Is it music what makes us humans?

Alright, the title is a blunt cliché admittedly. But that is what a new study on rhesus monkeys has found: that our intelligent cousins from India cannot discern the beat, the regularity that makes up a rhythm. Human babies can instead and so is the case of some birds.

Henkjang Honing et al., Rhesus Monkeys (Macaca mulatta) Detect Rhythmic Groups in Music, but Not the Beat. PLoS ONE 2012. Open access → LINK [doi:10.1371/journal.pone.0051369]

Abstract

It was recently shown that rhythmic entrainment, long considered a human-specific mechanism, can be demonstrated in a selected group of bird species, and, somewhat surprisingly, not in more closely related species such as nonhuman primates. This observation supports the vocal learning hypothesis that suggests rhythmic entrainment to be a by-product of the vocal learning mechanisms that are shared by several bird and mammal species, including humans, but that are only weakly developed, or missing entirely, in nonhuman primates. To test this hypothesis we measured auditory event-related potentials (ERPs) in two rhesus monkeys (Macaca mulatta), probing a well-documented component in humans, the mismatch negativity (MMN) to study rhythmic expectation. We demonstrate for the first time in rhesus monkeys that, in response to infrequent deviants in pitch that were presented in a continuous sound stream using an oddball paradigm, a comparable ERP component can be detected with negative deflections in early latencies (Experiment 1). Subsequently we tested whether rhesus monkeys can detect gaps (omissions at random positions in the sound stream; Experiment 2) and, using more complex stimuli, also the beat (omissions at the first position of a musical unit, i.e. the ‘downbeat’; Experiment 3). In contrast to what has been shown in human adults and newborns (using identical stimuli and experimental paradigm), the results suggest that rhesus monkeys are not able to detect the beat in music. These findings are in support of the hypothesis that beat induction (the cognitive mechanism that supports the perception of a regular pulse from a varying rhythm) is species-specific and absent in nonhuman primates. In addition, the findings support the auditory timing dissociation hypothesis, with rhesus monkeys being sensitive to rhythmic grouping (detecting the start of a rhythmic group), but not to the induced beat (detecting a regularity from a varying rhythm).

Sadly for the enthusiasts of "complex modern behavior", who'd love to draw an absolutist line between before and after of being humans, music leaves no or almost no remains, so their line, even if it might exist in blurry or whatever other state, cannot be identified in the archaeological record.

Edward Harris conference (video)

Edward C. Harris, Director of the Bermuda Maritime Museum is best known for his inception, back in the 1970s, of the Harris matrix, today the standard method for archaeological digs.

Along with a host of other reputed scholars he participated in the International Congress on Iruña-Veleia, which took place on November 24 in Vitoria-Gasteiz (Basque Country).

Harris' conference, which is essentially an introduction to modern stratigraphy, has been now been made available in video (good quality, 40 mins., English):

The specific mentions to Iruña-Veleia are at the end of the video.

See also:

• Iruña-Veleia Congress: papers and synthesis
• Edward Harris on the Iruña-Veleia affaire
• Category: Iruña-Veleia

Was the first ever cheese from Poland?

Modern oscypki cheese from Poland
(CC by Pawel Swiegoda)

While today it is maybe France the most famed cheese-making and cheese-eating region on Earth*, we knew very little about cheese-making origins... until now.

Melanie Salque et al., Earliest evidence for cheese making in the sixth millennium bc in northern Europe. Nature 2012. Pay per view → LINK [doi:10.1038/nature11698]

Abstract

The introduction of dairying was a critical step in early agriculture, with milk products being rapidly adopted as a major component of the diets of prehistoric farmers and pottery-using late hunter-gatherers^{1, 2, 3, 4, 5}. The processing of milk, particularly the production of cheese, would have been a critical development because it not only allowed the preservation of milk products in a non-perishable and transportable form, but also it made milk a more digestible commodity for early prehistoric farmers^{6, 7, 8, 9, 10}. The finding of abundant milk residues in pottery vessels from seventh millennium sites from north-western Anatolia provided the earliest evidence of milk processing, although the exact practice could not be explicitly defined¹. Notably, the discovery of potsherds pierced with small holes appear at early Neolithic sites in temperate Europe in the sixth millennium bc and have been interpreted typologically as ‘cheese-strainers’¹⁰, although a direct association with milk processing has not yet been demonstrated. Organic residues preserved in pottery vessels have provided direct evidence for early milk use in the Neolithic period in the Near East and south-eastern Europe, north Africa, Denmark and the British Isles, based on the δ¹³C and Δ¹³C values of the major fatty acids in milk^{1, 2, 3, 4}. Here we apply the same approach to investigate the function of sieves/strainer vessels, providing direct chemical evidence for their use in milk processing. The presence of abundant milk fat in these specialized vessels, comparable in form to modern cheese strainers¹¹, provides compelling evidence for the vessels having being used to separate fat-rich milk curds from the lactose-containing whey. This new evidence emphasizes the importance of pottery vessels in processing dairy products, particularly in the manufacture of reduced-lactose milk products among lactose-intolerant prehistoric farming communities^{6, 7}.

See also the related article by Niddhi Subamaran at Nature News and the one by Hanna Briggs at BBC News.

The dating for the cheese-making artifacts (holed pots used to press curdled milk, discarding the whey, which is a preliminary step in cheese making) is of similar age as the arrival of Neolithic itself and the first evidences of dairying in Europe and Africa. So I guess that we can conclude that farming arrived to Europe, at least to Central and Northern Europe, together with cattle herding, dairying and cheese-making.

While the potsherds are known to exist elsewhere in Central Europe, the ones analyzed for this paper are specifically from Cuyavia, Poland, which used to be the most Northeastern offshoot of the Danubian Neolithic.

Cuajada or mamia
(GFDL+CC-BY-SA-2.5)

Just one weak caveat. While Richard Evershed (in the BBC article) asks rhetorically what other milk product could it be? This question is not as trivial as it may look on first sight because there is indeed another such milk product: the cuajada (Spanish name) or mamia (Basque name) which is nothing else but the preliminary product of cheese making (curdled milk) and a much coveted delicatessen when properly made.

But, well, I guess it can be considered a form of cheese... more or less. Also real fully-processed cheese achieves a further purpose: to preserve milk (or rather key parts of it) for delayed consumption and easier transport.

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* Actually Greeks eat quite more cheese per capita than the French, but they are the only ones. 

"Megadrought" may have affected NW Australia some 5500 years ago

Depictions of the Wondjina rain spirits
(CC by Whinging Pom)

Researchers have detected an apparent "megadrought" affecting at least the region of Kimberley (NW Australia), which hosts some of the most important collections of Aboriginal rock art and may have been one of the first inhabited regions of the island-continent.

The drought may explain a change in artistic style between the Gwion (or Bradshaw) style and the Wondjina one, more modern. Memory of the drought persists in the legends from the Dream Time of the Aboriginal peoples of Australia.

Hamish McGowan et al., Evidence of ENSO* mega-drought triggered collapse of prehistory Aboriginal society in northwest Australia. GEOPHYSICAL RESEARCH LETTERS, VOL. 39, 2012. Pay per view → LINK [doi:10.1029/2012GL053916]

Abstract

The Kimberley region of northwest Australia contains one of the World's largest collections of rock art characterised by two distinct art forms; the fine featured anthropomorphic figures of the Gwion Gwion or Bradshaw paintings, and broad stroke Wandjina figures. Luminescence dating of mud wasp nests overlying Gwion Gwion paintings has confirmed an age of at least 17,000 yrs B.P. with the most recent dates for these paintings from around the mid-Holocene (5000 to 7000 yrs B.P.). Radiocarbon dating indicates that the Wandjina rock art then emerged around 3800 to 4000 yrs B.P. following a hiatus of at least 1200 yrs. Here we show that a mid-Holocene ENSO forced collapse of the Australian summer monsoon and ensuing mega-drought spanning approximately 1500 yrs was the likely catalyst of this change in rock art. The severity of the drought we believe was enhanced through positive feedbacks triggered by change in land surface condition and increased aerosol loading of the atmosphere leading to a weakening or failure of monsoon rains. This confirms that pre-historic aboriginal cultures experienced catastrophic upheaval due to rapid natural climate variability and that current abundant seasonal water supplies may fail again if significant change in ENSO occurs. 

See also article at Past Horizons (h/t Pileta). 

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* ENSO = El Niño Southern Oscillation.

MixMapper: wrong again!

Some of you already know that I'm reluctant to take the results produced by TreeMix seriously because they mostly seem to make very little sense and rather induce to the weirdest of confusions than to provide any useful, reliable info on ancient admixture episodes.

Now a new version with allegedly greater power and ability to detect two-source admixture events is being presented but I hold the same caveats: the results are not consistent with what we already know, so the product can only cause the weirdest of confusions if trusted beyond the level of an experimental toy with no reliability whatsoever.

Mark Lipson et al., Efficient moment-based inference of admixture parameters and sources of gene flow. arXiv 2012 (pre-pub). Freely accessible → LINK [ref: arXiv:1212.2555 [q-bio.PE]]

Abstract

The recent explosion in available genetic data has led to significant advances in understanding the demographic histories of and relationships among human populations. It is still a challenge, however, to infer reliable parameter values for complicated models involving many populations. Here we present MixMapper, an efficient, interactive method for constructing phylogenetic trees including admixture events using single nucleotide polymorphism (SNP) genotype data. MixMapper implements a novel two-phase approach to admixture inference using moment statistics, first building an unadmixed scaffold tree and then adding admixed populations by solving systems of equations that express allele frequency divergences in terms of mixture parameters. Importantly, all features of the tree, including topology, sources of gene flow, branch lengths, and mixture proportions, are optimized automatically from the data and include estimates of statistical uncertainty. MixMapper also uses a new method to express branch lengths in easily interpretable drift units. We apply MixMapper to recently published data for HGDP individuals genotyped on a SNP array designed especially for use in population genetics studies, obtaining confident results for 30 populations, 20 of them admixed. Notably, we confirm a signal of ancient admixture in European populations---including previously undetected admixture in Sardinians and Basques---involving a proportion of 20-40% ancient northern Eurasian ancestry.  

The relevant graph is this one:

Figure 4. Inferred anceint admixture in Europe. (A) Detail of the inferred ancestral admixture for Sardinians (other European populations are similar). One mixing population splits from the unadmixed tree along the common ancestor branch of Americans (“Ancient Northern Eurasian”) and the other along the common ancestor branch of all non-Africans (“Ancient Western Eurasian”). Median parameter values are shown; 95% bootstrap confidence intervals can be found in Table 1. The branch lengths a, b, and c are confounded, so we show a plausible combination.

Who says Sardinians here, says any other European or Highland West Asian (represented only by the Adygei in fig. 3; we know from other studies that North Caucasians cluster rather tightly with Higland West Asians like Turks, Kurds or Iranians, as well as with Western Jews). There are alleged (and expected) minor differences  between Russians, Basques and Sardinians but not in essence.

However we know for a fact that it is Native Americans who display obvious ancient admixture between a West Eurasian source (represented by Y-DNA Q and mtDNA X) and a more dominant East Asian one (represented notably by mtDNA A, B, C and D and also by Y-DNA C3). 

Native Americans are a clear case of ancient admixture between Western and Eastern Eurasians and this MixMapper algorithm is unable to detect that well known, obvious admixture. Instead (and I guess it could be worse) it detects a false admixture in reverse, maybe by conflating these ancient Native American (and some other Siberians') dual origins with recent inflow in Europe from Siberia (Uralic peoples and such, well known also). 

The conclusion can only be that, like its ancestor TreeMix, MixMapper is a mere experimental toy with no practical applications other than laughs. 

Keep trying, guys. 

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Note: in preliminary email exchanges on this matter, I was asked why I state so confidently that mtDNA X and Y-DNA Q are West Eurasian by origin. The matter is clear as soon as you look at their phylogenetically structured or basal haplogroup diversity.

This one is concentrated in West Asia for X (with even marked penetration in Africa with the X1 (also known as X1'3) clade, which is probably of Egyptian coalescence) and also for X2, with a more Central Asian tendency and scattered rare clades in Altai and Central Siberia. 

Almost the same is true for Y-DNA Q, the main Amerindian patrilineage, whose basal diversity seems centered around Iran at least until the Q1 and Q1b nodes. Q1a may have a Central Asian center of spread but it is not until the Q1a3 level when we can really speak of Native American lineages specifically. 

Nobody has ever expressed to me any doubts about mtDNA A, B, C and D, or Y-DNA C3, being of East Asian origin, so I won't discuss them here. 

Iruña-Veleia congress: papers and synthesis

The linguistic-cultural association Euskararen Jatorria (The Origin of the Basque Language) has published the reports presented for the International Congress on Iruña-Veleia that took place in late November in Vitoria-Gasteiz. 

All papers have trilingual (Basque, English, Spanish) introductory sections and then each one is in the language chosen by the author. They can all be found HERE.

Among them there is a "conclusions" synthesis (PDF) whose headlines I synthesize here:

• The dig [by Gil, Filloy et al.] was performed correctly
• Chain of evidence has been broken - as the judge has not controlled it
• Iconography and most graffiti are coherent
• Controlled local digs were not performed to contrast with the findings
• The archaeometrical datings now being performed in Madrid should have been the first thing to do
• Graffiti on bone are easy to date [but was not done either]
• It is only logical that Iberian signs are found among the rest
• So far 19 reports have declared the graffiti genuine
• The Advisory Commission did not do anything of what they should have done

Paraphrasing the late linguist Gorka Knörr, the paper concludes that 

If Iruña-Veleia would be a house, datings would be the foundations, controlled digs the first floor, auditions the first floor, history the second, philology the third... Therefore when the Advisory Commission "began building the house by the ceiling" and that is why we are now just as the beginning, because the datings required by Eliseo Gil were never performed.

Background:

As you may already know, Iruña-Veleia is a Vasco-Roman city of Antiquity not far from Vitoria-Gasteiz. In 2006 a large number of inscribed graffiti on pottery shards (ostrakas) was found, most of them in ancient Basque and Vulgar Latin. 

The finding had the potential of rewriting linguistic and historical understanding of Basque language and also Romances, what apparently scared to death some popes of linguistics led by Gorrochategui and Lakarra, who, by means of smearing, abuse of power and cronyism, managed to get the archaeologists in charge (Gil, Filloy and their company Lurmen) out and put instead the only archaeologist who was ready to play their game Luis Núñez, whose management of the site has consisted essentially into digging wildly with a caterpillar until popular clamor stopped his misgivings (since then he seems to do nothing at, what is surely good considering what he did when he dared to).

Gil and Filloy have been charged with "falsification" and in this trial is where the hopes of truth being revealed stand now. After many years, a sample of the ostrakas have been sent to researchers in Madrid to perform archeometry tests.

See also: category Iruña-Veleia for further details.

Italian haploid genetics (messy paper)

Important update (Feb 9 2014): the paper was formally corrected, after a long bureaucratic struggle, in February 2014. I wrote a new review for the occasion: → HERE.

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This study is rather chaotic and poorly presented with potentially interesting but very confusingly reported data Italian paternal and maternal lineages, after we wade through the hyper-obsolete and sometimes sloppy nomenclature they use and the many bugs in the presentation of the data.

Their attempt to say anything of the autosomal genetics is rather useless, confusing and pointless however and will not be discussed here.

Francesca Brisighelli et al., Uniparental Markers of Contemporary Italian Population Reveals Details on Its Pre-Roman Heritage. PLoS ONE 2012. Open access → LINK [doi:10.1371/journal.pone.0050794]

Abstract

Background

According to archaeological records and historical documentation, Italy has been a melting point for populations of different geographical and ethnic matrices. Although Italy has been a favorite subject for numerous population genetic studies, genetic patterns have never been analyzed comprehensively, including uniparental and autosomal markers throughout the country.

Methods/Principal Findings

A total of 583 individuals were sampled from across the Italian Peninsula, from ten distant (if homogeneous by language) ethnic communities — and from two linguistic isolates (Ladins, Grecani Salentini). All samples were first typed for the mitochondrial DNA (mtDNA) control region and selected coding region SNPs (mtSNPs). This data was pooled for analysis with 3,778 mtDNA control-region profiles collected from the literature. Secondly, a set of Y-chromosome SNPs and STRs were also analyzed in 479 individuals together with a panel of autosomal ancestry informative markers (AIMs) from 441 samples. The resulting genetic record reveals clines of genetic frequencies laid according to the latitude slant along continental Italy – probably generated by demographical events dating back to the Neolithic. The Ladins showed distinctive, if more recent structure. The Neolithic contribution was estimated for the Y-chromosome as 14.5% and for mtDNA as 10.5%. Y-chromosome data showed larger differentiation between North, Center and South than mtDNA. AIMs detected a minor sub-Saharan component; this is however higher than for other European non-Mediterranean populations. The same signal of sub-Saharan heritage was also evident in uniparental markers.

Conclusions/Significance

Italy shows patterns of molecular variation mirroring other European countries, although some heterogeneity exists based on different analysis and molecular markers. From North to South, Italy shows clinal patterns that were most likely modulated during Neolithic times.

As the data is so poorly presented, I decided to rework it all myself. This is the mtDNA map (made recycling figs. 1 and 4 on a map of Italy):

Italian mtDNA - on Brisighella 2012 - click to expand

We can see that the apportions of haplogroups are generally in agreement with what we can find in Western Europe, showing some minor but evident differences in the South: high frequency of J, more T and X than in the North and Center, less W, H and V, presence of rare lineages in the N* and M* categories.

However warning must be made that the Northern and Central pie charts are so exactly identical that it looks like an error was made (and either one was copied twice). I don't have time right now to research this so obvious error, checking the supp. material and what not, but be warned that there is a bug (this bug is reproduced here from fig. 1 as-it-is).

Southern highlight populations (Salentine Greeks and Lucerans, a town where Sicilian Muslims where deported to in the Middle Ages) appear to be very similar to Southern Italians in general. Instead the Ladins appear to retain a more Paleolithic-looking mtDNA pool, dominated by H, U and V. However notice that K (often considered a Neolithic haplogroup) is not mentioned separately from its parent U.

I did the same with Y-DNA, however here the difficulty is in the horribly chosen nomenclature:

Italian Y-DNA - on Brisighella 2012 - click to expand

Before you jump to any conclusion from the map above, you must note that the haplogroups are all poorly described. I checked ISOGG present day nomenclature and annotated fig. 3 (in grey) so we can get a more clear idea of what they are trying to describe:

Fig. 3 of Brisighella 2012
Phylogeny of Y-chromosome SNPs and haplogroup frequencies in different Italian populations.
(annotated by Maju)
- click to expand -

Notice also apparent inconsistencies on the labeling, notably how R1* becomes R1b3 (sic) among Ladins, Lucerans and Salentine Greeks.

In truth it's very difficult to get anything straight from this paper because there is such sloppiness in the presentation of the data that we can only end with a headache and greater confusion than when we started. 

Therefore I must renounce to make any attempt of analysis, sadly enough.