October 31, 2011

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

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

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

October 28, 2011

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.

October 26, 2011

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.

October 24, 2011

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.

Link

October 23, 2011

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.

October 22, 2011

ICHG 2011 webcast

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


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

October 20, 2011

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.

Link

Pre-Clovis Mastodon hunters from Manis, Washington

A related podcast. From the NY Times:
The study, in the journal Science, finds that a mastodon rib with a bone point lodged in it dates back 13,800 years.

“It’s the first hunting weapon found pre-Clovis,” said the lead author, Michael R. Waters, an archaeologist at Texas A&M University. “These people were hunting mastodons.”

The fossils had been discovered in the late 1970s near Manis, Wash., by Carl Gustafson, an archaeologist at Washington State University. At the time, Dr. Gustafson proposed that the skeleton was about 14,000 years old and that hunters had killed the mastodon with a bone point.

His theory was questioned by other scientists. But carbon dating technology has improved since then, and Dr. Waters and his colleagues were able to use mass spectrometry to date the rib, the bone point and tusks that were found at the site.
On an unrelated note, since Science missed out on the opportunity to publish Otzi's genome in conjunction with tomorrow's talk, all indications point towards Nature being the venue in conjunction with next Wednesday's (Oct 26) TV special. I don't know how much media there will be over the weekend, but any Italian readers or Mummy congress attendees are encouraged to send me an e-mail/leave a comment with any additional info.

Science 21 October 2011:
Vol. 334 no. 6054 pp. 351-353

Pre-Clovis Mastodon Hunting 13,800 Years Ago at the Manis Site, Washington

Michael R. Waters et al.

The tip of a projectile point made of mastodon bone is embedded in a rib of a single disarticulated mastodon at the Manis site in the state of Washington. Radiocarbon dating and DNA analysis show that the rib is associated with the other remains and dates to 13,800 years ago. Thus, osseous projectile points, common to the Beringian Upper Paleolithic and Clovis, were made and used during pre-Clovis times in North America. The Manis site, combined with evidence of mammoth hunting at sites in Wisconsin, provides evidence that people were hunting proboscideans at least two millennia before Clovis.

Link

Facial differences in autistic boys

If any readers have had the opportunity to interact with large numbers of autistic children, it would be interesting to see if these findings agree/disagree with their subjective impressions.

Autistic Facial Characteristics Identified
Aldridge and colleagues found the following distinct differences between facial characteristics of children with autism and those of typically developing children:
  • Children with autism have a broader upper face, including wider eyes.
  • Children with autism have a shorter middle region of the face, including the cheeks and nose.
  • Children with autism have a broader or wider mouth and philtrum -- the divot below the nose, above the top lip.
Molecular Autism 2011, 2:15 doi:10.1186/2040-2392-2-15

Facial phenotypes in subgroups of pre-pubertal boys with autism spectrum disorders are correlated with clinical phenotypes

Kristina Aldridge et al.

Abstract (provisional)
Background
The brain develops in concert and in coordination with the developing facial tissues, with each influencing the development of the other and sharing genetic signaling pathways. Autism spectrum disorders (ASDs) result from alterations in the embryological brain, suggesting that the development of the faces of children with ASD may result in subtle facial differences compared to typically developing children. In this study, we tested two hypotheses. First, we asked whether children with ASD display a subtle but distinct facial phenotype compared to typically developing children. Second, we sought to determine whether there are subgroups of facial phenotypes within the population of children with ASD that denote biologically discrete subgroups.

Methods
The 3dMD cranial System was used to acquire three dimensional stereophotogrammetric images for our study sample of 8- to 12-year-old boys diagnosed with essential ASD (n = 65) and typically developing boys (n = 41) following approved Institutional Review Board protocols. Three dimensional coordinates were recorded for 17 facial anthropometric landmarks using the 3dMD Patient software . Statistical comparisons of facial phenotypes were completed using Euclidean Distance Matrix Analysis and Principal Coordinates Analysis. Data representing clinical and behavioral traits were statistically compared among groups by using chi2 tests, Fisher's exact tests, Kolmogorov-Smirnov tests and Student's t-tests where appropriate.

Results
First, we found that there are significant differences in facial morphology in boys with ASD compared to typically developing boys. Second, we also found two subgroups of boys with ASD with facial morphology that differed from the majority of the boys with ASD and the typically developing boys. Furthermore, membership in each of these distinct subgroups was correlated with particular clinical and behavioral traits.

Conclusions
Boys with ASD display a facial phenotype distinct from that of typically developing boys, which may reflect alterations in the prenatal development of the brain. Subgroups of boys with ASD defined by distinct facial morphologies correlated with clinical and behavioral traits, suggesting potentially different etiologies and genetic differences compared to the larger group of boys with ASD. Further investigations into genes involved in neurodevelopment and craniofacial development of these subgroups will help to elucidate the causes and significance of these subtle facial differences.

Link

Putting it all together: DRACOS for fine-scale admixture estimation

I have previously developed new techniques and tools for ancestry estimation:
  • Clusters Galore
  • Zombies
  • The Dodecad Oracle
Clusters Galore allows very fine-scale ancestry estimation. In on of the most ambitious runs from last December, I was able to infer 124 different clusters on a global dataset. The downside is that individuals are placed on single clusters: the MCLUST algorithm estimates the probability that each individual belongs to each cluster, but does not estimate admixture proportions.

The Dodecad Oracle tries to address this problem, by using simple geometry to estimate 2-way mixes between populations. Individuals are projected onto lines formed by population pairs. An individual X that can be expressed as a mixture of A and B will tend to fall on the line segment AB, or close to it: the distance between X and AB is a measure of the closeness of fit. There are two downsides to this approach:
  • The limitation to two populations
  • The fact that different "populations" may in fact be different samples from the same population (e.g., the Behar et al. (2010) Ashkenazy_Jews and the Dodecad Project Ashkenazi_D populations)
The idea of Zombies is a powerful one. It allows one to convert the allele frequency data output by ADMIXTURE software to synthetic individuals representing the inferred ancestral populations. These individuals can then be used to estimate the ancestry of other individuals and populations. Not only does this have a tremendous performance benefit, but it also allows comparison across individuals and populations with the same "measuring stick".

The DRACOS pipeline

Fine-scale admixture estimation can be achieved by putting together these three ideas. I have called this new technique DRACOS:
  • Dimensionality Reduction
  • Analysis into COmponents
  • Structure estimation
Here are the steps of the full DRACOS pipeline:

1. Dimensionality Reduction: Use PCA or MDS to convert genotype data into a few principal components or MDS dimensions
2. Analysis into Components: Use MCLUST over the MDS/PCA representation to infer the presence of clusters at a fine scale
3. Identify sets of individuals that clearly belong to each of the clusters; one can use a filter based on posterior probability (e.g., greater 0.99) and/or distance from the cluster centroid (e.g., the 30 closest individuals)
4. Convert these sets of cluster-typical individuals into zombies for use with ADMIXTURE; alternatively, their allele frequencies themselves can be used, as in DIYDodecad, or any other structure-like analysis.

The DRACOS approach addresses all the drawbacks of the three individual methods:
  1. Compared to Clusters Galore, it allows for admixture
  2. It allows one to create zombies at a fine-scale. ADMIXTURE cannot do this, both because of its O(K^2) running time, as well as its lack of the model-based sophistication of MCLUST as applied over the first few principal components.
  3. Admixture can be estimated with any number of ancestral populations, not just two
There are of course drawbacks to the DRACOS approach as well; my recent post on increased error in short-range clines identifies the major issues with attempting to do admixture estimation at this level.

I have a few things running in parallel at this time, but I am pretty sure I will eventually release a DRACOS-based calculator on the Dodecad project page. I anticipate that such a tool, in conjunction with DIYDodecad's "byseg" and "target" modes may be helpful to genealogists, as it has the potential of inferring the geographical origin of segments of DNA at a finer level of detail.

Short-legged Neandertal mystery solved (and other interesting thoughts)

A nice new paper proposes that Neandertal short legs were not due to adaptation to cold but related to gait efficiency in a mountainous environment. A short-legged person usually has to use more strides/time unit to keep up with a long-legged one. What the researchers have shown is that on a slope this is not the case.

An interesting thought came to me as I was reading this: if Neandertal short legs were not due to cold adaptation, could it be that early Homo sapiens long legs were also not due to adaptation for a tropical climate?

It has been generally believed that the longer legs of early Upper Paleolithic humans in Europe compared to Neandertals evidenced their fairly recent arrival from a much warmer region.

But, in an age when there was no alternative to walking, we would expect populations that migrated over long distances to be efficient walkers, or to become so, en route, due to natural selection ("those who can't keep up stayed behind"). Moreover, while all humans are pretty much capable of walking anywhere, we would expect the pioneers in every region colonized by our species to be longer-limbed, since they "got there first".

The reverse could also be true, depending on the environment one walked through: early colonists of mountainous regions might be rather short-legged, and this is exactly what we find in the "hyper-polar" body types of early Neolithic farmers. These had to move across the fairly uneven terrain of southeastern Europe, at an age when there were no maps, no roads, and plenty of forest, making the shortest path between two points something different than a horizontal line.

The press release explains things quite well:
While most studies have concluded that a cold climate led to the short lower legs typical of Neandertals, researchers at Johns Hopkins have found that lower leg lengths shorter than the typical modern human's let them move more efficiently over the mountainous terrain where they lived. The findings reveal a broader trend relating shorter lower leg length to mountainous environments that may help explain the limb proportions of many different animals.

...

"Studies looking at limb length have always concluded that a shorter limb, including in Neandertals, leads to less efficiency of movement, because they had to take more steps to go a given distance," says lead author Ryan Higgins, graduate student in the Johns Hopkins Center of Functional Anatomy and Evolution. "But the other studies only looked at flat land. Our study suggests that the Neandertals' steps were not less efficient than modern humans in the sloped, mountainous environment where they lived."

...

Neandertals, who lived from 40,000 to 200,000 years ago in Europe and Western Asia, mostly during very cold periods, had a smaller stature and shorter lower leg lengths than modern humans. Because mammals in cold areas tend to be more compact, with a smaller surface area, scientists have normally concluded that it was the region's temperature that led to their truncated limbs compared to those of modern humans, who lived in a warmer environment overall.

...

The researchers decided to study different types of bovids--a group of mammals including gazelles, antelopes, goats and sheep--since these animals live in warm and cold environments on both flat and hilly terrain. The group took data from the literature on bovid leg bones and found that they fit the pattern: mountainous bovids, such as sheep and mountain goats, overall had shorter lower leg bones than their relatives on flat land, such as antelopes and gazelles, even when they lived in the same climates.

Investigating closely related bovids brought this trend into even sharper relief. Most gazelles live on flat land, and the one mountainous gazelle species examined had relatively shorter lower legs, despite sharing the same climate. Also, among caprids (goats and sheep), which mostly live on mountains, the one flat land member of the group exhibited relatively longer lower legs than all the others.

"Biologists have Bergman's and Allen's Rules, which predict reduced surface area to body size and shorter limbs in colder environments," says Higgins. "Our evidence suggests that we can also predict certain limb configurations based on topography. We believe adding the topic of terrain to ongoing discussions about limb proportions will allows us to better refine our understanding of how living species adapt to their environments. This improved understanding will help us better interpret the characteristics of many fossil species, not just Neandertals."


Am J Phys Anthropol DOI: 10.1002/ajpa.21575

The effects of distal limb segment shortening on locomotor efficiency in sloped terrain: Implications for Neandertal locomotor behavior

Ryan W. Higgins, Christopher B. Ruff

Past studies of human locomotor efficiency focused on movement over flat surfaces and concluded that Neandertals were less efficient than modern humans due to a truncated limb morphology, which may have developed to aid thermoregulation in cold climates. However, it is not clear whether this potential locomotor disadvantage would also exist in nonflat terrain. This issue takes on added importance since Neandertals likely spent a significant proportion of their locomotor schedule on sloped, mountainous terrains in the Eurasian landscape. Here a model is developed that determines the relationship between lower limb segment lengths, terrain slope, excursion angle at the hip, and step length. The model is applied to Neandertal and modern human lower limb reconstructions. In addition, for a further independent test that also allows more climate-terrain cross comparisons, the same model is applied to bovids living in different terrains and climates. Results indicate that: (1) Neandertals, despite exhibiting shorter lower limbs, would have been able to use similar stride frequencies per speed as longer-limbed modern humans on sloped terrain, due to their lower crural indices; and (2) shortened distal limb segments are characteristic of bovids that inhabit more rugged terrains, regardless of climate. These results suggest that the shortened distal lower limb segments of Neandertals were not a locomotor disadvantage within more rugged environments.

Link

October 17, 2011

Iceman stories begin arriving!

The National Geographic has info, a teaser for an October 26 Nova special:
The genetic results add both information and intrigue. From his genes, we now know that the Iceman had brown hair and brown eyes and that he was probably lactose intolerant and thus could not digest milk—somewhat ironic, given theories that he was a shepherd. Not surprisingly, he is more related to people living in southern Europe today than to those in North Africa or the Middle East, with close connections to geographically isolated modern populations in Sardinia, Sicily, and the Iberian Peninsula. The DNA analysis also revealed several genetic variants that placed the Iceman at high risk for hardening of the arteries. ("If he hadn't been shot," Zink remarked, "he probably would have died of a heart attack or stroke in ten years.") Perhaps most surprising, researchers found the genetic footprint of bacteria known as Borrelia burgdorferi in his DNA—making the Iceman the earliest known human infected by the bug that causes Lyme disease.
It seems that my prediction that the Iceman will turn out to be Mediterranean in terms of his autosomal genetic components was right!

I don't get, however, how lactose intolerance is incompatible with being a shepherd, since milk is widely used in southern Europe both as a raw product and for its cheese. I lack the lactose tolerance gene myself, but that doesn't keep me from having a glass of milk nearly every day. Lactose tolerance makes it possible for people to drink lots of milk; lactose intolerance does not make it impossible for them to drink any, or to enjoy its secondary products (such as cheese and butter).

Tyrolean Iceman week is upon us! (and some migrationist thoughts)

After a long wait, this week we are likely to read (and for the lucky few, hear) the long-awaited results of the genetic analysis of Ötzi, the Tyrolean Iceman. The talk on "Sequencing the Tyrolean Iceman" is scheduled for October 21 during the MUMMIES FROM THE ICE, 2nd BOLZANO MUMMY CONGRESS.

Thanks to intelligence from one of my readers, we already know that the Iceman belonged to Y-haplogroup G2a4. My experience with similar publicity bonanzas leads me to believe that the announcement at Bolzano may coincide with a major journal publication, but I have no inside information. Well, Friday is the day when the next issue of Science is due, so I'll take a bet on that journal having an Ötzi special this week. But, even if I'm wrong, there are likely to be media stories from the mummy congress itself; we will soon find out more.

(If any kind souls want to tip me, on promise of absolute confidentiality, feel free to do so: my e-mail's at the bottom)

Why is Ötzi so important? We already have genome sequence data on a ~4,000 year old Paleo-Eskimo, and even older Neandertals and Denisovans. Ötzi, at more than 5,000 years, will become the oldest Homo sapiens sequenced so far.

From a place like Europe, we almost never get anything other than bones and teeth from that period. An ice mummy is a real treasure, as it contains non-osseous tissues preserved in a natural refrigerator. Ötzi is likely to yield as good an ancient DNA genome as we are likely to get from prehistoric Europe anytime soon.

And, Ötzi's age is equally important, since he lived during the early Copper Age, at a time when humans in Europe transcended the use of bone and stone in their tool-making, and started using copper. Humans had used metals before (including gold and iron) in a haphazard way, but it was during the Copper and subsequent Bronze Age that there is clear evidence that metalworking began to transform society.

Ötzi's genome will be extremely important for a different reason: for a long time a conflict has simmered in archaeology between idea diffusionists, demic diffusionists, and migrationists.
  1. Idea diffusionists aka proponents of acculturation propose that ideas (such as the idea of crop-raising or metal-working) spread without large movements of people. They predict that Europeans did not change much since the Paleolithic, and Neolithic/post-Neolithic processes have little affected them.
  2. Demic diffusionists propose that humans behave like mindless automata, random walking across the landscape, mating with whom they find, and filling up a continent by the accretion of millennia-long processes of diffusion. They predict that Europeans are a fairly smooth cline of Neolithic+Paleolithic constituent elements from southeast to northwest.
  3. Migrationists adhere to an older and much-maligned arrows-on-the-map paradigm, whereby humans intentionally decide to move from A to B, even across great distances. According to this idea, colonists sometimes mix with/sometimes kill/sometimes avoid pre-existing inhabitants. Migrationists predict that prehistoric Europe was a dynamic patchwork of genetic-cultural units entering the continent from different routes at different times, gradually forming the cornucopia of its proto-historical ethnic groups.
It's been about two years since I came out as a migrationist. In my view, the colonization of Europe was less a random process and more akin to the much later colonization of the Mediterranean and Black Sea by the Greeks, and of the Americas by Europeans. We can envision initial forays of exploration, prompted by either curiosity or tales of strange sights and great riches (be it the riches of Marco Polo's East, El Dorado, the Golden Fleece, etc.). These were followed by colonists, either pushed from their homelands by social/economic malaise, or pulled towards their destinations by opportunity, establishing long-range communication/trade networks. Finally, more people could flow along the established routes in a directional, intentional flow of people.

Most of the ancient DNA published in the last few years has tended to support the migrationist paradigm. Indeed, we are uncovering even weirder data points every time we look. Who would have thought a few years ago, that Australian aborigines would show ties to Siberia, some prehistoric central-eastern Europeans to modern East Asians, and neither Mesolithic nor Neolithic Europeans any clear ties to modern ones?

It seems that the surest bet is on the unexpected, so I am hopeful that the Tyrolean Iceman will have some surprises in store for us; these may upset existing paradigms, but will pave the way for new ones.

October 16, 2011

China began cultivating millet 10,000 years ago

It is rather remarkable that after millions of years of living as foragers, humans on opposite sides of the Eurasian landmass adopted agriculture at roughly the same time. Some would interpret this as evidence of long-range diffusion of ideas, or even people.

I don't reject that idea; it's possible that the notion of agriculture became widely known among contemporary hunter-gatherers even if they did not adopt it right away. If that was the case, then "agriculture" (the concept) could have traveled far and wide without the spread of people or domesticates, explaining why eastern and western Eurasian peoples domesticated different species. It was later that "agriculture" started expanding from its cradles not only as a concept, but also as a people and as a complete economic package.

Alternatively, agriculture as an idea sprouted at the same time in West and East because of a law-like response of humans to the changing environment after the end of the last Ice Age. Under that hypothesis, prehistoric climate change either led to increases in population size or changes in ecosystems, and people on either side of the Eurasian landmass responded in sync to the same problem in similar ways.

Both explanations may be consistent with the later adoption of agriculture in Mesoamerica and Sub-Saharan Africa. Being at the periphery of human habitation, the idea of agriculture may have reached these lands later; alternatively, living close to the equator, inhabitants of these regions did not have to deal with the more dramatic consequences of deglaciation and climate change that more northerly humans had to contend with.

China began cultivating millet 10,000 years ago: archaeologists
SHIJIAZHUANG, Oct. 16 (Xinhua) -- Chinese archaeologists said Sunday that they have found evidence of the cultivation of glutinous millet in the northern province of Hebei that could date back to 10,000 years, the earliest evidence of people growing the crop in the world.

Lab results showed that remains of glutinous millet found at archaeological sites in Cishan Village in the city of Wu'an were harvested during the Neolithic Era between 8,700 to 10,000 years ago, scientists with the Institute of Geology and Geophysics of China Academy of Sciences (IGGCAS) said at a cultural festival held in Wu'an on Sunday.

This means Cishan was the birthplace of the crop, archaeologists said.

They have also found remains of foxtail millet in the pits, which could date back to between 8,700 and 7,500 years. This would be the earliest evidence of the crop's cultivation, which means that Cishan was the birthplace of foxtail millet, too, said Lu Houyuan, an IGGCAS scientist.

Cultivating small-seeded dry crops was more prevalent than cultivating rice in prehistoric times, especially in China's semi-arid northern regions, Lu said.

A total of 50,000 kilograms of grains have been stored in 88 pits for thousands of years at the Cishan Site, a Neolithic site discovered in 1972.

In addition to grain remnants, pottery, stone tools, animal bones and bone artifacts have also been excavated from the site, which archaeologists believe will help their research in the emergence of agriculture in China.

October 14, 2011

Ancient DNA suggests Greek amphorae carried more than wine

Journal of Archaeological Science doi:10.1016/j.jas.2011.09.025

Aspects of Ancient Greek trade re-evaluated with amphora DNA evidence

Brendan P. Foley et al.

Ancient DNA trapped in the matrices of ceramic transport jars from Mediterranean shipwrecks can reveal the goods traded in the earliest markets. Scholars generally assume that the amphora cargoes of 5th-3rd century B.C. Greek shipwrecks contained wine, or to a much lesser extent olive oil. Remnant DNA inside empty amphoras allows us to test that assumption. We show that short ∼100 nucleotides of ancient DNA can be isolated and analyzed from inside the empty jars from either small amounts of physical scrapings or material captured with non-destructive swabs. Our study material is previously inaccessible Classical/Hellenistic Greek shipwreck amphoras archived at the Ministry of Culture and Tourism Ephorate of Underwater Antiquities in Athens, Greece. Collected DNA samples reveal various combinations of olive, grape, Lamiaceae herbs (mint, rosemary, thyme, oregano, sage), juniper, and terebinth/mastic (genus Pistacia). General DNA targeting analyses also reveal the presence of pine (Pinus), and DNA from Fabaceae (Legume family); Zingiberaceae (Ginger family); and Juglandaceae (Walnut family). Our results demonstrate that amphoras were much more than wine containers. DNA shows that these transport jars contained a wide range of goods, bringing into question long-standing assumptions about amphora use in ancient Greece. Ancient DNA investigations open new research avenues, and will allow accurate reconstruction of ancient diet, medicinal compounds, value-added products, goods brought to market, and food preservation methods.

Link

October 13, 2011

Origin and evolution of word order

From the paper's conclusion:
The distribution of word order types in the world’s languages, interpreted in terms of the putative phylogenetic tree of human languages, strongly supports the hypothesis that the original word order in the ancestral language was SOV. Furthermore, in the vast majority of known cases (excluding diffusion), the direction of change has been almost uniformly SOV > SVO and, beyond that, primarily SVO > VSO/VOS. There is also evidence that the two extremely rare word orders, OVS and OSV, derive directly from SOV.

These conclusions cast doubt on the hypothesis of Bickerton that human language originally organized itself in terms of SVO word order. According to Bickerton, “languages that did fail to adopt SVO must surely have died out when the strict-order languages achieved embedding and complex structure” (50). Arguments based on creole languages may be answered by pointing out that they are usually derived from SVO languages. If there ever was a competition between SVO and SOV for world supremacy, our data leave no doubt that it was the SOV group that won. However, we hasten to add that we know of no evidence that SOV, SVO, or any other word order confers any selective advantage in evolution. In any case, the supposedly “universal” character of SVO word order (51) is not supported by the data.
UPDATE: An MSNBC article on the paper.

PNAS doi: 10.1073/pnas.1113716108

The origin and evolution of word order

Murray Gell-Mannn and Merritt Ruhlen

Recent work in comparative linguistics suggests that all, or almost all, attested human languages may derive from a single earlier language. If that is so, then this language—like nearly all extant languages—most likely had a basic ordering of the subject (S), verb (V), and object (O) in a declarative sentence of the type “the man (S) killed (V) the bear (O).” When one compares the distribution of the existing structural types with the putative phylogenetic tree of human languages, four conclusions may be drawn. (i) The word order in the ancestral language was SOV. (ii) Except for cases of diffusion, the direction of syntactic change, when it occurs, has been for the most part SOV > SVO and, beyond that, SVO > VSO/VOS with a subsequent reversion to SVO occurring occasionally. Reversion to SOV occurs only through diffusion. (iii) Diffusion, although important, is not the dominant process in the evolution of word order. (iv) The two extremely rare word orders (OVS and OSV) derive directly from SOV.

Link

Chromosome-wide haplotype sharing (Xu and Jin 2011)

This paper discovered that both haplotype sharing and recombination rate were correlated with genetic divergence between populations. The authors consider that haplotype sharing can be attributed to both drift and recombination, and study haplotype sharing for haplotypes of different lengths.

A potential problem is that humans may harbor archaic DNA sequences. Depending on when admixture with archaic humans took place, recombination may have reduced these archaic sequences to very small lengths. It is no longer tenable to suppose that only drift and recombination have affected haplotypes, the former removing some, the latter re-arranging others.

We must take into account the possibility that genetic divergence between human groups is partly the result of admixture with species outside the main H. sapiens phyletic line. Immediately following such admixture, there would have been long archaic haplotypes in affected humans, but -with enough time- these would have been reduced in size due to recombination.

Annals of Human Genetics doi: 10.1111/j.1469-1809.2011.00678.x

Chromosome-Wide Haplotype Sharing: A Measure Integrating Recombination Information to Reconstruct the Phylogeny of Human Populations

Shuhua Xu and Li Jin

The vast amount of recombination information in the human genome has long been ignored or deliberately avoided in studies on human population genetic relationships. One reason is that estimation of the recombination parameter from genotyping data is computationally challenging and practically difficult. Here we propose chromosome-wide haplotype sharing (CHS) as a measure of genetic similarity between human populations, which is an indirect approach to integrate recombination information. We showed in both empirical and simulated data that recombination differences and genetic differences between human populations are strongly correlated, indicating that recombination events in different human populations are evolutionarily related. We further demonstrated that CHS can be used to reconstruct reliable phylogenies of human populations and the majority of the variation in CHS matrix can be attributed to recombination. However, for distantly related populations, the utility of CHS to reconstruct correct phylogeny is limited, suggesting that the linear correlation of CHS and population divergence could have been disturbed by recurrent recombination events over a large time scale. The CHS we proposed in this study is a practical approach without involving computationally challenging and time-consuming estimation of recombination parameter. The advantage of CHS is rooted in its integration of both drift and recombination information, therefore providing additional resolution especially for populations separated recently.

Link

Should chimpanzees be used in entertainment?

There is an article in Scientific American covering a paper in PLoS ONE, arguing that chimpanzees should not be used on TV or Movies, and should not be used as pets. I will let readers evaluate the arguments for what they are worth, but I will just make a couple of comments:
  • I never quite understood the "endangered species" concept. Species come and go, that's Evolution 101 for you. And, some species go because of a new predator that they can't cope with, e.g., man. I am inherently suspicious of an antiquarian mentality that humans are supposed to preserve species as they are today, or even restore them to some older state: if we interfere with evolution, why should it always be to preserve species, and not to cull some of them?
  • There are good reasons why we should not want chimpanzees to go extinct, and they have nothing to do with the preservationist imperative. Chimpanzees are our closest relatives, and hence provide an important comparative baseline in studies of human evolution. The study of man and all its intellectual and practical benefits would suffer if there were no chimps around.
  • Who decides whether a species is endangered or not? According to the SciAm article, "the global population of wild chimpanzees is only 172,700 to 299,700 individuals." That corresponds to an effective population size well above estimates for the ancestral effective population size of either humans or the common ancestor of humans and chimpanzees.
  • It is true that TV and Movies present a distorted picture of chimpanzees. Most chimp appearances make them appear "cute" and "human-like". But, that could be said for nearly every animal on TV. You never see domestic dogs, for example, portrayed as killers on TV, and yet, there are dozens of fatal and many more non-fatal "dog bites man" incidents every year. According to the authors' logic, TV and Movies distort the behavior of dogs, making them appear like "Lassie" when they are in fact are often dangerous animals.
  • Nor is it true that if we did not use chimpanzees in TV and Movies we would have an accurate portrayal of them: if you don't watch chimps on TV ads, you will not automatically sit through scientifically-minded documentaries about them. TV and Movies happily portray all sorts of animals, domestic or otherwise in a stereotypical form. Ask a 5-year old whether they like a whole series of animals, and you will get back a whole series of positive and negative stereotypes, some of which go back to Aesop and beyond.
  • Should people's exposure to non-human primates in entertainment be limited to CGI creatures like King Kong, the apes in Planet of the Apes, or CGI chimps that will surely take the place of real ones if the use of the latter is outlawed?
  • It could be argued that the unprecedented wide-scale breeding and rearing of chimps is the initial stage of a process of domestication of that animal. Surely, early dogs, cats, horses, etc. were dangerous animals compared to modern breeds, but our ancestors did succeed in making them more amenable to human society. Why should it be illegal for people to keep whatever animal they see fit as pets, provided they are (a) not cruel to it, and (b) take proper precautions not to endanger their neighbors?

PLoS ONE 6(10): e26048. doi:10.1371/journal.pone.0026048

Use of “Entertainment” Chimpanzees in Commercials Distorts Public Perception Regarding Their Conservation Status

Kara K. Schroepfer et al.

Chimpanzees (Pan troglodytes) are often used in movies, commercials and print advertisements with the intention of eliciting a humorous response from audiences. The portrayal of chimpanzees in unnatural, human-like situations may have a negative effect on the public's understanding of their endangered status in the wild while making them appear as suitable pets. Alternatively, media content that elicits a positive emotional response toward chimpanzees may increase the public's commitment to chimpanzee conservation. To test these competing hypotheses, participants (n = 165) watched a series of commercials in an experiment framed as a marketing study. Imbedded within the same series of commercials was one of three chimpanzee videos. Participants either watched 1) a chimpanzee conservation commercial, 2) commercials containing “entertainment” chimpanzees or 3) control footage of the natural behavior of wild chimpanzees. Results from a post-viewing questionnaire reveal that participants who watched the conservation message understood that chimpanzees were endangered and unsuitable as pets at higher levels than those viewing the control footage. Meanwhile participants watching commercials with entertainment chimpanzees showed a decrease in understanding relative to those watching the control footage. In addition, when participants were given the opportunity to donate part of their earnings from the experiment to a conservation charity, donations were least frequent in the group watching commercials with entertainment chimpanzees. Control questions show that participants did not detect the purpose of the study. These results firmly support the hypothesis that use of entertainment chimpanzees in the popular media negatively distorts the public's perception and hinders chimpanzee conservation efforts.

Link

October 08, 2011

Pavlopetri: 4,000-year old underwater city brought to life

Pavlopetri: A window on to Bronze Age suburban life
Semi-detached houses with gardens, clothes drying in the courtyards, walls and well-made streets - Pavlopetri epitomises the suburban way of life. Except that it's a Bronze Age port, submerged for millennia off the south-east coast of Greece.

This summer it became the first underwater city to be fully digitally mapped and recorded in three dimensions, and then brought back to life with computer graphics.

The result shows how much it has in common with port cities of today - Liverpool, London, New York, San Francisco, Tokyo or Shanghai - despite the fact that its heyday was 4,000 years ago.

Apparently there is a 1-hour special on BBC Two: City Beneath the Waves: Pavlopetri
to be broadcast on Sunday:
Just off the southern coast of mainland Greece lies the oldest submerged city in the world. A city that thrived for 2000 years during the time that saw the birth of Western civilisation. An international team of experts uses the latest technology to investigate the site and digitally raise it from the seabed, to reveal the secrets of Pavlopetri.

Led by underwater archaeologist Dr Jon Henderson, the team use the latest in cutting-edge science and technology to prise age-old secrets from the complex of streets and stone buildings that lie less than five metres below the surface. State-of-the-art CGI helps to raise the city from the seabed revealing, for the first time in 3,500 years, how Pavlopetri would once have looked and operated.

Jon Henderson is leading this ground-breaking project in collaboration with a team from the Hellenic Ministry of Culture, and Nic Flemming, the man whose hunch led to the intriguing discovery of Pavlopetri in 1967. Also working alongside the archaeologists are a team from the Australian Centre for Field Robotics, who aim to take underwater archaeology into the 21st century.

The team scour the sea floor for any artefacts that have eroded from the sands. The site is littered with thousands of fragments, each providing valuable clues to the everyday lives of the people of Pavlopetri. From the buildings to the trade goods to the everyday tableware, every artefact provides a window into a long-forgotten world.

Together these precious relics provide us with a window on a time when Pavlopetri would have been at its height, showing us what life was like in this distant age, and revealing how this city marks the start of Western civilisation.


Wikipedia article on Pavlopetri

October 07, 2011

Major population expansion in mtDNA of East Asians


Table 2 has the expansion times.

PLoS ONE 6(10): e25835. doi:10.1371/journal.pone.0025835

Major Population Expansion of East Asians Began before Neolithic Time: Evidence of mtDNA Genomes

Hong-Xiang Zheng et al.

It is a major question in archaeology and anthropology whether human populations started to grow primarily after the advent of agriculture, i.e., the Neolithic time, especially in East Asia, which was one of the centers of ancient agricultural civilization. To answer this question requires an accurate estimation of the time of lineage expansion as well as that of population expansion in a population sample without ascertainment bias. In this study, we analyzed all available mtDNA genomes of East Asians ascertained by random sampling, a total of 367 complete mtDNA sequences generated by the 1000 Genome Project, including 249 Chinese (CHB, CHD, and CHS) and 118 Japanese (JPT). We found that major mtDNA lineages underwent expansions, all of which, except for two JPT-specific lineages, including D4, D4b2b, D4a, D4j, D5a2a, A, N9a, F1a1'4, F2, B4, B4a, G2a1 and M7b1'2'4, occurred before 10 kya, i.e., before the Neolithic time (symbolized by Dadiwan Culture at 7.9 kya) in East Asia. Consistent to this observation, the further analysis showed that the population expansion in East Asia started at 13 kya and lasted until 4 kya. The results suggest that the population growth in East Asia constituted a need for the introduction of agriculture and might be one of the driving forces that led to the further development of agriculture.

Link

Ancient mtDNA of Hokkaido Jomon

This is a very good paper that I don't have time right now to write a long post about; I will update this entry with some excerpts and/or additional thoughts when I can.

The gist of it is that the prehistoric Jomon people of Japan belonged to mtDNA haplogroups tying them to southeastern Siberia, but some haplogroups present there today were lacking in them. Then, the Ainu seem to have inherited the Jomon gene pool, but their major lineages tie them to the Okhotsk people. So, it seems that the deepest ancestry of Japan is not peculiar to it, but rather an extension of ancient Siberian variation with different population strata attributed to the Jomon, the Ainu, and (probably) the modern Japanese.

AJPA DOI: 10.1002/ajpa.21561

Mitochondrial DNA analysis of Hokkaido Jomon skeletons: Remnants of archaic maternal lineages at the southwestern edge of former Beringia

Noboru Adachi et al.

To clarify the colonizing process of East/Northeast Asia as well as the peopling of the Americas, identifying the genetic characteristics of Paleolithic Siberians is indispensable. However, no genetic information on the Paleolithic Siberians has hitherto been reported. In the present study, we analyzed ancient DNA recovered from Jomon skeletons excavated from the northernmost island of Japan, Hokkaido, which was connected with southern Siberia in the Paleolithic period. Both the control and coding regions of their mitochondrial DNA (mtDNA) were analyzed in detail, and we confidently assigned 54 mtDNAs to relevant haplogroups. Haplogroups N9b, D4h2, G1b, and M7a were observed in these individuals, with N9b being the predominant one. The fact that all these haplogroups, except M7a, were observed with relatively high frequencies in the southeastern Siberians, but were absent in southeastern Asian populations, implies that most of the Hokkaido Jomon people were direct descendants of Paleolithic Siberians. The coalescence time of N9b (ca. 22,000 years) was before or during the last glacial maximum, implying that the initial trigger for the Jomon migration in Hokkaido was increased glaciations during this period. Interestingly, Hokkaido Jomons lack specific haplogroups that are prevailing in present-day native Siberians, implying that diffusion of these haplogroups in Siberia might have been after the beginning of the Jomon era, about 15,000 years before present.

Link

October 05, 2011

Y-chromosomes of Marsh Arabs

What do the Marsh Arabs have to do with ancient Sumer? Nothing that can be determined on the basis of this data. There are plenty of ancient Sumerian skulls, so how about we study them directly?

As far as I can see, the only link between Marsh Arabs and Sumerians presented in this paper comes from dating Y-STR variation of their major J1-Page08 group using the evolutionary mutation rate, with a divergence time of 4.5 +/- 2.6 ky. Even if that mutation rate was correct (it is not) and the assumptions on which the confidence interval are based were exhaustive (they are not), we still have +/- 2.6 ky leeway to deal with, which spans not only the Sumerians but plenty more besides.

Not to mention that the evolutionary mutation rate is wrongly applied to every case under the sun, and that Y-STR based age estimation in general has been conclusively shown to be a rather futile exercise.

Nonetheless, the paper does have value in demonstrating the paucity of J2 and R1 in the Marsh Arabs compared to the more cosmopolitan general Iraqi population:
Different from the Iraqi control sample, the Marsh Arab gene pool displays a very scarce input from the northern Middle East (Hgs J2-M172 and derivatives, G-M201 and E-M123), virtually lacks western Eurasian (Hgs R1-M17, R1-M412 and R1-L23) and sub-Saharan African (Hg E-M2) contributions.
Rather than "Sumerian", it seems that the Marsh Arabs have rather preserved a more pristine Semitic patrilineal gene pool compared to the cosmopolitan Iraqi samples that have absorbed pre-Arab and pre-Semitic population elements.


BMC Evolutionary Biology 2011, 11:288doi:10.1186/1471-2148-11-288

In search of the genetic footprints of Sumerians: a survey of Y-chromosome and mtDNA variation in the Marsh Arabs of Iraq.

Nadia Al-Zahery et al.

Abstract (provisional)

Background
For millennia, the southern part of the Mesopotamia has been a wetland region generated by the Tigris and Euphrates rivers before flowing into the Gulf. This area has been occupied by human communities since ancient times and the present-day inhabitants, the Marsh Arabs, are considered the population with the strongest link to ancient Sumerians. Popular tradition, however, considers the Marsh Arabs as a foreign group, of unknown origin, which arrived in the marshlands when the rearing of water buffalo was introduced to the region.

Results
To shed some light on the paternal and maternal origin of this population, Y chromosome and mitochondrial DNA (mtDNA) variation was surveyed in 143 Marsh Arabs and in a large sample of Iraqi controls. Analyses of the haplogroups and sub-haplogroups observed in the Marsh Arabs revealed a prevalent autochthonous Middle Eastern component for both male and female gene pools, with weak South-West Asian and African contributions, more evident in mtDNA. A higher male than female homogeneity is characteristic of the Marsh Arab gene pool, likely due to a strong male genetic drift determined by socio-cultural factors (patrilocality, polygamy, unequal male and female migration rates).

Conclusions
Evidence of genetic stratification ascribable to the Sumerian development was provided by the Y-chromosome data where the J1-Page08 branch reveals a local expansion, almost contemporary with the Sumerian City State period that characterized Southern Mesopotamia. On the other hand, a more ancient background shared with to Northern Mesopotamia is revealed by the less represented Y-chromosome lineage J1-M267*. Overall our results indicate that the introduction of water buffalo breeding and rice farming, most likely from the Indian sub-continent, only marginally affected the gene pool of autochthonous people of the region. Furthermore, a prevalent Middle Eastern ancestry of the modern population of the marshes of southern Iraq implies that if the Marsh Arabs are descendants of the ancient Sumerians, also the Sumerians were most likely autochthonous and not of Indian or South Asian ancestry.

Link

October 04, 2011

Reconstruction of 7,500 years old forager from Norway

Source (in Norwegian)

FOTO: ARKEOLOGISK MUSEUM/UNIVERSITETET I STAVANGER

October 02, 2011

Rapid onset of Aurignacian in Southwest France

Journal of Archaeological Science doi:10.1016/j.jas.2011.09.019

A Radiocarbon chronology for the complete Middle to Upper Palaeolithic transitional sequence of Les Cottés (France)

Sahra Talamo et al.

The Middle to Upper Palaeolithic transition is the key period for our understanding of Neanderthal and modern human interactions in Europe. The site of Les Cottés in south-west France is one of the rare sites with a complete and well defined sequence covering this transition period. We undertook an extensive radiocarbon dating program on mammal bone which allows us to propose a chronological framework of five distinct phases dating from the Mousterian to the Early Aurignacian at this site. We found that the Mousterian and Châtelperronian industries are separated from the overlying Protoaurignacian by a gap of approximately 1000 calendar years. Based on a comparison with Upper Paleolithic sites in Europe we see an overlap in the ages of Châtelperronian industries and Aurignacian lithic assemblages, which are usually associated with Anatomical Modern Humans, which is consistent with an acculturation at distance model for these late Neanderthals. The Proto and Early Aurignacian appear contemporaneous indicating that this transition was rapid in this region. Anatomically Modern Humans are present at the site of Les Cottés at least at 39,500 cal BP roughly coincident with the onset of the cold phase Heinrich 4.

Link

October 01, 2011

Further caution on admixture estimates: at the edges of variation

My recent analysis of the Yunusbayev et al. (2011) revealed an interesting anomaly: the Armenians_Y sample tested much more "European" than the existing Armenians_D and Armenians (from Behar et al. (2010)).

A related "anomaly" was the use of some of my newer Dodecad tools that have been targeted to particular regions (e.g., Europe and West Asia for the newer euro7 calculator) by individuals from outside these regions (e.g., South Asia for euro7). Of course, I have cautioned against such use, but can we say something about why their use is not a very good idea.

Suspecting a systematic effect, I decided to investigate.

My geometric intuition is encapsulated in the following figure:

Suppose that a cline has been inferred from B to A1. Suppose that dist(A1, B) = dist(A2, B). So, A1 and A2 differ from each other in an orthogonal direction relative to their difference from B.

Now, if we project A2 onto the BA1 line, we see that A2 appears "intermediate" between them. The converse would occur if we project A1 onto the BA2 line.

This is reminiscent of my ciriticism of Moorjani et al. (2011) in that shifts away from a linear cline cause spurious admixture to be inferred. But, it is more general:
  • A2 may differ from A1 because it has cryptic admixture from an unsampled group, or vice versa
  • A2 may differ from A1 because of random genetic drift
We can go one step further and consider a population that is not only "off-cline", but beyond its edges. This can be seen in the following figure:
As you can see, now A2 (which is beyond the edge of the horizontal cline) cannot be projected between B and A1.

In order to examine this intuition, I carried out a few simple tests.

I set B to be HGDP North_Italians, A1 to be Behar et al. (2010) Armenians (with 3 outliers excluded), and A2 to be Yunusbayev et al. (2011) Armenians_Y.

1) Unsupervised analysis

North_Italian 100.0 0.0
Armenians_Y 1.3 98.7
Armenians 2.8 97.2

2) Supervised analysis: Armenians_Y as test population; North_Italian, Armenians fixed

North_Italian 100.0 0.0
Armenians_Y 0.6 99.4
Armenians 0.0 100.0

3) Supervised analysis: Armenians as test population; North_Italian, Armenians_Y fixed

North_Italian 100.0 0.0
Armenians_Y 0.0 100.0
Armenians 2.7 97.3


These results seem to confirm the geometric intuition.

Populations beyond the cline

Now, I will add Assyrians_D, a population that seems closely related to Armenians, but appear to be a little more "eastern" in most analyses. So, it is "beyond" the North_Italian-Armenian cline.

1) Unsupervised analysis

North_Italian 100.0 0.0
Armenians_Y 3.6 96.4
Armenians 5.3 94.7
Assyrians 0.6 99.4

2) Supervised analysis: Assyrians, Armenians as test populations; North_Italian, Armenians_Y fixed

North_Italian 100.0 0.0
Armenians_Y 0.0 100.0
Armenians 3.8 96.2
Assyrians 0.5 99.5

Again, the intuition is confirmed. A reasonable recommendation is to avoid mapping populations that are geographically outside the convex hull of the fixed populations.

Long clines

The effect described in this post is expected to abate in "long clines". For example, the amount of drift between Miaozu and She populations from east Asia is expected to be miniscule relative to the distance of either population to North Italians:

1) Unsupervised analysis

North_Italian 100 0
Miaozu 0 100
She 0 100

2) Supervised analysis: She as test population; North_Italian, Miaozu fixed

(identical)

3) Supervised analysis: Miaozu as test population; North_Italian, She fixed

(identical)

Conclusion

In determining the relative position of individuals along clines it is useful to remember:
  • The position is most accurately determined when the edges of the cline are most securely "fastened". Use as many populations and individuals from the perimeter of the region under study as possible.
  • The position is most accurately determined when the cline is long; small deviations due to drift or incomplete sampling at the edges are miniscule compared to the length of the cline. Components marking continent-wide distances (e.g., Europeans vs. East Asians) are estimated more accurately than those marking shorter distances (e.g., Southern Europeans vs. West Asians)

The way forward

There is no simple solution to the problem identified in this post. For short clines (e.g., within Europe) that are not securely fastened (few individuals from outlying groups), we can expect relatively large systematic errors.

As an analogy, imagine trying to measure the height of a 5-year old on the wall with measuring tape and a book. If you don't keep the book steady, one of the endpoints of your measurement will be "wobbly". If you don't keep your measuring tape vertical, your measurement will be off.

What can we do to solve this problem? Sample, sample, sample. There is no shortcut. The gross details of the genetic landscape (such as the relationship between major continental groups) are easy to infer, but the details will always have room for improvement.