Tag Archives: Y chromosome

Eurasian Y chromosome R1b in Africa.

Human Y chromosome haplogroup R-V88: a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages

Fulvio Cruciani et al.


Although human Y chromosomes belonging to haplogroup R1b are quite rare in Africa, being found mainly in Asia and Europe, a group of chromosomes within the paragroup R-P25* are found concentrated in the central-western part of the African continent, where they can be detected at frequencies as high as 95%. Phylogenetic evidence and coalescence time estimates suggest that R-P25* chromosomes (or their phylogenetic ancestor) may have been carried to Africa by an Asia-to-Africa back migration in prehistoric times. Here, we describe six new mutations that define the relationships among the African R-P25* Y chromosomes and between these African chromosomes and earlier reported R-P25 Eurasian sub-lineages. The incorporation of these new mutations into a phylogeny of the R1b haplogroup led to the identification of a new clade (R1b1a or R-V88) encompassing all the African R-P25* and about half of the few European/west Asian R-P25* chromosomes. A worldwide phylogeographic analysis of the R1b haplogroup provided strong support to the Asia-to-Africa back-migration hypothesis. The analysis of the distribution of the R-V88 haplogroup in >1800 males from 69 African populations revealed a striking genetic contiguity between the Chadic-speaking peoples from the central Sahel and several other Afroasiatic-speaking groups from North Africa. The R-V88 coalescence time was estimated at 9200–5600 kya, in the early mid Holocene. We suggest that R-V88 is a paternal genetic record of the proposed mid-Holocene migration of proto-Chadic Afroasiatic speakers through the Central Sahara into the Lake Chad Basin, and geomorphological evidence is consistent with this view.

I haven’t had a look at the full text for this yet, but relevant to this is the mt DNA study of Chadic speakers which showed a passage from East Africa (somewhere to the West of the Nile in the Sudan is my guess, it’s the only place the v88 and L3f3 would meet up).

 A date ~8,000 YBP was estimated for the L3f3 sub-haplogroup, which is in good agreement with the supposed migration of Chadic speaking pastoralists and their linguistic differentiation from other Afro-Asiatic groups of East Africa.

Which isn’t inconsistent with the date for V88 proposed at 9,200-5,600 years, and is also a very close match for the arrival of the Neolithic in Africa.

 Just a brief  note on the mt DNA  study: the only Afro-Asiatic speaking group that the Chadic speakers plot closely to is Cushitic, which will probably make Blench happy, as he claims Chadic speakers are a split-off from Cushitic speaking pastoralists. It’s fairly obvious that the male line of Chadic speakers followed a path into Africa via the Sinai, then down the West bank of the Nile and then struck out West to Lake Chad, acquiring wives as they went. The only issue is the exact date. Holocene or Neolithic? Whatever the exact date, this brings the argument for an Asian origin for Afro-Asiatic out again, as (from the DNA here) the odds are 50% that it followed the male line in from Asia. I would like to comment that Chadic has cognates for sheep and goats that look like they share a root with Cushitic and Egyptian, which would at least date proto Chadic to the Neolithic, making the mt DNA date of 8,000 more likely to be close to the actual date for V88 to enter Africa.


Y chromosome J quick reference page

My blogging lately has been slowed down by my MS flaring up and my boy discovering Lego Indiana Jones online – my  apologies to anyone I haven’t responded to in the comments.

A basic page for reference on J1 and J2 so I don’t have to root through multiple papers and blog entries every time I want to find something.

This is a homemade table and mainly from Cruciani’s 2004 figures and Hassan 2008  for a one-glace overview . The Egyptian figures are my own from several combined sources and are about as accurate as you’ll get for that country. The other countries are from single paper sources and probably aren’t as accurate overall, but it’s a decent rough guide.


The actual Cruciani table, another chart (can’t remember which paper).

cruciani's 2004 J tables jfreq

From Giacomo 2004 and Battaglia 2008

jneo2 jneo


greekj  cintj  etj

Greece, From Martinez 2007. Turkey; Cinnioglu 2003 and  Semino 2002.

jiran  mulj  omegar

Iran, from Cadenas 2006, from Al-Zahery 2002 and Luis 2004

From Giacomo 2004



While not the neatest page, it should be useful for quicker referencing. A good look through the J hg’s around the near East has reinforced a Neolithic or older entry date for the J2 in North Africa as far as I’m concerned, as the ratio of J2 to J1/other hg’s is incompatible with it having a historical arrival from any of the known invading areas. I’m also wondering if upper Egypt is the switch over  area from Arab J1 to Capsian J1.

Reference list.

If anyone else finds a Y chromosome J reference for the near East, Europe, North Africa or India/Pakistan that I haven’t included leave the name of the paper ( I expect there’s a few) in the comments, as I’ll be adding to this one as I go along. Also a decent recent tree of J would be nice – if anyone find one send me a link!

Tree for Y chromosome Haplogroup R


For my own reference from here. The Cameroon R1b marked in green.



 Also, digging out an Anatolian paper, I’m sure I saw M335 present there, location three being Armenia, I think.Very odd.  The Sudanese Copts have P25, as do the Hausa. I guess the simplest explanation would be that some  Ouldeme man ended up in Turkey at some point.

 While you get a little p25 in Turkey, there’s a dearth of it in the Jordan area- you only seem to get derived m269 there, which is what you’d expect if it took an overland route from Turkey to get to Africa. I’m suspecting the p25 (R1b1) went across the Red Sea at a fairly southerly point to get into the Northern part of the Sudan. I’m having a dig for Y chromosome information from that part of the Arabian/Yemeni coast but I’m not having much luck. Anyone who knows where I can dig out that info let me know. I’m  looking for a reasonable source for the R1b1 in East Africa, in Asia. So far I’m really only finding m269 in the fertile crescent and very low p25 in Turkey, so either the plain p25 that was ancestral to East Africa has been wiped out or it’s hiding on the East Red sea coast in a study I haven’t seen.

Y-chromosomal evidence of a pastoralist migration through Tanzania to southern Africa

Y-chromosomal evidence of a pastoralist migration through Tanzania to southern Africa

Although geneticists have extensively debated the mode by which agriculture diffused from the Near East to Europe, they have not directly examined similar agropastoral diffusions in Africa. It is unclear, for example, whether early instances of sheep, cows, pottery, and other traits of the pastoralist package were transmitted to southern Africa by demic or cultural diffusion. Here, we report a newly discovered Y-chromosome-specific polymorphism that defines haplogroup E3b1f-M293. This polymorphism reveals the monophyletic relationship of the majority of haplotypes of a previously paraphyletic clade, E3b1-M35*, that is widespread in Africa and southern Europe. To elucidate the history of the E3b1f  haplogroup, we analyzed this haplogroup in 13 populations from southern and eastern Africa. The geographic distribution of the E3b1f  haplogroup, in association with the microsatellite diversity estimates for populations, is consistent with an expansion through Tanzania to southern-central Africa. The data suggest this dispersal was independent of the migration of Bantu-speaking peoples along a similar route. Instead, the phylogeography and microsatellite diversity of the E3b1f lineage correlate with the arrival of the pastoralist economy in southern Africa. Our Y-chromosomal evidence supports a demic diffusion model of pastoralism from eastern to southern Africa ≈2,000 years ago



Fig. 2. Contour maps of the frequencies of E3b1-M35*(former) (A) and E3b1f-M293 (B) in Africa. Populations without M293 in B are based on unpublished data. The geographic distributions of M35*(former) and M293 frequencies across Africa were created using the Kringing method in Surfer 8 (Golden Software). Locations of populations in Table 1 are indicated by cross hatches. Because M35* is a paraphyletic haplogroup, the sharing of M35* does not indicate a close genetic relationship. Areas of high frequency are similar in the two maps as 90% of the M35*(former) samples are M293+. M293 is only found in sub-Saharan Africa, indicating a separate phylogenetic history for M35*(former) samples further north.

If I remember right, the oldestdates for cattle in Southern Africa are sbout 2,000 BP from Boteng in the Kalahari, which would suggest that  pastoralists started their move south earlier than that date.

The M78 Y chromosome and M1 Mt DNA as makers for the expansion of the Halfan culture.

I managed to access the distribution maps  of M1 recently, and decided to assemble it with the information on the M78 Y chromosome. These, in my opinion, definitely show an upper Egyptian focal point for M1, M1a and M78, which is supported by the coalescence dates on the mt DNA (Y chromosomes are slightly out)..


The coalescence time estimates for M1 is 36.8 ± 7.1 ky, but this is known to have originated in Asia now, so the hot spot in Egypt seems to be from a secondary distribution point. The coalescence for M1b is 25.7 ± 6.6 ky, and for M1a is 22.6 ± 8.1 ky. M1a is present in upper Egypt at roughly the ratio to M1 as it is in Ethiopians, which would again suggest that it moved out from North East Africa keeping company with M1 and m78 in a large population migration

The M1b  (M1c to Gonzalez) marked here is  believed to somewhat older than the other M1 subclades, and doesn’t seem to be part of the Pleistocene expansion from upper Egypt, it has a North west African origin. I’m assuming the date for the start of expansion to be in the 24,000 years or more, as it reached North Africa/Iberia  (Ibero Maurussian culture) and the near East (Kebaran culture) about 22,000 years ago, so any later would be logically impossible. M1a certainly seems to fall into this era. This North East African expansion would also make much more sense of the M1 and M1a in Portugal than an East African origin for M1a.

Also of note is how Mt DNa U derived haplotypes follow M1 and m78 into east Africa. This seems to have entered North East Africa first, with no entry across the red sea, logically suggesting it was part of the same population expansion from the Northern Nile valley. I do find the faint clusters of U6 and  M1b in the near east quite odd. Possibly explicable by much later movements between north Africa and the near east in the Phoenician era.

Olivieri also calculates the coalescence date for M1a2 as 24.0 ± 5.7 ky, and for M1a1 20.6 ± 3.4 ky. This would also place M1a2 in North East Africa prior to the expansion, and possibly M1a1,  depending on when the migration penetrated east Africa.


The m78 distribution pattern is a pretty good match for M1 and M1a. As always, the age for the Y chromosome is too recent- a bugbear of mine in all Y DNA studies- with an upper age estimate of 20ky (18.6, 17.3 to 20ky) but since it’s distribution is such a good match to the mt DNA I’ll presume that it’s more likely that it matches the 24ky for the start of the population expansion.

The expansion of this population seems to be as a result of either it’s new microlithic tool culture, or (more likely) it’s new diet that was based on wild grain. Its focal point seems to be upper Egypt, around Wadi Kubbaniya. The population expansion seemed to run of of steam in Northern Syria (the much later Natufians); possibly overcome by an expanding wave of proto-Neolithic Anatolians that left no visible traces of their upper Egyptian ancestry by the time the Neolithic expansion overtook the near East.

Independent histories of human Y chromosomes from Melanesia and Australia.

Independent histories of human Y chromosomes from Melanesia and Australia.

Kayser M, Brauer S, Weiss G, Schiefenhövel W, Underhill PA, Stoneking M.
Max Planck Institute for Evolutionary Anthropology, Department for Evolutionary Genetics, D-04103 Leipzig, Germany.

To investigate the origins and relationships of Australian and Melanesian populations, 611 males from 18 populations from Australia, Melanesia, and eastern/southeastern Asia were typed for eight single-nucleotide polymorphism (SNP) loci and seven short tandem-repeat loci on the Y chromosome. A unique haplotype, DYS390.1del/RPS4Y711T, was found at a frequency of 53%-69% in Australian populations, whereas the major haplotypes found in Melanesian populations (M4G/M5T/M9G and DYS390.3del/RPS4Y711T) are absent from the Australian populations. The Y-chromosome data thus indicate independent histories for Australians and Melanesians, a finding that is in agreement with evidence from mtDNA but that contradicts some analyses of autosomal loci, which show a close relationship between Australian and Melanesian (specifically, highland Papua New Guinean) populations. Since the Australian and New Guinean landmasses were connected when first colonized by humans > or =50,000 years ago but separated some 8,000 years ago, a possible way to reconcile all the genetic data is to infer that the Y-chromosome and mtDNA results reflect the past 8,000 years of independent history for Australia and New Guinea, whereas the autosomal loci reflect the long preceding period of common origin and shared history. Two Y-chromosome haplotypes (M119C/M9G and M122C/M9G) that originated in eastern/southeastern Asia are present in coastal and island Melanesia but are rare or absent in both Australia and highland Papua New Guinea. This distribution, along with demographic analyses indicating that population expansions for both haplotypes began approximately 4,000-6,000 years ago, suggests that these haplotypes were brought to Melanesia by the Austronesian expansion. Most of the populations in this study were previously typed for mtDNA SNPs; population differentiation is greater for the Y chromosome than for mtDNA and is significantly correlated with geographic distance, a finding in agreement with results of similar analyses of European populations

 Figure 1 Y-chromosome haplotypes, as defined by six Y-chromosome SNPs and two specific deletions at the Y-chromosome STR locus DYS390, and their frequency distribution in human populations from eastern/southeastern Asia, Melanesia, Polynesia, and Australia. Color codings are as follows: black, complete ancestral haplotype (with respect to the markers analyzed); gray, M9G; red, M4G/M5T/M9G; yellow, M119C/M9G; orange, M122C/M9G; green, RPS4Y711T; dark blue, DYS390.1del/RPS4Y711T; purple, DYS390.3del/M9G; and light blue, DYS390.3del/RPS4Y711T. Abbreviations are as follows: Aus1 p Australia, Arnhem Land; Aus2 p Australia, Sandy Desert; Bor p southern Borneo; Chi p China; Coo p Cook Islands; Jav p Java; Kor p Korea; Mal p Malaysia; Mol p Moluccas; Phi p Philippines; PNC p PNG coast; PNH p PNG highlands; TaC p Taiwan Chinese; Tai p Taiwan aborigines; Ten p Nusa Tenggara; TNB p Tolai New Britain; Tro p Trobriand Islands; Vie p Vietnam

Gene flow from the Indian subcontinent to Australia: evidence from the Y chromosome

Gene flow from the Indian subcontinent to Australia: evidence from the Y chromosome.

Redd AJ, Roberts-Thomson J, Karafet T, Bamshad M, Jorde LB, Naidu JM, Walsh B, Hammer MF.
Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA.

Phenotypic similarities between Australian Aboriginal People and some tribes of India were noted by T.H. Huxley during the voyage of the Rattlesnake (1846-1850). Anthropometric studies by Birdsell led to his suggestion that a migratory wave into Australia included populations with affinities to tribal Indians. Genetic evidence for an Indian contribution to the Australian gene pool is contradictory; most studies of autosomal markers have not supported this hypothesis (; and references therein). On the other hand, affinities between Australian Aboriginal People and southern Indians were suggested based on maternally inherited mitochondrial DNA. Here, we show additional DNA evidence in support of Huxley’s hypothesis of an Indian-Australian connection using single-nucleotide polymorphisms (SNPs) and short tandem repeats (STRs) on the nonrecombining portion of the Y chromosome (NRY). Phylogenetic analyses of STR variation associated with a major Australian SNP lineage indicated tight clustering with southern Indian/Sri Lankan Y chromosomes. Estimates of the divergence time for these Indian and Australian chromosomes overlap with important changes in the archaeological and linguistic records in Australia. These results provide strong evidence for an influx of Y chromosomes from the Indian subcontinent to Australia that may have occurred during the Holocene.

Croatian mt DNA and Y chromosomes

Review of Croatian genetic heritage as revealed by mitochondrial DNA and Y chromosomal lineages.

Pericic M, Barac Lauc L, Martinovic Klaric I, Janicijevic B, Rudan P.
Institute for Anthropological Research, Amruseva 8, 10000 Zagreb, Croatia.

The aim of this review is to summarize the existing data collected in high-resolution phylogenetic studies of mitochondrial DNA and Y chromosome variation in mainland and insular Croatian populations. Mitochondrial DNA polymorphisms were explored in 721 individuals by sequencing mtDNA HVS-1 region and screening a selection of 24 restriction fragment length polymorphisms (RFLPs), diagnostic for main Eurasian mtDNA haplogroups. Whereas Y chromosome variation was analyzed in 451 men by using 19 single nucleotide polymorphism (SNP)/indel and 8 short tandem repeat (STR) loci. The phylogeography of mtDNA and Y chromosome variants of Croatians can be adequately explained within typical European maternal and paternal genetic landscape, with the exception of mtDNA haplogroup F and Y-chromosomal haplogroup P* which indicate a connection to Asian populations. Similar to other European and Near Eastern populations, the most frequent mtDNA haplogroups in Croatians were H (41.1%), U5 (10.3%), and J (9.7%). The most frequent Y chromosomal haplogroups in Croatians, I-P37 (41.7%) and R1a-SRY1532 (25%), as well as the observed structuring of Y chromosomal variance reveal a clearly evident Slavic component in the paternal gene pool of contemporary Croatian men. Even though each population and groups of populations are well characterized by maternal and paternal haplogroup distribution, it is important to keep in mind that linking phylogeography of various haplogroups with known historic and prehistoric scenarios should be cautiously performed.

No real surprises in this paper.


Y chromosome haplogroups: a correlation with testicular dysgenesis syndrome?

Y chromosome haplogroups: a correlation with testicular dysgenesis syndrome?

McElreavey K, Quintana-Murci L.
Reproduction, Fertility and Populations, Institut Pasteur, Paris, France. kenmce@pasteur.fr

Testicular dysgenesis syndrome encompasses low sperm quality, hypospadias, cryptorchidism and testicular cancer. Epidemiological studies and genetic data from familial cases suggest that testicular dysgenesis syndrome has a common etiology. The Y chromosome is known to encode genes that are involved in germ cell development or maintenance. We have therefore investigated if different classes of Y chromosomes in the general population (Y chromosome haplogroups) are associated with aspects of the testicular dysgenesis syndrome. We defined the Y chromosome haplogroups in individuals from different European counties who presented with either (i) oligo- or azoospermia associated with a Y chromosome microdeletion, (ii) unexplained reduced sperm counts (<20 x 10(6)/ml) or (iii) testicular cancer. We failed to find Y chromosome haplotype associations with either microdeletion formation or testicular cancer. However, in a study of the Danish population, we found that a specific Y chromosome haplogroup (hg26) is significantly overrepresented in men with unexplained reduced sperm counts compared with a Danish control population. The factors encoded by genes on this class of Y chromosome may be particularly susceptible to environmental influences that cause testicular dysgenesis syndrome. Our current data highlight the need for further analyses of clinically well-defined patient groups from a wide range of ethnic and geographic origins.

Another study that suggests a Y chromosome prone to infertility.

Evidence for the association of Y-chromosome haplogroups with susceptibility to spermatogenic failure in a Chinese Han population

Evidence for the association of Y-chromosome haplogroups with susceptibility to spermatogenic failure in a Chinese Han population

Yang Y, Ma M, Li L, Zhang W, Xiao C, Li S, Ma Y, Tao D, Liu Y, Lin L, Zhang S.
Department of Medical Genetics and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, P R China.

INTRODUCTION: Y chromosomes are genetically highly variable due to frequent structural rearrangements. The variations may create a genetic background for the susceptibility to Y-related spermatogenic impairment, although few data have been accumulated about the possible correlation between the Y-chromosome haplotype and the predisposition of men to spermatogenic failure.

 OBJECTIVE: To investigate the possible association of Y-chromosome background with spermatogenic failure.

METHODS: The distribution of 18 Y-chromosome haplogroups was compared between 414 infertile men with azoospermia or oligozoospermia and 262 normozoospermic men with or without AZFc deletions in a Han population of Southwest China.

RESULTS: A significant population difference in Y-haplogroup distribution was found between the groups of normozoospermia and azoospemia or oligozoospermia, and between the patient groups with oligozoospermia and azoospermia without AZFc deletions. Interpopulation comparison of Y haplogroup frequencies showed that the distribution of the haplogroups C, K* and O3* were significantly different between the groups.

CONCLUSION: This study provides evidence for the association of Y-chromosome background with impaired spermatogenesis, suggesting that Y variations play a role in the occurrence and even the severity of spermatogenic failure. Furthermore, both AZFc deletions and other Y-chromosome structural variations may be important for determining the susceptibility to spermatogenic failure. Our findings emphasise the necessity of more extensive study on Y-chromosome variations for better understanding of spermatogenesis and its pathology.

I’m very pro the idea of the Y chromsome being subject to natural selection. Some types being better sperm producers than others would explain that.