Showing posts with label Y DNA. Show all posts
Showing posts with label Y DNA. Show all posts

Ancient Irish genomes confirm Bronze Age steppe incursion

Press release: First ancient Irish human genomes sequenced.

BBC: Ancient DNA sheds light on Irish origins.

Guardian: Origins of the Irish down to mass migration, ancient DNA confirms.

These settlers were followed by people, initially from the Pontic steppe of southern Russia, who knew how to mine for copper and work with gold, and who carried the genetic variant for a blood disorder called haemochromatosis, a hereditary genetic condition so common in Ireland that it is sometimes called Celtic disease.

These people also brought with them the inherited variation that permits the digestion of milk in maturity – much of the world becomes intolerant to the milk sugar lactose after infancy – and they may even have brought the language that became what is now Irish. Some of them, too, had blue eyes.

“There was a great wave of genome change that swept into Europe from above the Black Sea into Bronze Age Europe and we now know it washed all the way to the shores of its most westerly island,” said Dan Bradley, professor of population genetics at Trinity College Dublin.

“And this degree of genetic change invites the possibility of other associated changes, perhaps even the introduction of language ancestral to western Celtic tongues.”

The Dublin team and colleagues from Queens University Belfast report in the Proceedings of the National Academy of Sciences that the two great changes in European prehistory – the emergence of agriculture and the advance of metallurgy – were not just culture shifts: they came with new blood. An earlier population of hunter gatherers was successively overwhelmed by new arrivals. And in Ireland, these new settlers began to define a nation.

But the latest study throws more light on the birth of a nation. All three dead men from Rathlin Island carried what is now the most common type of Irish Y chromosome, inherited only from male forebears. [. . .]

And Lara Cassidy, a researcher in genetics at Trinity College Dublin and another co-author, said “Genetic affinity is strongest between Bronze Age genomes and modern Irish, Scottish and Welsh, suggesting establishment of central attributes of the insular Celtic genome 4,000 years ago.”

The PNAS paper: Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome
The Neolithic and Bronze Age transitions were profound cultural shifts catalyzed in parts of Europe by migrations, first of early farmers from the Near East and then Bronze Age herders from the Pontic Steppe. However, a decades-long, unresolved controversy is whether population change or cultural adoption occurred at the Atlantic edge, within the British Isles. We address this issue by using the first whole genome data from prehistoric Irish individuals. A Neolithic woman (3343–3020 cal BC) from a megalithic burial (10.3× coverage) possessed a genome of predominantly Near Eastern origin. She had some hunter–gatherer ancestry but belonged to a population of large effective size, suggesting a substantial influx of early farmers to the island. Three Bronze Age individuals from Rathlin Island (2026–1534 cal BC), including one high coverage (10.5×) genome, showed substantial Steppe genetic heritage indicating that the European population upheavals of the third millennium manifested all of the way from southern Siberia to the western ocean. This turnover invites the possibility of accompanying introduction of Indo-European, perhaps early Celtic, language. Irish Bronze Age haplotypic similarity is strongest within modern Irish, Scottish, and Welsh populations, and several important genetic variants that today show maximal or very high frequencies in Ireland appear at this horizon. These include those coding for lactase persistence, blue eye color, Y chromosome R1b haplotypes, and the hemochromatosis C282Y allele; to our knowledge, the first detection of a known Mendelian disease variant in prehistory. These findings together suggest the establishment of central attributes of the Irish genome 4,000 y ago.

More carriers of deeply diverged Y lineage (haplogroup A00) found in Cameroon

This possibly archaic African Y lineage was discovered a few years ago by hobbyists, and a project run and funded by hobbyists to collect and test additional A00 samples has started to report results:
There are some striking patterns in the results already. 85% of the A00 so far are from the Bangwa (Nweh) people, and 15% from the Nkongho-Mbo. This is despite the fact that nearly 57% of the samples collected were from Mbo, and only 37% were from Bangwa. Once all the results have been fully tabulated, we can provide more complete statistics. It will take a while to transcribe all the rich data from those handwritten sheets into electronic spreadsheets. [. . .]

What's next? Matthew would like to head back to the field quite soon, in the second half of October, when the school where he teaches has a break. Our current plan is for him to visit the region of the Bamileke people. Matthew, an ethno-historian, has said "The similarity in names, language, dancing style and all other aspects of life suggest that the Bangwa are 90 percent Bamileke." By testing a good number of Bamileke, we'll be able to see whether the heritage they share includes A00, or not. It is possible that the A00 among the Bangwa comes from the indigenous people who originally inhabited the hills, before they arrived several centuries ago, or it could also have been present among the Bamileke earlier. Our results should give strong evidence to answer that question.

The next field trips should be even more exciting. One of our goals is to collect the most diverse samples of A00 possible, to uncover its internal structure. By sequencing the Y-DNA of A00 lines that have diverged and settled in different parts of Cameroon, we should be able to get a good idea of when those different lineages had a common ancestor, and understand better how the peoples among whom it's found are related.

One trip will take Matthew westward into the lowland regions close to Nigeria, where the Banyangi and Ejagham peoples live, toward the Cross River, home of the endangered Cross River Gorilla. These villages are also on the roads that led to the old Nigerian port of Calabar, where captives from Cameroon's highlands, including some Bangwa, were sold into slavery in the past. He has never before sampled in the western regions, and only 16 Banyangi have been tested in his past research, but there are versions of Bangwa history which say that these peoples make up a significant element of their founders. Members of the A0 haplogroup have been found in Nigeria, but we have no idea yet whether A00 are also found in that direction. The famed Iwo Eleru cave is in southern Nigeria, where a skull with archaic features has been found that dates to only 13,000 years ago, suggesting long survival of diverse humans in that region.

In his other trip, he'll seek to sample members of several of the different Pygmy communities of Cameroon, who live to the South and East. Among the Pygmy peoples, Matthew collected 53 samples in 2006, and two of them belonged to A00! These communities are far from the highlands where the Bangwa and Mbo live, so we can expect that their A00 will be quite distinct. This should be extremely interesting!

ASHG 2015: growth rate estimates from whole Y chromosome sequences

Estimation of growth rates for populations and haplogroups using full Y chromosome sequences.

F. L. Mendez; G. D. Poznik; C. D. Bustamante; 1000 Genomes Project Consortium

Department of Genetics, Stanford University, Stanford, CA.

Evolutionary processes affecting a population influence gene genealogies across the genome. Coalescent theory provides the mathematical framework to connect realized genealogies to the underlying evolutionary processes. However, in most cases, information about the genealogies is obtained only indirectly through the observation of genetic variation. Therefore, in general, very limited information about any individual locus is available. As the longest non-recombining portion of the human genome, the Y chromosome accumulates mutations relatively quickly. When large amounts of sequence are used, the Y chromosome provides an unparalleled ability to resolve the structure and coalescence times of its genealogy. Because patterns of variation in the Y chromosome are only influenced by processes affecting men, they can be used to study both demographic and social phenomena. The 1000 Genomes Project includes whole Y-chromosome data from more than 1000 men and has an extensive representation of most lineages that have experienced recent massive expansions in size. Though the dynamics of population growth have likely changed over time, we are more interested in the growth rates at the times of these rapid expansions than on an average effect. To study this, we have developed a new method that takes advantage of the temporal resolution provided by Y-chromosome data and of historical data, while accounting for the uncertainties associated with the coalescent and mutational processes. We estimate the growth rates for several branches of the Y-chromosome tree, including those in Europe, sub-Saharan Africa and South Asia. We estimate that several lineages within the European R1b, sub-Saharan African E1b, and South Asian R1a haplogroups experienced growth rates of at least 20-60% per generation at the onset of their massive expansions, some 3-5 thousand years ago. These high growth rates are comparable to those experienced by human populations during the 20th century. However, we find that most observed genealogies are unlikely to be the result of whole population expansion or of natural selection.

The ancestry and affiliations of Kennewick Man

Kennewick Man ancient DNA. The paper is openly accessible. Results pretty much as I expected.
We find that Kennewick Man is closer to modern Native Americans than to any other population worldwide.
The paper is marred by strained, politically-motivated attempts to tie Kennewick Man specifically to "the Confederated Tribes of the Colville Reservation (Colville), one of the five tribes claiming Kennewick Man". So those interested in aboriginal American population structure are probably better off ignoring much of the authors's narrative and looking directly at the data.

Persistence of Lombard Y chromosomes in old Northern Italian families?

Traces of medieval migrations in a socially stratified population from Northern Italy. Evidence from uniparental markers and deep-rooted pedigrees.

Heredity (Edinb). 2015 Feb;114(2):155-62

Authors: Boattini A, Sarno S, Pedrini P, Medoro C, Carta M, Tucci S, Ferri G, Alù M, Luiselli D, Pettener D

Abstract

Social and cultural factors had a critical role in determining the genetic structure of Europe. Therefore, socially stratified populations may help to focus on specific episodes of European demographic history. In this study, we use uniparental markers to analyse the genetic structure of Partecipanza in San Giovanni in Persiceto (Northern Italy), a peculiar institution whose origins date back to the Middle Ages and whose members form the patrilineal descent of a group of founder families. From a maternal point of view (mtDNA), Partecipanza is genetically homogeneous with the rest of the population. However, we observed a significant differentiation for Y-chromosomes. In addition, by comparing 17 Y-STR profiles with deep-rooted paternal pedigrees, we estimated a Y-STR mutation rate equal to 3.90 * 10(-3) mutations per STR per generation and an average generation duration time of 33.38 years. When we used these values for tentative dating, we estimated 1300-600 years ago for the origins of the Partecipanza. These results, together with a peculiar Y-chromosomal composition and historical evidence, suggest that Germanic populations (Lombards in particular) settled in the area during the Migration Period (400-800 AD, approximately) and may have had an important role in the foundation of this community.

http://dx.doi.org/10.1038/hdy.2014.77

Exploring Surnames, DNA & Genealogy in The Low Countries

Maarten Larmuseau - Exploring Surnames, DNA & Genealogy in The Low Countries

Published on Apr 27, 2015

There is limited knowledge on the biological relatedness between citizens and on the demographic dynamics within villages, towns and cities in pre-17th-century Western Europe. By combining Y-chromosomal genotypes, in-depth genealogies and surname data in a strict genetic genealogical approach, it has been possible to gain insights into the genetic diversity and the relatedness among indigenous paternal lineages within six Flemish communities at the time of surname adoption between 14th-15th century. Since these communities have been selected based on differences in geography and historical development, the genetic results provide relevant information in historical sciences, demography, forensic genetics and genealogy.

Dr. Maarten Larmuseau, evolutionary geneticist, University of Leuven - Dr. Maarten Larmuseau is a senior postdoctoral researcher at the University of Leuven (KU Leuven, Belgium). He is an evolutionary geneticist interested in the interaction between genetics, evolution and history in humans and animals. Currently he is making use of genetic genealogical tools within forensic, historical and human sociobiological research. His research in e.g. historical cuckoldry rates, the false identification of relics attributed to French kings, and the detection of forgotten historical migration events in the 16th century is well known by both academics and the broad public.

High Y-chromosomal diversity and low relatedness between paternal lineages on a communal scale in the Western European Low Countries during the surname establishment

There is limited knowledge on the biological relatedness between citizens and on the demographical dynamics within villages, towns and cities in pre-17th century Western Europe. By combining Y-chromosomal genotypes, in-depth genealogies and surname data in a strict genetic genealogical approach, it is possible to provide insights into the genetic diversity and the relatedness between indigenous paternal lineages within a particular community at the time of the surname adoption. To obtain these insights, six Flemish communities were selected in this study based on the differences in geography and historical development. After rigorous selection of appropriate DNA donors, low relatedness between Y chromosomes of different surnames was found within each community, although there is co-occurrence of these surnames in each community since the start of the surname adoption between the 14th and 15th century. Next, the high communal diversity in Y-chromosomal lineages was comparable with the regional diversity across Flanders at that time. Moreover, clinal distributions of particular Y-chromosomal lineages between the communities were observed according to the clinal distributions earlier observed across the Flemish regions and Western Europe. No significant indication for genetic differences between communities with distinct historical development was found in the analysis. These genetic results provide relevant information for studies in historical sciences, archaeology, forensic genetics and genealogy.

Massive migration from the steppe is a source for Indo-European languages in Europe

New preprint confirming what those of us who were paying attention were able to infer years ago:
We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost four hundred thousand polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of western and far eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ~8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary, and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ~24,000 year old Siberian6. By ~6,000-5,000 years ago, a resurgence of hunter-gatherer ancestry had occurred throughout much of Europe, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ~4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ~3/4 of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ~3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for the theory of a steppe origin of at least some of the Indo-European languages of Europe. [. . .]

R1a and R1b are the most common haplogroups in many European populations today 18,19 , and our results suggest that they spread into Europe from the East after 3,000 BCE. Two hunter-gatherers from Russia included in our study belonged to R1a (Karelia) and R1b (Samara), the earliest documented ancient samples of either haplogroup discovered to date. These two hunter-gatherers did not belong to the derived lineages M417 within R1a and M269 within R1b that are predominant in Europeans today 18,19 , but all 7 Yamnaya males did belong to the M269 subclade 18 of haplogroup R1b.

Ust'-Ishim: Ancient DNA offers the first of what I expect in the coming years will be many disappointments to those emotionally invested in a SE Asian origin for K-M526

It's been asserted, on crude phylogeographic grounds, that K-M526 originated in South East Asia. A SE Asian origin for K-M526 is credible if you ignore the rest of the Y phylogeny, starting with K-M9, and all other available information. Sadly for Hector, reality, with this recent publication, has again chosen to side with "Eurocentrists".

I don't expect the Hectors will gracefully accept their beating, but to others the presence of a previously unknown branch of K(xLT) in Siberia 45,000 years ago should be a pretty clear signal that the idea of a 500 year sprint from West or Central Asia to an already-inhabited SE Asia, followed, after an indefinite pause, by a repopulating of the world from Sundaland (if not the islands of Wallacea), all while failing to carry any trace of Denisovan admixture back to the future civilized world is an unnecessary and improbable fantasy.

The cline of Denisovan admixture, from faint, highly-selected remnants in mainland SE Asia to maxima among Melanesians and Australian Aborigines, has always pointed to gene flow into the region after its initial settlement rather than out of it, the K-bearers being one obvious candidate for the major source of this dilution. I'd also say it's more likely than not that they (an M526-carrying population of Central Asian origin) are the ones who brought culture to Hector's ancestors.

ESHG 2014: Y chromosome haplogroups C, N and Q in Eurasian populations for the perspectives of proto-Bulgarian ancestry

Title: P17.92-M - Meta-analysis of Y chromosome haplogroups C, N and Q in Eurasian populations for the perspectives of proto-Bulgarian ancestry
Keywords: Y-chromosome; haplogroup; proto-Bulgarians
Authors: S. Karachanak1, D. Nesheva1, V. Grugni2, N. Al-Zahery2, V. Battaglia,2, A. S. Galabov3, D. Toncheva1; 1Department of Medical Genetics, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria, 2Department of Biology and Biotechnologies “Lazzaro Spallanzani”. University of Pavia, Pavia, Italy, 3The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria.

Abstract: Bulgaria is situated on the presumed trajectory of the pioneer colonization of Europe. Since then it has been subjected to a series of demographic events with disputable impact on the contemporary Bulgarian gene pool. One of the most controversial issues of the Bulgarian past is the origin of the proto-Bulgarians, which were previously considered as a sparse Turkic population.

In order to delve into Bulgarian patrilineal origins we have performed a survey of Y-chromosome haplogroups followed by meta-analysis of haplogroups C, N and Q distinctive for Altaic populations. The analysis was performed on a sample comprising 808 Bulgarian males using RFLP and DHPLC analysis. We have found that only 1.49 % of the contemporary gene pool belongs to haplogroups C, N and Q. Our results were used to upgrade and extend the distribution maps of these haplogroups and to compare their frequency in 240 Eurasian (sub-) populations with more than 20 000 samples.

The comparison reveals a statistically significant difference in the distribution of the studied haplogroups between Bulgarians and Altaic populations as well as between Bulgarians and Eastern Slavic populations. Based on the novel historical studies which point to a substantial contribution of the proto-Bulgarians to the modern Bulgarian gene pool the obtained results suggest that there is no common genetic ancestry between proto-Bulgarians and present day Altaic populations as they reject the hypothesis of the Turkic origin of proto-Bulgarians.

ESHG 2014: Y-chromosome Polymorphisms in Kazakh Populations from the Perspective of Tribal-clan structure

Title: J17.65 - Characteristics of Y-chromosome Polymorphisms in Kazakh Populations from the Perspective of Tribal-clan structure
Keywords: Y-chromosome Polymorphisms; Kazakh Populations; Tribal-clan structure
Authors: M. Zhabagin1,2, Z. Sabitov3, H. Dibirova4, E. Balanovska4, I. Zakharov2, O. Balanovsky2; 1Center for Life Sciences, Nazarbayev University, Astana, Kazakhstan, 2Vavilov Institute of General Genetics RAS, Moscow, Russian Federation, 3Gumilyov Eurasian National University, Astana, Kazakhstan, 4Research Centre of Medical Genetics RAMS, Moscow, Russian Federation.

Abstract: The characteristic feature of the Kazakh nomadic society was the presence of a hierarchically organized and widely branched tribal-clan structure called “Shezhire”, which reflected complex system of ethno-social organization. In the context of the Shezhire, Kazakh populations are divided into three ethno-territorial association of tribes called "Zhuz" (Great, Middle, and Small Zhuzes) and a group of aristocratic tribes (Tore, Kozha, Sunak).

This study aims to compare Y-chromosomal polymorphism of three Kazakh Zhuzs and group of aristocratic tribes (total sample size N= 1407). We analyzed 40 SNP and 17 STR Y-chromosomal markers. Summary statistics were calculated using Arlequin 3.5. Neighbor-joining tree was constructed by the program MEGA 5.0. Multidimensional scaling plot was drawn by the software package Statistica v.7.1.

Population pairwise FST values were calculated from the Y-chromosomal haplogroup frequencies to assess the genetic similarity among studied groups of Kazakh tribes. The most distant ones were the tribe of Sunak and the Small Zhuz (0.393), whereas the shortest distance was found between the tribe of Tore and the Great Zhuz (0,021). These genetic distances are associated with the geographic distances between studied populations. The distribution of Y-chromosomal haplogroups is strongly correlated with the tribal-clan structure of Kazakhs. Presence of certain haplogroups at high frequency at particular tribes is in favor to the hypothesis that many tribes go back to one biological founder, confirming the link between Kazakh family tree Shezhire with the genetic composition.

Y haplogroups and aggression in humans

Greg Cochran writes:
If a new environment favored lower (or higher) aggressiveness in males , a Y-chromosome that induced lower (or higher) aggressiveness would take off. And since different Y chromosomes do indeed affect the level of aggressiveness in mice [which I just found out], possibly by affecting testosterone production – this mechanism is plausible. [. . .]

Fortunately for all concerned, the selective value of aggressiveness, etc. has been the same for all human populations forever and ever, before and after the development of agriculture. Otherwise you might see weirdly rapid expansions of particular Y-chromosome haplogroups – common, yet only a few thousand years old.

A 2009 study of 156 Pakistanis found an association opposite what one might expect, but I doubt it would replicate in a larger sample:
Five Y haplogroups that are commonly found in Eurasia and Pakistan comprised 87% (n=136) of the population sample, with one haplogroup, R1a1, constituting 55% of the sampled population. A comparison of the total and four subscale mean scores across the five common Y haplogroups that were present at a frequency > or =3% in this ethnic group revealed no overall significant differences. However, effect-size comparisons allowed us to detect an association of the haplogroups R2 (Cohen's d statistic=.448-.732) and R1a1 (d=.107-.448) with lower self-reported aggression mean scores in this population.
A PhD thesis published this year ("The Y chromosome in cardiovascular disease") looks at reasonably large samples of Polish men and evidently finds no associations between Y haplogroup and sex hormones or aggression:
Though no analysis of the human Y chromosome has ever been completed in the context of these \male-relateda or \sex-specifica phenotypes, evidence from animal models supports a hypothetical role for the Y chromosome in regulation of both aggression and sex hormones. Firstly, the Y chromosome has been repeatedly implicated in aggression in murine models; Gatewood et al. found that female mice carrying an SRY-deleted Y chromosome had significantly higher aggression levels than wild-type female mice, similar to those found in males (Gatewood et al. 2006). Similarly, the Y chromosome was associated with sex steroids through its function in sex determination (Wilhelm et al. 2007).

To identify the mechanism of association between haplogroup I of the Y chromosome and CAD, the effect of this haplogroup on \sex-associateda and \sex-specifica phenotypes was investigated in a series of experiments highlighted in this chapter. No relationship between the Y chromosome and any facet of aggression or sex steroid was identified. These data indicate that these traits are unlikely to drive the association between haplogroup I and increased predisposition to CAD.

(More interestingly, while I haven't looked at the thesis closely it does apparently confirm in Polish men an association between Y haplogroup I and cardiovascular disease, which I hadn't taken too seriously when it was previously reported in British men.)

Although a lack of convincing evidence that major extant European Y haplogroups are differentially associated with aggression doesn't rule out the possibility that Y chromosomes associated with, e.g., lower aggressiveness constituted a larger share of European male lineages in the past, I doubt this possibility as an explanation for the recent expansion of haplogroups like R1b and R1a.

Possible archaic African Y lineage

The paper has now been published: An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree
We report the discovery of an African American Y chromosome that carries the ancestral state of all SNPs that defined the basal portion of the Y chromosome phylogenetic tree. We sequenced ∼240 kb of this chromosome to identify private, derived mutations on this lineage, which we named A00. We then estimated the time to the most recent common ancestor (TMRCA) for the Y tree as 338 thousand years ago (kya) (95% confidence interval = 237–581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils. The extremely ancient age combined with the rarity of the A00 lineage, which we also find at very low frequency in central Africa, point to the importance of considering more complex models for the origin of Y chromosome diversity. These models include ancient population structure and the possibility of archaic introgression of Y chromosomes into anatomically modern humans. The A00 lineage was discovered in a large database of consumer samples of African Americans and has not been identified in traditional hunter-gatherer populations from sub-Saharan Africa. This underscores how the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during the interpretation of the geographic location of divergent branches of the Y chromosome phylogenetic tree for the elucidation of human origins.

Incomplete Y DNA results from two Corded Ware skeletons

The data:

The seemingly highly-confused interpretation offered by the authors:

Determining polymorphisms of SNP type from chromosome Y resulted in categorizing skeleton from grave no. 1 with very high probability into haplogroup G, whereas skeleton from grave no. 2 with very high probability into one of three haplogroups J, I or E*. Detailed results of determinations are included in the attached table 2. On the basis of the above mentioned expertise one can state that the skeletons are male individuals with no relationship between each other. [. . .]

An analysis of polymorphism of single nucleotide (SNP) of chromosome Y from genetic material derived from both burials has brought in different results than in the case of so far analyzed aDNA materials of burials of the Corded Ware culture or partly contemporary Beaker culture which revealed the presence of haplogroups R1a1 and R1b among them (Haak et al., 2008; Lee et al., 2012). In case of the dead from Wrocław-Jagodno genetic diversity of both individuals was observed. One of them does not have clearly determined haplogroup. We should reject his affiliation to paragroup E* characteristic mainly for Africa and identified among population of Bantu (Karafet et al., 2008). On the other hand, haplogroup J was probably formed about 30000 years ago in Arabian Peninsula and it is often identified as a indicator of the Neolithic demic diffusion associated with spreading agriculture (Semino et al., 2004, 1996). Its contemporary distribution covers mainly the area of Middle East and the Mediterranean Sea basin; it sporadically occurs in Central Europe. Latest analyses show that its spreading might be a marker of later migrations (Giacomo et al., 2004). Hence the most probable is acceptance of haplogroup I as a proper one for the examined individual. It is considered that it was developed between 15000 and 30000 years ago (Karafet et al., 2008) and its spreading is associated with the expansion of the Paleolithic Gravettian culture (Semino, 2000) or population from the beginning of Holocene (Rootsi et al., 2004). Thus we should think that this individual is most probably descendant of native hunting and gathering community. Haplogroup G, identified in the second individual, belongs to widespread multiethnic groups of Europe, Asia and northern Africa. This haplogroup is largely identified among analyzed aDNA materials from Europe including the early Neolithic in Spain and Germany and the late Neolithic in France. It is a serious factor supporting a conception of spreading of Neolithic from the area of Middle East (Haak et al., 2010; Lacan et al., 2011; Rootsi et al., 2012). It may indicate very complicated development processes of communities of the Corded Ware culture in which diverse populations participated – autochtonous deriving from hunting and gathering ancestors as well as Neolithic populations, genetically deriving from the Middle East areas but already living there since the beginning of Neolithic.

[Assessment of late Neolithic pastoralist's life conditions from the Wroclaw-Jagodno site (SW Poland) on the basis of physiological stress markers]

I see no basis whatsoever in the reported results for "categorizing skeleton from grave no. 1 with very high probability into haplogroup G". Possibly there is some miscommunication among the authors, or else a complete failure of logic. It appears the authors merely failed to exclude haplogroup G in sample 1 because of an unsuccessful test (and arbitrarily decided to make haplogroup G their "very highly probable" default assumption).

At the locations where both samples returned results, the only difference is at P25 (which we'll come back to). If I and J are possibilities for the haplogroup of sample 2, then possibilities for sample 1 include I, J, and G. [Edit: I originally wrote that among these choices haplogroup I would also be my guess, and it still is; but we shouldn't have to guess, and there are still other options not ruled out beyond I, J, and G.]. Note that if we ignore P25 (as the authors appear to have chosen to do), the Y haplotypes are identical at the available resolution and provide no basis for asserting the individuals are unrelated.

I'm not sure what to make of the fact that sample 1 shows CA and sample 2 shows C at P25. P25 exists in multiple copies in a palindromic region and is not the most reliable marker. But if in sample 1 any copy of P25 is A, it would suggest sample 1 is R1b.

Against this, the authors apparently take their results to indicate that sample 1 is ancestral for M207 (which would rule out R) and M45 (which would rule out P). [Update: removed speculation about errors due to strand issues. In this case, it should be safe to rule out R as a possibility for both samples, and to rule out P for skeleton 1 (though I'd still like to see comments from the authors about the "CA" at P25 for skeleton 1). The more fundamental point remains: more data will be needed to confidently assign haplogroups to these samples.]

"New" R1a1 SNPs

New Y-chromosome binary markers improve phylogenetic resolution within haplogroup R1a1:

Despite the limited data available for Z280 and Z93, some general inferences can be drawn from the geographic distributions of these two haplogroups. The R1a1- Z280 subclade is a strong candidate for covering the R1a1a* (xM458) in Eastern Europe, which was found in high frequency by Underhill et al. (2010).The tested set of 53 Malaysian Indian samples presented 100% frequency for the R1a1-Z93 subclade, without co-existence Z280 or M458 sub-haplogroups. Inner and Central Asia seem to be the overlap zones for the R1a1-Z280 and R1a1-Z93 chromosomes as both forms were observed at low frequencies. This is again consistent with the observations described for R1a1a* spread in Central Asia and in the Altai region by Underhill et al. (2010). This pattern suggests that the origin of R1a1-M198 arguably occurred somewhere between South Asia and Eastern Europe. Potential candidates could be the Eurasian Steppes (Ukraine – Southern Russia – Kazakhstan – Caucasus) or the Middle East. European populations showed higher M458 and Z280, whereas Asian populations presented higher Z93 frequencies, indicating that the new markers can be effectively used to distinguish between the European and Asian branches of the haplogroup R1a1-M198. [. . .]

The coalescent time calculated by us for R1a1-M458 carriers is consistent with the age calculated by Underhill et al. (2010) in Europe yielding 7.3 KYA versus 7.9 KYA (thousands of years ago). Underhill et al. (2010) also noted the potential association of R1a1-M458 with the Linear Pottery Neolithic culture in the territory of present-day Hungary—this observation is supported by our data. The TMRCA calculated for R1a1-Z280 diversification (10.3 KYA) is approximately in agreement with the estimation of Underhill et al. (2010) for R1a1a*(xM458) chromosomes in Eastern Europe ( 11 KYA). However, the coalescent age of 10.3 KYA for R1a1- Z93 chromosomes in this study is lower than that of populations of the Indus Valley (14 KYA) for the STR associated diversity of R1a1a*(xM458) chromosomes calculated by Underhill et al. (2010).

Of course, these markers and other markers defining additional layers of structure under M417 have been known for over a year. Budgetary constraints and the magic of peer review combine to render this paper relatively uninformative. One of the authors explains:
I have to agree with all, but those who never tried to push an article through a serious academic journal has no idea how difficult this is. The first version was submitted like 1 year ago, and also contained pedigree rates plus 500+ FTDNA samples from different ethnic groups. But unfortunately the reviewers were so narrow-minded that we had finally to drop all FTDNA samples plus the pedigree calcs.

Personally I also do not consider Zhiv. rate valid, but I had to accept this compromise to get the paper accepted. Anyway, as Lukasz pointed out, the main goal was to introduce Z93 and Z280 into the "academic circles" so in the future we may have a comprehensive paper from a more wealthy lab. The Budapest forensics are not full of money so we had no chance to have more than 12 markers tested and "low-chance SNPs" like Z284 in Hungary. Actually we submitted the first draft before Z283 was established securely on the FTDNA tree so we could not include it later...

My comments from last year on the dna-forums postings of an Underhill(lab that brought us Zhivotovsky "evolutionary" mutation rates)-affiliated academic stand:
Another poster points out: "Dividing by 3 [to bring the estimate more in line with real mutation rates] gives an age of 3300 years, almost exactly the estimate from Nordtvedt's spreadsheet." Someone else recently estimated the TMRCA for L342.2+ at around 3,600 years. So: if current patterns hold, the bulk of South Asian R1a unambiguously falls within European R1a variation. While I fully expect, when we eventually see results for these markers in large academic samples published, the papers will feature evolutionary mutation rates and less than parsimonious attempts to fit the distribution of M417 sublineages to archaeology, it's pretty clear to me Z93 and L342.2 originated on the Steppe within the past 4000 years or so and spread with Indo-Iranian.
Again: the most straightforward interpretation of the evidence is that Z93 is a relatively young branch of an evidently European lineage. Accurate, unbiased dates using SNPs instead of STRs should be here soon enough, definitively settling this and other issues.

Haplogroups as evolutionary markers of cognitive ability

A reader emails a link (pdf) to a recent paper from Rindermann:
Studies investigating evolutionary theories on the origins of national differences in intelligence have been criticized on the basis that both national cognitive ability measures and supposedly evolutionarily informative proxies (such as latitude and climate) are confounded with general developmental status. In this study 14 Y chromosomal haplogroups (N = 47 countries) are employed as evolutionary markers. These are (most probably) not intelligence coding genes, but proxies of evolutionary development with potential relevance to cognitive ability. Correlations and regression analyses with a general developmental indicator (HDI) revealed that seven haplogroups were empirically important predictors of national cognitive ability (I, R1a, R1b, N, J1, E, T[+L]). Based on their evolutionary meaning and correlation with cognitive ability these haplogroups were grouped into two sets. Combined, they accounted in a regression and path analyses for 32–51% of the variance in national intelligence relative to the developmental indicator (35–58%). This pattern was replicated internationally with further controls (e.g. latitude, spatial autocorrelation etc.) and at the regional level in two independent samples (within Italy and Spain). These findings, using a conservative estimate of evolutionary influences, provide support for a mixed influence on national cognitive ability stemming from both current environmental and past environmental (evolutionary) factors.
The association with cognitive ability is positive for haplogroups I, R1a, R1b, and N and negative for J1, E, and T[+L], a pattern that also holds within Spain and Italy.
I1 arose in southern Scandinavia between 4000 and 6000 years ago (Rootsi et al., 2004). R1a and R1b arose in southwestern Asia (Caucasus, Pontic–Caspian steppe, Kurgan culture) around 22,000 ybp or somewhat later at 18,500 ybp. N and its relevant European subclades arose in Siberia and central Asia 12–27,000 ybp (Rootsi et al., 2007). This suggests that these environments may have been evolutionarily significant for cognitive ability: The presence of environmental harshness (i.e. extreme winter cold) suggests that factors relevant to the cold winters theory could have contributed to an increase in intelligence among the ancestors of those possessing these haplogroups. It is also likely that factors such as the development of agriculture, tools and dairy farming (milk from horses and cattle around 6000 ybp) were themselves an evolutionary catalyst for increasing cognitive ability (Cochran & Harpending, 2009; Hawks, Wang, Cochran, Harpending, & Moyzis, 2007; Wade, 2006), possibly enhancing neurological maturation via the provision of better nutrition during pregnancy, in youth and adulthood. The Neolithic transition to agriculture in cold climates would have been particularly evolutionarily demanding in terms of the need for heightened cognitive resources (e.g. farsightedness and planning).

[. . .]

Finally the steppe presents an unprotected environment, people living in such an environment are different to the people living in mountains, near to large oceans, in dense forests or in oases surrounded by large deserts, as they are permanently in danger of being attacked by neighboring peoples. This challenge could have selected for enhanced military preparedness a component of which may have been higher cognitive ability.

Analysis of surname origins identifies genetic admixture events undetectable from genealogical records

In the name of the migrant father—Analysis of surname origins identifies genetic admixture events undetectable from genealogical records

M H D Larmuseau et al.

Patrilineal heritable surnames are widely used to select autochthonous participants for studies on small-scale population genetic patterns owing to the unique link between the surname and a genetic marker, the Y-chromosome (Y-chr). Today, the question arises as to whether the surname origin will be informative on top of in-depth genealogical pedigrees. Admixture events that happened in the period after giving heritable surnames but before the start of genealogical records may be informative about the additional value of the surname origin. In this context, an interesting historical event is the demic migration from French-speaking regions in Northern France to the depopulated and Dutch-speaking region Flanders at the end of the sixteenth century. Y-chr subhaplogroups of individuals with a French/Roman surname that could be associated with this migration event were compared with those of a group with autochthonous Flemish surnames. Although these groups could not be differentiated based on in-depth genealogical data, they were significantly genetically different from each other. Moreover, the observed genetic divergence was related to the differences in the distributions of main Y-subhaplogroups between contemporary populations from Northern France and Flanders. Therefore, these results indicate that the surname origin can be an important feature on top of in-depth genealogical results to select autochthonous participants for a regional population genetic study based on Y-chromosomes.

Keywords: admixture; genetic genealogy; historical gene flow; human population structure; Y-chromosome

http://www.nature.com/hdy/journal/vaop/ncurrent/abs/hdy201217a.html

Ötzi's Y-DNA haplogroup: G2a4

A few days ago a commenter at Dienekes' posted that this information had been revealed by "Dr. Eduard Egarter-Vigl, Head of Conservation and Assistant to research projects of the Archaeological Museum in Bozen [. . .] in a documentary [Ötzi, ein Archäologie-Krimi] broadcast by 3sat on 10th august 2011." Now someone has uploaded the relevant clip:
Subtitles: "Since six months, the full decoding of the genome of the Iceman is done. [. . .] Certain genes that are relevant to the origin, Y-chromosome, for example, can be examined well. [. . .] And the haplogroup to which the Iceman belonged is the haplogroup G2a4. [. . .] And this group is known, that it is now very rare in Europe. Interestingly, it is still in Sardinia. Sardinia is as an island a so-called micro-isolate where the poulation has hardly changed and so has developed genetically fairly constant. But there is this haplogroup in Eurasian regions, ie those from which we know that Europe was actually populated."

Sample size equals one, but the presence of G2a and absence of R1b is consistent with previous ancient DNA findings for Neolithic western and central Europe.

Sex Chromosome Evolution and Medicine

A talk from earlier this year by David Page. Slides available here (pdf).
Contra the view promoted by Bryan Sykes, the Y chromosome is not dying.

Another R1b paper

The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269 (full text freely accessible):
Recently, the debate on the origins of the major European Y chromosome haplogroup R1b1b2-M269 has reignited, and opinion has moved away from Palaeolithic origins to the notion of a younger Neolithic spread of these chromosomes from the Near East. Here, we address this debate by investigating frequency patterns and diversity in the largest collection of R1b1b2-M269 chromosomes yet assembled. Our analysis reveals no geographical trends in diversity, in contradiction to expectation under the Neolithic hypothesis, and suggests an alternative explanation for the apparent cline in diversity recently described. We further investigate the young, STR-based time to the most recent common ancestor estimates proposed so far for R-M269-related lineages and find evidence for an appreciable effect of microsatellite choice on age estimates. As a consequence, the existing data and tools are insufficient to make credible estimates for the age of this haplogroup, and conclusions about the timing of its origin and dispersal should be viewed with a large degree of caution.
I find it hard to get too excited about this paper. As discussed previously, amateurs looking at more finely-resolved subclades using larger numbers of STRs do find trends in diversity that seem to point to an E. European origin for W. European R1b. I expect we'll have to wait a couple years, for overwhelming evidence to accumulate in the form of ancient DNA results and SNP-based dating, before seeing the correct route and timing of the entry of R1b into Europe widely agreed upon by academics. BBC article:
The extent to which modern Europeans are descended from these early farmers versus the indigenous hunter-gatherers who settled the continent thousands of years previously is a matter of heated debate. [. . .]

More than 100 million European men carry a type called R-M269, so identifying when this genetic group spread out is vital to understanding the peopling of Europe. [. . .]

A more recent origin for R-M269 than the Neolithic is also possible. But researchers point out that after the advent of agriculture, populations in Europe exploded, meaning that it would have been more difficult for incoming migrants to displace local people.

From the paper:
If the R-M269 lineage is more recent in origin than the Neolithic expansion, then its current distribution would have to be the result of major population movements occurring since that origin. For this haplogroup to be so ubiquitous, the population carrying R-S127 would have displaced most of the populations present in western Europe after the Neolithic agricultural transition.
Although the debate is commonly framed as Paleolithic vs. Neolithic, many lines of evidence suggest the correct answer is the third option: major post-Neolithic population movement.

Y haplogroup R1b and light hair in Italy

Via Italian Wikipedia.
 

Update addressing some questions/comments:

(1) The map specifically shows the frequency of blond hair; so yes the frequency of light hair in general will be higher.

(2) The map is adapted from Biasutti's Razze e popoli della Terra. The data was originally collected by Ridolfo Livi in 1859-1863.

(3) The Biasutti/Livi map shows a higher frequency of blond hair in Corsica than in Sardinia. In keeping with the apparent pattern elsewhere in Italy, the frequency of R1b appears to be markedly higher in Corsicans than in Sardinians (in this paper, "HG 1" in combination with "HG 22" roughly corresponds to R1b).

(4) "Does R1b necessarily correlate with light hair?" In Italy it pretty clearly does. If you mean am I suggesting a strict correspondence between light hair and haplogroup R1b, obviously I am not. Looking at Europe as a whole, I doubt much of a correlation exists. But the evidence is consistent with the bearers of R1b (or more specifically subclades of R-L11) being lighter than the previous inhabitants of Italy. This doesn't mean the original carriers of R-M417 and some subclades of I weren't probably also lighter-haired, or that as R1b spread throughout Europe and mixing occurred, R1b always remained associated with light hair. It does tend to add yet more weight against attempts to link R1b in Europe to migration of Neolithic farmers from Anatolia, but dispensing with that question for good awaits large, high-resolution studies of ancient and modern DNA.

"haplogroup R1b is found in some of it's highest concentrations among European peoples in Spain and Portugal -- two countries hardly known for blondes."

Within Iberia, though, it's certainly possible the pattern will hold. Among Iberians, Basques have some of the highest frequencies of both R1b and blondism. According to Coon: 'The French Basques are by no means all brunet; Collignon finds 22 per cent of blue eyes, 44 per cent of "medium," and 34 per cent of dark. Black hair is found in 7 per cent of the group, brown in 77 per cent, and light brown to blond in 16 per cent. Among the Spanish Basques the incidence of blondism is somewhat lower, but the Basques are still light when compared to most other inhabitants of Spain.'