Thesis of Oleg Balonovsky

is available here as pdf. Lots of interesting information, and a few striking maps. Hopefully, the fact that it's all in Russian won't be much of a problem in this day and age.
I will highlight a few pieces of information. First, a distribution of Y-chromosome haplogroups in Russian groups:

Notice:

• N1c-Tat is a general feature of the Russians, but N1b-P43 is only really found at any significant frequency in the northern groups.
• A strong contrast of E-M78 between central (present) and northern (absent) groups, consistent with a late introduction of this haplogroup in easternmost Europe.
• South-Central-North decreasing frequency of R1a; now, it's not clear how R1a came to be in Russians: some of it may be legacy of its initial entry into Europe from the east, other could be of historical import, and may have even arrived during the Slavic expansion from Central Europe. The pattern probably is the reverse of the high frequency of N1, indicating increasing importance of Finno-Ugric substratum in the north.
• Fairly interesting that of the two likely "Balkan" haplogroups E-M78 and I-P37, the former is modal in central region, the latter in southern one. The absence of both in "deep Asia" suggests a late introduction, as mentioned before, but when?

Also of interest a haplotype analysis within R1a1a-M198:

My most immediate observation is the set of mainly Indian highly divergent haplotypes on the left. There has been (well-deserved) excitement about recent Y-SNP progress within this haplogroup, but we should not neglect the occurrence of outliers/relics in our reconstruction of a haplogroup's history. I'd love to see those few Indian haplotypes SNP-tested using the currently available SNPs, or even used to develop new SNPs for this important Eurasian haplogroup.

Y chromosomes of Bulgarians (Karachanak et al. 2013)

Bulgaria had been something of a blank area in studies of uniparental markers, so it's nice to finally see a comprehensive Y-chromosome study of the country.
The dates in the paper are based on the "evolutionary mutation rate". I suspect that ancient DNA will be the final arbiter in this issue, because, for example, a Mesolithic TMRCA of E-V13 in Bulgaria implies that we'll find a lot of it in Neolithic contexts, whereas a Bronze Age one implies that we'll find a little if any of it, and a discontinuity across time.
Of interest is the occurrence of some E*(xM35, M2) in this sample in Burgas, Varna, and Plovdiv. It would be interesting to trace the ancestry of the bearers of these Y-chromosomes. I know that there still exists a minority-within-a-minority of Black Muslims in Greek Thrace, and it's not inconceivable that these Y-chromosomes may represent the legacy of a similar population; in any case, their haplotypes can be found in Table S5 for anyone wanting to investigate.
SNP Diversity within R seems substantial, and as always, it is difficult to say much, since this may be a consequence of either (i) a plausible role of the Balkans as a staging point of the likely invasion of Europe in late prehistory, or (ii) back-migration of derived R-bearers into the Balkans, be them Slavs or Goths or "eastern" folks of various stripes during history. Once again, I suspect that ancient DNA might solve this riddle, or, alternatively, routine high-coverage sequencing of the Y chromosome that might inform us, e.g., about the TMRCA of a Bulgarian and a German R-U152 or a Bulgarian and Polish R-M458.
PLoS ONE 8(3): e56779. doi:10.1371/journal.pone.0056779
Y-Chromosome Diversity in Modern Bulgarians: New Clues about Their Ancestry
Sena Karachanak et al

To better define the structure and origin of the Bulgarian paternal gene pool, we have examined the Y-chromosome variation in 808 Bulgarian males. The analysis was performed by high-resolution genotyping of biallelic markers and by analyzing the STR variation within the most informative haplogroups. We found that the Y-chromosome gene pool in modern Bulgarians is primarily represented by Western Eurasian haplogroups with ~ 40% belonging to haplogroups E-V13 and I-M423, and 20% to R-M17. Haplogroups common in the Middle East (J and G) and in South Western Asia (R-L23*) occur at frequencies of 19% and 5%, respectively. Haplogroups C, N and Q, distinctive for Altaic and Central Asian Turkic-speaking populations, occur at the negligible frequency of only 1.5%. Principal Component analyses group Bulgarians with European populations, apart from Central Asian Turkic-speaking groups and South Western Asia populations. Within the country, the genetic variation is structured in Western, Central and Eastern Bulgaria indicating that the Balkan Mountains have been permeable to human movements. The lineage analysis provided the following interesting results: (i) R-L23* is present in Eastern Bulgaria since the post glacial period; (ii) haplogroup E-V13 has a Mesolithic age in Bulgaria from where it expanded after the arrival of farming; (iii) haplogroup J-M241 probably reflects the Neolithic westward expansion of farmers from the earliest sites along the Black Sea. On the whole, in light of the most recent historical studies, which indicate a substantial proto-Bulgarian input to the contemporary Bulgarian people, our data suggest that a common paternal ancestry between the proto-Bulgarians and the Altaic and Central Asian Turkic-speaking populations either did not exist or was negligible.
Link

Y chromosomes of pastoralists and farmers from the Sahel

Am J Phys Anthropol DOI: 10.1002/ajpa.22236
Multiple and differentiated contributions to the male gene pool of pastoral and farmer populations of the African Sahel
Jana Bučková et al.
The African Sahel is conducive to studies of divergence/admixture genetic events as a result of its population history being so closely related with past climatic changes. Today, it is a place of the co-existence of two differing food-producing subsistence systems, i.e., that of sedentary farmers and nomadic pastoralists, whose populations have likely been formed from several dispersed indigenous hunter-gatherer groups. Using new methodology, we show here that the male gene pool of the extant populations of the African Sahel harbors signatures of multiple and differentiated contributions from different genetic sources. We also show that even if the Fulani pastoralists and their neighboring farmers share high frequencies of four Y chromosome subhaplogroups of E, they have drawn on molecularly differentiated subgroups at different times. These findings, based on combinations of SNP and STR polymorphisms, add to our previous knowledge and highlight the role of differences in the demographic history and displacements of the Sahelian populations as a major factor in the segregation of the Y chromosome lineages in Africa. Interestingly, within the Fulani pastoralist population as a whole, a differentiation of the groups from Niger is characterized by their high presence of R1b-M343 and E1b1b1-M35. Moreover, the R1b-M343 is represented in our dataset exclusively in the Fulani group and our analyses infer a north-to-south African migration route during a recent past.
Link

Extremely old (237–581 kya) root of human Y-chromosome phylogeny

I had mentioned this research before, and now it has officially been published. There are three things to be excited about this new paper:
First, it forces us to consider the possibility of either (i) archaic admixture in Africa, or (ii) a much more ancient time depth of modern humans than the first fossils from Ethiopia dated to about ~200 thousand years ago.
Second, it underscores the importance of collaboration between academia and regular folk, since it was the combined contributions of academics, genetic genealogists, and the owners of the new A00 basal Y-chromosomes that made this new discovery possible.
And, third, it shows that the extraordinary can be discovered without contacting isolated tribes or seeking human bones in remote regions, but rather through careful scrutiny of large volumes of data for the proverbial needle in the haystack.
The paper developed a model of Y-chromosome mutation based on the estimate of Kong et al. Significantly, though:

If we were to use the higher mutation rate (1.0x10^-9 per base per year6) rather than a realistic range derived from whole-genome sequencing (4.39x10^-9  -   7.07x10^- 9), the estimated TMRCA for the tree incorporating A00 as the basal lineage would be 209 kya, which is only slightly older than current estimates of the TMRCA of mtDNA and the age of the oldest AMH fossil remains. We note, however, that the higher mutation rate produces an estimate for the common ancestor of all non-African Y chromosome haplogroups (C through T) of ~39 kya6 (i.e., versus ~63 kya for the mutation rate used here).

A 39kya common ancestor for Eurasian Y-chromosomes makes no sense, since we now know for sure that by that time, the differentiation of Eurasians was already well on its way and modern humans in remote parts of the Old World have been documented much earlier than that time.
A ~63kya common ancestor, on the other hand, fits nicely with my "two deserts" theory of modern human origins, according to which the ancestors of Eurasians faced an ecological crisis in Arabia when it became much drier post-70kya; that seems like a most opportune time for the major Eurasian bottleneck and the corresponding coalescence of Eurasian Y-chromosomes to a single man. And, while there is no a priori reason for Y chromosomes and mtDNA to behave similarly, the age of the "older" Eurasian ur-mother, haplogroup N at 59 thousand years, with presumably an older ancestor within mtDNA haplogroup L3 founding the Eurasian population.
Also, if modern human-Neandertal admixture had occurred  "most likely 47,000–65,000 years ago", then the expansion of modern Proto-Eurasians within a 70-60kya timeframe north Out-of-Arabia would have brought them in contact with their northern Neandertal neighbors. On the other hand, it would be incredible if modern humans experienced admixture with Neandertals but were still much later a very small population (to allow for the coalescence of their Y-chromosomes to one man ~39kya).
So, in summary, the mutation rate used by the authors seems consistent with what we know about an important calibration point of the human story.
But, who were the people in Africa responsible for the introgression of A00 chromosomes? Mendez et al. used the haplotype of the African American A00 individual and discovered his patrilineal kin among theMbo of Cameroon, who are Bantu farmers.
I have observed before that Pygmies and Bushmen represent only a tiny fraction of pre-existing African genetic diversity, the part that had not yet been absorbed into the farmers' expanding population by the time that Africa came to the attention of of modern science. We see traces of Pygmy and Bushman ancestry in some African farmers, and there were probably other groups, no longer extant as distinct ethno-cultural entities, but, nonetheless, surviving as genetic fragments in the genomes of the farmers.
Thus, while it still makes sense to study the surviving hunter-gatherers of Africa who make up perhaps a percent or less of the population of Africa, it may be equally important to study different groups of African farmers who may possess a much richer treasure trove (albeit diluted) of such "Palaeoafrican" ancestry.
Finally:

Although the stochastic nature of the evolutionary process can explain the aforementioned incongruences, the extreme age and rarity of the A00 lineage point to the possibility of a highly structured ancestral population, consistent with recent work on the autosomes.40,41,43,44 This could take the form of long-standing population structure among AMH populations45 or archaic introgression from an archaic form into the ancestors of AMHs.46 Interestingly, the Mbo live less than 800 km away from a Nigerian site known as Iwo Eleru, where human skeletal remains with both archaic and modern features were found and dated to ~13 kya.47 Further surveys in sub- Saharan Africa and in the African Diaspora might uncover more diverged basal lineages, which will help to disentangle some of the complex evolutionary processes that shape patterns of Y chromosome diversity.

AJHG 10.1016/j.ajhg.2013.02.002
An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree
Fernando L. Mendez et al.
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.
Link

Y chromosomes of Corded Ware at Wroclaw-Jagodno (SW Poland)

From the paper:

Two teeth coming from fossil human skeletons were examined in the Molecular Technology Institute of Forensic Medicine Department, Wroclaw Medical University. It was stated that both teeth came from two men on the basis of the gene of amelogenin variants study. 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*.

Table 2:

It appears that dots represent identity with the reference sequence, so for example M201 has a dot for skeleton 1 which indicates a T at position 15,027,529 (GRCh37) which is the position where this mutation has occurred. So, the attribution of skeleton 1 to haplogroup G seems reasonable, and suggests continuity between the Neolithic population of Europe (where G is over-represented) and this CW individual.
It's not clear to me how skeleton 2 is attributed to J or I or E* on the basis of these SNPs. If anyone can figure it out, post in the comments.

Journal of Archaeological Science doi:10.1016/j.jas.2013.02.002
Assessment of late Neolithic pastoralist's life conditions from the Wroclaw-Jagodno site (SW Poland) on the basis of physiological stress markers
Bohdan Gworys et al.
So-called physiological stress markers are extremely valuable in assessing life conditions of old human populations. They constitute effects of adverse environmental conditions, which leave traces on skeleton. Those traces allow for partial assessment of life conditions not only in environmental and social but also cultural aspects for prehistoric populations. The aim of this study is to estimate the influence of general environmental conditions on human organism at the final stage of the Neolithic period – in the Corded Ware culture. Two skeletons discovered in a tumulus on the outskirts of Wroclaw in the Jagodno district have been subjected to assessment. Their age at the moment of death has been determined in both cases on the basis of multi-feature analysis of changes occurring in formation of particular morphologic features of skeleton and teeth. Attention has been paid to the obliteration degree of skull sutures and the surface state of chewing tooth crowns. A comprehensive DNA analysis has been conducted determining sex of the remains. Also bacteriological analysis of the research material has been conducted. Measurements of all available metric features of the skeletons have been performed with the use of the Martin method. Inventory and basic description of the finds accompanying skeleton remains have been carried out as well. Intensity of the following physiological stress markers have been defined and evaluated: Harris lines; cribra orbitalia; cribra cranii. Skull morphology, degree of suture obliteration, surface state of chewing tooth crowns and estimation of degree of bone development of postcranial skeleton indicate that both skeletons detailed age was about 16 – 18 years. Harris lines on the femur were formed in the 2nd and the 3rd year of life and on both tibias – in the 2nd year of life. Obtained results indicate that those people were expose to stress connected with food deficit when they were very young. Poor porotic changes on the skull and isotopic data suggest that their life quality increased at later age.
Link

Algerian Y chromosomes and mtDNA

Algerian Y chromosomes and mtDNA

From the paper:

For the R-M343 subdivision, the Iberian Peninsula reflects a genuine European profile [45] except for the presence of one Sahel R-V88 type. In contrast, all R-M343 detected in W. Saharan-Mauritanian belong to sub-group R-V88, reaching a frequency of 7%, similar to those observed in other Sahel samples [40]. In the Maghreb countries, the frequency of R-V88 drops to around 1%. On the other hand, the presence in this area of representatives of the European sub-groups R-M412, R-S116, R-U152 and R-M529 points to North-South maritime contacts across the Mediterranean

It would be interesting to estimate the depth of common ancestry of the North African "European" Y chromosomes to determine the epoch during which they arrived there, i.e., whether the common ancestry stems from recent historical contacts (Roman Empire, Vandals, etc.) or from the early settlement of both Mediterranean coasts during the arrival of R-M269 into Europe.

A few observations on Y-haplogroup frequencies:

• The ubuquity of haplogroup Q at trace frequencies in most regions except North Africa (only a little in ALG) is interesting and it's high time that someone looked at the relationship between West Eurasian Q-bearers and their much more numerous East Eurasian cousins.
• I find the paucity of Y-haplogroup I in North Africa noteworthy; given its high levels in most of Western Europe, its relative absence might indicate that the people who brought "European" R-M269 into N Africa were not occasional recent migrants, but rather earlier settlers. 
• The relative absence of J2 is expected, given that neither of the two main strata of population ("Berber" and "Arab") may have possessed it initially; it has also not been found in a historical sample from the Canary Islands, whereas its J1 counterpart has.
• The paucity of haplogroup G, which is the European Neolithic lineage par excellence probably argues against the involvement of the people who colonized Europe during the Early Neolithic in similar events on the south shore of the Mediterranean.
• The further study of F chromosomes could also be further attempted, given their possible involvement in the Upper Paleolithic of Eurasia

The authors highlight that 80% of mtDNA is Eurasian vs. 90% of Y chromosomes. This might point to asymmetric gene flow from Sub-Saharan Africa. Alternatively, it might point to some mtDNA that is characterized as non-Eurasian (because it does not belong to the M, N macro-haplogroups) being in fact so. It is a persistent question whether lineages that have a wide frequency differential in two regions do so because of gene flow (from the high- to low-frequency area), or because of other processes.

PLoS ONE 8(2): e56775. doi:10.1371/journal.pone.0056775

Introducing the Algerian Mitochondrial DNA and Y-Chromosome Profiles into the North African Landscape

Asmahan Bekada et al.

North Africa is considered a distinct geographic and ethnic entity within Africa. Although modern humans originated in this Continent, studies of mitochondrial DNA (mtDNA) and Y-chromosome genealogical markers provide evidence that the North African gene pool has been shaped by the back-migration of several Eurasian lineages in Paleolithic and Neolithic times. More recent influences from sub-Saharan Africa and Mediterranean Europe are also evident. The presence of East-West and North-South haplogroup frequency gradients strongly reinforces the genetic complexity of this region. However, this genetic scenario is beset with a notable gap, which is the lack of consistent information for Algeria, the largest country in the Maghreb. To fill this gap, we analyzed a sample of 240 unrelated subjects from a northwest Algeria cosmopolitan population using mtDNA sequences and Y-chromosome biallelic polymorphisms, focusing on the fine dissection of haplogroups E and R, which are the most prevalent in North Africa and Europe respectively. The Eurasian component in Algeria reached 80% for mtDNA and 90% for Y-chromosome. However, within them, the North African genetic component for mtDNA (U6 and M1; 20%) is significantly smaller than the paternal (E-M81 and E-V65; 70%). The unexpected presence of the European-derived Y-chromosome lineages R-M412, R-S116, R-U152 and R-M529 in Algeria and the rest of the Maghreb could be the counterparts of the mtDNA H1, H3 and V subgroups, pointing to direct maritime contacts between the European and North African sides of the western Mediterranean. Female influx of sub-Saharan Africans into Algeria (20%) is also significantly greater than the male (10%). In spite of these sexual asymmetries, the Algerian uniparental profiles faithfully correlate between each other and with the geography.

Link

Whole genome Y-SNP calling

Whole genome Y-SNP calling

BMC Genomics 2013, 14:101 doi:10.1186/1471-2164-14-101

AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications

Anneleen Van Geystelen et al.

Abstract (provisional)

Background

Due to the rapid progress of next-generation sequencing (NGS) facilities, an explosion of human whole genome data will become available in the coming years. These data can be used to optimize and to increase the resolution of the phylogenetic Y chromosomal tree. Moreover, the exponential growth of known Y chromosomal lineages will require an automatic determination of the phylogenetic position of an individual based on whole genome SNP calling data and an up to date Y chromosomal tree.

Results

We present an automated approach, 'AMY-tree', which is able to determine the phylogenetic position of a Y chromosome using a whole genome SNP profile, independently from the NGS platform and SNP calling program, whereby mistakes in the SNP calling or phylogenetic Y chromosomal tree are taken into account. Moreover, AMY-tree indicates ambiguities within the present phylogenetic tree and points out new Y-SNPs which may be phylogenetically relevant. The AMY-tree software package was validated successfully on 118 whole genome SNP profiles of 109 males with different origins. Moreover, support was found for an unknown recurrent mutation, wrong reported mutation conversions and a large amount of new interesting Y-SNPs.

Conclusions

Therefore, AMY-tree is a useful tool to determine the Y lineage of a sample based on SNP calling, to identify Y-SNPs with yet unknown phylogenetic position and to optimize the Y chromosomal phylogenetic tree in the future. AMY-tree will not add lineages to the existing phylogenetic tree of the Y-chromosome but it is the first step to analyse whole genome SNP profiles in a phylogenetic framework.

Link

Y chromosome and mtDNA study of modern Middle Eastern populations (Badro et al. 2013)

Y chromosome and mtDNA study of modern Middle Eastern populations (Badro et al. 2013)

I will just briefly comment on the occurrence of L3* mtDNA in the Near East. This is a critical haplogroup because of its age of ~70ky. If all L3* in the Near East represents African migrants, then only the M and N macrogroups appeared in Eurasia, and a good case can be made for a "late" OoA event.

On the other hand, it is quite possible that some of the L3* in the Near East does not represent recent admixture, but rather native forms of L3 with deep ancestry in the region. If that is the case, then the Near East will emerge as the origin of L3, with M, N representing Out-of-Near East-into-Eurasia founders, and the various L3*(xM, N) representing Out-of-Near East-into-Africa founders.

It is difficult to say at present what will turn out to be the case. Ancient DNA has the potential of resolving this issue, because if L3*(xM, N) in Eurasia is really recent (e.g., associated with Islamic/Arab dispersals spanning Africa and Eurasia), then it ought to be missing from the earliest genetic layers.

Also of interest the geographical distribution of Y-haplogroups; nothing much new here, but still useful as a reference:

PLoS ONE 8(1): e54616. doi:10.1371/journal.pone.0054616

Y-Chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations 

Danielle A. Badro et al.

The Middle East was a funnel of human expansion out of Africa, a staging area for the Neolithic Agricultural Revolution, and the home to some of the earliest world empires. Post LGM expansions into the region and subsequent population movements created a striking genetic mosaic with distinct sex-based genetic differentiation. While prior studies have examined the mtDNA and Y-chromosome contrast in focal populations in the Middle East, none have undertaken a broad-spectrum survey including North and sub-Saharan Africa, Europe, and Middle Eastern populations. In this study 5,174 mtDNA and 4,658 Y-chromosome samples were investigated using PCA, MDS, mean-linkage clustering, AMOVA, and Fisher exact tests of FST's, RST's, and haplogroup frequencies. Geographic differentiation in affinities of Middle Eastern populations with Africa and Europe showed distinct contrasts between mtDNA and Y-chromosome data. Specifically, Lebanon's mtDNA shows a very strong association to Europe, while Yemen shows very strong affinity with Egypt and North and East Africa. Previous Y-chromosome results showed a Levantine coastal-inland contrast marked by J1 and J2, and a very strong North African component was evident throughout the Middle East. Neither of these patterns were observed in the mtDNA. While J2 has penetrated into Europe, the pattern of Y-chromosome diversity in Lebanon does not show the widespread affinities with Europe indicated by the mtDNA data. Lastly, while each population shows evidence of connections with expansions that now define the Middle East, Africa, and Europe, many of the populations in the Middle East show distinctive mtDNA and Y-haplogroup characteristics that indicate long standing settlement with relatively little impact from and movement into other populations.

Link

Indonesian mega-study (Tumonggor et al. 2013)

Indonesian mega-study (Tumonggor et al. 2013)

A new comprehensive survey of Y chromosome/mtDNA variation in Indonesia has just appeared online. From the paper:

The first stage of Indonesian prehistory represents the archipelago’s initial settlement as part of the African dispersal ~50 kya. The geography of the region was then markedly different from today. Sea levels were much lower, most modern islands had merged into larger landmasses, and the westernmost parts of Indonesia were physically contiguous with mainland Asia. This first stage is recorded by deep mtDNA lineages (M17a, M73, M47, N21, N22, R21, R22 and R23), which trace back to the main branching of macrohaplogroups M and N, and have a spotty distribution across both mainland and island southeast Asia today.

and:

The second stage reflects recurrent colonization events from mainland Asia throughout the later Paleolithic. Many haplogroups (B4a, B4b, B4c, B4c1b3, B5a, B5b, B5b1, D and E) show origin dates of 10-40 kya (Supplementary Table 6) 25, 63 and are distributed across a wide range of mainland and island southeast Asian populations. 

and:

The third stage represents Neolithic movements into and around island southeast Asia. Some of these may involve population dispersals from (and perhaps to) Taiwan, while others reflect movements between Indonesian island groups. Representative haplogroups include M7b3, E1a1a, M7c3c and Y2. Autosomal data strongly supports large demic movements of Asian populations into eastern Indonesia from around 4 kya 67.

and, finally:

The fourth stage reflects historic movements into Indonesia, largely involving trade and the associated spread of major religions from India, Arabia and China 71. Although found at relatively low frequency today, Y chromosome lineages representing these movements occur across Indonesia 20, notably in the west, such as the Hindu dominated island of Bali

It would be useful to study Indonesian haplogroups as a means of testing the hypothesis of Indian settlement in Australia, since it is difficult to see any such settlement that would not have passed through the Indonesian archipelago.

Of the lineages found in Indonesia, the deepest ancestry appears to be associated with mtDNA haplogroups P (54+/-16ky) and Q (38+/-9ky), both of which appear to have clear "Australo-Melanesian" associations. Of the B subclades that are lately of interest due to the publication of Tianyuan ancient DNA, the oldest one appears to be B4a (33+/-13ky).

One of the major puzzles in prehistory is the co-occurrence of mtDNA macro-haplogroups M and N in the eastern portion of Eurasia vs. the dominance of N in the western part thereof. The peninsulas of Arabia and India probably hold a key to this riddle, although in both cases the situation is obscured by subsequent events: in Arabia, there has probably been substantial population turnover during its "desert" phases, while in India there has been recent admixture between the aboriginal population and West Eurasian-derived inhabitants.

Journal of Human Genetics , (24 January 2013) | doi:10.1038/jhg.2012.154

The Indonesian archipelago: an ancient genetic highway linking Asia and the Pacific 

Meryanne K Tumonggor et al.

Indonesia, an island nation linking mainland Asia with the Pacific world, hosts a wide range of linguistic, ethnic and genetic diversity. Despite the complexity of this cultural environment, genetic studies in Indonesia remain surprisingly sparse. Here, we report mitochondrial DNA (mtDNA) and associated Y-chromosome diversity for the largest cohort of Indonesians examined to date—2740 individuals from 70 communities spanning 12 islands across the breadth of the Indonesian archipelago. We reconstruct 50 000 years of population movements, from mitochondrial lineages reflecting the very earliest settlers in island southeast Asia, to Neolithic population dispersals. Historic contacts from Chinese, Indians, Arabs and Europeans comprise a noticeable fraction of Y-chromosome variation, but are not reflected in the maternally inherited mtDNA. While this historic immigration favored men, patterns of genetic diversity show that women moved more widely in earlier times. However, measures of population differentiation signal that Indonesian communities are trending away from the matri- or ambilocality of early Austronesian societies toward the more common practice of patrilocal residence today. Such sex-specific dispersal patterns remain even after correcting for the different mutation rates of mtDNA and the Y chromosome. This detailed palimpsest of Indonesian genetic diversity is a direct outcome of the region’s complex history of immigration, transitory migrants and populations that have endured in situ since the region’s first settlement.

Link

Beware of who you kiss

Beware of who you kiss

Forensic Sci Int Genet. 2013 Jan;7(1):124-8. doi: 10.1016/j.fsigen.2012.07.007. Epub 2012 Aug 20.

Prevalence and persistence of male DNA identified in mixed saliva samples after intense kissing.

Kamodyová N, Durdiaková J, Celec P, Sedláčková T, Repiská G, Sviežená B, Minárik G.

Abstract

Identification of foreign biological material by genetic profiling is widely used in forensic DNA testing in different cases of sexual violence, sexual abuse or sexual harassment. In all these kinds of sexual assaults, the perpetrator could constrain the victim to kissing. The value of the victim's saliva taken after such an assault has not been investigated in the past with currently widely used molecular methods of extremely high sensitivity (e.g. qPCR) and specificity (e.g. multiplex Y-STR PCR). In our study, 12 voluntary pairs were tested at various intervals after intense kissing and saliva samples were taken from the women to assess the presence of male DNA. Sensitivity-focused assays based on the SRY (single-copy gene) and DYS (multi-copy gene) sequence motifs confirmed the presence of male DNA in female saliva after 10 and even 60min after kissing, respectively. For specificity, standard multiplex Y-STR PCR profiling was performed and male DNA was found in female saliva samples, as the entire Y-STR profile, even after 30min in one sample. Our study confirms that foreign DNA tends to persist for a restricted period of time in the victim's mouth, can be isolated from saliva after prompt collection and can be used as a valuable source of evidence.

Link

Moldavian Y-chromosomes

Moldavian Y-chromosomes

The most salient feature is probably the absence of E-V13 (which is modal in Balkan populations) in Ukrainians. The position of Moldavians in the MDS plot of haplogroup frequencies is as expected, with a clear differentiation of "southern" populations from Italy, Greece/Albania, and Anatolia, and "northern" ones from the west Balkans (ex-Yugoslavs) and eastern Europe: Moldavians occupy an intermediate position along this second group of populations.

PLoS ONE 8(1): e53731. doi:10.1371/journal.pone.0053731

Paleo-Balkan and Slavic Contributions to the Genetic Pool of Moldavians: Insights from the Y Chromosome

Alexander Varzari et al.

Moldova has a rich historical and cultural heritage, which may be reflected in the current genetic makeup of its population. To date, no comprehensive studies exist about the population genetic structure of modern Moldavians. To bridge this gap with respect to paternal lineages, we analyzed 37 binary and 17 multiallelic (STRs) polymorphisms on the non-recombining portion of the Y chromosome in 125 Moldavian males. In addition, 53 Ukrainians from eastern Moldova and 54 Romanians from the neighboring eastern Romania were typed using the same set of markers. In Moldavians, 19 Y chromosome haplogroups were identified, the most common being I-M423 (20.8%), R-M17* (17.6%), R-M458 (12.8%), E-v13 (8.8%), R-M269* and R-M412* (both 7.2%). In Romanians, 14 haplogroups were found including I-M423 (40.7%), R-M17* (16.7%), R-M405 (7.4%), E-v13 and R-M412* (both 5.6%). In Ukrainians, 13 haplogroups were identified including R-M17 (34.0%), I-M423 (20.8%), R-M269* (9.4%), N-M178, R-M458 and R-M73 (each 5.7%). Our results show that a significant majority of the Moldavian paternal gene pool belongs to eastern/central European and Balkan/eastern Mediterranean Y lineages. Phylogenetic and AMOVA analyses based on Y-STR loci also revealed that Moldavians are close to both eastern/central European and Balkan-Carpathian populations. The data correlate well with historical accounts and geographical location of the region and thus allow to hypothesize that extant Moldavian paternal genetic lineages arose from extensive recent admixture between genetically autochthonous populations of the Balkan-Carpathian zone and neighboring Slavic groups.

Link

Ancient Y chromosomes from China

Ancient Y chromosomes from China

This appears to be an abstract of a 2012 dissertation from Jilin University (using Google Translate):

Northern China is the hub of East Asia connecting North Asia, Central Asia and the European civilization, it is a vast variety of natural ecological environment, suitable for farming, nomadic, hunting and fishing and other economic lifestyle coexist, since ancient times is fertile ground for human life, many ancient ethnic groups in here thrive and leave a valuable intangible cultural heritage. Ancient ancestors of the region but also a number of occasions by force to seize power, large-scale war had thrown the history of the North China southward to accelerate China Southern, northern populations gene fusion. Part of the ancient nation even Expeditionary Europe, its descendants across the country to play a role in promoting the exchange of population of the entire Eurasian continent. These events northern populations occupy an important position in the history of human migration. Therefore, this region of the ancient population genetics research for the original genetic retrospective of the Chinese nation, and speculated Eurasia population migration, fusion mode has great significance. This study of 13 archaeological sites in northern China - Xinjiang river cemetery, Hami Tianshan Road cemetery, Barkol the black Gouliang cemetery, the Ning Xia Pengyang cemetery, Xining Tao Wangjiazai cemetery, of Shanxi Jiangxian cross Kitamura cemetery, Hebei Yuxian three hurdles cemetery, Temple Zaigou site Niuheliang site, Sahara Trench cemetery, DADIANZI site, large piedmont ruins, wells ditch sub cemetery - human remains unearthed parent molecular genetics research, summed up the various ancient population Y chromosome haplotype groups paternal genetic diversity of the distribution rules and characteristics, combined with related ancient the modern crowd molecular genetics data reveal ancient population of the different regions of northern China, to explore the genetic makeup of the different periods of the ancient population dynamic process, in order to clarify the north fusion between ethnic origin, flow and crowd differentiation provides evidence of molecular genetics. The results are as follows: First, five archaeological site northeast western Liaoning Province 78 males unearthed ancient human remains of 44 cases of samples Y-DNA results are attributed to the C, N and O three single haplotype groups. Haplogroup N in western Liaoning Province the ancient population for a long, extensive presence, and account for a large proportion, dated to 5500-3000 years ago, is the most important ingredient in the genetic composition of the area of the ancient population paternal; based on single frequency of the haplotype groups O ancient population of western Liaoning Province and their cultural attributes and lifestyle of the crowd, and the combination of the relevant ancient population Y-SNP findings, we speculate that the haplogroup O northward by the Central Plains, emigrated to the the ancient agricultural population of western Liaoning Province carried haplogroup. The emergence of haplogroup C may be related to the nomads of the south of the North Asia. These data suggest that paternal genetic structure of the indigenous populations of the western Liaoning Province while maintaining continuity, integration into the ancient Central Plains and North Asian populations paternal genetic component. , From 64 cases of the Northwest men of ancient human remains successful Y-DNA results of 46 cases of samples, attributable to four single haplotype N, O, Q and R groups. Paternal genetic make-up of the ancient population of the Northwest Territories has obvious geographical specificity, for example, the westernmost Creek crowd as the main western lineage of R1a1 haplogroup; the adjoining Inner Mongolia Pengyang crowd all individuals can be attributed to a single type groups Q, North Asian populations in the high-frequency haplogroup; while the the approaching the Central Plains Dow Wangjiazai crowd of paternal Y-DNA to the East Asian haplogroup O, similar to the modern Han population. Comprehensive analysis of the ancient population of the Northwest Territories paternal genetic structure, in the paternal genetic form of the ancient population of the Northwest Territories there are significantly different, the reason for these different genetic data obtained speculated, is mainly due to the different groups of people have different paternal origin, everyone group accepted by the ancestors of the crowd gene contribution is different, and the from Sire terms, fewer exchanges between people own unique genetic component, so that it is preserved. Third, the success obtained from ancient human remains of the 48 cases in North China's male Y-DNA results of 29 cases of samples, attributable to the N, O and Q three single haplotype groups. The largest proportion of haplogroup O, diversity highest in two archaeological sites of the ancient Central Plains region of North China have been found; the haplogroup Q high frequency existence of Shanxi was the ancient nomads " Di "active area; haplogroup N appears that there may be the exchange of genes between populations in the Central Plains and western Liaoning Province. Comprehensive analysis of the Y-DNA of the various regions of the ancient population study results, northwest and northeast regions of the ancient population of most East Asian specific single haplotype groups can be found in the ancient population of the Central Plains, Ancient crowd paternal genetic diversity high. Central Plains region, since the Shang and Zhou dynasties is the Huaxia their descendants Han settlements, so the characteristics of the ancient population genetic structure in the Central Plains region of North China from one side of corroboration ancestors of the Han - Huaxia the Source is diverse rather than a single the integration of the different sources of the ancient population genetic component in the process of its formation. Based on the above analysis of the results, the paternal genetic structure of the ancient population in northern China in different regions have different distribution patterns: Northeast western Liaoning Province, while maintaining continuity in the of indigenous populations paternal genetic, you can see that the foreign genetic component exists in the population of the region, the foreign genetic component is likely to come from the Central Plains and North Asia and other regions. About 3000-2500 years ago, and the increasing trend of foreign genetic component. Northwest Territories of paternal inheritance there are significant differences between different geographical area of ancient population. 5 northwest of the ancient population of this study, Y chromosome genetic data, the reasons for these differences may be due to different populations have different sources of paternal and less genetic exchange between different populations, so that the the inherent genetic structure is maintained; in North China, the the patrilineal genetic structure is located in the ancient Central Plains region of the ancient population with modern Han closest, the modern Han paternal genes contributors.

The full text appears to be behind a paywall. Any native speakers who can add some information and/or correct possible mistranslations, feel free to do so in the comments.

Y-haplogroup Q and Native American origins (Regueiro et al. 2013)

Y-haplogroup Q and Native American origins (Regueiro et al. 2013)

From the paper:

Table 2 provides coalescence time estimations based on 15 Y-STR loci for haplogroup Q-M242 and subhaplogroups Q1a3-M346, Q1a3a-L54 and Q1a3a1-M3. Due to the limitations and assumptions associated with the current calibrations of Y-STR mutation rates (Zhivotovsky et al., 2004; Goedbloed et al., 2009; Ravid-Amir and Rosset, 2010; Burgarella and Navascue/s, 2011), the dates generated in this study should only be taken as relative estimates. However, these relative values may be useful for comparisons among populations. Using the pedigree mutation rate (average mutation rate of 0.0025 per locus per generation; Goedbloed et al., 2009), we obtained coalescence estimates that were approximately three times younger than those calculated with the evolutionary rate (average mutation rate of 0.00069 per locus per generation; Zhivotovsky et al., 2004). In general, the genealogical estimates are more compatible with archeological data than the evolutionary rates 

According to Table 2, the oldest TMRCA for M242 chromosomes is ~11ky using the pedigree rate and ~29ky using the evolutionary rate. In a previous post, I argued that in order to account for the fact that modern-day haplogroups have millions of modern representatives, a fairly high growth rate must be assumed for them, with one estimate of the effective rate being 0.84μ, where μ is the genealogical rate. Ergo, the ~11ky time estimate must be updated to something like ~13ky, which corresponds reasonably well -within the confidence limits- to the first colonization of the Americas.

The paper's conclusion:

Overall, our data are best explained by invoking a single major pre-Holocene migration that proceeded eastward in a trans-continental trek across Beringia and then southward to transverse the length of Americas-a scenario that fits nicely with the South Altaian origin of Native Americans as proposed by Dulik et al. (2012). The subsequent winnowing of the Native American gene pool via repeated founder effects and bottleneck events could have produced the Y chromosome distribution illustrated on the pie map (Fig. 2). The Q haplogroup frequency pattern of the Native Americans features: 1) a dramatic reduction of the ancestral L54 and MEH2 lineages of Central Asia and/or northeast Siberia and 2) a concomitant increase in the derived M3 state, which exerts total domination of the Q landscape in nearly all of South American reference populations examined. We also see evidence of a dramatic Mesoamerican postmigration population growth in the ubiquitous and diverse Y-STR profiles of the Mayan and other Mesoamerican populations in the PCA (Fig. 4), and the M242 and M3 networks (Fig. 5A,D). In the case of the Mayans, this demographic population growth was most likely fueled by the agricultural- and trade-based subsistence adopted during the pre-Classic age of their empire. Our results indicate that the oldest dates for Q-M242 are found in Northeast Siberia followed by populations from Mesoamerica, which is most likely a consequence of demographic expansion as discussed above. The diversity levels observed in the Altaian and Tuvinian regions of Central Asia, the lowest of all populations examined may be the consequence of bottleneck events fostered by the spatial isolation and low effective population size characteristic of a nomadic lifestyle. 

It seems likely that the migration of Q-M242 descendants corresponds mainly to the "First Americans" sensu Reich et al. (2012) which makes up the bulk of Amerindian Y-chromosomes. Interestingly:

The recently sequenced genome of a Paleo-Eskimo _ 4,000 years old, belonging to the Saqqaq culture, provides evidence for a more recent migration from Siberia into the New World some 5.5 kya, independent of the pre-Holocene penetration that gave rise to the modern Native Americans and Inuit (Rasmussen et al., 2010). In addition, the Paleo-Eskimo individual is a member of the haplogroup Q1a*-MEH2 suggesting that this lineage likely traces a population migration originating in Northeast Siberia across the Bering Strait (Rasmussen et al., 2010). 

and:

In the MDS plot, we observe a segregation between Eskimo populations from northeast Siberia and the Native American populations, differentiation likely due to the northeast Siberian presence of the MEH2 mutation which defines the Q1a* haplogroup.  

So, it would appear that the additional "Eskimo" wave may be discernible within Q itself; the third "Na-Dene" wave cannot be distinguished on the basis of Q alone, and probably reflects the later entry of haplogroup C.


Am J Phys Anthropol DOI: 10.1002/ajpa.22207

On the Origins, Rapid Expansion and Genetic Diversity of Native Americans From Hunting-Gatherers to Agriculturalists

Maria Regueiro et al.

Given the importance of Y-chromosome haplogroup Q to better understand the source populations of contemporary Native Americans, we studied 8 biallelic and 17 microsatellite polymorphisms on the background of 128 Q Y-chromosomes from geographically targeted populations. The populations examined in this study include three from the Tuva Republic in Central Asia (Bai-Tai, Kungurtug, and Toora-Hem, n = 146), two from the northeastern tip of Siberia (New Chaplino and Chukchi, n = 32), and two from Mesoamerica (Mayans from Yucatan, Mexico n = 72, and Mayans from the Guatemalan Highlands, n = 43). We also see evidence of a dramatic Mesoamerican post-migration population growth in the ubiquitous and diverse Y-STR profiles of the Mayan and other Mesoamerican populations. In the case of the Mayans, this demographic growth was most likely fueled by the agricultural- and trade-based subsistence adopted during the Pre-Classic, Classic and Post-Classic periods of their empire. The limited diversity levels observed in the Altaian and Tuvinian regions of Central Asia, the lowest of all populations examined, may be the consequence of bottleneck events fostered by the spatial isolation and low effective population size characteristic of a nomadic lifestyle. Furthermore, our data illustrate how a sociocultural characteristic such as mode of subsistence may be of impact on the genetic structure of populations. We analyzed our genetic data using Multidimensional Scaling Analysis of populations, Principal Component Analysis of individuals, Median-joining networks of M242, M346, L54, and M3 individuals, age estimations based on microsatellite variation utilizing genealogical and evolutionary mutation rates/generation times and estimation of Y- STR average gene diversity indices.

Link

Y-chromosome and mtDNA of Henri IV

Y-chromosome and mtDNA of Henri IV

A recent paper had determined the Y-chromosome haplotype of Louis XVI of France from a handkerchief preserving his blood after his execution. A new study looks at the mummified head of Henri IV, the first Bourbon King of France. Even though only a limited number of Y-STRs were successfully typed, they match those of Louis XVI, who belonged to the not-so-frequent-anymore haplogroup G2a. So, while we cannot be entirely sure that the two Y-chromosomes were related in a genealogical time frame, the evidence is consistent with their known genealogical relationship and with the attribution of the two samples (mummified head/blood) to the respective kings.

Also of interest, Henri IV's mtDNA haplotype:

The majority of the clones generated show an U5b* mtDNA haplotype defined by three nucleotide changes at positions 16239T 16270T 16311C (see Supplementary material). The three HVR1 diagnostic positions were confirmed in two different amplifications of the L16185-H16378 HVR1 fragment, proving that the results are reproducible. This mtDNA haplotype is present so far in one single individual from France (originally published in [10]) in an in-house database of 22,807 published European sequences, and it is absent in all people involved in the laboratory analysis.

 If I followed the trail of ancestry correctly, this matrilineage leads all the way to a Tochter von Egisheim in the 11th century.

Forensic Science International Available online 30 December 2012

Genetic comparison of the head of Henri IV and the presumptive blood from Louis XVI (both Kings of France)

Philippe Charlier et al.

A mummified head was identified in 2010 as belonging to Henri IV, King of France. A putative blood sample from the King Louis XVI preserved into a pyrographically decorated gourd was analyzed in 2011. Both kings are in a direct male-line descent, separated by seven generations. We have retrieved the hypervariable region 1 of the mitochondrial DNA as well as a partial Y-chromosome profile from Henri IV. Five STR loci match the alleles found in Louis XVI, while another locus shows an allele that is just one mutation step apart. Taking into consideration that the partial Y-chromosome profile is extremely rare in modern human databases, we concluded that both males could be paternally related. The likelihood ratio of the two samples belonging to males separated by seven generations (as opposed to unrelated males) was estimated as 246.3, with a 95% confidence interval between 44.2 and 9729. Historically speaking, this forensic DNA data would confirm the identity of the previous Louis XVI sample, and give another positive argument for the authenticity of the head of Henri IV.

Link

Higher female effective population size in recent human evolution

Higher female effective population size in recent human evolution

The common maternal ancestor of all living humans appears to be much older than the common paternal ancestor of all living men. It has been suggested that selection on the Y-chromosome is responsible for this discrepancy, that is, that a recent male line has wiped out older lines because of some unspecified advantage. This new study indicates that this is not the case, and rather that the female effective population size was higher than the male one, which is likely due to the practice of successful males to have many children with different wives (polygyny).

Mol Biol Evol. 2004 Aug 18 [Epub ahead of print]

Genetic Evidence for Unequal Effective Population Sizes of Human Females and Males.

Wilder JA et al.

The time to the most recent common ancestor (TMRCA) of the human mitochondria (mtDNA) is estimated to be older than that of the non-recombining portion of the Y chromosome (NRY). Surveys of variation in globally distributed humans typically result in mtDNA TMRCA values just under 200 thousand years (kya) while those for the NRY range between 46 and 110 kya. A favored hypothesis for this finding is that natural selection has acted on the NRY leading to a recent selective sweep. An alternate hypothesis is that sexbiased demographic processes are responsible. Here we re-examine the disparity between NRY and mtDNA TMRCAs using data collected from individual human populations--a sampling strategy that minimizes the confounding influence of population subdivision in global datasets. We survey variation at 782 bp of the mitochondrial cytochrome c oxidase subunit 3 gene as well as at 26.5 kb of non-coding DNA from the NRY in a sample of 25 Khoisan, 24 Mongolians, and 24 Papua New Guineans. Data from both loci in all populations are best described by a model of constant population size, with the exception of Mongolian mtDNA which appears to be experiencing rapid population growth. Taking these demographic models into account, we estimate the TMRCAs for each locus in each population. A pattern that is remarkably consistent across all three populations is an approximately two-fold deeper coalescence for mtDNA than for the NRY. The oldest TMRCAs are observed for the Khoisan (73.6 kya for the NRY and 176.5 kya for mtDNA) while those in the non-African populations are consistently lower (averaging 47.7 kya for the NRY and 92.8 kya for mtDNA). Our data do not suggest that differential natural selection is the cause of this difference in TMRCAs. Rather, these results are most consistent with a higher female effective population size.
Link (pdf)

Y chromosomal haplogroup J as a signature of the post-neolithic colonization of Europe

Y chromosomal haplogroup J as a signature of the post-neolithic colonization of Europe

A very important new paper about Y chromosome haplogroup J. I will have more to say once I have finished reading it carefully.

Update:
The main finding of the authors is that haplogroup J was not carried by a single advance from the Middle East into Europe. Rather, at least two expansions can be detected, a "Neolithic" one and a "Greek" one:

In summary, our data are in agreement with a major discontinuity for the peopling of southern Europe. Here, haplogroup J constitutes not only the signature of a single wave-of-advance from the Levant but, to a greater extent, also of the expansion of the Greek world, with an accompanying novel quota of genetic variation produced during its demographic growth. In the analysis by Cavalli-Sforza et al. (1994), the two peopling contributions can be distinguished, as they are caught in the first and the fourth principal component, respectively, but the relevance of the latter may have been underestimated. The two processes, widely spaced in time, are associated with dramatically different travel technologies. This implies that, in the central and west Mediterranean, the entry of J chromosomes may have occurred mainly by sea, i.e., in the south–east of both Spain and Italy.

Human Genetics (online first)

Y chromosomal haplogroup J as a signature of the post-neolithic colonization of Europe
F. Di Giacomo et al.

Abstract In order to attain a finer reconstruction of the peopling of southern and central-eastern Europe from the Levant, we determined the frequencies of eight lineages internal to the Y chromosomal haplogroup J, defined by biallelic markers, in 22 population samples obtained with a fine-grained sampling scheme. Our results partially resolve a major multifurcation of lineages within the haplogroup. Analyses of molecular variance show that the area covered by haplogroup J dispersal is characterized by a significant degree of molecular radiation for unique event polymorphisms within the haplogroup, with a higher incidence of the most derived sub-haplogroups on the northern Mediterranean coast, from Turkey westward; here, J diversity is not simply a subset of that present in the area in which this haplogroup first originated. Dating estimates, based on simple tandem repeat loci (STR) diversity within each lineage, confirmed the presence of a major population structuring at the time of spread of haplogroup J in Europe and a punctuation in the peopling of this continent in the post-Neolithic, compatible with the expansion of the Greek world. We also present here, for the first time, a novel method for comparative dating of lineages, free of assumptions of STR mutation rates.

Link

Celtic Origins on the Atlantic Facade of Europe

Celtic Origins on the Atlantic Facade of Europe

A new study re-evaluates mtDNA evidence, in conjunction with Y-chromosomal and autosomal DNA, to trace the origins of Celtic-speaking populations of Western Europe. The main conclusion is that while some Central European origin can't be ruled out using genetic data, current and former Celtic speakers seem to share a common ancestry with other non-Celtic populations of the Atlantic zone of Europe.

Am. J. Hum. Genet., 75:000, 2004

The Longue Durée of Genetic Ancestry: Multiple Genetic Marker Systems and Celtic Origins on the Atlantic Facade of Europe

Brian McEvoy et al.

Celtic languages are now spoken only on the Atlantic facade of Europe, mainly in Britain and Ireland, but were spoken more widely in western and central Europe until the collapse of the Roman Empire in the first millennium A.D. It has been common to couple archaeological evidence for the expansion of Iron Age elites in central Europe with the dispersal of these languages and of Celtic ethnicity and to posit a central European "homeland" for the Celtic peoples. More recently, however, archaeologists have questioned this "migrationist" view of Celtic ethnogenesis. The proposition of a central European ancestry should be testable by examining the distribution of genetic markers; however, although Y-chromosome patterns in Atlantic Europe show little evidence of central European influence, there has hitherto been insufficient data to confirm this by use of mitochondrial DNA (mtDNA). Here, we present both new mtDNA data from Ireland and a novel analysis of a greatly enlarged European mtDNA database. We show that mtDNA lineages, when analyzed in sufficiently large numbers, display patterns significantly similar to a large fraction of both Y-chromosome and autosomal variation. These multiple genetic marker systems indicate a shared ancestry throughout the Atlantic zone, from northern Iberia to western Scandinavia, that dates back to the end of the last Ice Age.

Link

Samaritan mtDNA and Y chromosomes

Samaritan mtDNA and Y chromosomes

Hum Mutat. 2004 Sep;24(3):248-60.

Reconstruction of patrilineages and matrilineages of Samaritans and other Israeli populations from Y-Chromosome and mitochondrial DNA sequence Variation.
P. Shen et al.

The Samaritan community, which numbered more than a million in late Roman times and only 146 in 1917, numbers today about 640 people representing four large families. They are culturally different from both Jewish and non-Jewish populations in the Middle East and their origin remains a question of great interest. Genetic differences between the Samaritans and neighboring Jewish and non-Jewish populations are corroborated in the present study of 7,280 bp of nonrecombining Y-chromosome and 5,622 bp of coding and hypervariable segment I (HVS-I) mitochondrial DNA (mtDNA) sequences. Comparative sequence analysis was carried out on 12 Samaritan Y-chromosome, and mtDNA samples from nine male and seven female Samaritans separated by at least two generations. In addition, 18-20 male individuals were analyzed, each representing Ethiopian, Ashkenazi, Iraqi, Libyan, Moroccan, and Yemenite Jews, as well as Druze and Palestinians, all currently living in Israel. The four Samaritan families clustered to four distinct Y-chromosome haplogroups according to their patrilineal identity. Of the 16 Samaritan mtDNA samples, 14 carry either of two mitochondrial haplotypes that are rare or absent among other worldwide ethnic groups. Principal component analysis suggests a common ancestry of Samaritan and Jewish patrilineages. Most of the former may be traced back to a common ancestor in the paternally-inherited Jewish high priesthood (Cohanim) at the time of the Assyrian conquest of the kingdom of Israel.
Link

mtDNA and Y chromosomes of Yakuts

mtDNA and Y chromosomes of Yakuts

In agreement with a recent autosomal DNA study on the Yakuts, this ethnic group is characterized by mainly Mongoloid mtDNA haplogroups (A, B, C, D, G, and F) as well as the Uralic-Mongoloid Y-haplogroup N3.

Genetika. 2003 Jul;39(7):975-81. Related Articles, Links

[MtDNA and Y-chromosome lineages in the Yakut population]
Puzyrev VP et al.

The structure of female (mtDNA) and male (Y-chromosome haplotypes) lineages in the Yakut population was examined. To determine mtDNA haplotypes, sequencing of hypervariable segment I and typing of haplotype-specific point substitutions in the other parts of the mtDNA molecule were performed. Y haplogroups were identified through typing of biallelic polymorphisms in the nonrecombining part of the chromosome. Haplotypes within haplogroups were analyzed with seven microsatellite loci. Mitochondrial gene pool of Yakuts is mainly represented by the lineages of eastern Eurasian origin (haplogroups A, B, C, D, G, and F). In Yakuts haplogroups C and D showing the total frequency of almost 80% and consisting of 12 and 10 different haplopypes, respectively, were the most frequent and diverse. The total part of the lineages of western Eurasian origin ("Caucasoid") was about 6% (4 haplotypes, haplogroups H, J, and U). Most of Y chromosomes in the Yakut population (87%) belonged to haplogroup N3 (HG16), delineated by the T-C substitution at the Tat locus. Chromosomes of haplogroup N3 displayed the presence of 19 microsatellite haplotypes, the most frequent of which encompassed 54% chromosomes of this haplogroup. Median network of haplogroup N3 in Yakuts demonstrated distinct "starlike phylogeny". Male lineages of Yakuts were shown to be closest to those of Eastern Evenks.

Link

Reduced genetic structure of the Iberian peninsula revealed by Y-chromosome analysis: implications for population demography

Reduced genetic structure of the Iberian peninsula revealed by Y-chromosome analysis: implications for population demography

A new comprehensive Y-chromosomal study on Iberian populations demonstrates that despite a small level of admixture, modern Iberians remain relatively homogeneous and untouched by contacts during historical times.

European Journal of Human Genetics
advance online publication 28 July 2004; doi:10.1038/sj.ejhg.5201225

Carlos Flores et al.

Abstract

Europe has been influenced by both intra- and intercontinental migrations. Since the Iberian peninsula was a refuge during the Last Glacial Maximum, demographic factors associated with contraction, isolation, subsequent expansion and gene flow episodes have contributed complexity to its population history. In this work, we analysed 26 Y-chromosome biallelic markers in 568 chromosomes from 11 different Iberian population groups and compared them to published data on the Basques and Catalans to gain insight into the paternal gene pool of these populations and find out to what extent major demographic processes account for their genetic structure. Our results reveal a reduced, although geographically correlated, Y-chromosomal interpopulation variance (1.2%), which points to a limited heterogeneity in the region. Coincidentally, spatial analysis of genetic distances points to a focal distribution of Y-chromosome haplogroups in this area. These results indicate that neither old or recent Levantine expansions nor North African contacts have influenced the current Iberian Y-chromosome diversity so that geographical patterns can be identified.