December 29, 2009

Imperfection of the Molecular Clock of Hominid Mitochondria (Loogväli et al. 2009)

Another paper which shows that post-Last Ice Age mtDNA evolution did not proceed "slowly", i.e., with a rate similar to that inferred from human-chimpanzee divergence. As the authors note, the mechanism for the "slow" mutation rate, i.e. purifying selection of deleterious mtDNA mutations was "sluggish".

Note also how post-Last Ice Age population expansions are responsible for the weakness of purifying selection: as populations expand, even slightly deleterious alleles (and even non-deleterious ones) have a higher chance of surviving in a population. Genetic diversity increases faster in an expanding than in a static population.

From the paper:
In conclusion, human mitochondrial DNA clock is time-dependent mainly because of the time-dependence of purifying selection. There is also evidence that purifying selection has been counteracted by other population genetic factors during the course of human history. Our results imply that the proportion of synonymous substitutions has alternated between growth and decrease. This interpretation is strengthened given the shape of the human mtDNA tree, which reflects the bottlenecks and subsequent population expansions associated with the out-of-Africa migration and the hectic climatic conditions of the last glacial period. The wavy growth of the proportion of synonymous substitutions implies biases in the published correction of the mtDNA clock, which assumed a monotonic growth curve [15]. Therefore, the clock of synonymous substitutions should be preferred. In addition, it seems that a good consensus has been achieved on the rate of accumulation of synonymous substitutions in human mtDNA, which applies at the population as well as the interspecies level (this study, [15]).
[15] is Soares et al. (see below)

PLoS ONE doi:10.1371/journal.pone.0008260

Explaining the Imperfection of the Molecular Clock of Hominid Mitochondria

Eva-Liis Loogväli et al.


The molecular clock of mitochondrial DNA has been extensively used to date various genetic events. However, its substitution rate among humans appears to be higher than rates inferred from human-chimpanzee comparisons, limiting the potential of interspecies clock calibrations for intraspecific dating. It is not well understood how and why the substitution rate accelerates. We have analyzed a phylogenetic tree of 3057 publicly available human mitochondrial DNA coding region sequences for changes in the ratios of mutations belonging to different functional classes. The proportion of non-synonymous and RNA genes substitutions has reduced over hundreds of thousands of years. The highest mutation ratios corresponding to fast acceleration in the apparent substitution rate of the coding sequence have occurred after the end of the Last Ice Age. We recalibrate the molecular clock of human mtDNA as 7990 years per synonymous mutation over the mitochondrial genome. However, the distribution of substitutions at synonymous sites in human data significantly departs from a model assuming a single rate parameter and implies at least 3 different subclasses of sites. Neutral model with 3 synonymous substitution rates can explain most, if not all, of the apparent molecular clock difference between the intra- and interspecies levels. Our findings imply the sluggishness of purifying selection in removing the slightly deleterious mutations from the human as well as the Neandertal and chimpanzee populations. However, for humans, the weakness of purifying selection has been further exacerbated by the population expansions associated with the out-of Africa migration and the end of the Last Ice Age.


December 28, 2009

Το προσχέδιο νόμου για την πολιτογράφηση των μεταναστών σε διαβούλευση στο

Όλοι πάμε στο σχολιάζουμε με σοβαρότητα άρθρο προς άρθρο, απαντούμε σε όσους έχουν αντίθετη άποψη, και ζητάμε για ένα τόσο σοβαρό κοινωνικό ζήτημα να εγκρίνει την πρωτοβουλία της Κυβέρνησης ο λαός με δημοψήφισμα.

Κάντε κλικ στην εικόνα για να πάρετε έγκυρη πληροφόρηση και επιχειρήματα εναντίον της μεταρρύθμισης. Κάθε νέα πληροφορία θα προστίθεται σε νέο ποστ και συγκεντρωτικά σε αυτή τη διεύθυνση.

Οι πολίτες παίρνουν την υπόθεση στα χέρια τους! Όχι ιθαγένεια και ψήφος στους πάντες χωρίς ουσιαστικές προϋποθέσεις!

Προσοχή: η διαβούλευση διαρκεί έως τις 7/1/2010.

Y chromosomes of Dagestan highlanders

Journal of Human Genetics 54, 689–694 (1 December 2009) | doi:10.1038/jhg.2009.94

The key role of patrilineal inheritance in shaping the genetic variation of Dagestan highlanders

Laura Caciagli


The Caucasus region is a complex cultural and ethnic mosaic, comprising populations that speak Caucasian, Indo-European and Altaic languages. Isolated mountain villages (auls) in Dagestan still preserve high level of genetic and cultural diversity and have patriarchal societies with a long history of isolation. The aim of this study was to understand the genetic history of five Dagestan highland auls with distinct ethnic affiliation (Avars, Chechens-Akkins, Kubachians, Laks, Tabasarans) using markers on the male-specific region of the Y chromosome. The groups analyzed here are all Muslims but speak different languages all belonging to the Nakh-Dagestanian linguistic family. The results show that the Dagestan ethnic groups share a common Y-genetic background, with deep-rooted genealogies and rare alleles, dating back to an early phase in the post-glacial recolonization of Europe. Geography and stochastic factors, such as founder effect and long-term genetic drift, driven by the rigid structuring of societies in groups of patrilineal descent, most likely acted as mutually reinforcing key factors in determining the high degree of Y-genetic divergence among these ethnic groups.


December 27, 2009

mtDNA haplogroup C4c as a founding lineage in the Americas

American Journal of Physical Anthropology doi:10.1002/ajpa.21238

Brief communication: Mitochondrial haplotype C4c confirmed as a founding genome in the Americas

Ripan S. Malhi et al.


Mitochondrial DNA analysis of 31 unrelated Shuswap speakers from a previously poorly sampled region of North America revealed two individuals with haplogroups rarely found in the Americas, C4c and C1d. Comparison of the complete genomes of the two individuals with others found in the literature confirms that C4c is a founding haplotype and gives insight into the evolution of the C1d haplotype. This study demonstrates the importance of collecting and analyzing data from Native North Americans when addressing hypotheses about the peopling of the Americas.

December 26, 2009

mtDNA evidence for Caucasoid-Mongoloid admixture in Xinjiang 2,500 years ago

American Journal of Physical Anthropology doi:10.1002/ajpa.21237

Prehistorical East-West admixture of maternal lineages in a 2,500-year-old population in Xinjiang

Fan Zhang et al.


As an area of contact between Asia and Europe, Central Asia witnessed a scenario of complex cultural developments, extensive migratory movements, and biological admixture between West and East Eurasians. However, the detanglement of this complexity of diversity requires an understanding of prehistoric contacts of the people from the West and the East on the Eurasia continent. We demonstrated the presence of genetic admixture of West and East in a population of 35 inhabitants excavated in Gavaerk in southern Xinjiang and dated 2,800-2,100 years before present by analyzing their mitochondrial DNA variations. This result indicates that the initial contact of the East and the West Eurasians occurred further east than Central Asia as early as 2,500 years ago.


December 22, 2009

New major study on African ancestry

This looks like a great continuation of the previous study on African structure from the Tishkoff lab. I will add the abstract when it's posted in the PNAS site.

From the press release, Genetic study clarifies African and African-American ancestry:
This newly acquired genetic data revealed a number of important advances, including:
  • The rich mosaic of African-American ancestry. Among the 365 African-Americans in the study, individuals had as little as 1 percent West African ancestry and as much as 99 percent. There are significant implications for pharmacogenomic studies and assessment of disease risk. It appears that the range of genetic ancestry captured under the term African-American is extremely diverse, suggesting that caution should be used in prescribing treatment based on differential guidelines for African-Americans.
  • A median proportion of European ancestry in African-Americans of 18.5 percent, with large variation among individuals.
  • The predominately African origin of X chromosomes of African-Americans. This is consistent with the pattern of gene flow where mothers were mostly of African ancestry while fathers were either of African or European ancestry.
  • A technique which can reliably distinguish African and European ancestry for any particular region of the genome in African-Americans. This could have implications for personalized ancestry reconstructions, personalized medicine and more effective drug treatments and could aid in developing more effective methods for mapping genetic risk factors for diseases common in African-Americans, such as hypertension, diabetes and prostate cancer.
  • The similarity of the West African component of African-American ancestry to the profile from non-Bantu Niger-Kordofanian speaking populations, which include the Igbo and Yoruba from Nigeria and the Brong from Ghana
  • A comparison of the West African segments of African-American genomes. This is wholly in line with historical documents showing that the Igbo and Yoruba are two of the 10 most frequent ethnicities in slave trade records; however, most African-Americans also have ancestry from Bantu-speaking populations in western Africa.
  • Population structure within the West African samples reflecting primarily language and secondarily geographical distance, echoing the Bantu expansion from a homeland in West Africa across much of sub-Saharan Africa around 4,000 years ago.
The paper is open access and is now online.

PNAS doi:10.1073/pnas.0909559107

Genome-wide patterns of population structure and admixture in West Africans and African Americans

Katarzyna Bryc et al.


Quantifying patterns of population structure in Africans and African Americans illuminates the history of human populations and is critical for undertaking medical genomic studies on a global scale. To obtain a fine-scale genome-wide perspective of ancestry, we analyze Affymetrix GeneChip 500K genotype data from African Americans (n = 365) and individuals with ancestry from West Africa (n = 203 from 12 populations) and Europe (n = 400 from 42 countries). We find that population structure within the West African sample reflects primarily language and secondarily geographical distance, echoing the Bantu expansion. Among African Americans, analysis of genomic admixture by a principal component-based approach indicates that the median proportion of European ancestry is 18.5% (25th–75th percentiles: 11.6–27.7%), with very large variation among individuals. In the African-American sample as a whole, few autosomal regions showed exceptionally high or low mean African ancestry, but the X chromosome showed elevated levels of African ancestry, consistent with a sex-biased pattern of gene flow with an excess of European male and African female ancestry. We also find that genomic profiles of individual African Americans afford personalized ancestry reconstructions differentiating ancient vs. recent European and African ancestry. Finally, patterns of genetic similarity among inferred African segments of African-American genomes and genomes of contemporary African populations included in this study suggest African ancestry is most similar to non-Bantu Niger-Kordofanian-speaking populations, consistent with historical documents of the African Diaspora and trans-Atlantic slave trade.

Link (pdf)

December 19, 2009

The Ecumenical Patriarch on 60 Minutes

The Ecumenical Patriarch Bartholomew, leader of 300 million Orthodox Christians, feels "crucified" and "second-class " living in Turkey. Bob Simon reports, this Sunday, Dec. 20, at 7 p.m. ET/PT.

Video excerpt (2:27)

Update: The Complete segment

December 17, 2009

New comprehensive study on continental ancestry of Argentineans (Corach et al. 2010)

An interesting find from the study:
Whereas 96% of the individuals with European surnames carried European Y-chromosomes, 50% of the samples from individuals with Amerindian surnames had
European Y chromosomes.
The combined use of Y-chromosome, mtDNA, and autosomal markers in a sample gives us a rare opportunity to see how well inferences of ancestry from uniparental markers matches with that from autosomal ones:

European ancestry in mtDNA (44.3%) and Y-chromosome (94.1%) gives an estimate of 69.2%, compared to 78.6% for autosomal markers. Native S. American in mtDNA (53.7%) and Y-chromosome (4.9%) gives an estimate of 29.3%, compared to 17.28% for autosomal markers. Finally, African mtDNA (2%) and Y-chromosomes (0.9%) gives an estimate of 1.45% compared to 4.15% for the autosomal markers.

It is difficult to guess how much of the difference is due to the small number of markers used, how much is due to the choice of parental populations for the admixture estimate (which cannot match perfectly the actual parental populations), and how much is due to the inclusion of pigmentation-related markers which have substantial inter-continental differences, but may have shifted frequencies due to social selection.

Annals of Human Genetics doi:10.1111/j.1469-1809.2009.00556.x

Inferring Continental Ancestry of Argentineans from Autosomal, Y-Chromosomal and Mitochondrial DNA

Daniel Corach et al.


We investigated the bio-geographic ancestry of Argentineans, and quantified their genetic admixture, analyzing 246 unrelated male individuals from eight provinces of three Argentinean regions using ancestry-sensitive DNA markers (ASDM) from autosomal, Y and mitochondrial chromosomes. Our results demonstrate that European, Native American and African ancestry components were detectable in the contemporary Argentineans, the amounts depending on the genetic system applied, exhibiting large inter-individual heterogeneity. Argentineans carried a large fraction of European genetic heritage in their Y-chromosomal (94.1%) and autosomal (78.5%) DNA, but their mitochondrial gene pool is mostly of Native American ancestry (53.7%); instead, African heritage was small in all three genetic systems (less than 4%). Population substructure in Argentina considering the eight sampled provinces was very small based on autosomal (0.92% of total variation was between provincial groups, p = 0.005) and mtDNA (1.77%, p = 0.005) data (none with NRY data), and all three genetic systems revealed no substructure when clustering the provinces into the three geographic regions to which they belong. The complex genetic ancestry picture detected in Argentineans underscores the need to apply ASDM from all three genetic systems to infer geographic origins and genetic admixture. This applies to all worldwide areas where people with different continental ancestry live geographically close together.


Facial attractiveness ratios for Caucasoid women

Vision Research doi:10.1016/j.visres.2009.11.003

New “golden” ratios for facial beauty

Pamela M. Pallett et al.


In four experiments, we tested the existence of an ideal facial feature arrangement that could optimize the attractiveness of any face given its facial features. Participants made paired comparisons of attractiveness between faces with identical facial features but different eye–mouth distances and different interocular distances. We found that although different faces have varying attractiveness, individual attractiveness is optimized when the face’s vertical distance between the eyes and the mouth is approximately 36% of its length, and the horizontal distance between the eyes is approximately 46% of the face’s width. These “new” golden ratios match those of an average face.


December 15, 2009

Physical appearance predicts personality

The paper is open access.

Personality and Social Psychology Bulletin Vol. 35, No. 12, 1661-1671, DOI: 10.1177/0146167209346309

Personality Judgments Based on Physical Appearance

Laura P. Naumann et al.


Despite the crucial role of physical appearance in forming first impressions, little research has examined the accuracy of personality impressions based on appearance alone. This study examined the accuracy of observers’ impressions on 10 personality traits based on full-body photographs using criterion measures based on self and peer reports. When targets’ posture and expression were constrained (standardized condition), observers’ judgments were accurate for extraversion, self-esteem, and religiosity. When targets were photographed with a spontaneous pose and facial expression (spontaneous condition), observers’ judgments were accurate for almost all of the traits examined. Lens model analyses demonstrated that both static cues (e.g., clothing style) and dynamic cues (e.g., facial expression, posture) offered valuable personality-relevant information. These results suggest that personality is manifested through both static and expressive channels of appearance, and observers use this information to form accurate judgments for a variety of traits.


December 11, 2009

Mapping Human Genetic Diversity in Asia

From the press release:
Several genome-wide studies of human genetic diversity have been conducted on European populations. Now, for the first time, these studies have been extended to 73 Southeast Asian (SEA) and East Asian (EA) populations.

In a paper titled, "Mapping Human Genetic Diversity in Asia," published online Science on 10 Dec. 2009, over 90 scientists from the Human Genome Organisation's (HUGO's) Pan-Asian SNP Consortium report that their study conducted within and between the different populations in the Asia continent showed that genetic ancestry was highly correlated with ethnic and linguistic groups.

The scientists also reported a clear increase in genetic diversity from northern to southern latitudes. Their findings also suggest that there was one major inflow of human migration into Asia arising from Southeast Asia, rather than multiple inflows from both southern and northern routes as previously proposed. This indicates that Southeast Asia was the major geographic source of East Asian and North Asian populations.

(A figure illustrating the paper shows plausible routes of pre-historical migration of Asian human populations. According to the study, the PanAsia SNP Initiative, the most recent common ancestors of Asians arrived first in India and later, some of them migrated to Thailand, and South to the lands known today as Malaysia, Indonesia, and the Philippines. The first group of settlers must have gone very far south before they settled successfully. These included the Malay Negritos , Philippine Negritos , the East Indonesians, and early settlers of the Pacific Islands. Thereafter, one or several groups of people migrated North, mixed with previous settlers there and, finally, formed various populations we now refer to as Austronesian, Austro-Asiatic, Tai-Kadai, Hmong-Mien, and Altaic. The figure is titled, "Putative Pre-Historical Migration Routes of Asian Human Populations.")

The researchers noted that the geographical and linguistic basis of genetic subgroups in Asia clarifies the need for genetic stratification when conducting genetic and pharmacogenomic studies in this continent, and that human genetic mapping of Asia has important implications for the study of genetics and disease and for research to understand migratory patterns in human history.

HUGO President Edison Liu, M.D., who is Executive Director of the Genome Institute of Singapore (GIS), said, "This study was a milestone not only in the science that emerged, but the consortium that was formed. Ten Asian countries came together in the spirit of solidarity to understand how we were related as a people, and we finished with a truly Asian scientific community. We overcame shortage of funds and diverse operational constraints through partnerships, good will, and cultural sensitivity.

"Our next goal is to expand this collaboration to all of Asia including Central Asia and the Polynesian Islands," said Dr. Liu, one of the corresponding authors of the paper. "We also aim to be more detailed in our genomic analysis and plan to include structural variations, as well as over a million single nucleotide polymorphisms in the next analysis."

While HUGO initiated and coordinated the research, Dr. Liu pointed out, "Affymetrix, led by Dr. Giulia C. Kennedy and based in the US, is our primary technology partner in this endeavour. We greatly appreciate their support."
As usual for a Science paper there are voluminous (and free) supplementary materials. The Neighbor-Joining tree shows the clear correlation between linguistic affiliation and genetic identity of individuals.

UPDATE: As to the main thesis of the paper, namely that East Asians are descended from Southeast Asians rather than Central Asians, I have to say that I am not convinced. This thesis is based on two observations: minimum sharing between East Asians and Central/South Asians and south-north reduction of genetic diversity in East Eurasians. However, the high genetic diversity in Southeast Asians can be explained if they are taken to be old hybrids of Mongoloid northerners with "Australoid"-like southerners as physical anthropology suggests, and the seeming absence of influence of present-day Central/South Asians is due to the fact that the latter are largely Caucasoids of western Eurasian origin, and, thus, do not represent any putative ancestral populations to modern Mongoloids.


Mapping Human Genetic Diversity in Asia

The HUGO Pan-Asian SNP Consortium


Asia harbors substantial cultural and linguistic diversity, but the geographic structure of genetic variation across the continent remains enigmatic. Here we report a large-scale survey of autosomal variation from a broad geographic sample of Asian human populations. Our results show that genetic ancestry is strongly correlated with linguistic affiliations as well as geography. Most populations show relatedness within ethnic/linguistic groups, despite prevalent gene flow among populations. More than 90% of East Asian (EA) haplotypes could be found in either Southeast Asian (SEA) or Central-South Asian (CSA) populations and show clinal structure with haplotype diversity decreasing from south to north. Furthermore, 50% of EA haplotypes were found in SEA only and 5% were found in CSA only, indicating that SEA was a major geographic source of EA populations.


December 09, 2009

Jews intermediate between Middle Eastern and European populations (Kopelman et al. 2009)

Fairly interesting that at K=5 a Palestinian cluster emerges, and Jews show mixed affiliations with this cluster and the European one. This is also consistent with the idea that different Jewish populations have a Levantine element in common, and have also undergone admixture with European (or more properly European-like) populations.

A weakness of the study is that it does not look into Gentile populations in the region between Italy and Palestine.

The main issue in Jewish origins is no longer whether they are of Middle Eastern or European (or European-like) origin. It seems pretty clear by now that they are both. The main issue is to determine the origin of their Middle Eastern and European components. This study does offer some new insight by showing the affinity between Jews and Palestinians at K=5 (purple); however the origin of the European (or European-like) component remains elusive.

BMC Genetics 2009, 10:80 doi:10.1186/1471-2156-10-80

Genomic microsatellites identify shared Jewish ancestry intermediate between
Middle Eastern and European populations

Naama M Kopelman et al.

Background: Genetic studies have often produced conflicting results on the
question of whether distant Jewish populations in different geographic locations
share greater genetic similarity to each other or instead, to nearby non-Jewish
populations. We perform a genome-wide population-genetic study of Jewish
populations, analyzing 678 autosomal microsatellite loci in 78 individuals from four
Jewish groups together with similar data on 321 individuals from 12 non-Jewish
Middle Eastern and European populations.
Results: We find that the Jewish populations show a high level of genetic similarity
to each other, clustering together in several types of analysis of population structure.
Further, Bayesian clustering, neighbor-joining trees, and multidimensional scaling
place the Jewish populations as intermediate between the non-Jewish Middle
Eastern and European populations.
Conclusion: These results support the view that the Jewish populations largely
share a common Middle Eastern ancestry and that over their history they have
undergone varying degrees of admixture with non-Jewish populations of European

December 06, 2009

Kinship, marriage, and the genetics of past human dispersals (Bentley et al. 2009)

Hum Biol. 2009 Apr;81(2-3):159-79

Kinship, marriage, and the genetics of past human dispersals.

Bentley RA, Layton RH, Tehrani J

Abstract The extent to which colonizing farmer populations have overwhelmed or "replaced" indigenous forager populations, as opposed to having intermarried with them, has been widely debated. Indigenous-colonist "admixture" is often represented in genetic models as a single parameter that, although parsimonious and simple, is incongruous with the sex-specific nature of mtDNA and Y-chromosome data. To help interpret genetic patterns, we can construct useful null hypotheses about the generalized migration history of females (mtDNA) as opposed to males (Y chromosome), which differ significantly in almost every ethnographically known society. We seek to integrate ethnographic knowledge into models that incorporate new social parameters for predicting geographic patterns in mtDNA and Y-chromosome distributions. We provide an example of a model simulation for the spread of agriculture in which this individual-scale evidence is used to refine the parameters.


December 05, 2009

Y chromosome and mtDNA of Udegeys

American Journal of Physical Anthropology doi:10.1002/ajpa.21232

Genetic diversity of two haploid markers in the Udegey population from southeastern Siberia

Han-Jun Jin et al.


The Udegeys are a small ethnic group who live along the tributaries of the Amur River Basin of southeastern Siberia in Russia. They are thought to speak a language belonging to a subdivision of the Tungusic-Manchu branch of the Altaic family. To understand the genetic features and genetic history of the Udegeys, we analyzed two haploid markers, mitochondrial DNA (mtDNA), and Y-chromosomal variation, in 51 individuals (including 21 males) from the Udegey population. In general, the Udegeys' mtDNA profiles revealed similarities to Siberians and other northeastern Asian populations, although a moderate European contribution was also detected. Interestingly, pairwise values of FST and the MDS plots based on the mtDNA variation showed that the Orok and Nivkh inhabiting the very same region of the Udegey were significantly different from the Udegey, implying that they may have been isolated and undergone substantial genetic drift. The Udegeys were characterized by a high frequency (66.7%) of Y chromosome haplogroup C, indicating a close genetic relationship with Mongolians and Siberians. On the paternal side, however, very little admixture was observed between the Udegeys and Europeans. Thus, the combined haploid genetic markers of both mtDNA and the Y chromosome imply that the Udegeys are overall closest to Siberians and northeast Asians of the Altaic linguistic family, with a minor maternal contribution from the European part of the continent.


December 04, 2009

mtDNA continuity between Bronze Age and some modern Sardinians

Molecular Biology and Evolution, doi:10.1093/molbev/msp292

Inferring Genealogical Processes from Patterns of Bronze-Age and Modern DNA variation in Sardinia

Silvia Ghirotto et al.


The ancient inhabitants of a region are often regarded as ancestral, and hence genetically related, to the modern dwellers (for instance, in studies of admixture), but so far this assumption has not been tested empirically using ancient DNA data. We studied mitochondrial DNA variation in Sardinia, across a time span of 2,500 years, comparing 23 Bronze-Age (nuragic) mitochondrial DNA sequences with those of 254 modern individuals from two regions, Ogliastra (a likely genetic isolate) and Gallura, and considering the possible impact of gene flow from mainland Italy. To understand the genealogical relationships between past and present populations we developed seven explicit demographic models; we tested whether these models can account for the levels and patterns of genetic diversity in the data, and which one does it best. Extensive simulation based on a serial coalescent algorithm allowed us to compare the posterior probability of each model and estimate the relevant evolutionary (mutation and migration rates) and demographic (effective population sizes, times since population splits) parameters, by Approximate Bayesian Computations. We then validated the analyses by investigating how well parameters estimated from the simulated data can reproduce the observed data set. We show that a direct genealogical continuity between Bronze-Age Sardinians and the current people of Ogliastra, but not Gallura, has a much higher probability than any alternative scenarios, and that genetic diversity in Gallura evolved largely independently, owing in part to gene flow from the mainland.


December 03, 2009

Biological basis for musical scales

I find it fascinating that the two highest ranked scales are precisely the two ones allowed by Plato for his Republic:
Quite the reverse, he replied; and if so the Dorian and the Phrygian are the only ones which you have left.

I answered: Of the harmonies I know nothing, but I want to have one warlike, to sound the note or accent which a brave man utters in the hour of danger and stern resolve, or when his cause is failing, and he is going to wounds or death or is overtaken by some other evil, and at every such crisis meets the blows of fortune with firm step and a determination to endure; and another to be used by him in times of peace and freedom of action, when there is no pressure of necessity, and he is seeking to persuade God by prayer, or man by instruction and admonition, or on the other hand, when he is expressing his willingness to yield to persuasion or entreaty or admonition, and which represents him when by prudent conduct he has attained his end, not carried away by his success, but acting moderately and wisely under the circumstances, and acquiescing in the event. These two harmonies I ask you to leave; the strain of necessity and the strain of freedom, the strain of the unfortunate and the strain of the fortunate, the strain of courage, and the strain of temperance; these, I say, leave.

And these, he replied, are the Dorian and Phrygian harmonies of which I was just now speaking.

Then, I said, if these and these only are to be used in our songs and melodies, we shall not want multiplicity of notes or a panharmonic scale?

I suppose not.
CORRECTION: A reader correctly points out in the comments that the names of musical scales are a bit ambivalent, so I looked into the paper itself. By "Dorian" they mean do-re-mib-fa-sol-la-sib-do which corresponds to the ancient Phrygian mode (the peace-like one according to Plato). The ancient Dorian mode (the war-like one according to Plato) seems to correspond to the "Phrygian" one. So, as far as I can tell, the highest ranked is the ancient Dorian and the next highest-ranked is the ancient Phrygian one, but any music experts are free to chime in and correct me.

From the paper:
The 50 heptatonic scales with the highest mean percentage similarity among the >4×107 possible scales evaluated are shown in Table 3. Three of the seven heptatonic modes (see Figure 1) emerge at the top of this list. The Phrygian mode holds the highest rank followed by the Dorian mode and the Ionian mode (the major scale). The fourth ranked scale is similar to the Phrygian mode but contains a neutral second (12:11) instead of a minor second; this collection is the Husayni scale in Arabic music [27]. The Aeolian mode (the natural minor scale) and Lydian mode are the fifth and sixth ranked scales. The next three scales are similar to the Dorian mode but with slight alterations in one or two scale degrees. The seventh ranked scale may represent the Kafi scale in classical Indian music with an alternative sharp sixth scale degree [22]. The eighth ranked scale is the Kardaniya scale in Arabic music [op cit.]. Although the ninth ranked scale does not represent any well-known musical tone collection, the Mixolydian mode is ranked tenth. The Locrian, which is the least used of the Western modes, is ranked fiftieth. Thus both the five-note and seven-note scales preferred in much music worldwide comprise intervals that conform optimally to a harmonic series.

In humans, vocal stimuli arise in a variety of complex ways, not all of which are harmonic. Harmonic series depend on vocal fold vibrations and are characteristic of the “voiced speech” responsible for vowel sounds and some consonants [1]. Although the relative amplitudes of harmonics are altered by filtering effects of the supralaryngeal vocal tract resonances to produce different vowel phones, the frequencies of harmonics remain unchanged [op cit.]. In consequence, the presence of a harmonic series is a salient feature of human vocalizations and essential to human speech and language. It follows that the similarity of musical intervals to harmonic series provides a plausible biological basis for the worldwide human preference for a relatively small number of musical scales defined by their overall similarity to a harmonic series.

PLoS ONE doi:10.1371/journal.pone.0008144

A Biological Rationale for Musical Scales

Kamraan Z. Gill, Dale Purves


Scales are collections of tones that divide octaves into specific intervals used to create music. Since humans can distinguish about 240 different pitches over an octave in the mid-range of hearing [1], in principle a very large number of tone combinations could have been used for this purpose. Nonetheless, compositions in Western classical, folk and popular music as well as in many other musical traditions are based on a relatively small number of scales that typically comprise only five to seven tones [2]–[6]. Why humans employ only a few of the enormous number of possible tone combinations to create music is not known. Here we show that the component intervals of the most widely used scales throughout history and across cultures are those with the greatest overall spectral similarity to a harmonic series. These findings suggest that humans prefer tone combinations that reflect the spectral characteristics of conspecific vocalizations. The analysis also highlights the spectral similarity among the scales used by different cultures.


December 01, 2009

Why Some Women Look Young for Their Age (Gunn et al. 2009)

On the left facial composites of younger/older (left/right) monozygotic/dizygotic twins (top/bottom).

PLoS ONE doi:10.1371/journal.pone.0008021

Why Some Women Look Young for Their Age

David A. Gunn et al.


The desire of many to look young for their age has led to the establishment of a large cosmetics industry. However, the features of appearance that primarily determine how old women look for their age and whether genetic or environmental factors predominately influence such features are largely unknown. We studied the facial appearance of 102 pairs of female Danish twins aged 59 to 81 as well as 162 British females aged 45 to 75. Skin wrinkling, hair graying and lip height were significantly and independently associated with how old the women looked for their age. The appearance of facial sun-damage was also found to be significantly correlated to how old women look for their age and was primarily due to its commonality with the appearance of skin wrinkles. There was also considerable variation in the perceived age data that was unaccounted for. Composite facial images created from women who looked young or old for their age indicated that the structure of subcutaneous tissue was partly responsible. Heritability analyses of the appearance features revealed that perceived age, pigmented age spots, skin wrinkles and the appearance of sun-damage were influenced more or less equally by genetic and environmental factors. Hair graying, recession of hair from the forehead and lip height were influenced mainly by genetic factors whereas environmental factors influenced hair thinning. These findings indicate that women who look young for their age have large lips, avoid sun-exposure and possess genetic factors that protect against the development of gray hair and skin wrinkles. The findings also demonstrate that perceived age is a better biomarker of skin, hair and facial aging than chronological age.