The X chromosome in population genetics

The X chromosome in population genetics

Something I’m posting a link to for later reference, in case I see any more X chr studies. The bit I want to find quickly is…

Taken together, these studies indicate an Out of Africa origin for modern humans. Individually, however, the studies point to diverse conclusions. For example, two studies reconstructed haplotypes in introns of X chromosome-linked genes, using chromosomes drawn from many populations around the world. The first study7 found a pattern that was strongly indicative of a recent expansion (and subsequent isolation by distance) of humans from a single geographical source. The chromosomes showed two common, old (200,000–800,000 years) haplotypes with worldwide distribution, as well as many younger, derived haplotypes (~100,000 years old) with limited geographical distribution.Africa was identified as the probable source for the expansion on the basis of the higher genetic diversity there, and by the continued presence of the ancestral human haplotype (as  determined by comparison with other primates). The second study44, on the other hand, found a pattern that was more consistent with multiregionalism.

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.

Abstract

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.

The trans-Saharan slave trade – clues from interpolation analyses and high-resolution characterization of mitochondrial DNA lineages

The trans-Saharan slave trade – clues from interpolation analyses and high-resolution characterization of mitochondrial DNA lineages

Background: A proportion of ¼ to ½ of North African female pool is made of typical sub- Saharan lineages, in higher frequencies as geographic proximity to sub-Saharan Africa increases. The Sahara was a strong geographical barrier against gene flow, at least since 5,000  years ago, when desertification affected a larger region, but the Arab trans-Saharan slave trade could have facilitate enormously this migration of lineages. Till now, the genetic consequences of these forced trans-Saharan movements of people have not been ascertained.

Results: The distribution of the main L haplogroups in North Africa clearly reflects the known trans-Saharan slave routes: West is dominated by L1b, L2b, L2c, L2d, L3b and L3d; the Center by L3e and some L3f and L3w; the East by L0a, L3h, L3i, L3x and, in common with the Center, L3f and L3w; while, L2a is almost everywhere. Ages for the haplogroups observed in both sides of the Saharan desert testify the recent origin (holocenic) of these haplogroups in sub-Saharan Africa, claiming a recent introduction in North Africa, further strengthened by the no detection of local expansions.

Conclusions: The interpolation analyses and complete sequencing of present mtDNA sub-Saharan lineages observed in North Africa support the genetic impact of recent trans-Saharan migrations, namely the slave trade initiated by the Arab conquest of North Africa in the seventh century. Sub-Saharan people did not leave traces in the North African maternal gene pool from the time of its settlement, some 40,000 years ago.

I haven’t read the whole paper through yet, but just from reading the bit I put in bold.. I’m sure that a paper on ancient Guanche mtDNA showed an L haplotype or two present which meant they had to be present a few thousand years ago during the colonisation of the Canary islands.

 The majority of lineages (93%) were from West Eurasian origin, being the rest (7%) from sub-Saharan African ascription

And a very ancient age for L6 crossing over into Spain (about 20 kya) from another paper. So I’m going to state emphatically this can’t be correct. Not to mention that the ceramic using Saharan Negroid ’roundhead’ population reached as far as the Acacus mountains (about 10,500 bp) and would have had some contact/gene flow with the coastal Capsians (who were  a near Eastern /Mechtoid mixed people from the cranial studies I’ve seen and the expansion dates of Y chr J1 and H mtDNA). Although  the majority of the L haplotypes in North Africa are due to the slave trade, they can’t ALL be.
Edit:

I read through this this morning. The most interesting bits of the whole pdf for me were…

Clearly, the main component of the West Eurasian lineages was made of possible Iberian
expanded lineages following the post-glacial climate improvement: H1 (12.35%), V (9.88%)
and U5b (1.23%).

I’d debate the 14k age for this given in the paper… but they had to have arrived before the Taforalt people died as the H, HV /V turns up in those 12k old samples..

A few L3 sequences observed in North Africa have older co-ancestry with other sub-Saharan
regions, but as this occurs in the rarer haplogroups (almost restricted to East Africa), most
probably the scenario will change as these become better characterized. This is the case for
one L3x2 sequence observed in Algeria, which shares an older most recent common ancestor
with two Ethiopian, one Israeli and one Kuwait, at 33,165 ± 4,499 years ago, but one
Ethiopian and the Israeli and Kuwait sequences share a younger ancestor at 19,012 ± 4,200.
Also, one Egyptian L3f2b sequence shares an ancestor with a Chadic one at around 24,809 ±
5,935 years ago. For L3h1a2 haplogroup, one Egyptian and one Lebanese sequences share a
coalescence age of 26,281 ± 6,139 years old. And for L3h1b, with an age of 36,827 ± 3,772
years, one of the North African sequences (one Tunisian and one Moroccan) has a most recent
common ancestor of 14,766 ± 4,448 years old with a sequence from Guinea Bissau.

I’ve been looking for mtDNA that could have accompanied the M78 out of Africa (arriving in the near east and NW Africa about 22k ago). While M1 obviously fits that date, it’s nice to see that some of the L3 dates aren’t incompatible with the m78;  being found in Natufian areas of Israel and Lebanon. The Israel/Kuwait/Ethiopian L3 may be a back-migrating L haplotype, not incompatible with the return of M1 and U, or another haplotype caught up in the Lower Nubian expansion and fanned out into the same areas as the m78/M1.

So far, the two only complete published samples belonging to haplogroup L3k have a North
African origin, one from Libya and one from Tunisia. This haplogroup has a coalescent age of
around 29,251 ± 6,524 years old

Who/where did that come from?

But the most useful thing in the whole paper are the maps, which give a quick over view of L distribution in Africa. I’ve reworked this one in colour, as the original is a bit hard to make out in places.

One of the interesting patterns I noticed was the (quite possibly superficial) relation to the expansion of non-L haplotypes and L3h in E/SE Africa. Also the hotspot for L3h in Northern Sudan, makes me wonder if it may not have been a travelling companion to the non-African mt DNA’s at some time. Unlike Maju, I’d say this looks like it has an origin on the Nile rather in Ethiopia, as it seems to have a relation to the expansion pattern of the M1/M1a/m78  from Lower Nubia/Egypt.

I’m going to have a dig to see what I can find on L3h now…

A Draft Sequence of the Neandertal Genome

A Draft Sequence of the Neandertal Genome

Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.

To cut a long story short…

The authors suggest that non-Africans having about 1-4% Neanderthal ancestry is the most likely explanation for the variation in the DNA they have found. It’s not an absolute. A much less likely but not impossible scenarios is that the variation is due to population structure in Africa prior to the OOA, which may relate with the earlier separation of the ancestors of modern Africans and non-Africans inside Africa, although John Hawkes thinks this is so unlikely he was surprised they gave it space on the paper.

But, considering the number of genes in non Africans that have a time depth that is considerably older than the OOA movement (over 1 million years on one in one study by Hammer et al), and I think there is now decent evidence for Neanderthal ancestry in non-Africans.

I have some issues with the paper. Modern humans were in the near East about 120k ago, keeping company with Neanderthals for many millennia, but the interbreeding date comes out at 80,000 to 50,000 years. What were they doing with the rest of the time?

Such a scenario is compatible with the archaeological record, which shows that modern humans appeared in the Middle East before 100,000 years ago whereas the Neandertals existed in the same region after this time, probably until 50,000 years ago.

  And they observe that modern Europeans don’t seem to have a higher amount of Neanderthal ancestry than anyone else. But then they add:

 This possibility can be addressed by the determination of genome sequences from pre agricultural early modern humans in Europe (85). It is also possible that if the expansion of modern humans occurred differently in Europe than in the Middle East, for example by already large populations interacting with Neandertals, then there may be little or no trace of any gene flow in present-day Europeans even if interbreeding occurred.  

Which is what I suspect is more likely. I’d also like to address the apparent lack of modern human ancestry in the Neanderthals: well a quick look at the dates of the remains sampled; not younger than 38,000 BP. Which is prior to the date modern humans started to move into that part of Europe. Possibly a future investigation of later dated remains would show some AMH ancestry in them, as their appearance suugests they may be hybrids. I think the  Lagar Velho specimen would be a possible source, although it would be a pity to damage the specimen, possibly the Gorham’s Cave bones could yield relevant information.

So, non-Africans are definitely part Neanderthal

Finally the DNA evidence is in from Paabo ect. I thought I detected signs of a back track last year when he said they had probably had sex.

Neanderthal Genome Yields Insights Into Human Evolution and Evidence of Interbreeding With Modern Humans

 “We can now say that, in all probability, there was gene flow from Neanderthals to modern humans,” said the paper’s first author, Richard E. (Ed) Green of the University of California, Santa Cruz.

I’m trying to locate the full text for the Science article later. But my PC time is a bit limited today. However, I am officially entering smug mode now. Told you so.

I image there are a few anthropologists hopping up and down like excited orangutans right now at the news. To quote John Hawks:

Out-of-Africa movement was a major mechanism of recent human evolution. The genetic ancestry of living people is multiregional.

And

It does define all non-Africans today as an interspecific hybrid population.

From the article..

“The scenario is not what most people had envisioned,” Green said. “We found the genetic signal of Neanderthals in all the non-African genomes, meaning that the admixture occurred early on, probably in the Middle East, and is shared with all descendants of the early humans who migrated out of Africa.”

Which would suggest that the Levant, where modern humans and Neanderthals co-existed for some time about 120k ago was a mixing place for the two. According to the article, between 1% nd 4% of the genomes of non-Africans in Neanderthal in origin, which pretty much tallies with some of the older studies done (they are on the blog if you want to hunt them down).

The estimate of the time of admixture is around 50,000-80,000 years, however I’m not really sure why that should be correct, seeing as they first encountered each other prior to the ‘beach buggy’ colonisation of S/SE Asia, which would kind of place 80k as a bare minimum age, and more like 100k as there is some evidence of modern humans in SE Asia 74k ago under the Toba ash (necessitating a dispersal date for SE Asian populations of about 95k min). I also wonder what implications this has for the route out of Africa, as an exit via the Gate of Tears would make it less likely they’d come into contact with the Med coast Neanderthals of the era. I wonder if the number is more a composite of the very early mix in the Levant, followed by a later addition of Neanderthal DNA in Europe.

Having a happy day 🙂

The lineage of King Tutankhamun from ancient DNA analysis

The news of the month, kindly posted to me by a friend, is that they have proved via ADNA that the mummy from tomb Kv55 is Akhenaten, son of Amenhotep III and king Tutankhamun’s father, and that the younger lady (KV35) is his mother. It also seems Tut died of malaria and suffered congenital deformities, which I’d guess were the result of incestuous marriages in the royal family. This means that the prior ageing of KV55 as 18 was way off.

This also mean that queen the red-haired queen Tiye (elder lady mummy) was the mother of Kv35 (using logic, they all have the same mt DNA), which might explain why they were found in the same tomb.

I’ve prepared a brief genealogy.

      

Known grandparents  

 Amenhotep III  and Tiye (whose parents were Tuya and Yuya)

        

Known parents

Akhenaten (Kv 55)  and  (KV 35).

The actual name of KV35 uncertain but she has been suggested as Nefertiti, these were brother and sister.

 

 Tutankhamun, who appears to have also married his sister Ankhesenamun.

It would be interesting to see if the mummy in Kv21A is indeed Tut’s wife Ankhesenamun, as she is known to be the daughter of Nefertiti and Akhenaten, and this could give a definitive answer as to whether Kv35 is in fact Nefertiti.  Ankhesenamun has been identified as the mother of one of the fetuses from Tut’s tomb, so this might be on the cards for the future.

Ancestry and Pathology in King Tutankhamun’s Family
Zahi Hawass, PhD; Yehia Z. Gad, MD; Somaia Ismail, PhD; Rabab Khairat, MSc; Dina Fathalla, MSc; Naglaa Hasan, MSc; Amal Ahmed, BPharm; Hisham Elleithy, MA; Markus Ball, MSc; Fawzi Gaballah, PhD; Sally Wasef, MSc; Mohamed Fateen, MD; Hany Amer, PhD; Paul Gostner, MD; Ashraf Selim, MD; Albert Zink, PhD; Carsten M. Pusch, PhD
JAMA. 2010;303(7):638-647.

Context

  The New Kingdom in ancient Egypt, comprising the 18th, 19th, and 20th dynasties, spanned the mid-16th to the early 11th centuries BC. The late 18th dynasty, which included the reigns of pharaohs Akhenaten and Tutankhamun, was an extraordinary time. The identification of a number of royal mummies from this era, the exact relationships between some members of the royal family, and possible illnesses and causes of death have been matters of debate.

Objectives

  To introduce a new approach to molecular and medical Egyptology, to determine familial relationships among 11 royal mummies of the New Kingdom, and to search for pathological features attributable to possible murder, consanguinity, inherited disorders, and infectious diseases.

Design

  From September 2007 to October 2009, royal mummies underwent detailed anthropological, radiological, and genetic studies as part of the King Tutankhamun Family Project. Mummies distinct from Tutankhamun’s immediate lineage served as the genetic and morphological reference. To authenticate DNA results, analytical steps were repeated and independently replicated in a second ancient DNA laboratory staffed by a separate group of personnel. Eleven royal mummies dating from circa 1410-1324 BC and suspected of being kindred of Tutankhamun and 5 royal mummies dating to an earlier period, circa 1550-1479 BC, were examined.

Main Outcome Measures

  Microsatellite-based haplotypes in the mummies, generational segregation of alleles within possible pedigree variants, and correlation of identified diseases with individual age, archeological evidence, and the written historical record.

Results

Genetic fingerprinting allowed the construction of a 5-generation pedigree of Tutankhamun’s immediate lineage. The KV55 mummy and KV35YL were identified as the parents of Tutankhamun. No signs of gynecomastia and craniosynostoses (eg, Antley-Bixler syndrome) or Marfan syndrome were found, but an accumulation of malformations in Tutankhamun’s family was evident. Several pathologies including Köhler disease II were diagnosed in Tutankhamun; none alone would have caused death. Genetic testing for STEVOR, AMA1, or MSP1 genes specific for Plasmodium falciparum revealed indications of malaria tropica in 4 mummies, including Tutankhamun’s. These results suggest avascular bone necrosis in conjunction with the malarial infection as the most likely cause of death in Tutankhamun. Walking impairment and malarial disease sustained by Tutankhamun is supported by the discovery of canes and an afterlife pharmacy in his tomb.

Conclusion  Using a multidisciplinary scientific approach, we showed the feasibility of gathering data on Pharaonic kinship and diseases and speculated about individual causes of death.

According to someone (not me) who has been bothered to enter the Y chr markers as seen on the video, Tut is coming up as R1b. I’d have put money on it being something more like an E1 Y chr, or maybe J as an outside chance…R1b isn’t unknown in Egypt, (see Wood 2005) but isn’t exactly common. R1b appears to have entered Africa from Asia sometime in the Neolithic along with Afro-Asiatic, which is really all I have to say until I get a published source and more detail. Can’t get any detail on the mt DNA, unfortunately. 

For anyone interested, there’s a bunch of videos at the Discovery Channel site about this, with some good shots of Akhenaten in his coffin.

Mitochondrial DNA and Y-Chromosome Variation in the Caucasus

Mitochondrial DNA and Y-Chromosome Variation in the Caucasus

We have analyzed mtDNA HVI sequences and Y chromosome haplogroups based on 11 binary markers in 371 individuals, from 11 populations in the Caucasus and the neighbouring countries of Turkey and Iran. Y chromosome haplogroup diversity in the Caucasus was almost as high as in Central Asia and the Near East, and significantly higher than in Europe. More than 27% of the variance in Y-haplogroups can be attributed to differences between populations, whereas mtDNA showed much lower heterogeneity between populations (less then 5%), suggesting a strong influence of patrilocal social structure. Several groups from the highland region of the Caucasus exhibited low diversity and high differentiation for either or both genetic systems, reflecting enhanced genetic drift in these small, isolated populations. Overall, the Caucasus groups showed greater similarity with West Asian than with European groups for both genetic systems, although this similarity was much more pronounced for the Y chromosome than for mtDNA, suggesting that male-mediated migrations from West Asia have influenced the genetic structure of Caucasus populations.

An older paper, but one I hadn’t taken a look at.

Unfortunately there isn’t as much detail on the mt DNA.

From one long ago read text, I can remember that one North Caucasus late neolithic site had a tendency to have Mediterranean male crania with the more robust local females. This could support that  population movements into the area from the Iran/Turkey area (birthplace of the Neolithic) may have been male lead, which might give a clue as to how each the Caucasus population has such a heterogenous Y chromosome profile.

Lewontin’s fallacy

No, I’m not dead, just recovering from an MS attack that ‘turned off’ my curiosity and messed up my memory for a couple of months. I will look at the comments (all 254 of them) eventually.

I was slightly irked at watching channels 4’s shockingly bad and biased series on race, in which it trotted out Lewontin’s fallacy on the programs and on its supporting material on its site. All the criticisms I posted (they had an OOA date of 50k ago, don’t get me started…) have not been allowed through to the site, so I’m going to have a mini rant here. It’s not that they are supporting the ‘no race’ line (hey, you can disagree with me), but that they are pretending that it is the consensus view among anthropologists and geneticists- no-one is allowed to post the recent work that outright states that race is real.

First of all here is the article which explained why the claims for low diversity in humans were over exaggerated…

Human genetic diversity: Lewontin’s fallacy

In popular articles that play down the genetical differences among human populations, it is often stated that about 85% of the total genetical variation is due to individual differences within populations and only 15% to differences between populations or ethnic groups. It has therefore been proposed that the division of Homo sapiens into these groups is not justified by the genetic data. This conclusion, due to R.C. Lewontin in 1972, is unwarranted because the argument ignores the fact that most of the information that distinguishes populations is hidden in the correlation structure of the data and not simply in the variation of the individual factors. The underlying logic, which was discussed in the early years of the last century, is here discussed using a simple genetical example.

Worth a read.

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.