Earliest sapiens remains in Europe

From the BBC:

They may be yellowed and worn but these ancient teeth and jaw fragment have something very revealing to say about how modern humans conquered the globe.

The specimens, unearthed in Italy and the UK, have just been confirmed as the earliest known remains of Homo sapiens in Europe.

Careful dating suggests they are more than 41,000 years old, and perhaps as much as 45,000 years old in the case of the Italian "baby teeth".

...

The re-assessments have further importance because palaeoanthropologists can now put modern humans in the caves at the same time as the stone and bone tool technologies discovered there.

There has been some doubt over who created the so-called Aurignacian artefacts at Kents Cavern and the slightly older Uluzzian technologies at Grotta del Cavallo. It could have been Neanderthals, but there is now an obvious association in time with Homo sapiens.

From the NY Times:

They had in fact discovered the oldest known skeletal remains of anatomically modern humans in the whole of Europe, two international research teams reported Wednesday.

The scientists who made the discovery and others who study human origins say they expect the findings to reignite debate over the relative capabilities of the immigrant modern humans and the indigenous Neanderthals, their closest hominid relatives; the extent of their interactions; and perhaps the reasons behind the Neanderthal extinction. The findings have already prompted speculation that the Homo sapiens migrations into Europe may have come in at least two separate waves, rather than just one.

I'll add the abstracts later. This certainly seems to be incompatible with substantial Neandertal interbreeding. If humans and Neandertals were genetically compatible species, then why would they maintain very separate morphological populations for ~10ka? We would expect the two populations to quickly merge into one. Moreover, a longer period of interbreeding in West Eurasia would have left an excess of "Neandertal" ancestry in modern West Eurasians, something we simply don't observe.

Press release:

"What the new dates mean", Benazzi summarised, "is that these two teeth from Grotta del Cavallo represent the oldest European modern human fossils currently known. This find confirms that the arrival of our species on the continent – and thus the period of coexistence with Neanderthals – was several thousand years longer than previously thought. Based on this fossil evidence, we have confirmed that modern humans and not Neanderthals are the makers of the Uluzzian culture. This has important implications to our understanding of the development of 'fully modern' human behaviour. Whether the colonisation of the continent occurred in one or more waves of expansion and which routes were followed is still to be established."

Nature (2011) doi:10.1038/nature10484

The earliest evidence for anatomically modern humans in northwestern Europe

Tom Higham et al.

The earliest anatomically modern humans in Europe are thought to have appeared around 43,000-42,000 calendar years before present (43-42 kyr cal BP), by association with Aurignacian sites and lithic assemblages assumed to have been made by modern humans rather than by Neanderthals. However, the actual physical evidence for modern humans is extremely rare, and direct dates reach no farther back than about 41-39 kyr cal BP, leaving a gap. Here we show, using stratigraphic, chronological and archaeological data, that a fragment of human maxilla from the Kent’s Cavern site, UK, dates to the earlier period. The maxilla (KC4), which was excavated in 1927, was initially diagnosed as Upper Palaeolithic modern human1. In 1989, it was directly radiocarbon dated by accelerator mass spectrometry to 36.4-34.7 kyr cal BP2. Using a Bayesian analysis of new ultrafiltered bone collagen dates in an ordered stratigraphic sequence at the site, we show that this date is a considerable underestimate. Instead, KC4 dates to 44.2-41.5 kyr cal BP. This makes it older than any other equivalently dated modern human specimen and directly contemporary with the latest European Neanderthals, thus making its taxonomic attribution crucial. We also show that in 13 dental traits KC4 possesses modern human rather than Neanderthal characteristics; three other traits show Neanderthal affinities and a further seven are ambiguous. KC4 therefore represents the oldest known anatomically modern human fossil in northwestern Europe, fills a key gap between the earliest dated Aurignacian remains and the earliest human skeletal remains, and demonstrates the wide and rapid dispersal of early modern humans across Europe more than 40 kyr ago.

Link

Nature (2011) doi:10.1038/nature10617

Early dispersal of modern humans in Europe and implications for Neanderthal behaviour

Stefano Benazzi et al.


The appearance of anatomically modern humans in Europe and the nature of the transition from the Middle to Upper Palaeolithic are matters of intense debate. Most researchers accept that before the arrival of anatomically modern humans, Neanderthals had adopted several transitional technocomplexes. Two of these, the Uluzzian of southern Europe and the Châtelperronian of western Europe, are key to current interpretations regarding the timing of arrival of anatomically modern humans in the region and their potential interaction with Neanderthal populations. They are also central to current debates regarding the cognitive abilities of Neanderthals and the reasons behind their extinction1, 2, 3, 4, 5, 6. However, the actual fossil evidence associated with these assemblages is scant and fragmentary7, 8, 9, 10, and recent work has questioned the attribution of the Châtelperronian to Neanderthals on the basis of taphonomic mixing and lithic analysis11, 12. Here we reanalyse the deciduous molars from the Grotta del Cavallo (southern Italy), associated with the Uluzzian and originally classified as Neanderthal13, 14. Using two independent morphometric methods based on microtomographic data, we show that the Cavallo specimens can be attributed to anatomically modern humans. The secure context of the teeth provides crucial evidence that the makers of the Uluzzian technocomplex were therefore not Neanderthals. In addition, new chronometric data for the Uluzzian layers of Grotta del Cavallo obtained from associated shell beads and included within a Bayesian age model show that the teeth must date to ~45,000-43,000 calendar years before present. The Cavallo human remains are therefore the oldest known European anatomically modern humans, confirming a rapid dispersal of modern humans across the continent before the Aurignacian and the disappearance of Neanderthals.

Link

Homo floresiensis: dramatically dwarfed Homo erectus descendant

Journal of Human Evolution doi:10.1016/j.jhevol.2011.08.008

Craniofacial morphology of Homo floresiensis: Description, taxonomic affinities, and evolutionary implication

Yousuke Kaifu et al.

This paper describes in detail the external morphology of LB1/1, the nearly complete and only known cranium of Homo floresiensis. Comparisons were made with a large sample of early groups of the genus Homo to assess primitive, derived, and unique craniofacial traits of LB1 and discuss its evolution. Principal cranial shape differences between H. floresiensis and Homo sapiens are also explored metrically.

The LB1 specimen exhibits a marked reductive trend in its facial skeleton, which is comparable to the H. sapiens condition and is probably associated with reduced masticatory stresses. However, LB1 is craniometrically different from H. sapiens showing an extremely small overall cranial size, and the combination of a primitive low and anteriorly narrow vault shape, a relatively prognathic face, a rounded oval foramen that is greatly separated anteriorly from the carotid canal/jugular foramen, and a unique, tall orbital shape. Whereas the neurocranium of LB1 is as small as that of some Homo habilis specimens, it exhibits laterally expanded parietals, a weak suprameatal crest, a moderately flexed occipital, a marked facial reduction, and many other derived features that characterize post-habilis Homo. Other craniofacial characteristics of LB1 include, for example, a relatively narrow frontal squama with flattened right and left sides, a marked frontal keel, posteriorly divergent temporal lines, a posteriorly flexed anteromedial corner of the mandibular fossa, a bulbous lateral end of the supraorbital torus, and a forward protruding maxillary body with a distinct infraorbital sulcus. LB1 is most similar to early Javanese Homo erectus from Sangiran and Trinil in these and other aspects. We conclude that the craniofacial morphology of LB1 is consistent with the hypothesis that H. floresiensis evolved from early Javanese H. erectus with dramatic island dwarfism. However, further field discoveries of early hominin skeletal remains from Flores and detailed analyses of the finds are needed to understand the evolutionary history of this endemic hominin species.

Link

Roman DNA Project

Kristina "Bone Girl" Killgrove is launching a Roman DNA Project

This is a pilot project to study the DNA from the skeletal remains of lower-class Romans dating to the Imperial period. Some DNA analysis has been done in ancient Italy, but it hasn't yet been explored as a method for understanding the geographic origins of immigrants to Rome. In particular, the combination of DNA with results I obtained from isotope analyses (Sr/O/C/N/Pb) in my dissertation research will be a powerful way of investigating the life histories of groups under-represented in history, particularly slaves, immigrants, women, and children.

She is asking for contributions to the Roman DNA Project. There is also a video associated with the Project:



This is a good idea, and I encourage readers to contribute, if, after reading the project materials, they want to pitch in.

Just one quick comment: testing lower-class Imperial Romans is, indeed, admirable, but I am pretty sure there are ancient remains from Latium that date to before the period when cremation burial became the norm, with inhumation never entirely dying out even among the patrician gentes.

In studying the origin of foreigners in Rome, it makes sense to first have a picture of what the Romans of old were like. They may not have been "under-represented" in history, but they are certainly under-represented when it comes to ancient DNA research.

Y-haplogroups E-V13 and G2a in Neolithic Spain

I have not read the paper, so I can't comment in detail. Two quick comments:

• The discovery of G2a is added to the finds from Treilles, Derenburg, and the Alps. It is now virtually certain that the Neolithic transition in much of Europe, both inland, and coastal involved G2a-bearing men.
• The discovery of E-V13 in Spain is unexpected on a number of different reasons: there is relatively little of it there now; it had previously been associated with the inland route of the spread of agriculture, as well as the spread of the Greeks to Sicily and Provence, or Roman soldiers at a much later date.

While this Neolithic E-V13 may well have come from the Balkans, and the common ancestor of the very uniform present-day Balkan cluster may have lived after this Spanish find, it is now certain that E-V13 was established in Europe long before the Bronze Age. This highlights the need to avoid Y-STR based calculations on modern populations for inferring patterns of ancient history, and not to conflate TMRCAs with "dates of arrival": "In short: a particular TMRCA is consistent with either the arrival of the lineage long before and long after the TMRCA in a particular geographical area."

At least for now, three of the major players of the European genetic landscape (E-V13, G2a, and I2a) have made their Neolithic appearance. Hopefully, as more ancient DNA is published, and even from later dates, more of them will turn up.

I will comment more when I get to read the paper.

UPDATE I:

From the paper:

For the six male samples, two complete and four partial Y-STRs haplotypes were obtained (Table 3). They allowed classification of individuals into two different haplogroups: G2a (individuals ave01, ave02, ave03, ave05, and ave06, which seem to share the same haplotype) and E1b1b1 (individual ave07). The four markers chosen to confirm belonging to these haplogroups (Y-E1b1b1-M35.1, Y-E1b1b1a1b-V13, Y-G2-M287, and Y-G2a-P15) were typed with a rate of 66%, which permitted confirmation that four males were G2a and one was E1b1b1a1b (Table 3).

Analysis of shared haplotypes showed that the G2a haplotype found in ancient specimens is rare in current populations: its frequency is less than 0.3%(Table S3). The haplotype of individual ave07 is more frequent (2.44%), particularly in southeastern European populations (up to 7%). The Ave07 haplotype was also compared with current Eb1b1a2 haplotypes previously published (10–14). It appeared identical at the seven markers tested to five Albanian, two Bosnian, one Greek, one Italian, one Sicilian, two Corsican, and two Provence French samples and are thus placed on the same node of the E1b1b1a1b-V13 network as eastern, central, and western Mediterranean haplotypes (Fig. S1).

The ancient remains all appeared to lack the common European lactase persistence genotype.

On the mtDNA:

Mitochondrial HVS-I sequences were obtained for the seven individuals and can be classified into four different haplotypes (Table 2). All are still frequent in current European populations (Table S1), and three of them were also found in ancient Neolithic samples (Table S2). These haplotypes permitted the determination that the individuals ave01, ave02, and ave06 belonged to K1a, ave04 and ave05 to T2b, ave03 to H3, and ave07 to U5 haplogroups.

The supporting information (pdf) has a lot of additional information.

PNAS doi: 10.1073/pnas.1113061108

Ancient DNA suggests the leading role played by men in the Neolithic dissemination

Marie Lacan et al.

The impact of the Neolithic dispersal on the western European populations is subject to continuing debate. To trace and date genetic lineages potentially brought during this transition and so understand the origin of the gene pool of current populations, we studied DNA extracted from human remains excavated in a Spanish funeral cave dating from the beginning of the fifth millennium B.C. Thanks to a “multimarkers” approach based on the analysis of mitochondrial and nuclear DNA (autosomes and Y-chromosome), we obtained information on the early Neolithic funeral practices and on the biogeographical origin of the inhumed individuals. No close kinship was detected. Maternal haplogroups found are consistent with pre-Neolithic settlement, whereas the Y-chromosomal analyses permitted confirmation of the existence in Spain approximately 7,000 y ago of two haplogroups previously associated with the Neolithic transition: G2a and E1b1b1a1b. These results are highly consistent with those previously found in Neolithic individuals from French Late Neolithic individuals, indicating a surprising temporal genetic homogeneity in these groups. The high frequency of G2a in Neolithic samples in western Europe could suggest, furthermore, that the role of men during Neolithic dispersal could be greater than currently estimated.

Link

Archaic human ancestry in East Asia (Skoglund and Jakobsson 2011)

This is an open access article. I had first blogged about this research here.

Related: Reich et al. (2011), Rasmussen et al. (2011), Abi-Rached et al. (2011)

Interestingly, Reich et al. (2011) did not find evidence of substantial Denisova admixture in Eastern Eurasia, with the exception of the islands of the Southeast into Australasia. If I have any ideas on the possible discrepancy between the two, I'll add them here.

PNAS doi: 10.1073/pnas.1108181108

Archaic human ancestry in East Asia

Pontus Skoglund, and Mattias Jakobsson

Recent studies of ancient genomes have suggested that gene flow from archaic hominin groups to the ancestors of modern humans occurred on two separate occasions during the modern human expansion out of Africa. At the same time, decreasing levels of human genetic diversity have been found at increasing distance from Africa as a consequence of human expansion out of Africa. We analyzed the signal of archaic ancestry in modern human populations, and we investigated how serial founder models of human expansion affect the signal of archaic ancestry using simulations. For descendants of an archaic admixture event, we show that genetic drift coupled with ascertainment bias for common alleles can cause artificial but largely predictable differences in similarity to archaic genomes. In genotype data from non-Africans, this effect results in a biased genetic similarity to Neandertals with increasing distance from Africa. However, in addition to the previously reported gene flow between Neandertals and non-Africans as well as gene flow between an archaic human population from Siberia (“Denisovans”) and Oceanians, we found a significant affinity between East Asians, particularly Southeast Asians, and the Denisova genome—a pattern that is not expected under a model of solely Neandertal admixture in the ancestry of East Asians. These results suggest admixture between Denisovans or a Denisova-related population and the ancestors of East Asians, and that the history of anatomically modern and archaic humans might be more complex than previously proposed.

Link

Sardinian continuity against a backdrop of European discontinuity

Ancient DNA research from Europe has tended to paint a picture of substantial population discontinuity. In a Neolithic sample from Derenburg, neither of the two major Y-chromosome haplogroups prevalent in Central-Northern Europe, R1 and I were found. The Tyrolean Iceman belongs to haplogroup G2a4, a minor lineage in modern-day Europeans. In a Neolithic site from the French south, Treilles, haplogroups G2 and I2 were found, the major R1 lineage again being absent. Megalithic mtDNA from France complements that from the Linearbandkeramik in suggesting a picture of discontinuity, or, at least, substantial change, in the occupation of Europe since the Neolithic. An upcoming study suggest that mtDNA haplogroup X2 did not arrive in Central Europe with the early LBK Neolithic, but with the later Bell Beaker folk. The picture of discontinuity, at least for the Mesolithic-Neolithic transition is supported from Scandinavia, as well as Luxembourg. To cap it all off, a pair of unexpected results from Hungary and Ukraine stretch the contact zone of West/East Eurasian populations well to the west of what has already been determined by ancient DNA work in the Tarim basin and Siberia.


There is, however, one population that stands as an outlier against the backdrop of discontinuity: Sardinians. Ghirotto et al. inferred population continuity in Sardinian mtDNA at least until the Bronze Age. Stories about the Tyrolean Iceman, confirmed in the NOVA TV documentary suggest that a 5,000-year old denizen of Central Europe was genetically closest to Sardinians. A study of craniofacial variation confirms population continuity in Sardinia since the Neolithic, with the population of peninsular Italy gradually diverging, consistent with the Iceman findings. Substantial frequencies of Y-haplogroups G and I are found in modern Sardinian newborns, the same two haplogroups detected in Neolithic southern France at Treilles. And, a study of European genetic isolates finds Sardinians to be lacking in some European polymorphic sites, suggesting a degree of genetic isolation compared to mainland Europeans; this is consistent with my own finding that Sardinians are maximally "western" along the east-west Eurasian axis.

Two cryptic bits of revealed information suggest that a major event may have happened in Europe. In an ICHG 2011 talk, David Reich revealed that his lab has unpublished work of ancient admixture in Europe and that "Europeans are anciently mixed just like South Asians." A blog post by Ewen Callaway suggests that Zink's Tyrolean Iceman investigators are asking "whether he and his kin died out and were replaced by migrants from elsewhere, such as the Middle East."

In the absence of concrete data, it is difficult to interpret such hints of things to come. But the idea of an episode of admixture in Europe from the East that would leave a South Asian-like cline of diminishing West Asian ancestry is supported by admixture studies of West Eurasians, showing that the Near-East to Atlantic-Baltic vector captures the principal aspect of variation in this region.


Interestingly, a "West Asian" ancestral component centered on the South Caucasus region has an Fst distance of 0.028 with the main European "Atlantic-Baltic" component, and of 0.058 with a "Southern" component present at non-trivial amount in southern populations from both sides of the Mediterranean and the Near East.

The possibility of a major east-west population movement into Europe that left Sardinians least affected is intriguing. At K=7 Sardinians have almost none of the "West Asian" ancestral component and most of the "Southern" one in Europe. This appears to be consistent with a population that was least affected by population movements from the northern parts of West Asia.

If I had to guess, I would propose that most extant Europeans will be discovered to be a 2-way West Asian/Ancestral European mix, just as most South Asians are a simple West Asian/Ancestral South Indian mix. In both cases, the indigenous component is no longer in existence and the South Asian/Atlantic_Baltic components that emerge in ADMIXTURE analyses represent a composite of the aboriginal component with the introduced West Asian one. And, like in India, some populations will be discovered to be "off-cline" by admixture with different elements: in Europe these will be Paleo-Mediterraneans like the Iceman, an element maximally preserved in modern Sardinians, as well as the East Eurasian-influenced populations at the North-Eastern side of the continent.


In a roundabout manner, the Caucasus and its environs may soon reclaim their position as the fons gentium that Blumenbach, more than two centuries ago, ascribed to them. More than one century ago, Italian anthropologist Giuseppe Sergi, proposed a model of the double origin of Europeans, supposing that the Mediterraneans of southern Europe (a branch of the "Eurafricans") were invaded by peoples from the east, the "Eurasiatics." Naturally, the ideas of Blumenbach and Sergi cannot be adopted today in their entirety, but they do well to remind us that inklings of truth can be found in the most unexpected of places.


And, when one reads this quote from Carleton Coon's classic 1939 synthesis The Races of Europe (section "The western Mediterranean Islands")... "Sardinia and Corsica were peopled at the beginning of the Neolithic by a race of short-statured, dolichocephalic, low-vaulted, brunet Mediterraneans, coming probably from several quarters, including the adjacent European coasts, North Africa, and the eastern Mediterranean. Subsequent immigrations of other Mediterranean peoples have affected the racial composition of these islands but little." ... one is inclined to say "Dr. Coon, you were right!"

More on Al-Magar horses

I had covered a news story about the Al-Magar site and its possible early use of the domesticated horse. Now, Horsetalk has some more information, including some pictures:

The discoveries in Al-Magar, in Saudi Arabia, are equally startling.

They not only push evidence of horse domestication back to about 9000 years ago, but may also point to the very roots of the Arabian horse breed.

One statue shows the unique neck and head characteristics of the breed. Two are said to show evidence of harness and a bridle. A nearby cave drawing appears to show a man riding a horse, and other evidence points to horses and other animals being part of the inhabitants' daily lives.

Among more than 80 artifacts found at Al-Magar is a one-metre long statue of a horse, comprising head, neck and chest.

Officials say the statue, which could well be the largest known sculpture of a horse during that period, has features similar to that of the original Arabian horses, characterised by a long neck and unique head shape.

The head of the statue carries what officials say are clear signs of a bridle.

Long live the 28th October 1940

The Taíno are extinct

Nature corrects itself for stating that the Taíno, pre-Columbian inhabitants of the Caribbean were extinct:

This article originally stated that the Taíno were extinct, which is incorrect. Nature apologizes for the offence caused, and has corrected the text to better explain the research project described.

This is, of course, nonsense. How timorous has the modern scientific culture become, that it is willing to acquiesce so easily, lest one be perceived as not having sufficient "sensitivity" in matters ethnic?

When we say that the Taíno are extinct, we are, in fact claiming that a population group is extinct. We do not say that pieces of DNA are extinct, or that words in a language are extinct. There are pieces of Taíno DNA in modern Puerto Ricans, and there are Taíno words in the Spanish spoken there. But the Taíno group is extinct.

For example, you will not found any aurochsen (Bos primigenius) in Europe today, even though they did pass on some of their genes to modern European cattle. The aurochsen are extinct, even though some of their genes persist. You can say that modern European cattle are just Bos taurus influenced by Bos primigenius in Europe, but you can't say that B. primigenius is in existence today.

Similarly, there are Etruscan words and genes floating around in Europe today, but there are no longer any Etruscans. The Etruscans are extinct. There were, there are not => they are extinct.

A group is defined by a set of common genetic (and, in some animals, cultural) features. The survival of a few of these features is not the same as the survival of the group. The fact that some modern humans have preserved bits of Neandertal immunogenetics does not reverse the fact of Neandertal extinction, because Neandertals were not reducible to bits of their immune systems.

It is well-known that Egyptian pyramids have been used for building materials since the demise of ancient Egyptian civilization. If the building blocks of the pyramids had all found themselves in Cairo buildings, we would be justified in saying that "the pyramids are gone", because the arrangement of parts called "pyramids" was no longer in existence, even though their parts remain.

It is somewhat ironic that the same crowd of "ethnically sensitive" people can simultaneously propose that differences between races and ethnic groups have no biological basis, and, at the same time, affirm the non-extinction of an ethnic group precisely on account of its having preserved a few bits of distinctive DNA.

Let us suppose, for the sake of argument, that five hundred years into the future, there is a United Europe, with English as its common language. Further suppose, that in a province of that United Europe, say Finland, the population's gene pool is composed of 10% current Finnish DNA and 90% other European/non-European DNA. Would we be justified in saying that the Finns were extinct?

Bits of our DNA have reached us from the remotest depths of time, joined, more recently, by bits of our culture. They aggregate, for a time, into distinctive biocultural packages, such as the Taíno, they are transformed, and then they are dissolved: some dying out, some latching onto new units. The Taíno are extinct, but parts of them remain.

Press release about Bolzano Mummy congress

A Rest, a Meal, Then Death for 5,000-Year-Old Glacier Mummy: Scientists Consolidate Results of Research Into Ötzi’s State of Health and His Death

There was broad agreement at the Bolzano Congress about the last hour of his life. Albert Zink, Head of the Institute for Mummy Research at EURAC, reports as follows about the circumstances of the Iceman's death: "He felt safe enough to take a break, and settled down to a copious meal. While thus resting, he was attacked, shot with an arrow and left for dead." There was no evidence pointing to a possible burial as some scientists have suggested in the past. "The position of the mummified body with his arm pointing obliquely upwards, the lack of any piles of stones or other features which often accompany burial sites, runs counter to the burial theory," he continues.

But there is still the problem of what was Ötzi doing up there, at a height of 3,200 metres? At the Bolzano Congress, the Innsbruck based scientists Andreas Putzer, Daniela Festi and Klaus Oeggl refuted the theory, first put forward in 1996, according to which Ötzi was a shepherd who had taken his herd to pastures high up in the mountains to graze during the summer months. According to the latest archaeological and botanical findings, there was no seasonal migration of cattle during the Chalcolithic period, the Copper Stone Age. The so called transhumance did not start until around 1500 BC.

Ötzi was not on the run. On the contrary, between 30 and 120 minutes before his death he had settled down to a hearty meal, as evidenced by stomach samples investigated by Albert Zink and his team this past summer. Goat meat, grains of corn, pieces of leaves, apples and flies' wings were clearly discernible under the microscope.

...

Since then, scientists from almost all disciplines have been investigating these samples from their own specific scientific angles using subject-specific methods: medics, nanotechnologists, anthropologists, biochemists, archaeologists and physicists. There are now over 100 "Ötzi researchers," and the Bolzano Mummy Congress represents a so far unique opportunity for them to discuss the present state of research face-to-face at a gathering which was specifically dedicated to the famous iceman.

This is all we are likely to get folks. It seems that Tyrolean Iceman week was a dud, and I have no doubt that the TV special today will be along the same lines, i.e., no real genetic information that we don't already know.

The 90% of the Iceman genome that has been sequenced will remain locked up. This will ensure that some of the "100 Ötzi researchers" will have the time to write their papers without fear of competition, and that the journals that will publish them will have the exclusivity necessary to make a profit. Only losers: (a) the public in several nations, which makes possible, directly or indirectly this type of research, and (b) Science, which must take second place behind more ephemeral concerns.

Mastery through practice, but not for all

From the press release:

In one survey of chess players in Argentina, Campitelli and Gobet found that, indeed, practice is important. All of the players that became masters had practice at least 3,000 hours. "That was not surprising," he says. There is a theory in psychology that the more you practice, the better you'll do in areas like sports, music, and chess. "But the thing is, of the people that achieved the master level, there are people that achieved it in 3,000 hours. Other people did, like, 30,000 hours and achieved the same level. And there are even people that practiced more than 30,000 hours and didn't achieve this."

...

Campitelli and Gobet suggest that more intelligent children may be attracted to chess, and use their good reasoning skills to play well, but later they need to practice hard to learn all the strategies and plans that make a good chess player -- and intelligence isn't much help.

Intelligence is definitely necessary for achieving mastery in chess, but one of the most critical components of current practice is having a good memory. Without a substantial knowledge of opening and endgame theory, chess players of higher ability are at a disadvantage against less able but better prepared opponents. This knowledge can only be obtained by diligent study, but having the right hardware helps. But, even in the middle game one needs a good working memory, since one needs to basically do a tree traversal with a lot of redundancy whenever one analyzes variants.

Chess seems like the perfect game to use for analyzing learning and high-performance human brain functioning, as it is entirely rational, and there are literally millions of test subjects around the world.

Current Directions in Psychological Science October 2011 vol. 20 no. 5 280-285

Deliberate Practice Necessary But Not Sufficient

Guillermo Campitelli, Fernand Gobet

Deliberate practice (DP) occurs when an individual intentionally repeats an activity in order to improve performance. The claim of the DP framework is that such behavior is necessary to achieve high levels of expert performance. The proponents of the framework reject evidence that suggests that other variables are also necessary to achieve high levels of expert performance, or they claim that the relationship between those variables and expert performance is mediated by DP. Therefore, the DP framework also implies that DP is sufficient to achieve high levels of expert performance. We test these claims by reviewing studies on chess expertise. We found strong evidence that abundant DP is necessary (but not sufficient) and estimated that the minimum requirement to achieve master level is 3,000 hours of DP. We also review evidence showing that other factors play a role in chess skill: general cognitive abilities, sensitive period, handedness, and season of birth.

Link

The Iceman's genome cometh... not yet

The Iceman genome cometh - October 24, 2011

To get a better grip on his ancestry and predisposition to disease, Albert Zink, head of the Institute for Mummies and the Iceman in Bolzano, and his team sequenced Ötzi’s 3 billion base pair nuclear genome from a shard of hip bone. Their sequence covers more than 90 percent of the Iceman’s genome. Their team also analysed DNA preserved in Ötzi’s stomach in hopes of revealing the microbes that colonized his gut.

Zink says his team is keeping most of the results of these studies under wraps, pending publication. They had hoped to have the paper out in time for last week’s Mummy Congress and a television special called Iceman Murder Mystery.

His team plans to use the sequence to determine Ötzi’s status for genetic variations linked to diseases in modern humans, particularly arthrosclerosis. A full nuclear genome will also paint a more detailed picture of the Iceman’s ancestry and his relationship to present-day humans. Zink’s team will ask whether Ötzi is an ancestor of people living in Central Europe today, or whether he and his kin died out and were replaced by migrants from elsewhere, such as the Middle East. To buff up this analysis, they are analysing DNA preserved in the skeletons of other ancient inhabitants of central Europe.

I don't get why we can't have Otzi's genome sequence out in the open already. I realize that it's a precious resource that can lead to lots of publications for the people involved, but at the expense of delaying the use of the genome by everyone else. Otzi wasn't a milk drinker but he is sure as hell being milked dry by the people in charge.

(Sometimes) time dependent mtDNA evolution rate

Genome Biol Evol. 2011 Oct 19. [Epub ahead of print]

Time dependency of molecular evolutionary rates? Yes and No.

Subramanian S, Lambert D.

Abstract

Some previous studies have suggested that rates of evolution inferred using molecular sequences vary substantially depending on the time frame over which they are measured, while a number of other studies have argued against this proposition. We examined this issue by separating positions of primate mitochondrial genomes that are under different levels of selection constraints. Our results revealed an order of magnitude variation in the evolutionary rates at constrained sites (including nonsynonymous sites, D-loop and RNA) and virtually an identical rate of evolution at synonymous sites, independent of the timescales over which they were estimated. While the evolutionary rate at nonsynonymous sites obtained using the European (H1 haplogroup) mitogenomes is 9-15 times higher than that estimated using the human-chimpanzee pair, in contrast the rates at synonymous sites are similar between these comparisons. We also show that the ratio of divergence at nonsynonymous- to synonymous sites estimated using intra- and inter-specific comparisons vary up to 9 times, which corroborates our results independent of calibration times.

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Citizen genetics

Razib posted his analysis of the 23andMe data of Betsileo individual from Madagascar. This analysis was made possible by a number of different people:

1. Razib, who took the initiative and carried out the analysis
2. Scientists who wrote the software used
   
3. 23andMe, who sold a product providing genotype data
4. Donors, who paid for the test
5. The actual individual who contributed his/her DNA for science

Yesterday, I twitted in exasperation that Otzi's genome, which must have been available in at least some sort of draft form since at least the beginning of this year, has been under lock and key, presumably because of the need to make a big splash with the simultaneous Bolzano conference, TV special, likely imminent journal publication, and all the media stories that will follow.

Scientific progress = active brains using tools to examine data and produce new knowledge

In the grand scheme of things it may be a trifle that the Betsileo are Bantu+Malay. But, the fact that ordinary people can band together and produce new knowledge within a few months is anything but a trifle. An equivalent academic study would have taken years: drafting proposals, dealing with funding agencies, getting consent forms, navigating institutional review boards, dealing with bureaucrats, convincing reviewers and editors, and finally producing an article that might end up hidden behind a paywall for the profit of some publishing company.

Would the end product be better? Perhaps, but the whole point of citizen science is that you can do it better, and you can tell the whole world if it's bad.

Citizen science is no longer a sideshow, and traditional science must take her into account, lest she be reduced to a sideshow before long.

There are, of course, things that citizen science can't, or won't do.

It won't do the kind of meaningless navel-gazing work that scientists in some disciplines are able to get away with at the public expense. It won't inveigle in the hope of being printed in the pages of a high-status publication. It won't split and bundle itself into least publishable units. It won't sit in a drawer afraid of having its data and ideas co-opted by the competition.

But, it can't do the type of highly sophisticated, technical and expensive work that requires a concerted interdisciplinary effort and substantial human and monetary resources.

There is plenty of common ground between traditional and citizen science, so let's hope that their noble competition and ability to learn from each other will benefit the lady Science herself.

ICHG 2011 webcast

Webcast: Next-Generation Genome Sequencing Methods Reveal New Findings on Evolution and Population Genetics at ICHG/ASHG 2011 Meeting

PDF: Press release (pdf)

The following topics are covered:

• Lynn B. Jorde, PhD (Moderator) – “Using Whole-genome Data to Reveal Distant Relationships Between Individuals by Analysis of Genomic Segments Shared Identically by Descent”
• Lalji Singh, PhD – “Genetic Diversity in Indian Populations and its Health Implications”
• Carlos D. Bustamante, PhD – “Genomic Reconstruction of an Extinct Population from Next-Generation Sequence Data: Insights from the Taìno Genome Project”
• David E. Reich, PhD – “Denisova Genetic Admixture and the First Modern Human Population Dispersals into Southeast Asia and Oceania”

Some comments:

• Interesting tidbit from David Reich's talk, referring to the earliest ANI/ASI work: "We now know in unpublished work from our laboratory that Europeans are anciently mixed just like South Asians".
• Lynn Jorde mentions that one of the advantages of full genome sequencing is that it is not as susceptible to biases related to SNP discovery in micorarrays, and David Reich adds that current microarrays don't even begin to cover variation in Indians, e.g., missing a major disease susceptibility locus

Cultured orangutans

The is a long-standing debate about the origins of human uniqueness. Specific human adaptations (such as the use of sophisticated tools, fire, clothing, ornaments, etc.) seem to have occurred at different times. What seems to be most human, however, is language and culture. Our species, it turns out, is not the only one to have culture, i.e., transmission of know-how via non-genetic means, but we are certainly awfully good at it, aided by our ability to communicate with language.

One camp thinks that there was one or more genetic mutations that turned us from apes to humans. According to that point of view, we are genetically special, and our complex language and culture was made possible by our genetic endowment.

An alternative view is that humans are not that special genetically, or that their adaptations took hold long before the emergence of fully modern behavior during the Upper Paleolithic. According to that view, one can think of humans as kindling that took the spark of culture by accident, long after it was ready to receive it. As an analogy, we can say that Upper Paleolithic brains probably had the capacity to go to the Moon, but did not have the culture for it yet: settled agriculture, science, and the industrial revolution were needed first.

I tend to the latter view myself. If a Neandertal or even Homo heidelbergensis child were raised in a modern society, they would no doubt be able to function in it, even if they weren't very bright or if they talked/moved/looked funny. The fact that these species never developed the complex cultures that modern humans did is not in itself evidence that they were innately incapable to produce them.

In any case, the comparison of the modern human/Neandertal genomes, in conjunction with developmental studies/studies of pathological variants may yet shed more light on whether modern humans do have, after all, genetic mutations that acted as the great enablers of their cultural efflorescence.

The new study frames the debate by establishing that one part of "being human", cultural transmission across the generations isn't "only human".

Culture in Humans and Apes Has the Same Evolutionary Roots

ScienceDaily (Oct. 20, 2011) — Culture is not a trait that is unique to humans. By studying orangutan populations, a team of researchers headed by anthropologist Michael Krützen from the University of Zurich has demonstrated that great apes also have the ability to learn socially and pass them down through a great many generations. The researchers provide the first evidence that culture in humans and great apes has the same evolutionary roots, thus answering the contentious question as to whether variation in behavioral patterns in orangutans are culturally driven, or caused by genetic factors and environmental influences.

Current Biology, 10.1016/j.cub.2011.09.017

Culture and Geographic Variation in Orangutan Behavior

Michael Krützen et al.

Although geographic variation in an organism's traits is often seen as a consequence of selection on locally adaptive genotypes accompanied by canalized development [1], developmental plasticity may also play a role [2,3], especially in behavior [4]. Behavioral plasticity includes both individual learning and social learning of local innovations (“culture”). Cultural plasticity is the undisputed and dominant explanation for geographic variation in human behavior. It has recently also been suggested to hold for various primates and birds [5], but this proposition has been met with widespread skepticism [6,7,8]. Here, we analyze parallel long-term studies documenting extensive geographic variation in behavioral ecology, social organization, and putative culture of orangutans [9] (genus Pongo). We show that genetic differences among orangutan populations explain only very little of the geographic variation in behavior, whereas environmental differences explain much more, highlighting the importance of developmental plasticity. Moreover, variation in putative cultural variants is explained by neither genetic nor environmental differences, corroborating the cultural interpretation. Thus, individual and cultural plasticity provide a plausible pathway toward local adaptation in long-lived organisms such as great apes and formed the evolutionary foundation upon which human culture was built.

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