q1a* haplogroup.  

So, it would appear that the additional "Eskimo" wave may be discernible within Q itself; the third "Na-Dene" wave cannot be distinguished on the basis of Q alone, and probably reflects the later entry of haplogroup C.


Am J Phys Anthropol DOI: 10.1002/ajpa.22207

On the Origins, Rapid Expansion and Genetic Diversity of Native Americans From Hunting-Gatherers to Agriculturalists

Maria Regueiro et al.

Given the importance of Y-chromosome haplogroup Q to better understand the source populations of contemporary Native Americans, we studied 8 biallelic and 17 microsatellite polymorphisms on the background of 128 Q Y-chromosomes from geographically targeted populations. The populations examined in this study include three from the Tuva Republic in Central Asia (Bai-Tai, Kungurtug, and Toora-Hem, n = 146), two from the northeastern tip of Siberia (New Chaplino and Chukchi, n = 32), and two from Mesoamerica (Mayans from Yucatan, Mexico n = 72, and Mayans from the Guatemalan Highlands, n = 43). We also see evidence of a dramatic Mesoamerican post-migration population growth in the ubiquitous and diverse Y-STR profiles of the Mayan and other Mesoamerican populations. In the case of the Mayans, this demographic growth was most likely fueled by the agricultural- and trade-based subsistence adopted during the Pre-Classic, Classic and Post-Classic periods of their empire. The limited diversity levels observed in the Altaian and Tuvinian regions of Central Asia, the lowest of all populations examined, may be the consequence of bottleneck events fostered by the spatial isolation and low effective population size characteristic of a nomadic lifestyle. Furthermore, our data illustrate how a sociocultural characteristic such as mode of subsistence may be of impact on the genetic structure of populations. We analyzed our genetic data using Multidimensional Scaling Analysis of populations, Principal Component Analysis of individuals, Median-joining networks of M242, M346, L54, and M3 individuals, age estimations based on microsatellite variation utilizing genealogical and evolutionary mutation rates/generation times and estimation of Y- STR average gene diversity indices.

Link

Chromosomal rearrangements and human-chimp speciation

Chromosomal rearrangements and human-chimp speciation

Mol Biol Evol (2012) doi: 10.1093/molbev/mss272

Recombination Rates and Genomic Shuffling in Human and Chimpanzee—A New Twist in the Chromosomal Speciation Theory

Marta Farré et al.

A long-standing question in evolutionary biology concerns the effect of recombination in shaping the genomic architecture of organisms and, in particular, how this impacts the speciation process. Despite efforts employed in the last decade, the role of chromosomal reorganizations in the human–chimpanzee speciation process remains unresolved. Through whole-genome comparisons, we have analyzed the genome-wide impact of genomic shuffling in the distribution of human recombination rates during the human–chimpanzee speciation process. We have constructed a highly refined map of the reorganizations and evolutionary breakpoint regions in the human and chimpanzee genomes based on orthologous genes and genome sequence alignments. The analysis of the most recent human and chimpanzee recombination maps inferred from genome-wide single-nucleotide polymorphism data revealed that the standardized recombination rate was significantly lower in rearranged than in collinear chromosomes. In fact, rearranged chromosomes presented significantly lower recombination rates than chromosomes that have been maintained since the ancestor of great apes, and this was related with the lineage in which they become fixed. Importantly, inverted regions had lower recombination rates than collinear and noninverted regions, independently of the effect of centromeres. Our observations have implications for the chromosomal speciation theory, providing new evidences for the contribution of inversions in suppressing recombination in mammals.

Link

Bulging modern human foreheads

Bulging modern human foreheads

AJPA DOI: 10.1002/ajpa.22202

Geometric variation of the frontal squama in the genus homo: Frontal bulging and the origin of modern human morphology

Emiliano Bruner et al.

The majority of studies of frontal bone morphology in paleoanthropology have analyzed the frontal squama and the browridge as a single unit, mixing information from different functional elements. Taking into account that the bulging of the frontal bone is often described as a species-specific trait of Homo sapiens, in this article we analyze variation in the midsagittal profile of the genus Homo, focusing on the frontal squama alone, using landmark-based superimpositions and principal components analysis. Our results demonstrate that anatomically modern humans are definitely separated from extinct human taxa on the basis of frontal bulging. However, there is minor overlap among these groups, indicating that it is necessary to exercise caution when using this trait alone to make taxonomic inferences on individual specimens. Early modern humans do not show differences with recent modern humans, and “transitional” individuals such as Jebel Irhoud 1, Maba, and Florisbad, show modern-like frontal squama morphology. The bulging of the frontal squama in modern humans may represent a structural consequence of more general cranial changes, or it could be a response to changes in the morphology of the underlying prefrontal brain elements. A subtle difference between Neandertals and the Afro-European Middle Pleistocene Homo sample is associated with flattening at bregma in the former group, a result that merits further investigation.

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