Tunisian and Moroccan Y Chromosomes

Y-chromosome markers distribution in Northern Africa: High-resolution SNP and STR analysis in Tunisia and Morocco populations

Valerio Onofria, Federica Alessandrinia, Chiara Turchia, Mauro Pesaresia and Adriano Tagliabracci, a,
Abstract
At the beginning of 2006 more than 301,000 immigrants resident in Italy resulted to come from Tunisia and Morocco, 66% of which are male subjects; in addition, it is estimated that some other thousand are clandestine. Our data show that there is an increasing involvement of Tunisian and Moroccan individuals in paternity testing and in individual identification cases. For these reasons, the aim of this work was to enrich forensic Y-chromosome databases with Northern Africa data to better know markers frequency and their distribution across these populations. 103 Tunisian and Moroccan healthy male donors were typed by 17 microsatellites extended haplotype and 41 Y-SNPs. A high-resolution level database was created, including both haplotype and haplogroup for each sample. This study confirmed that precious informations might come both from Y-SNPs haplogroup distribution besides Y-STRs data.

After just re-reading the Guanche Y chr the total abscence of  ‘I’ across this part of N Africa is a mystery. How did it get to the Canaries when it skipped Morocco? Admittedly the sample size is a bit small. Maybe it got missed.

Guanche Y chromosomes

Demographic history of Canary Islands male gene-pool: replacement of native lineages by European

Abstract
 The origin and prevalence of the prehispanic settlers of the Canary Islands has attracted great multidisciplinary interest. However, direct ancient DNA genetic studies on indigenous and historical 17th-18th century remains, using mitochondrial DNA as a female marker, have only recently been possible. In the present work, the analysis of Ychromosome polymorphisms in the same samples, has shed light on the way the European colonization affected male and female Canary Island indigenous genetic pools, from the conquest to present-day times.

Results
Autochthonous (E-M81) and prominent (E-M78 and J-M267) Berber Y-chromosome lineages were detected in the indigenous remains, confirming a North West African origin for their ancestors which confirms previous mitochondrial DNA results. However, in contrast with their female lineages, which have survived in the present-day population since the conquest with only a moderate decline, the male indigenous lineages have dropped constantly being substituted by European lineages. Male and  female sub-Saharan African genetic inputs were also detected in the Canary population, but their frequencies were higher during the 17th-18th centuries than today.

Conclusions
The European colonization of the Canary Islands introduced a strong sex-biased change in the indigenous population in such a way that indigenous female lineages survived in the extant population in a significantly higher proportion than their male counterparts.

Unashamedly nicked from Maju- but topped off with a genuine portrait of a Guanche male called Hairy Harry (centre) shown to me by Ricardo.

Interesting to see the J1, which a couple of studies have placed in North Africa from about 10k ago. A fair amount of other older Eurasian lines. I’ll have another read of this one later.

mtDNA diversity in Sudan (East Africa)

mtDNA diversity in Sudan (East Africa)

A major effort must be put in East and sub-Saharan African mtDNA diversity characterisation for the construction of an informative database. We contribute 102 new HVRI + HVRII Sudanese sequences. As expected this sample is highly diverse, mainly constituted of unique haplotypes (2.07% random match probability for HVRI alone), 72.5% of which belong to sub-Saharan haplogroups.

Somehow this slipped past me last year- I think because it came out in the school holidays. It’s a bit short on detail unfortunately. A bit like this blog entry.

Genetic variation of 15 autosomal STR loci in Upper (Southern) Egyptians

Genetic variation of 15 autosomal STR loci in Upper (Southern) Egyptians

Abstract
A sample of 265 unrelated individuals inhabiting five governorates in Upper (south) Egypt was collected with informed consent. The samples were amplified using the AmpFℓSTR®Identifiler™PCR Amplification Kit (containing 15 loci: D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA), and genotyped subsequent to capillary electrophoresis. Statistical analysis of the generated data indicated neither departure from expectation of Hardy–Weinberg Equilibrium (HWE) in most of the tested loci nor dependence of alleles between loci. All tested loci were polymorphic; the most discriminating is D18S51 while the least is TPOX. The combined power of exclusion was 0.99999868 and the combined match probability was 1.93×10−18. The genetic diversity of the Upper Egyptians was compared with those of other populations at the local, regional and global levels.

Multi-dimensional scaling (MDS) based on pair-wise FST genetic distances of Upper Egyptian and other diverse global populations. OCE, Oceanian; ME, Middle Eastern; NAF, North African; EAS, East Asian; SSA, sub-Saharan African; UEGY, Upper Egyptian; SAS, South Asian; EUR, European. The figure shows that Oceania and American populations are very distant from Upper Egyptians (marked by a grey triangle) and other populations. The Upper Egyptian population is closer to the Middle Eastern, North African, South Asian and European populations than others.

Not a mega surprise that upper Egyptians grouped closer to north African and near Eastern rather than West African samples. It would have been nice to see Ethiopian samples too, for a better sense of perspective.

Detecting ancient admixture and estimating demographic parameters in multiple human populations

Detecting ancient admixture and estimating demographic parameters in multiple human populations (pdf)

A rather odd looking pdf- runs a lot like a mini PowerPoint presentation, by the man who published the recent paper that concluded there probably was archaic admixture in humans. And yet again.. I see the 40k-60k OOA date in print. Grr.

Detecting ancient admixture and estimating demographic parameters in multiple human populations

We analyze patterns of genetic variation in extant human polymorphism data from the NIEHS SNPs project to estimate human demographic parameters. We update our previous work by considering a larger data set (more genes and more populations), and by explicitly estimating the amount of putative admixture between modern humans and archaic human groups (e.g., Neandertals, Homo erectus, H. floresiensis). We find evidence for this ancient admixture in European, East Asian and West African samples, suggesting that admixture between diverged hominin groups may be a general feature of recent human evolution.

Yet another DNA study that finds evidence of archaic contributions in modern human groups. Odd how these don’t make the news but anything that finds in favour of the OOA gets splattered all over the media.

We estimate admixture proportions of 14 % (95% CI: 8 – 20 %) in the European-American sample and 1.5% (95% CI: 0.5 – 2.5 %) in the East Asian sample. In both cases, the relative log-likelihood for a = 0 (i.e., no ancient admixture) is significantly lower than the maximum likelihood (likelihood-ratio test, p < 10-3) , which provides additional evidence (along with the S* results in the previous paragraph) that ancient admixture occurred. The estimates of admixture rates in Europeans are consistent with estimates of Neandertal admixture obtained from analyses of Neandertal DNA (Serre et al. 2004; Noonan et al. 2006), [. . .] Unlike previous studies, we incorporated admixture between archaic and modern humans as an additional demographic parameter to be co-estimated. Interestingly, we could exclude no admixture (i.e., exclude a = 0) in both of the non-African populations studied

 The observation that all (three) populations studied seem to have evidence for ancient admixture suggests that ancient population structure may be a common feature of all contemporary human populations, and this ancient structure may predate the initial expansion of modern humans out of Africa.

Although some of the archaic DNA isn’t found in Africa, which would make the archaic admixture prior to the OOA hard to explain. This paper also finds evidence for archaic admixture in the Yoruba. I remember reading previously that the X chromosome showed signs of archaic ancestry in one pygmy group, so archaic ancestry in West Africa is supported by another paper. More detail… Testing for Archaic Hominin Admixture on the X Chromosome, which concluded the TMRCA was about 2 million years for one locus on the X chromosome and concludes..

For now, this locus represents a genealogical history that is most consistent with recent admixture from an archaic hominin population in Asia

Which is a far cry from Svante Paabo’s ‘no admixture but they were within the range of modern humans’ claim, which I found a bit odd. So you found they had essentially human DNA with us but decided they didn’t mingle …how?

I’d just like to comment that the OOA/RAR theory leaves absolutely NO room for any ancient DNA cropping in non Africans that doesn’t have a root in Africa- but it does, with remarkable frequency. In other words, the OOA doesn’t ‘fit’. That OOA is true of mostof our ancestry means sod all, it has to be true for all of it and it’s rather blatantly NOT the case, as there are a plethora of non-African but ancient in Eurasia mutations that invalidate it. Particularly the non African MC1R mutation ages that have ages of 100k-250k and a TMRCA of a million years.

Both African and non-African data suggest that the time to the most recent common ancestor is ª1 million years and that the age of the global 314 variant is 650,000 years. On this time scale, ages for the Eurasian distributed Val60Leu, Val92Met, and Arg163Gln variants are 250,000–100,000 years;

I’m going to have to make up a proper list of the DNA studies that find against the OOA theory.

J1-M267 Y lineage marks climate-driven pre-historical human displacements

J1-M267 Y lineage marks climate-driven pre-historical human  displacements

Sergio Tofanelli et al.
The present day distribution of Y chromosomes bearing the haplogroup J1 M267*G variant has been associated with different episodes of human demographic history, the main one being the diffusion of Islam since the Early Middle Ages. To better understand the modes and timing of J1 dispersals, we reconstructed the genealogical relationships among 282 M267*G chromosomes from 29 populations typed at 20 YSTRs and 6 SNPs. Phylogenetic analyses depicted a new genetic background consistent with climate-driven demographic dynamics occurring during two key phases of human pre-history: (1) the spatial expansion of hunter gatherers in response to the end of the late Pleistocene cooling phases and (2) the displacement of groups of foragers/herders following the mid-Holocene rainfall retreats across the Sahara and Arabia. Furthermore, J1 STR motifs previously used to trace Arab or Jewish ancestries were shown unsuitable as diagnostic markers for ethnicity.

One to add to the J page. I ‘ll have to access the paper later- so no deep insights on this one as yet. Take a month of sick and you do get behind with this stuff.

Near Eastern Neolithic genetic input in a small oasis of the Egyptian Western Desert

Near Eastern Neolithic genetic input in a small oasis of the Egyptian Western Desert

The Egyptian Western Desert lies on an important geographic intersection between Africa and Asia. Genetic diversity of this region has been shaped, in part, by climatic changes in the Late Pleistocene and Holocene epochs marked by oscillating humid and arid periods. We present here a whole genome analysis of mitochondrial DNA (mtDNA) and high-resolution molecular analysis of nonrecombining Y-chromosomal (NRY) gene pools of a demographically small but autochthonous population from the Egyptian Western Desert oasis el-Hayez. Notwithstanding signs of expected genetic drift, we still found clear genetic evidence of a strong Near Eastern input that can be dated into the Neolithic. This is revealed by high frequencies and high internal variability of several mtDNA lineages from haplogroup T. The whole genome sequencing strategy and molecular dating allowed us to detect the accumulation of local mtDNA diversity to 5,138 ± 3,633 YBP. Similarly, theY-chromosome gene pool reveals high frequencies of the Near Eastern J1 and the North African E1b1b1b lineages, both generally known to have expanded within North Africa during the Neolithic. These results provide another piece of evidence of the relatively young population history of North Africa.

Spotted on Dienekes, I’ll dig up the full text to add to my Egyptian DNA page later. I’d debate that the J1 was all historic though, bearing in mind the Capsian J1 input into the area, but it is pretty far North. It’s a pretty small sample size (35) for the Y chr info.

Single, Rapid Coastal Settlement of Asia Revealed by Analysis of Complete Mitochondrial Genomes

Single, Rapid Coastal Settlement of Asia Revealed by Analysis of Complete Mitochondrial Genomes

A recent dispersal of modern humans out of Africa is now widely accepted, but the routes taken across Eurasia are still disputed. We show that mitochondrial DNA variation in isolated “relict” populations in southeast Asia supports the view that there was only a single dispersal from Africa, most likely via a southern coastal route, through India and onward into southeast Asia and Australasia. There was an early offshoot, leading ultimately to the settlement of the Near East and Europe, but the main dispersal from India to Australia 65,000 years ago was rapid, most likely taking only a few thousand years.

An older paper, but I like to keep everything I find for reference As a minor point, the calculted age for M here is 64k, but last time I saw it in print it was more like 74k ago. The last age for L3 I saw was more in the 100k area.

Holocene human peopling of Libyan Sahara

Holocene human peopling of Libyan Sahara – Molecular analysis of maternal lineages in ancient and extant populations of Fezzan

The present work provides an important view of a region of Africa that is still almost unknown: the Central Sahara. The aim of the project as a whole, was to reconstruct from the maternal side, through the genetic analysis of mitochondrial DNA (mtDNA), the origins of a Pastoral nomad population in the Libyan Sahara, the Tuareg. The availability of both modern and ancient samples from the Fezzan (Libyan Sahara), collected in collaboration with the Italian Archaeological Mission in Libya directed by Prof. Savino Di Lernia, represented an important means of relating the mtDNA pool of extant Libyan Tuareg, with that of Pastoral people inhabiting the Central Sahara in prehistoric times, and with the Garamantes, the hypothetical ancestors of Libyan Tuareg. Nevertheless, molecular analysis carried out on the bones collected from the archaeological sites of the Acacus region, showed a very low state of preservation of the DNA, this probably due to the high temperatures that characterised burials over the centuries. Failure of the genetic analyses in the ancient individuals, necessarily limited the present work to the study of the extant Tuareg sample. Nevertheless, comparison with other genetic data collected so far in the modern African populations, and moreover the multidisciplinary integration with archaeological and ethnological data, helped to hypothetically reconstruct the origins of Libyan Tuareg, and their relationship with the ancient human migratory dynamics that occurred in Northern Africa during the Holocene.

A total of 129 individuals from two villages in the Acacus region, in Fezzan, were genetically analysed at the mtDNA level. The results here reported clearly show the low level of genetic diversity in the Libyan Tuareg sample, that is hypothetically due to high endogamy. Furthermore, phylogenetic analyses indicate that the mtDNA genetic pool of the Libyan Tuareg is characterized by a major “West- Eurasian” component, that is shared with many Berber groups and hypothetically comes from the Iberian Peninsula, and a minor “South-Saharan” component that shows some kind of  relationship with Central and Eastern African populations.

A pdf I located with a lot of information on North Africa and The Tuareg, for anyone interested in their history and culture and maternal ancestry.

The pdf book (it’s very long) shows H1 to be dominant in the Tuareg sample tested at  frequencies higher than 60%, H1 having roughly an 11,000 year old presence in North Africa. Eurasian lines H and V  make up nearly 2/3 of Libyan Tuareg mtDNA. This paper also finds traces of Eastern African ancestry in the Tuareg via the L2a lineage which has a coalescence date of around 5,000 years, which is tolerably close to the theorised Beja/Tuareg split of 6,000 years. It’s got a pretty detailed breakdown all all the Hg’s found.

Luis, you’ll like this one. Places the U in N Africa as Iberian in origin.

Analysis of mtDNA HVRII in several human populations

Analysis of mtDNA HVRII in several human populations using an  immobilised SSO probe hybridisation assay

Several populations were typed for the hypervariable region II (HVRII) of the mitochondrial DNA (mtDNA) control region using immobilised sequence-specific oligonucleotide (SSO) probes. A total of 16 SSO probes was used to type 1081 individuals from eight different ethnic groups (African Americans, Somali, US Europeans, US Hispanics, Bosnians, Finns, Saami and Japanese). Data was compared with already published sequence data by analysis of principal components, genetic distances and analysis of the molecular variance (AMOVA). The analyses performed group the samples in several clusters according to their geographical origins. Most of the variability detected is assigned to differences between individuals and only 7% is assigned to differences among groups of populations within and between geographical regions. Several features are patent in the samples studied: Somali, as a representative East African population, seem to have experienced a detectable amount of Caucasoid maternal influence; different degrees of admixture in the US samples studied are detected; Finns and Saami belong to the European genetic landscape, although Saami present an outlier position attributable to a strong maternal founder effect. The technique used is a rapid and simple method to detect human variation in the mtDNA HVRII in a large number of samples, which might be useful in forensic and population genetic studies.

Finally some info on Somali mt DNA, although it’s not very detailed, probably due to it’s age (‘99).

It’s also got a little snippet of autosomal info on Somalis.

Our Somali sample presents features that clearly locate it close to the African samples, but European features are also evident…. For a simple approach to measure the Caucasoid influence in East Africa, the triangle method described by Cavalli-Sforza et al was used to compute the proportion of admixture from the genetic distance matrix. Taking the British as a representative Caucasoid sample and the Mandenka as a sub-Saharan population, the proportion m of caucasoid lineages in the Somali is m = 0.46. This value is similar to the estimate based on autosomal studies (m = 0.40), and clearly higher than the estimates for the mtDNA found in Ethiopians 1 (m = 0.05–0.27)

The last paper I saw put M1 down as 20%, so I’d guess a lot of this input is  ancient. This makes Somalis (at least, the ones tested) about the same as Ethiopians for Eurasian ancestry (40% ish). I’d guess some of this dates back to the expansion from Egypt. The Ethiopian maternal Eurasian contributions is now more like 40%  (GOT paper) so I assume the data they are reffering to had M1 as African (incorrect now).

The paper describes Hispanics as well, quite a mixed bag genetically, no surprise, and estimates African ancestry in white Americans at 0.8%, and European in black Americans as about 22%, which are very close to the later studies done (I believe the latest tests by Shriver had African ancestry in white Americans as 0.7%).