Armenian Y-chromosomes revisited (Herrera et al. 2011)

Armenian Y-chromosomes have been a largely ignored since the publication of the classic Weale et al. (2001) paper a decade ago. The Armenian DNA Project has largely covered the void during the intervening years, but it is nice that the topic is revisited by academics.

Armenia is sandwiched between Anatolia, the Fertile Crescent, the Iranian plateau, the Caucasus, and the Black and Caspian seas, making the study of Armenian Y-chromosomes extremely interesting for the student of Eurasian prehistory.

Gene flow from the surrounding regions may have affected the Armenian population over historical time, but the remoteness of the Armenian highlands, coupled with the national church -- which distinguished Armenians from both the Orthodoxy of the Roman Empire, the Zoroastrianism of the Persians, and, later the Islam of Arabs and Ottomans -- may have prevented it.

My comments on the paper will follow below once I read it.

UPDATE I: The paper spends a lot of time on analysis of Y-STR variance; my opinion of Y-STRs as a tool for inferring past population movements is, to put it mildly, low. When Bahamian Y-STR variance is higher than African one, and E-V13, one of the youngest European Y-haplogroups (in terms of Y-STR variance) turns up in Spain in one of the earliest ancient DNA samples, it goes without saying that the burden of proof is on those who wish to continue to talk about Neolithic or other population movements to make the assumptions of their models clearer. Nonetheless, there is still some utility in Y-STRs, so I reproduce some tree diagrams from the paper (top left), and link to the supplementary info that has a collection of haplotypes that may be useful to genealogists.

From the paper:

However, owing to the contentions associated with the current calibrations of the Y-STR mutation rates,32,34,35,41 as well as the limitations of the assumptions utilized by the methodologies for time estimations, the absolute dates generated in this study should only be taken as rough estimates of upper bounds.

Indeed. We are at the point where Y-STRs are at the end of their utility, but the replacement technology of extensive Y-chromosome sequencing has not quite arrived in an economical way yet.

UPDATE II: I will have some additional thoughts on Y-chromosome distribution in the third update, but, for the time being, the two most important "nuggets" of information are: (i) the unusual haplogroup frequencies in Sasun (high R2 and T), which may be due to a founder effect, but it would be interesting if Armenian historians could find some explanation for their occurrence there, and (ii) the occurrence of R-M269*(xL23) in Ararat Valley. I invite more knowledgeable readers to comment on the issue; the haplotypes are in Table 2 of the supplement.

UPDATE III: The ubuiquity of haplogroup G2a in Neolithic Europe, coupled with the absence of other prominent present-day European haplogroups, has important implications about European discontinuity.

But, it also has implications about West Asian discontinuity. The Neolithic in Europe arrived by all accounts from either of two principal areas: Anatolia or the Levant. Today, in Anatolia and the Levant, we see a set of haplogroups of which haplogroup J is the most important and ubiquitous one. Haplogroup R1b is also quite frequent in Armenia, the east Caucasus, Anatolia, and Iran, but its frequency drops dramatically to the east and south. And, there is a whole assortment of other haplogroups with varying frequency.

Why didn't all these non-G2a haplogroups participate in the early Neolithic colonization of Europe? It could very well be that a very small founder population crossed the Aegean into Europe, one that happened to be G2a-dominated. But, that is ultimately not very satisfying: if there was plenty of J and R1b in West Asia at the time of the Neolithic expansion, why are these haplogroups so conspicuous in their absence -at least so far- from Neolithic Europe?

The case of haplogroup J is particularly problematic. If we had to guess, by looking at present-day distribution, which lineage tracks population movements from the Near East to Europe, there is simply no better candidate: every map of this haplogroup, and especially of its J2a sublineage shows an unambiguous pattern of radiation, with a core area consisting of Southern Italy, Greece, Anatolia, West Asia, Mesopotamia and the northern parts of the Levant. All these regions are crucial to the story of the Neolithic, so the absence of J in Neolithic Europe is perplexing.

And, the story has other complications. From the current paper:

The relative expansion times for haplogroup J2-M172 (Table 4) generally correspond with those yielded for R1b-M343, with the exception of Greece and Crete, which, unlike haplogroup R1b-M343, are slightly older than the dates yielded for several of the Near Eastern groups as well as the four Armenian populations.

As mentioned above, I don't give much weight on Y-STR evidence, but observations such as the above certainly add to the feeling of unease that something is not quite right with the default picture of prehistory.

Another observation on the Armenian population, is its very low frequency of haplogroup R1a1. Proponents of the Kurgan model of Indo-European dispersals sometimes associate this haplogroup with the Proto-Indo-European community, and it is strange why -if their ideas are right- Armenia is so lacking in this haplogroup, like its Caucasian neighbors. Why would these hypothetical migrants make such a huge impact in faraway India and barely a dent in nearby Armenia?

Finally, the occurrence of some I2, E-V13, and, perhaps, J2b in Armenia may point to Balkan contacts. But, when did these contacts occur? Are they traceable to the migration of Phrygians to Anatolia, according to the Herodotean account of Armenian origins, or can they be attributed to later contacts with Greeks or other Europeans?

The veil of mystery seems to be raised even higher by every new study: we may be less certain of what really happened today than in the days of happy ignorance, ten years ago. Ultimately it is new data, like the ones included in this paper, that will make every piece of evidence fit, and the grand puzzle of the history of Eurasia will be revealed in all its glory.

European Journal of Human Genetics , (16 November 2011) | doi:10.1038/ejhg.2011.192

Neolithic patrilineal signals indicate that the Armenian plateau was repopulated by agriculturalists

Kristian J Herrera, Robert K Lowery, Laura Hadden, Silvia Calderon, Carolina Chiou, Levon Yepiskoposyan, Maria Regueiro, Peter A Underhill and Rene J Herrera

Abstract
Armenia, situated between the Black and Caspian Seas, lies at the junction of Turkey, Iran, Georgia, Azerbaijan and former Mesopotamia. This geographic position made it a potential contact zone between Eastern and Western civilizations. In this investigation, we assess Y-chromosomal diversity in four geographically distinct populations that represent the extent of historical Armenia. We find a striking prominence of haplogroups previously implicated with the Agricultural Revolution in the Near East, including the J2a-M410-, R1b1b1*-L23-, G2a-P15- and J1-M267-derived lineages. Given that the Last Glacial Maximum event in the Armenian plateau occured a few millennia before the Neolithic era, we envision a scenario in which its repopulation was achieved mainly by the arrival of farmers from the Fertile Crescent temporally coincident with the initial inception of farming in Greece. However, we detect very restricted genetic affinities with Europe that suggest any later cultural diffusions from Armenia to Europe were not associated with substantial amounts of paternal gene flow, despite the presence of closely related Indo-European languages in both Armenia and Southeast Europe.

Link

Does capitalism reduce fitness? (part II)

Rasmus Nielsen responds to my commentary of his students' ‘rEvolutionary Biologists say: Capitalism Reduces Fitness!’ sign and the blog post associated with it:

Dienekes was shocked by this travesty and decided to make a blog post about it. To my surprise his outrage was not about the social conditions in West Oakland but rather about the loose use of fitness employed in the blog. He took the statement by my students and postdocs literally and pointed out that if you include all the different components of fitness, and not just viability, there is in fact no good scientific evidence that the absolute fitness of individuals growing up in capitalist societies is reduced.

I largely ignore economics and politics in this blog, not because I have no interest in them, but because this is an anthropology blog. And, while I'm sure social conditions in West Oakland may be in great need of improvement, it's not my business to improve them; apparently there are plenty of kind souls working toward that goal already.

It is one thing to hold a political opinion as an individual and another to link that opinion to one's scientific discipline. An electrical engineer, a medical doctor, and a biologist may think that capitalism is a terrible or wonderful system, but if they attempted to link that opinion with electrical engineering, medicine, or biology, I would like to see the evidence for it.

The people in question explicitly linked their political opinions with evolutionary biology, both by ascribing those opinion to "rEvolutionary biologists" and by explicitly linking their dismissal of capitalism to fitness, a central concept in evolutionary biology.

Dr. Nielsen continues:

Most of the students and postdocs in my group are from Europe, and many have not been here for long. They have perhaps not quite gotten use to American political discourse and may not express themselves in a way that most Americans find convincing. But at least they haven’t quite lost their sense of empathy and care for other people. I figure that if I keep them here, in an American academic environment, for a couple of years more they will get cured of that problem and will be able to concentrate fully on their research careers without getting distracted by the economic and social problems they encounter in the neighborhoods around campus on their commute from and to work. If I push them hard, the may even eventually end up getting real jobs and move up in the East Oakland hills. They will then never have to worry about the problems in West Oakland again, and can spend all their time making sure they include all components of fitness when making blog posts.

Last time I checked, both East Oakland and West Oakland, and indeed the entire United States have a capitalist economy. If someone cares why people in West Oakland have a different life expectancy than those in East Oakland, they must seek the explanation elsewhere, and not in their common economic system. If they wanted to examine the influence of capitalism on life expectancy, they could, perhaps, compare South vs. North Korea, two countries with similar populations, that also happen to have a difference in life expectancy of about 10 years, with capitalist South Koreans outliving non-capitalist North Koreans.

Splits or Waves? Trees or Webs?

Tree models are used in both linguistics and genetics for inferring population history. The trouble with them is that human populations do not really evolve (either genetically or culturally, as in language), tree-like, but rather exchange both genes and words.

Linguistic evolution has been mostly described in terms of tree models, but languages are not insulated from each other, and they interact after their initial differentiation. This interaction is facilitated by geographic proximity, and also by linguistic proximity.

Geographic proximity makes it possible for speakers of different languages to talk to each other, learn each other's languages, or develop hybrid languages or a lingua franca. Linguistic proximity facilitates communication: it is fairly easy, for example, for speakers of Germanic languages to interact, and much more difficult for those of, say, English and Chinese.

If speakers of a language become separated by distance or geographical barriers, then lateral exchange between different groups becomes minimal, and language evolution can be well-described by a tree model. If, on the other hand, there exists a language continuum across a wide area, effected by a common process (say, the spread of agriculture), then there is room for substantial cross-interaction of different emergent languages at the stage when they can be still thought as dialects of the parent language.

While the current paper's focus is on Germanic languages, the endgame seems to be on the much harder and more vigorously contested field of Indo-European studies.

The author has put up a nice supplementary page online on a first attempt of using NeighborNet with an Indo-European dataset, pictured on the right. A publication on the topic is listed as being in preparation:

The utility of Germanic as a case-study is that it provides a (reasonably) known external history against which to assess our methodological approaches. On the strength of the findings here, a similar logic can now be extended to probing the unknown of how the early divergence history of Indo-European unfolded. In the full exploration in Heggarty (in preparation a), it transpires that even the data underlying figures 1 and 2 here suggest an early divergence along the lines of a dialect continuum. And for all the purported analytical elegance of binary branches, as a real-world demographic scenario it is this Indo-European continuum that offers the more straightforward and economical explanation. A splits-then-borrowing scenario has instead to invoke not just a complex series of divergent migrations, but then later movements to attenuate this by bringing certain groups back into contact again. This in turn entails consequences for which of the main rival hypotheses—the migratory Kurgan ‘horse culture’, or the progressive demic diffusion of agriculture—best fits as the driving force that shaped the pattern of the earliest Indo-European expansion.

Phil. Trans. R. Soc. B 12 December 2010 vol. 365 no. 1559 3829-3843

Splits or waves? Trees or webs? How divergence measures and network analysis can unravel language histories

Paul Heggarty et al.

Linguists have traditionally represented patterns of divergence within a language family in terms of either a ‘splits’ model, corresponding to a branching family tree structure, or the wave model, resulting in a (dialect) continuum. Recent phylogenetic analyses, however, have tended to assume the former as a viable idealization also for the latter. But the contrast matters, for it typically reflects different processes in the real world: speaker populations either separated by migrations, or expanding over continuous territory. Since history often leaves a complex of both patterns within the same language family, ideally we need a single model to capture both, and tease apart the respective contributions of each. The ‘network’ type of phylogenetic method offers this, so we review recent applications to language data. Most have used lexical data, encoded as binary or multi-state characters. We look instead at continuous distance measures of divergence in phonetics. Our output networks combine branch- and continuum-like signals in ways that correspond well to known histories (illustrated for Germanic, and particularly English). We thus challenge the traditional insistence on shared innovations, setting out a new, principled explanation for why complex language histories can emerge correctly from distance measures, despite shared retentions and parallel innovations.

Link

Doing science right

I recently complained about the non-arrival of the Tyrolean Iceman's genome this October, despite the fact that at least parts of it have been available for almost a year.

More recently, I plugged the Roman DNA Project that has already exceeded its funding goal, and seems to be going strong. Kristina Killgrove promises:

Donors will also be able to follow my progress through Twitter and blog feeds not available to the general public, getting real-time updates and learning the DNA results along with me.

Personally, I would prefer if project progress would be visible to the world at large, rather than only to project donors, in accordance with my default stance in favor of completely open science. Nonetheless, I appreciate that this limitation may serve as an incentive for donations. I hope that there will not be formal limitations barring donors from communicating news about the Project's progress to the community at large.

And, it seems that we won't have to wait too long for results. Kristina tweeted back to me that:

@dienekesp Funding will be released in mid-Dec. Samples shipped mid-Jan. First results expected 2-3 months after that.

@dienekesp Depends on # of samples, but before summer will probably have all results.

The success of this and other projects from the SciFund challenge would be a very positive sign that regular people with a passion for science are willing to fund experts to do the kind of research they want. The funding and success of such endeavors may be the best answer to those who think that digging deeper into the public purse is the only way to advance science and education.

Does capitalism reduce fitness?

I was much surprised to find this blog post on my feed today:

nielsen lab, occupy, and berkeley protests

I don't have much to say about the Occupy movement itself. People can differ in their opinions about the causes of the current economic malaise, and to argue about them. But, I will comment on a point:

We’ve thus been taking part in multiple ‘Occupy’ activities, starting the first meeting of Occupy Oakland in mid-October, marches in SF, and the Nov 2 Oakland general strike. This was a great moment – young and old, blue and white collar workers walked and rejoiced together the whole day. Our sign said ‘rEvolutionary Biologists say: Capitalism Reduces Fitness!’

Well, it’s the objective truth. An flyer distributed in the demonstration was pointing out that an African-American boy born in West Oakland has 15 shorter life expectancy than someone born up in the hills. If that’s not reduction in fitness, what is?

A reduction of life expectancy by 15 years is not evidence of reduction of fitness. Fitness is measured in offspring, it is not measured in years lived. African countries, for example, have very high population growth rates, and very low life expectancies. That is fitness. Fitness is not a comfortable long life, but having lots of babies and living long enough to ensure their survival as independent entities.

It is strange that evolutionary biologists from a top institution would make such a simple mistake. Perhaps public spending is not the best way to advance science and education?

Falsification in action

I am an occasional critic of Anatole Klyosov's Y-STR based age estimation methodology on the GENEALOGY-DNA-L list. As I have mentioned before, I am boycotting Y-STRs because they are simply worthless for the student of prehistory due to their poor qualities as molecular clocks and lack of any clear correspondence with population movements.

Nonetheless, Klyosov's professional credentials and substantial "dna genealogy" paper production, may lead some to give his work, characterized by very narrow confidence intervals and rather imaginative archaeological reconstructions, undue attention.

Klyosov resurfaced on GENEALOGY-DNA-L, taking a swipe at my criticism of his narrow confidence intervals:

Instead of walking in circles considering "bushy trees" all these years and complaining on "huge confidence intervals", one better take ACTUAL genealogy data, ACTUAL haplotype datasets, and compare actual dates with those resulted from DNA genealogy. This will show what ACTUAL margins of error looks like. With "bushy trees", they should be first subdivided on separate branches, and each branch should be analyzed individually.

Thankfully, the arrival of ancient DNA analysis can be used to falsify Klyosov's assertions. In December 2010 he discussed the possibility that some E1b1b1 subclades may have played a role in wiping out the "Bell Beakers":

However, E-V13 is already out, since it was formed around 2600 ybp (Lutak and Klyosov, Proceedings, 2009, April, pp. 639-669). E-V65 is out on the same reason (2625 ybp). E-V22 is a good candidate, with its common ancestor around 5075 ybp (ibid). E1b1b1a1-V12 also could be there, with its common ancestor of 4300+/-680 ybp. E3b1, as Adams et al (2008) called them (it is apparently E-81), has a common ancestor in Iberia around 4825 ybp (Klyosov, Proceedings, 2009, March, pp. 390-421), which nicely fit to the concept.

The recent publication of 7,000-year-old E-V13 from Neolithic Spain, indicates that this haplogroup was in existence at least that long ago, and hence could not have been formed 2,600 years before present. Klyosov's error is at least 2.5x, consistent with my assertions that Y-STR based age estimates carry huge confidence intervals, and inconsistent with his self-assurance that they do not.

I see nothing wrong in advancing speculative hypotheses based on the available evidence. I've advanced some of my own ideas for the spread of E-V13 that appear to be less plausible in the light of the ancient DNA evidence, even though a historical, Greek-mediated spread of a subset of E-V13 as proposed by Di Gaetano et al. and King et al. is still possible.

What is certainly wrong is to have over-confidence in one's assertions and not to admit the limitations of Y-STR based age estimates when they are staring us in the face on both theoretical and empirical grounds.

To survive: be fat or be smart

The bottom line is that it makes sense for an animal to combine the "fat" and "smart" strategies to survive. It makes sense: a very fat but very dumb animal has all the energy reserves it will ever need, but at the expense of locomotion efficiency, avoidance of predators, etc. A very smart but very lean animal has all the brain power needed to survive, but has very little "in the tank" if it finds itself in a bad spot and has to go without food for a long time.

The versatile strategy is best, and humans are the one species that seems to have gone the "brain power" way, without sacrificing completely other traits needed for survival.

Nature (2011) doi:10.1038/nature10629

Energetics and the evolution of human brain size

Ana Navarrete et al.

The human brain stands out among mammals by being unusually large. The expensive-tissue hypothesis1 explains its evolution by proposing a trade-off between the size of the brain and that of the digestive tract, which is smaller than expected for a primate of our body size. Although this hypothesis is widely accepted, empirical support so far has been equivocal. Here we test it in a sample of 100 mammalian species, including 23 primates, by analysing brain size and organ mass data. We found that, controlling for fat-free body mass, brain size is not negatively correlated with the mass of the digestive tract or any other expensive organ, thus refuting the expensive-tissue hypothesis. Nonetheless, consistent with the existence of energy trade-offs with brain size, we find that the size of brains and adipose depots are negatively correlated in mammals, indicating that encephalization and fat storage are compensatory strategies to buffer against starvation. However, these two strategies can be combined if fat storage does not unduly hamper locomotor efficiency. We propose that human encephalization was made possible by a combination of stabilization of energy inputs and a redirection of energy from locomotion, growth and reproduction.

Link

Cave painters painted spotted horses as they saw them.

I am innately skeptical of "symbolism" when it comes to most ancient art (see e.g., the destruction of the "mother goddess" theory). So, an article that shows that ancient artists painted horses as they saw them, and did not put dots on them for some strange symbolic reason, is very welcome.

From ScienceNOW:

About 25,000 years ago, humans began painting a curious creature on the walls of European caves. Among the rhinos, wild cattle, and other animals, they sketched a white horse with black spots. Although such horses are popular breeds today, scientists didn't think they existed before humans domesticated the species about 5000 years ago. Now, a new study of prehistoric horse DNA concludes that spotted horses did indeed roam ancient Europe, suggesting that early artists may have been reproducing what they saw rather than creating imaginary creatures.

Related: Ancient DNA for horse coat color

PNAS doi: 10.1073/pnas.1108982108

Genotypes of predomestic horses match phenotypes painted in Paleolithic works of cave art

Melanie Pruvost et al.

Archaeologists often argue whether Paleolithic works of art, cave paintings in particular, constitute reflections of the natural environment of humans at the time. They also debate the extent to which these paintings actually contain creative artistic expression, reflect the phenotypic variation of the surrounding environment, or focus on rare phenotypes. The famous paintings “The Dappled Horses of Pech-Merle,” depicting spotted horses on the walls of a cave in Pech-Merle, France, date back ∼25,000 y, but the coat pattern portrayed in these paintings is remarkably similar to a pattern known as “leopard” in modern horses. We have genotyped nine coat-color loci in 31 predomestic horses from Siberia, Eastern and Western Europe, and the Iberian Peninsula. Eighteen horses had bay coat color, seven were black, and six shared an allele associated with the leopard complex spotting (LP), representing the only spotted phenotype that has been discovered in wild, predomestic horses thus far. LP was detected in four Pleistocene and two Copper Age samples from Western and Eastern Europe, respectively. In contrast, this phenotype was absent from predomestic Siberian horses. Thus, all horse color phenotypes that seem to be distinguishable in cave paintings have now been found to exist in prehistoric horse populations, suggesting that cave paintings of this species represent remarkably realistic depictions of the animals shown. This finding lends support to hypotheses arguing that cave paintings might have contained less of a symbolic or transcendental connotation than often assumed.

Link

Y-chromosomes of the Bahamas

I like the line about there being substantially more Y-STR variation in E1b1a7a-U174 and E1b1ba8-U175 in the Bahamas than any African collection. I have argued for years that the central assumption of phylogeography, that the location of highest Y-STR diversity is not necessarily the point of origin of a haplogroup, since Y-STR diversity can be affected both by antiquity and by admixture. Nonetheless, I keep reading papers where tiny differences in Y-STR variation, even if we forget about the noisiness of Y-STRs themselves, are taken as evidence of ancient migrations. Thankfully, the time when Y-STRs were used to infer ancient migrations is over, and the huge collection of Y-STR haplotypes amassed by population geneticists, forensic specialists, and genealogists alike can be put to uses for which it is more amenable.

I can't say I know much about the history of the Bahamas, but this was something I had not heard of before:

Over the last 150 years, the Bahamas has been witness to a varied array of settlers, including Chinese immigrant workers, Greek spongers, Jewish business-men and individuals of Lebanese descent fleeing religious persecution. The extent to which each group has contributed genetically to the Bahamian paternal gene pool, however, is unknown. Our findings suggest that the Greeks, which exhibit relatively high frequencies of haplogroups E1b1b1a*-M78, J2a*-M410, and R1b1b1*-L23 (Semino et al., 2004; Myres et al., 2011), are a likely source of these lineages in the Bahamas, although the presence of M78 derived chromosomes may also signal gene flow from Lebanon (Zalloua et al., 2008). J1e-P58 lineages, on the other hand, which are characteristic of Jewish populations (Hammer et al., 2009) and Arab speaking groups (Chiaroni et al., 2010), may represent genetic signatures of Eastern European Jews and/or Lebanese migrants entering the Bahamas in the early twentieth century.

Another interesting tidbit:

Western European colonialism, although short-lived, appears to have left marked genetic imprints throughout the Bahamian archipelago, with Long Island receiving the strongest European genetic signals and Exuma, the weakest; a distribution pattern consistent with our earlier reports utilizing autosomal STR markers (Simms et al., 2008, 2011). The higher frequency of M269 derived individuals in the Long Island population (55.8%), when compared with the other five Bahamian islands surveyed (ranging from 8.5% to 18.3%), suggests higher gene flow from European males (Saunders, 2003b). According to the 1851 census, Long Island possessed one of the smallest European components (13.1%) yet, by 1953, almost 50% of this population was of ‘‘mixed’’ ancestry (Craton, 1998).

R-M269 seems quintessentially European today, and most living R-M269 men probably have West European ancestry. But, the finding of a high frequency in a Bahamian spot ought to remind us that Y-chromosomes can achieve high frequencies in little time, given the right conditions. Indeed, we can very well draw a parallel between the prehistoric spread of R-M269 into Europe, an event that is still shrouded in mystery, with the late historical movement of the same haplogroup into the Americas. Taking the broad view, these two unrelated events represent two pulses of the same westward spread of a successful Y-chromosome lineage.

It is also nice that scientists are beginning to take notice of very basal Y-chromosomes, going back to Y-chromosome Adam.

Two samples that fell outside of haplogroups B-T (defined by M42) were observed in Abaco (1.5%) and New Providence (0.7%), two Bahamian islands separated by a total of 139.4 km, as well as in a single sample from Haiti (unpublished data). When tested for V171, which, according to Cruciani et al. (2011a) defines the A2-T lineage, all three samples exhibited the ancestral allele. Instead, each individual was derived for the paralogous V152 mutation that determines the A1b lineage. It should be noted that each of the three samples possessed an eight base pair long Poly-T stretch at the M91 locus, indicative of the monophyletic haplogroup A defined by Karafet et al. (2008). However, as a result of the rearrangement of the tree by Cruciani et al. (2011a), haplogroup A no longer represents a monophyletic group, as the A2 and A3 lineages are now united with all haplogroup A lineages other than A1 by their shared possession of V171.

Haplogroup A chromosomes have been collected as isolated examples in many genealogical projects and scientific studies. It's a great idea for someone to take the initiative and collect the most divergent ones, invest in genotyping them fully, and push the boundaries of what we know about the most ancient history of modern human patrilineages.

AJPA DOI: 10.1002/ajpa.21616

Paternal lineages signal distinct genetic contributions from British Loyalists and continental Africans among different Bahamian islands

Tanya M. Simms et al.

Over the past 500 years, the Bahamas has been influenced by a wide array of settlers, some of whom have left marked genetic imprints throughout the archipelago. To assess the extent of each group's genetic contributions, high-resolution Y-chromosome analyses were performed, for the first time, to delineate the patriarchal ancestry of six islands in the Northwest (Abaco and Grand Bahama) and Central (Eleuthera, Exuma, Long Island, and New Providence) Bahamas and their genetic relationships with previously published reference populations. Our results reveal genetic signals emanating primarily from African and European sources, with the predominantly sub-Saharan African and Western European haplogroups E1b1a-M2 and R1b1b1-M269, respectively, accounting for greater than 75% of all Bahamian patrilineages. Surprisingly, we observe notable discrepancies among the six Bahamian populations in their distribution of these lineages, with E1b1a-M2 predominating Y-chromosomes in the collections from Abaco, Exuma, Eleuthera, Grand Bahama, and New Providence, whereas R1b1b1-M269 is found at elevated levels in the Long Island population. Substantial Y-STR haplotype variation within sub-haplogroups E1b1a7a-U174 and E1b1ba8-U175 (greater than any continental African collection) is also noted, possibly indicating genetic influences from a variety of West and Central African groups. Furthermore, differential European genetic contributions in each island (with the exception of Exuma) reflect settlement patterns of the British Loyalists subsequent to the American Revolution.

Link

The advantage of being first

From press release:

"We find that families who are at the forefront of a range expansion into new territories had greater reproductive success. In other words, that they had more children, and more children who also had children," Labuda explained. "As a result, these families made a higher genetic contribution to the contemporary population than those who remained behind in what we call the range core, as opposed to the wave front.

The research confirms in humans a phenomenon that has already been observed in other species with much shorter generation spans. "We knew that the migration of species into new areas promoted the spread of rare mutations through a phenomenon known as 'gene surfing', but now we find that selection at the wave front could make this surfing much more efficient," Excoffier said. This evolutionary mechanism in combination with founder effects and social or cultural transmission of reproductive behavior could explain why some genetic diseases are found at an elevated frequency in the Charlevoix and Saguenay Lac Saint-Jean regions where the study was carried out, as rare mutations can also surf during a range expansion.

Science DOI: 10.1126/science.1212880

Deep Human Genealogies Reveal a Selective Advantage to Be on an Expanding Wave Front

Claudia Moreau et al.

Since their origin, human populations have colonized the whole planet, but the demographic processes governing range expansions are mostly unknown. We analyzed the genealogy of more than 1 million individuals resulting from a range expansion in Quebec between 1686 and 1960 and reconstructed the spatial dynamics of the expansion. We find that a majority of the present Saguenay Lac Saint-Jean population can be traced back to ancestors having lived directly on or close to the wave front. Ancestors located on the front contributed significantly more to the current gene pool than those from the range core, likely due to a 20% larger effective fertility of women on the wave front. This fitness component is heritable on the wave front and not in the core, implying that this life-history trait evolves during range expansions.

Link

Darwinian linguistic controversies

There is an interesting essay titled Darwin's Tongues, which covers some of the controversies associated with the use of biological evolutionary methods on linguistic problems. A couple of the papers mentioned in the article are Dunn et al. (2011) and Atkinson (2011). This little bit sparked my interest:

Using this database, Cysouw’s team repeated Atkinson’s technique and found two separate geographic origins for language, one in East Africa and another in West Asia’s Caucasus region, with a large swath of the Middle East and South Africa also possible. Crucially, Cysouw’s analysis suggests that none of these regions contain phoneme-rich languages that stand out as having far more speech sounds than any of the others.

I've contacted Dr. Cysouw to see if anything on this has been published/is available, and I will update this blog entry if it has.

Sardinian snails got around

Interesting, in the context of my recent musings.

PLoS ONE 6(6): e20734. doi:10.1371/journal.pone.0020734

Phylogeography of a Land Snail Suggests Trans-Mediterranean Neolithic Transport

Ruth Jesse et al.

Abstract
Background
Fragmented distribution ranges of species with little active dispersal capacity raise the question about their place of origin and the processes and timing of either range fragmentation or dispersal. The peculiar distribution of the land snail Tudorella sulcata s. str. in Southern France, Sardinia and Algeria is such a challenging case.

Methodology
Statistical phylogeographic analyses with mitochondrial COI and nuclear hsp70 haplotypes were used to answer the questions of the species' origin, sequence and timing of dispersal. The origin of the species was on Sardinia. Starting from there, a first expansion to Algeria and then to France took place. Abiotic and zoochorous dispersal could be excluded by considering the species' life style, leaving only anthropogenic translocation as parsimonious explanation. The geographic expansion could be dated to approximately 8,000 years before present with a 95% confidence interval of 10,000 to 3,000 years before present.

Conclusions
This period coincides with the Neolithic expansion in the Western Mediterranean, suggesting a role of these settlers as vectors. Our findings thus propose that non-domesticated animals and plants may give hints on the direction and timing of early human expansion routes.

Link

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