Neandertal flutes debunked

Royal Society Open Science DOI: 10.1098/rsos.140022

‘Neanderthal bone flutes’: simply products of Ice Age spotted hyena scavenging activities on cave bear cubs in European cave bear dens

Cajus G. Diedrich

Punctured extinct cave bear femora were misidentified in southeastern Europe (Hungary/Slovenia) as ‘Palaeolithic bone flutes’ and the ‘oldest Neanderthal instruments’. These are not instruments, nor human made, but products of the most important cave bear scavengers of Europe, hyenas. Late Middle to Late Pleistocene (Mousterian to Gravettian) Ice Age spotted hyenas of Europe occupied mainly cave entrances as dens (communal/cub raising den types), but went deeper for scavenging into cave bear dens, or used in a few cases branches/diagonal shafts (i.e. prey storage den type). In most of those dens, about 20% of adult to 80% of bear cub remains have large carnivore damage. Hyenas left bones in repeating similar tooth mark and crush damage stages, demonstrating a butchering/bone cracking strategy. The femora of subadult cave bears are intermediate in damage patterns, compared to the adult ones, which were fully crushed to pieces. Hyenas produced round–oval puncture marks in cub femora only by the bone-crushing premolar teeth of both upper and lower jaw. The punctures/tooth impact marks are often present on both sides of the shaft of cave bear cub femora and are simply a result of non-breakage of the slightly calcified shaft compacta. All stages of femur puncturing to crushing are demonstrated herein, especially on a large cave bear population from a German cave bear den.

Link

Music and population structure (Brown et al. 2013)

Proceedings of the Royal Society B doi: 10.1098/rspb.2013.2072

Correlations in the population structure of music, genes and language

Steven Brown et al.

We present, to our knowledge, the first quantitative evidence that music and genes may have coevolved by demonstrating significant correlations between traditional group-level folk songs and mitochondrial DNA variation among nine indigenous populations of Taiwan. These correlations were of comparable magnitude to those between language and genes for the same populations, although music and language were not significantly correlated with one another. An examination of population structure for genetics showed stronger parallels to music than to language. Overall, the results suggest that music might have a sufficient time-depth to retrace ancient population movements and, additionally, that it might be capturing different aspects of population history than language. Music may therefore have the potential to serve as a novel marker of human migrations to complement genes, language and other markers.

Link

Evolving music

I would say that this is a good indirect argument for democracy; by pooling raters' opinions, a compromise that wasn't too horrible was arrived at. Of course, democracy won't produce Bach, but it will also not produce something as horrible as Schoenberg.

The coverage of this paper in Science NOW has sample audio.

PNAS doi: 10.1073/pnas.1203182109


Evolution of music by public choice

Robert M. MacCallum et al.

Abstract

Music evolves as composers, performers, and consumers favor some musical variants over others. To investigate the role of consumer selection, we constructed a Darwinian music engine consisting of a population of short audio loops that sexually reproduce and mutate. This population evolved for 2,513 generations under the selective influence of 6,931 consumers who rated the loops’ aesthetic qualities. We found that the loops quickly evolved into music attributable, in part, to the evolution of aesthetically pleasing chords and rhythms. Later, however, evolution slowed. Applying the Price equation, a general description of evolutionary processes, we found that this stasis was mostly attributable to a decrease in the fidelity of transmission. Our experiment shows how cultural dynamics can be explained in terms of competing evolutionary forces.

Link

43,000-year old Aurignacian in Swabian Jura

A new paper continues the re-assessment of the radiocarbon dating record in Europe. It pushes the Aurignacian of Central Europe back in time, but not as far back as the appearance of modern humans in Europe. The implication is that the advanced music and art of the Aurignacian did not accompany modern humans as they made their first steps into Europe, but rather developed there.

The authors distinguish between a "strong" version of their model (which would posit a monocentric origin of music/art around the Geissenkoesterle site), and a "weak" one in which these innovations were contributed in parallel by different regions. A better understanding of the origin of different innovations and their assignment to specific groups of modern humans may help us better understand what was the "common core" of behavioral and technological modernity that facilitated the success of our species.

From the paper:

The majority of scholars conclude that the Aurignacian is the earliest signature of the first modern humans in Europe. Recent research suggests that this is not likely to be the case. Benazzi et al. (2011) have shown that the Uluzzian of Italy and Greece is likely to be a modern human industry based on the reanalysis of infant teeth in the archaeological site of Cavallo, and also demonstrated that it dates to 45,000-43,000 cal BP. Other dated examples from other Uluzzian sites (e.g., Higham et al., 2009) fall into the same period, and the Uluzzian is always stratigraphically below the Proto- Aurignacian in Italian sites where both co-occur. This adds an additional level of complexity to the emerging picture of early human dispersals and suggests that the Aurignacian does not represent the earliest evidence of our species in Europe. 

... 

Taken together, these results suggest that modern humans arrived in Europe as early as ~45,000 cal BP and spread rapidly across Europe to as far as southern England between 43,000 and41,000 cal BP. The dates for the lower Aurignacian at Geissenklosterle fall in the same period and appear to pre-date the ages for the Proto- Aurignacian and Early Aurignacian in other regions (Fig. 6). The new results suggest that the caves of the Swabian Jura document the earliest phase of the Aurignacian, and the region can be viewed as one of the key areas in which a variety of cultural innovations, including figurative art, mythical images, and musical instruments, are first documented. These dates are consistent with the Danube Valley serving as an important corridor for the movement of people and ideas (Conard, 2002; Conard and Bolus, 2003). 

... 

The new radiocarbon dates from Geissenklosterle document the presence of the Aurignacian in the Swabian Jura prior to the Heinrich 4 cold phase, with the Early Aurignacian beginning around 42,500 cal BP. In the coming years, excavations in the Swabian Jura will continue and new radiometric dates should contribute to an improved understanding of the spatial-temporal development of the Aurignacian and its innovative material culture.

From the press release:

Researchers from Oxford and Tübingen have published new radiocarbon dates from the from Geißenklösterle Cave in Swabian Jura of Southwestern Germany in the Journal of Human Evolution. The new dates use improved methods to remove contamination and produced ages between began between 42,000 – 43,000 years ago for start of the Aurignacian, the first culture to produce a wide range of figurative art, music and other key innovations as postulated in the Kulturpumpe Hypothesis. The full spectrum of these innovations were established in the region no later than 40 000 years ago.

Journal of Human Evolution doi:10.1016/j.jhevol.2012.03.003

Τesting models for the beginnings of the Aurignacian and the advent of figurative art and music: The radiocarbon chronology of Geißenklösterle

Thomas Higham et al.

The German site of Geißenklösterle is crucial to debates concerning the European Middle to Upper Palaeolithic transition and the origins of the Aurignacian in Europe. Previous dates from the site are central to an important hypothesis, the Kulturpumpe model, which posits that the Swabian Jura was an area where crucial behavioural developments took place and then spread to other parts of Europe. The previous chronology (critical to the model), is based mainly on radiocarbon dating, but remains poorly constrained due to the dating resolution and the variability of dates. The cause of these problems is disputed, but two principal explanations have been proposed: a) larger than expected variations in the production of atmospheric radiocarbon, and b) taphonomic influences in the site mixing the bones that were dated into different parts of the site. We reinvestigate the chronology using a new series of radiocarbon determinations obtained from the Mousterian, Aurignacian and Gravettian levels. The results strongly imply that the previous dates were affected by insufficient decontamination of the bone collagen prior to dating. Using an ultrafiltration protocol the chronometric picture becomes much clearer. Comparison of the results against other recently dated sites in other parts of Europe suggests the Early Aurignacian levels are earlier than other sites in the south of France and Italy, but not as early as recently dated sites which suggest a pre-Aurignacian dispersal of modern humans to Italy by ∼45000 cal BP. They are consistent with the importance of the Danube Corridor as a key route for the movement of people and ideas. The new dates fail to refute the Kulturpumpe model and suggest that Swabian Jura is a region that contributed significantly to the evolution of symbolic behaviour as indicated by early evidence for figurative art, music and mythical imagery.

Link

Tonal preferences in music/speech

PLoS ONE 6(5): e20160. doi:10.1371/journal.pone.0020160

Co-Variation of Tonality in the Music and Speech of Different Cultures

Shui' er Han et al.

Whereas the use of discrete pitch intervals is characteristic of most musical traditions, the size of the intervals and the way in which they are used is culturally specific. Here we examine the hypothesis that these differences arise because of a link between the tonal characteristics of a culture's music and its speech. We tested this idea by comparing pitch intervals in the traditional music of three tone language cultures (Chinese, Thai and Vietnamese) and three non-tone language cultures (American, French and German) with pitch intervals between voiced speech segments. Changes in pitch direction occur more frequently and pitch intervals are larger in the music of tone compared to non-tone language cultures. More frequent changes in pitch direction and larger pitch intervals are also apparent in the speech of tone compared to non-tone language cultures. These observations suggest that the different tonal preferences apparent in music across cultures are closely related to the differences in the tonal characteristics of voiced speech.

Link

ASHG 2010 abstracts

The 2010 meeting of the American Society of Human Genetics is in November. Here are some interesting abstracts that caught my eye:

It's nice to finally see a genomic study on the Greek population.
P. Paschou et al. Evaluation of the HapMap dataset as reference for the Greek population.

The HapMap project has provided a unique tool for the analysis of human genetic variation, providing reference information for allele frequency and genotype distributions as well as linkage disequilibrium patterns of Single Nucleotide Polymorphisms (SNPs) across the entire genome. The latest release of HapMap phase 3 data provides genotypes for millions of SNPs in 11 populations from around the world, with Europe being represented by the CEU (originating from Northwestern Europe) and the TSI populations (Tuscan Italians from Southern Europe). Although initial studies support the fact that the CEU can be used as reference for the selection of tagging SNPs in other European populations, a critical step in the design of genetic association studies, this hypothesis has not been extensively studied across Europe and in particular in Southern Europe. We set out to explore the extent to which the HapMap populations can be used as reference for a previously unstudied population of South-Eastern Europe, the Greek population. To do so we studied genomic variation in 1,813 SNPs, genotyped by our group in 56 individuals of Greek origin, and compared them to the CEU and TSI genotypes (1,813 SNPs from the CEU HapMap dataset and 1,205 from the TSI dataset). The studied SNPs are spread over 13 autosomal chromosomes and 26 regions, ranging in size from 120Kb to more than 4Mb. Genotype, allele frequency, and pairwise LD measures were compared across all three populations. PCA was used in order to identify those markers that are responsible for the observed inter-sample variance. Tagging SNPs were selected in the CEU and TSI samples and their transferability to the Greek population was tested, using both the r2 metric as well as the efficiency of genotype imputation of the non-selected SNPs. Our results demonstrate that, although the CEU population can to some extent be used as reference for the Greek population, it is preferable to use as reference a European population of closer genetic ancestry, like the TSI. These results are applicable in medical genetics, in order to inform the design of genetic association studies, as well as in studies of evolutionary relationships of Southern European populations.

One of the great problems of Eurasian anthropology is whether the Uralic populations are simply variable admixtures of Caucasoids and Mongoloids or they contain a tertium quid in the form of a Proto-Uralic element. The latter need not be distinct from the other two, as it can also be an old or stabilized blend of the two major Eurasian races that later admixed with more recent groups on either side. The abstract does not seem promising in this respect, i.e., in identifying a common core of ancestry among Uralic speakers in addition to their variable east-west admixture, but it would be nice to see if anything like that exists in the paper.

K. Tambets et al. Haploid and autosomal variation within a linguistic continuum of the Uralic-speaking people of Eurasia.

For about last two decades the examination of uniparentally inherited genetic marker systems revealing the variation embedded in mtDNA and Y chromosome has been the main tool in the studies of human genetic origins. Within few recent years the analysis of the genome-wide SNP data of individuals from different populations has started to give promising new insights in the field of human population genetics. The uniparentally inherited markers have shown slightly different demographic scenarios for the maternal and paternal lineages of North Eurasian, particularly of European Uralic-speaking populations. The geographical location of a population has evidently been the most important component that dictates the proportion of western and eastern mtDNA types in the gene pool of Uralic-speakers. Thus, the palette of maternal lineages of the Uralic-speakers resembles that of their geographically close European or Western Siberian Indo-European and/or Altaic-speaking neighbours, respectively. At the same time, the most frequent North Eurasian Y chromosome type N1c, that is also a common link between almost all Uralic-speakers, is with few exceptions rare, if present at all, among Indo-European-speakers of Western and Southern Europe. Here we combine genome-wide high density SNP data (650 000 SNPs, Illumina) with uniparentally inherited mtDNA and Y-chromosome variation of 16 Uralic-speaking populations to assess their place on the genetic landscape of North Eurasia. By the use of principal component and structure-like analysis on the autosomal data we show that the proportions of western and eastern ancestry components among the Uralic-speakers are determined mostly by geographical factors. The westernmost populations from Europe, both Uralic- and Indo-European speakers, are similar in their pattern of ancestry components and show low levels (less than 10%) of the eastern component. Conversely, the eastern ancestry component is dominant (60-70%) in the gene pool of the Siberian Uralic-speakers. In general, the genome-wide analyses corroborate the results of mtDNA analysis and do not reflect the common genetic characteristics between western and eastern Uralic-speakers at the level seen in case of N1c. Interestingly, among Saami from North Europe, who are often considered as „outliers“ in genetic studies, the dominant western component is accompanied by 30% of eastern component making them more similar to Volga-Uralic populations than to their closest neighbours.

This seems to validate my thoughts on relics and their importance in age estimation.

U. A. Perego et al. The Initial Peopling Of The Americas: An Ever-Growing Number Of Founding Mitochondrial Genomes From Beringia

Genetic evidence based on mitochondrial DNA (mtDNA) has recently revealed the existence of additional founding lineages that have contributed to the first peopling of America’s double-continent in addition to the more popular five Native American haplogroups (A2, B2, C1, D1 and X2a), and has demonstrated as well the need for additional sampling and analysis to be performed for some of the already known but poorly characterized lineages. One paradigmatic example is represented by the pan-American haplogroup C1. Two of its sub-branches (C1b and C1c) harbor ages and geographical distributions that are indicative of an early arrival from Beringia about 15-17,000 years ago, concomitantly with the other currently accepted Paleo-Indian founders. However, the estimated age of C1d - the third Native American subset of C1 - is only 8-10,000 years, which is suggestive of a much later entry and spread in the Americas. In this study, we shed light on the origin of this enigmatic Native American branch of C1 by completely sequencing a large number of C1d mitochondrial genomes from a wide range of geographically diverse, mixed and indigenous American populations. The revised phylogeny shows that the age previously reported for C1d was heavily underestimated and indicate that C1d is ancient enough to be among the founding Paleo-Indian mtDNA lineages. Moreover, our results reveal that there were two C1d founder genomes for Paleo-Indians that most likely arose early (~16kya), either in the dynamic Beringian gene pool, or at a very initial stage of the Paleo-Indian southward migration. This brings the recognized maternal founding lineages of Native Americans to the unexpected number of 15, and indicates that the overall number of Beringian or Asian founder mitochondrial genomes will probably continue to increase as more Native American haplogroups reach the same level of phylogenetic resolution as we obtained here for C1d. Additionally, we have confirmed a nearly identical geographic distribution pattern for haplogroup C1d when comparing samples collected in the general mixed population with those from native tribal groups, as it was also reported previously for haplogroups X2a and D4h3. This substantiates the validity of searching large public mtDNA databases (such as the one available through the Sorenson Molecular Genealogy Foundation, www.SMGF.org) for novel founder candidates able to reveal unknown details concerning the ancient human history of the Americas.

Another interesting abstract. I've written before about the association of Y-chromosome haplogroups with the spread of Semitic speakers and the agreement with language phylogenetics.

N. Al-Zahery et al. The male gene pool of the contemporary Mesopotamia marsh population supports their Semitic origin.

The origin of the modern Mesopotamia marsh people, which are locally called “Ma’dan” or “Marsh’s Arabs”, is a question of great interest. Based on their life-style (living in reed houses, grazing of water buffalo and other aspects) and local archaeological sites, many historians and archaeologists believe they may have Sumerian ancestry. Although little is known about the origin of Sumerians themselves, two main hypotheses have been advanced in this regard. According to the first, Sumerians were a group of populations which migrated from the “South East” following a seashore route through the Arabian Gulf, and settled down in the southern marshes of Iraq. According to the second, the advancement of the Sumerian civilization is the result of migration from the mountainous area of Anatolia to the southern marshes of Iraq where they settled, adsorbing previous populations. In order to shed some light on the genetic origin of the Mesopotamia marsh population, we investigated the male gene pool of 145 DNA samples of modern Mesopotamia people, still living in marshes in the south of Iraq. The analyses of Single Nucleotide Polymorphisms (SNPs) and Short Tandem Repeats (STRs) of the paternally transmitted Male Specific region of the Y chromosome (MSY) revealed that more than 80% of marsh Y chromosomes belong to (Hg) J1-M267, the autochthonous haplogroup of Middle Eastern/Semitic speakers with possible recent expansion and/or founder effect reflected by the reduced STRs variability. In particular, 90% of them were assigned to the J1e-M267-PAGE08 sub-haplogroup, which is the predominant Y chromosome lineage among Middle Eastern Arab populations (Yemen, Qatar, UAE, and Levant). Thus, these findings testify, at least from the paternal side, a strong Semitic Arabian component in the contemporary Mesopotamia marshes population, whereas no clear Anatolian and/or South Asian genetic evidence has been detected.

The finding of haplogroup I in China is surprising, as I is not generally found that far away from Europe. It would be interesting to see what the actual haplotypes are.
Y. Lu et al. Western Eurasian Y chromosomes found in the Chinese Salar ethnic group

Salar is a small Western-Turkish-speaking population living mostly in Qinghai province of China. The most similar languages to Salar are all far in Turkmenistan. Historical records suggested that they may be descendants of the Turkic nomadic tribes in Central Asia. In this study, 141 Salar Y chromosomes were analyzed for 39 SNP and 14 STR markers to investigate the potential imprints of their western ancestors. The most frequent haplogroup (hg) in this population sample is Hg R, comprising 40% of all Y chromosomes. Most of these Hg R samples belong to R1a1 (M17), which distributes in a wide geographic region including South Asia, East Europe, Central Asia, and South Siberia. Other four Western Eurasian haplogroups (G-2%, H-5%, I-3%, J-3%) were also found in Salar Y chromosome gene pool. These paternal lineages of Salar are absent in their East Asian neighbors but frequent in Central Asia. Y-STR-based analyses also grouped Salar to Central Asians. On the other side, Salar also has low frequencies of the East Asian specific Hg D and Hg O, suggesting possible gene flow from their neighboring populations. This Y chromosome study demonstrated that Salar well keeps the Western Eurasian paternal lineages of their Central Asian ancestors although they may have migrated to Central China for about 800 years.

I wish that more "people pairs" would be studied this way, as it would give us some good insight of how migration affects gene pools (allele frequency changes, founder effects, possible social selection etc.)

M. Davis et al. Ancient and recent demographic events influence mitochondrial DNA diversity in an immigrant Basque population

The Basques are an ancient people, considered by many anthropologists to represent the oldest extant European population. Because of this, they have been the subject of numerous sociological and biological investigations. The Basque Diaspora, a relatively recent demographic expansion of the Basque population, has until now been overlooked in genetic studies. Samples were taken from 53 individuals with Basque ancestry in Boise, Idaho, and the mitochondrial DNA (mtDNA) sequence variation of the first and second hypervariable regions were determined. Thirty-six mtDNA haplotypes were detected in the sample. Comparing the genetic diversity in the Idaho sample with other Basque populations, signatures of founder effects were observed, consistent with both the recent and ancient history of Basque mitochondrial lineages. There has been a marked alteration of haplogroup frequency and diversity, and there is a slight reduction in other measures of diversity in the NW Basque population compared to the native Basque population. We have found a relatively high percentage of the Cambridge Reference Sequence (rCRS) haplotype for hypervariable regions I and II, which is absent in previous studies of Basque mtDNA, and rare in other Spanish populations. The amount of nucleotide diversity is consistent with a sample that is predominantly haplogroup H, which is especially common in the Basque regions of Europe, due to ancient migrations and expansions out of glacial refugia. This is the first report of mtDNA diversity in an immigrant Basque population, and we find that the diversity in NW Basques can be explained by the recent history of migration, as well as the phylogeography and diversity of the major European haplogroups.

W. S. Watkins et al. Admixture in New World populations: an analysis of Y-chromosome, mtDNA, and genome-wide microarray data

The first major interaction between Native Americans and Europeans is documented historically and occurred less than 550 years ago. This recent time frame provides an excellent opportunity to investigate the effects of admixture between two populations that were previously separated for hundreds of generations. To characterize European admixture in Native American populations, we sampled and analyzed a group of isolated Totonac agriculturists from tropical Mexico near Veracruz and a group of native Bolivians predominantly from the mountainous region near La Paz, Boliva. Mitochondrial sequencing of HVS1 showed that all samples had pre-Columbian mtDNA haplogroups (A, B, C, and D). Using a panel of 48 STRs or 12 Y-chromosome SNPs, Totonac Y-chromosomes lineages were all assigned to the pre-Columbian haplogroup Q1a3a, and Bolivian Y-chromosome lineages were assigned to haplogroups Q1a3a, R1, and J2. Haplogroups R1 and J2 are common in European populations. Principal components analysis (PCA) using >800K autosomal SNPs typed in 24 Totonacs and 23 Bolivians showed that all Totonacs and 14 Bolivians clustered distinctly from Eurasian individuals. Nine Bolivians, however, were positioned between the New World and European PCA clusters. Admixture analysis showed that these nine samples had 21 - 33% European admixture using a European reference population. All three observed Y-chromosome haplogroups, including the well-studied pre-Columbian haplogroup Q1a3a, occurred in the admixed individuals. Two of the nine admixed individuals had pre-Columbian mtDNA and Y-chromosome haplogroups but 21-23% European ancestry. This result demonstrates that Y-chromosome and mtDNA haplogroups are only partial indicators of an individual’s complete ancestry.

Readers of the blog know that I don't agree with the scenario presented in the followin abstract. The serial founder effect idea is used by geneticists to explain the overall reduced genetic diversity of our species (that we appear to be young, in evolutionary terms). Personally, I don't see how a smart, expanding species that all of the sudden had access to the resources of the landmass of Eurasia went through these extreme bottlenecks.
I think that the alternative of a larger human population, genetic diversity reduced across the species by ongoing climate- and culture-mediated selection, and admixture within Africa itself -where a particular expanding H. sapiens group must've co-existed with pre-existed hominids, anatomically modern or not- has merit.
J. Long et al. Evidence for archaic admixture in contemporary non-African human populations

Analyses of large-scale genetic data sets show evidence for a series of founder effects that occurred as modern humans left Africa and settled the rest of the world. Nonetheless, research on modern humans has not ruled out the possibility that other processes, such as local gene flow, or mixing between archaic and modern humans, have also contributed to modern human diversity. Recent analyses of the Neanderthal genome make archaic admixture a salient issue because they show evidence for mixing between Neanderthals and out-of-Africa migrants. The present study examines evidence for archaic admixture in genotypes for 619 microsatellite loci collected from over 2,000 individuals from 100 human populations. We obtained these data from the Marshfield Clinic collection. The populations analyzed represent all inhabited continents of the world. In our analysis, we formulate the serial founder effects (SFE) model as a special case of a phylogenetic model promoted by Cavalli-Sforza and his associates. In this light, the SFE process makes four predictions: 1) A tree of descent according to the pattern of fissions. 2) The root of the tree lies in Africa. 3) The length of each branch is proportional to ratio of evolutionary time to effective population size. 4) The gene identity between all pairs of populations that share the same most recent common ancestor is equal in expectation. Using hypothesis tests based on generalized hierarchical statistical models, we find good agreement between the SFE predictions and diversity within and between African populations, and we find good agreement between the SFE predictions and diversity between non-African populations. However, there is more diversity within the non-African populations than the SRE model can account for. This makes for greater genetic distance between Africans and non-Africans than otherwise expected. How and where did the non-Africans obtain this diversity? A simple explanation for the finding is that the earliest migrants out-of-Africa mixed with an archaic population such as Neanderthals prior to their expansion throughout Europe and Asia. Coalescent based computer simulations of the SFE model with mixing support our interpretation. The time and place that we detect mixing coincides perfectly with that detected in a recent examination of Neanderthal genome sequences. Our study shows that genomic diversity in modern humans still reflects ancient events and processes.

C. Flores et al. Using EuroAIMs to measure admixture proportions in atypical European populations: the case of Canary Islanders

Using ancestry informative markers (AIMs) allows reducing the number of makers needed for population stratification adjustments in association studies. As few as 100 AIMs are sufficient to adjust for the largest European axis of differentiation (i.e. EuroAIMs). However, their use for ancestry inference and adjustment in association studies in atypical European populations such as the Canary Islanders, a recently African-admixed population from Spain, needs to be addressed. We aimed to explore whether EuroAIMs were suitable both for the inference of Spanish and Northwest African admixture proportions and for ancestry adjustments in association studies including samples from Canary Islanders. We analyzed samples from Canary Islanders, mainland Spanish (IBE) and Northwest Africans (NWA) for 93 EuroAIMs and compared the data with CEU and YRI from HapMap, Basques and Mozabite from HGDP, as well as from previously analyzed European samples. The major genetic difference was observed between NWA and all European populations, preserving the northwest-to-southeast differentiation of European populations in the second axis. Analyses revealed that Canary Islanders were intermediate between IBE and NWA, and that direct sub-Saharan African influences were negligible. Assessment of individual admixtures without prior population information clearly identified two subpopulations corresponding to NWA and IBE, while Canary Islanders were admixed with an average of 17.4% Northwest African contribution varying largely among individuals (range 0-95.7%). As few as 23 EuroAIMs correctly estimated population membership to IBE and NWA, while 69 EuroAIMs were required to accurately estimate individual admixture proportions in Canary Islanders. Ancestry estimates based on a subset of 69 EuroAIMs also controlled significant allele frequency differences between IBE and Canary Islanders. These data suggest that a handful of EuroAIMs would be useful to control false-positives in association studies performed in Spanish populations. Supported by FUNCIS 23/07 and grants from the Spanish Ministry of Science and Innovation PI081383 and EMER07/001 to CF.

As I have I mentioned before, the Maasai (and many other east Africans in various degrees) are intermediate between Negroids and Caucasoids, and hence admixture estimates considering Yoruba Nigerians would tend to underestimate the African element. It's important to remember that extant Africans are not uniform, ranging from Caucasoids to Negroids, Pygmies, and Khoi-San, with multiple identifiable clusters within the major Negroid group itself, and all sorts of between-group gene flow in a regional basis. It is always useful (as is the case e.g., with African Americans) to both use historical knowledge about population sources, and also to validate historical narratives with the genetic evidence.
R. L. Raaum et al. Autosomal African admixture in Yemeni populations.

Approximately 30% of mtDNA lineages in South Arabian samples are African L haplotypes, whose origin has usually been attributed to migration and assimilation of African females into the Arabian population over approximately the last 2,500 years. Few In contrast, few Y chromosome lineages of clear recent sub-Saharan African origin have been found in Southern Arabian populations. This bias in maternal and paternal lineages is in accord with historical accounts of the female bias in the Middle Eastern slave trade. In order to evaluate autosomal African ancestry, we collected high-resolution SNP genotype data from a geographically representative set of 62 Yemenis selected from a collection of 552 samples acquired in the Spring of 2007. The ancestry of chromosomal segments in the Yemeni population was estimated using a haplotype-based local ancestry estimation method, HAPMIX. The HAPMIX method is based on a two way admixture model that requires two phased reference populations; we used the HapMap Yoruba in Ibadan, Nigeria (YRI), Luhya in Webuye, Kenya (LWK), Maasai in Kinyawa, Kenya (MKK), and CEPH US residents with ancestry from northern and western Europe (CEU) samples. The three African reference populations include two Bantu-speaking groups (YRI and LWK) and one Nilotic-speaking group (MKK). We estimated local ancestry in the Yemeni sample with all three European-African reference population combinations (CEU-YRI, CEU-LWK, CEU-MKK). The correlations among African ancestry calculated using all three reference population combinations are high (r > 0.98 in all pairwise correlations). Furthermore, there is no significant difference between the average proportion of African ancestry in Yemenis calculated using either of the two Bantu-speaking reference populations: CEU-YRI (mean 0.062, sd 0.044) and CEU-LWK (mean 0.076, sd 0.049) (p=0.13, two-tailed Welch two sample t-test). However, the average African ancestry calculated using the Maasai reference population (CEU-MKK, mean 0.148, sd 0.060) is significantly greater from that calculated using either the Yoruba or Luhya reference populations (p less than 0.0001 in both comparison, two-tailed Welch two sample t-test). These data suggest that the source population for the African ancestry of the Yemeni population is more similar to the contemporary Maasai population than either the Luhya or Yoruba.

The next abstract seems fun; it's always nice to see something that isn't like everything that came before it.
T. Rzeszutek et al. Music as a novel marker in the study of prehistoric human migrations.

The study of prehistoric human population history is often fraught with controversy owing to incongruent evidence among various markers of present-day genetic and cultural diversity. While archaeological evidence can be used to calibrate the conclusions drawn from present-day diversity, the fickle nature of the fossil record leaves some migration histories unresolved. Our work analyzes the potential of music - in particular, vocal music - to serve as novel migration marker, bolstering established migration work and shedding light on regions of the world whose settlement history is contested. One such migration is the recent expansion of Austronesian-speaking peoples across the Pacific within the last 6000 years. The dominant hypothesis posits a recent origin in Taiwan, with a rapid movement southwards and eastwards to populate Polynesia during the following 3500 years. While this model is strongly supported by both archaeological evidence and the present-day distribution of linguistic diversity, our goal was to analyze whether music could serve as a novel line of evidence in the study of Pacific prehistory. A critical concern regarding any migration marker is its time depth. In order to examine this for music, we analyzed correlations between musical diversity and mitochondrial-DNA diversity in 9 Taiwanese aboriginal tribes for which both types of data were available. A sample of 226 choral songs was analyzed using 39 binary characters representing significant structural features of music (e.g., rhythm, interval size, melodic contour, etc.). The musical samples were restricted to ritual musics, which constitute the most conservative (i.e., slowly changing) component of a culture’s repertoire. Mantel tests showed a significant correlation between musical distance and genetic distance among these 9 tribes, suggesting that music may have a time depth comparable to widely-used genetic markers like mitochondrial DNA. This work demonstrates that music has the potential to enrich the conclusions drawn from other markers, and establishes methods for employing it as a tool in the study of prehistoric human movements throughout the world. At the same time, we want to capitalize on music’s own unique dynamics of change over time and place, particularly its capacity for admixture. In other words, music might not only be able to support the narratives told by other migration markers but shed new light on the histories of population movement and cultural contact.

The bolded part in the following abstract makes sense, as it indicates (i) the distinctiveness of Ashkenazi Jews compared to CEU Europeans, and (ii) the fairly recent widespread formation of admixed individuals (in the last couple of generations) which generated individuals that are 1/4 1/2 and 3/4 AJ genomically.

V. Vacic et al., Admixture in Ashkenazi Jewish cohorts and implications for association studies.

Studies of complex genetic disorders may benefit from focusing on population isolates, such as Ashkenazi Jews (AJ). However, in order to truly exploit the advantages of reduced genetic diversity the self-declared AJ ancestry of study participants should be independently confirmed with available genetic data. We investigate whether the AJ cohorts display genetic heterogeneity, such as e.g. different rate of admixing in cases and controls, which could potentially confound disease association studies. We applied principal component analysis (PCA) to AJ cohorts ascertained in Israel and the US East Coast with the goal of characterizing population structure. As described previously, when compared to the HapMap samples with CEU, YRI and CHB/JPT ancestry, virtually all AJ samples cluster with the CEU. Similar analysis done on CEU and Jewish HapMap samples from Ashkenazi, Sephardic and Middle Eastern Jewish communities revealed that 97.8% of AJ samples cluster along the AJ-CEU axis, with modes at AJ and CEU cluster centers and at approximately quartile distances between them. We postulate that these groups correspond to 100-0, 75-25, 50-50, 25-75, and 0-100% AJ-CEU admixtures. Notably, only 91.7% of self-reported AJ individuals fall into the reference JHapMap panel AJ cluster, with 1.6, 3.3, 0.5 and 0.7% in the admixed modes ordered by decreasing fraction of AJ ancestry. We also observe admixing with the non-AJ Jewish communities: 0.7% of samples fall within the non-AJ clusters and 1.4% at a subgroup approximately halfway between the AJ and non-AJ cluster centers. In our dataset we found that when compared to the sample as a whole or only to controls, individuals with Crohn’s disease (CD) show significantly more admixing: 78.1, 3.1, 8.5, 2.0 and 0.9% in the 100, 75, 50, 25 and 0% AJ subgroups respectively. Also, CD samples show more admixing with non-AJ groups (2.8 and 1.0% in the 50-50 and 0-100 AJ-non-AJ subgroups). Isolates typically exhibit a greater amount of cryptic relatedness compared to outbred populations, which motivates an orthogonal method for verifying AJ ancestry based on identity-by-descent (IBD). The high background level of IBD within the Ashkenazi Jewish community can be used to estimate degree of AJ ancestry by averaging the IBD between a sample under study and the AJ individuals in the JHapMap panel. Our preliminary results show that this method recapitulates the high-level results from the PCA analysis and provides better resolution.

Mathematical structure of Platonic dialogues (?)

J. B. Kennedy proposes that Plato organized his dialogues in mathematical form. His argument is mostly found in 'Plato's Forms, Pythagorean Mathematics, and Stichometry', but there is some interesting additional material in his site, and, apparently, a planned book on the subject. The story has found its way to the popular press, without, unfortunately, a lack of journalistic hyperbole thrown in.

I was first suspicious of the notion of a Plato Code, as the name itself reminds one of the discredit Bible Code, but Kennedy proposes something more down-to-earth, namely that Plato used Pythagorean musical principles in the organization of his dialogues. Three main claims stand out: (i) that dialogues have an internal organization in which high points are placed in 1/12ths, corresponding to notes of a musical scale, (ii) that positive and negative turns of the dialogue correspond to consonant intervals of the scale, and this may allow us to discover what Plato "really thought" in open-ended dialogues, and (iii) that different dialogues have a different length of their 1/12th unit, which stretch from 100 lines for the Apology to 1000 lines for the Republic and 1200 lines for the Laws. Kennedy makes several interesting observations on his material, including an apparent lack of this mathematical structure in some of the Platonica that are universally acknowledged to be spurious.

Is it plausible that Plato went into all this trouble? Kennedy cites some pieces of evidence in favor of his Platonic stichometry thesis. In my opinion, the thesis is plausible: the "secret structure" may sound like a conspiracy theory, yet Plato himself (in the 7th epistle) argued against revealing the highest doctrines to the polloi, and (in the Republic) proposed that the advanced study of geometry and astronomy should be revealed -after preparation- to the guardian class. The idea that Plato had a secret mathematical doctrine, discussed only within the walls of the Academy, also finds support in Aristotle, who recounts the tale of Plato's Lecture on the Good, which ended in disaster when Plato attempted to present his geometrical arguments about the One to a lay audience. And, the relationship between the world created by the demiurge, music, and mathematical proportion is famously presented in the Timaeus.

Could it be that as the Timaean demiurge looked at the eternal model of number and proportion to fashion the universe as an expression of a musical scale, so did Plato, as the demiurge of his philosophical universe? It is an intriguing idea.

Even though Kennedy's thesis does not sound like a simple case of quackery, and circumstantial evidence lends it a level of initial credibility, the main weakness of the paper is its lack of statistical elaboration, and its reliance on expert judgments.

Perhaps there is evidence that key themes coincide with 1/12ths, but how many key themes are placed in-between notes? A thorough breakdown of the dialogues based on who is speaking, the topic of discussion, the tone, etc. would allow us to better appreciate whether or not the proposed structure actually exists.

Listening to Mozart does not make you smart

It's a shame that it took us 17 years to put the "Mozart makes you smart" meme to rest. I wonder how much money in research grants was wasted over the years (40 studies!) on the question. So, a big thanks to Pietschnig, Voracek, and Formann for debunking the Mozart-effect theory. I predict that the theory will -unfortunately- survive in popular culture, for a long time to come; but if it leads to people learning to enjoy good music, it might be worth it.



Intelligence doi:10.1016/j.intell.2010.03.001

Mozart effect–Shmozart effect: A meta-analysis

Jakob Pietschnig et al.

The transient enhancement of performance on spatial tasks in standardized tests after exposure to the first movement “allegro con spirito” of the Mozart sonata for two pianos in D major (KV 448) is referred to as the Mozart effect since its first observation by Rauscher, Shaw, and Ky (1993). These findings turned out to be amazingly hard to replicate, thus leading to an abundance of conflicting results. Sixteen years after initial publication we conduct the so far largest, most comprehensive, and up-to-date meta-analysis (nearly 40 studies, over 3000 subjects), including a diversity of unpublished research papers to finally clarify the scientific record about whether or not a specific Mozart effect exists. We could show that the overall estimated effect is small in size (d = 0.37, 95% CI [0.23, 0.52]) for samples exposed to the Mozart sonata KV 448 and samples that had been exposed to a non-musical stimulus or no stimulus at all preceding spatial task performance. Additionally, calculation of effect sizes for samples exposed to any other musical stimulus and samples exposed to a non-musical stimulus or no stimulus at all yielded effects similar in strength (d = 0.38, 95% CI [0.13, 0.63]), whereas there was a negligible effect between the two music conditions (d = 0.15, 95% CI [0.02, 0.28]). Furthermore, formal tests yielded evidence for confounding publication bias, requiring downward correction of effects. The central finding of the present paper however, is certainly the noticeably higher overall effect in studies performed by Rauscher and colleagues than in studies performed by other researchers, indicating systematically moderating effects of lab affiliation. On the whole, there is little evidence left for a specific, performance-enhancing Mozart effect.

Link

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.

and:

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

Abstract

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.

Link

Paleolithic Flutes from the early Aurignacian in Germany

The Hohle Fels site was in the news recently for the discovery of the "first depiction of the human form".

Nature doi:10.1038/nature08169

New flutes document the earliest musical tradition in southwestern Germany

Nicholas J. Conard et al.

Considerable debate surrounds claims for early evidence of music in the archaeological record. Researchers universally accept the existence of complex musical instruments as an indication of fully modern behaviour and advanced symbolic communication1 but, owing to the scarcity of finds, the archaeological record of the evolution and spread of music remains incomplete. Although arguments have been made for Neanderthal musical traditions and the presence of musical instruments in Middle Palaeolithic assemblages, concrete evidence to support these claims is lacking. Here we report the discovery of bone and ivory flutes from the early Aurignacian period of southwestern Germany. These finds demonstrate the presence of a well-established musical tradition at the time when modern humans colonized Europe, more than 35,000 calendar years ago. Other than the caves of the Swabian Jura, the earliest secure archaeological evidence for music comes from sites in France and Austria and post-date 30,000 years ago

Link

AVPR1A and Musical Aptitude

AVPR1A has been previously implicated in dance ability and pair bonding.

PLoS ONE doi:10.1371/journal.pone.0005534

Musical Aptitude Is Associated with AVPR1A-Haplotypes

Liisa T. Ukkola et al.

Abstract

Artistic creativity forms the basis of music culture and music industry. Composing, improvising and arranging music are complex creative functions of the human brain, which biological value remains unknown. We hypothesized that practicing music is social communication that needs musical aptitude and even creativity in music. In order to understand the neurobiological basis of music in human evolution and communication we analyzed polymorphisms of the arginine vasopressin receptor 1A (AVPR1A), serotonin transporter (SLC6A4), catecol-O-methyltranferase (COMT), dopamin receptor D2 (DRD2) and tyrosine hydroxylase 1 (TPH1), genes associated with social bonding and cognitive functions in 19 Finnish families (n = 343 members) with professional musicians and/or active amateurs. All family members were tested for musical aptitude using the auditory structuring ability test (Karma Music test; KMT) and Carl Seashores tests for pitch (SP) and for time (ST). Data on creativity in music (composing, improvising and/or arranging music) was surveyed using a web-based questionnaire. Here we show for the first time that creative functions in music have a strong genetic component (h² = .84; composing h² = .40; arranging h² = .46; improvising h² = .62) in Finnish multigenerational families. We also show that high music test scores are significantly associated with creative functions in music (p<.0001). We discovered an overall haplotype association with AVPR1A gene (markers RS1 and RS3) and KMT (p = 0.0008; corrected p = 0.00002), SP (p = 0.0261; corrected p = 0.0072) and combined music test scores (COMB) (p = 0.0056; corrected p = 0.0006). AVPR1A haplotype AVR+RS1 further suggested a positive association with ST (p = 0.0038; corrected p = 0.00184) and COMB (p = 0.0083; corrected p = 0.0040) using haplotype-based association test HBAT. The results suggest that the neurobiology of music perception and production is likely to be related to the pathways affecting intrinsic attachment behavior. 

Link

Practicing a musical instrument and cognitive function

PLoS ONE doi: 10.1371/journal.pone.0003566

Practicing a Musical Instrument in Childhood is Associated with Enhanced Verbal Ability and Nonverbal Reasoning

Marie Forgeard et al.

Abstract

Background

In this study we investigated the association between instrumental music training in childhood and outcomes closely related to music training as well as those more distantly related.

Methodology/Principal Findings

Children who received at least three years (M = 4.6 years) of instrumental music training outperformed their control counterparts on two outcomes closely related to music (auditory discrimination abilities and fine motor skills) and on two outcomes distantly related to music (vocabulary and nonverbal reasoning skills). Duration of training also predicted these outcomes. Contrary to previous research, instrumental music training was not associated with heightened spatial skills, phonemic awareness, or mathematical abilities.

Conclusions/Significance

While these results are correlational only, the strong predictive effect of training duration suggests that instrumental music training may enhance auditory discrimination, fine motor skills, vocabulary, and nonverbal reasoning. Alternative explanations for these results are discussed.

Link