Tag Archives: Mitochondrial DNA.

Ancient Jomon DNA from Hokkaido

Mitochondrial DNA analysis of the Jomon and Epi-Jomon individuals in Hokkaido, Japan.

American Journal of Physical Anthropology doi: 10.1002/ajpa.20923

N. Adachi1, K. Shinoda2, K. Umetsu3, Y. Dodo1. 1Department of Anatomy and Anthropology, Tohoku University School of
Medicine, 2Department of Anthropology, National Science Museum, Tokyo, 3Department of Experimental and Forensic
Pathology, Faculty of Medicine, Yamagata University.

From the morphological point of view, prehistoric populations in Hokkaido are considered to have been least influenced by Yayoi immigrants. Therefore, genetic study of these people can be expected to provide important information on the genealogy of the early settlers of the Japanese archipelago. In the present study, we examined the genealogy of the seventy-six Jomon and Epi-Jomon skeletons excavated in Hokkaido, Japan by mitochondrial DNA analysis. To identify their genealogy securely, we analyzed the coding region of mtDNA by using amplified product-length polymorphisms (Umetsu et al., 2001, 2005) and direct sequencing. We also sequenced the segments of two hypervariable regions of mtDNA, and  assigned the mtDNA under study to relevant haplogroups using the known mtDNA databases.

Haplogroups D4, G1, M7a, and N9b were observed in the individuals, and N9b was by far the most predominant. The requencies of the haplogroups were quite different from any modern populations including Ainu and Okinawans. Haplogroup N9b is hitherto observed almost only in Japanese populations; therefore, this  haplogroup might be the (pre-) Jomon contribution to the modern Japanese mtDNA pool.

I’m looking for something on this journal summary, so I’ll be posting a lot of abtracts from it today.More on ancient Jomon DNA.

Mitochondrial DNA analysis of Jomon skeletons from the Funadomari site, Hokkaido, and its implication for the origins of Native American 
 
Ancient DNA recovered from 16 Jomon skeletons excavated from Funadomari site, Hokkaido, Japan was analyzed to elucidate the genealogy of the early settlers of the Japanese archipelago. Both the control and coding regions of their mitochondrial DNA were analyzed in detail, and we could securely assign 14 mtDNAs to relevant haplogroups. Haplogroups D1a, M7a, and N9b were observed in these individuals, and N9b was by far the most predominant. The fact that haplogroups N9b and M7a were observed in Hokkaido Jomons bore out the hypothesis that these haplogroups are the (pre-) Jomon contribution to the modern Japanese mtDNA pool. Moreover, the fact that Hokkaido Jomons shared haplogroup D1 with Native Americans validates the hypothesized genetic affinity of the Jomon people to Native Americans, providing direct evidence for the genetic relationships between these populations. However, probably due to the small sample size or close consanguinity among the members of the site, the frequencies of the haplogroups in Funadomari skeletons were quite different from any modern populations, including Hokkaido Ainu, who have been regarded as the direct descendant of the Hokkaido Jomon people. It appears that the genetic study of ancient populations in northern part of Japan brings important information to the understanding of human migration in northeast Asia and America.

Origin and Diffusion of mtDNA Haplogroup X

Origin and Diffusion of mtDNA Haplogroup X

AbstractA maximum parsimony tree of 21 complete mitochondrial DNA (mtDNA) sequences belonging to haplogroup X and the survey of the haplogroup-associated polymorphisms in 13,589 mtDNAs from Eurasia and Africa revealed that haplogroup X is subdivided into two major branches, here defined as “X1” and “X2.” The first is restricted to the populations of North and East Africa and the Near East, whereas X2 encompasses all X mtDNAs from Europe, western and Central Asia, Siberia, and the great majority of the Near East, as well as some North African samples. Subhaplogroup X1 diversity indicates an early coalescence time, whereas X2 has apparently undergone a more recent population expansion in Eurasia, most likely around or after the last glacial maximum. It is notable that X2 includes the two complete Native American X sequences that constitute the distinctive X2a clade, a clade that lacks close relatives in the entire Old World, including Siberia. The position of X2a in the phylogenetic tree suggests an early split from the other X2 clades, likely at the very beginning of their expansion and spread from the Near East.
Further northeast of the Altai area, haplogroup X sequences were detected in the Tungusic-speaking Evenks, of the Podkamennaya Tunguska basin (Central Siberia). In contrast to the Altaians, the Evenks did not harbor any West Eurasian mtDNA haplogroups other than X. However, neither of the two Evenk X haplotypes showed mutations characteristic of the Native American clade X2a. Instead, one sequence was a member of X2b and the other of X2* (fig. 2). Thus, one possible scenario is that several X haplotypes arrived in Siberia from western Asia during the Palaeolithic, but only X2a crossed Beringia and survived in modern Native Americans. Alternatively, the presence of two phylogenetically different haplogroup X mtDNA sequences in this particular subpopulation of Evenks might be due to recent gene flow

Part of my attempt to get to grips with the phantom ancestor of X2a. I have to say, that I find accepting an East Asian source for the X2 hard, and it’s largely to do with the dates that X2 as a hg has. If the coalescence of the entire X2 Hg is somewhere between 20 to 30k, and seems to be focused in West Asia, then how it managed to move itself so fast over all of Asia to colonise America via Siberia is a bit of a mystery, particularly since it seemed to do so without leaving a trace there. It seems the possibility it came across the Atlantic ocean is very unpopular.

Distinctive Paleo-Indian Migration Routes from Beringia Marked by Two Rare mtDNA Haplogroups

Distinctive Paleo-Indian Migration Routes from Beringia Marked by Two Rare mtDNA Haplogroups

Summary
It is widely accepted that the ancestors of Native Americans arrived in the New World via Beringia approximately 10 to 30 thousand years ago (kya). However, the arrival time(s), number of expansion events, and migration routes into the Western Hemisphere remain controversial because linguistic, archaeological, and genetic evidence have not yet provided coherent answers. Notably, most of the genetic evidence has been acquired from the analysis of the common pan-American mitochondrial DNA (mtDNA) haplogroups. In this study, we have instead identified and analyzed mtDNAs belonging to two rare Native American haplogroups named D4h3 and X2a. Phylogeographic analyses at the highest level of molecular resolution (69 entire mitochondrial genomes) reveal that two almost concomitant paths of migration from Beringia led to the Paleo-Indian dispersal approximately 1517 kya. Haplogroup D4h3 spread into the Americas along the Pacific coast, whereas X2a entered through the ice-free corridor between the Laurentide and Cordilleran ice sheets. The examination of an additional 276 entire mtDNA sequences provides similar entry times for all common Native American haplogroups, thus indicating at least a dual origin for Paleo-Indians. A dual origin for the first Americans is a striking novelty from the genetic point of view, and it makes plausible a scenario positing that within a rather short period of time, there may have been several entries into the Americas from a dynamically changing Beringian source. Moreover, this implies that most probably more than one language family was carried along with the Paleo-Indians.

image

I’m curious.. did they find a parent for X2a in East Asia? As far as I know the only possible HG ancestral to it is on the West coast of Europe. I shall have to check up.

The mitochondrial lineage U8a reveals a Paleolithic settlement in the Basque country

The mitochondrial lineage U8a reveals a Paleolithic settlement in the Basque country
Ana M González1 , Oscar García2 , José M Larruga1  and Vicente M Cabrera1

Published: 23 May 2006

Background
It is customary, in population genetics studies, to consider Basques as the direct descendants of the Paleolithic Europeans. However, until now there has been no irrefutable genetic proof to support this supposition. Even studies based on mitochondrial DNA (mtDNA), an ideal molecule for constructing datable maternal genealogies, have failed to achieve this. It could be that incoming gene flow has replaced the Basque ancient lineages but it could also be that these lineages have not been detected due to a lack of resolution of the Basque mtDNA genealogies. To assess this possibility we analyzed here the mtDNA of a large sample of autochthonous Basques using mtDNA genomic sequencing for those lineages that could not be unequivocally classified by diagnostic RFLP analysis and control region (HVSI and HVSII) sequencing.
Results
We show that Basques have the most ancestral phylogeny in Europe for the rare mitochondrial subhaplogroup U8a. Divergence times situate the Basque origin of this lineage in the Upper Palaeolithic. Most probably, their primitive founders came from West Asia. The lack of U8a lineages in Africa points to an European and not a North African route of entrance. Phylogeographic analysis suggest that U8a had two expansion periods in Europe, the first, from a south-western area including the Iberian peninsula and Mediterranean France before 30,000 years ago, and the second, from Central Europe around 15,000–10,000 years ago.

Conclusion
It has been demonstrated, for the first time, that Basques show the oldest lineages in Europe for subhaplogroup U8a. Coalescence times for these lineages suggest their presence in the Basque country since the Upper Paleolithic. The European U8 phylogeography is congruent with the supposition that Basques could have participated in demographic re-expansions to repopulate central Europe in the last interglacial periods.

I’ll read this one a bit more thoroughly when the kids calm down.

Mitochondrial DNA variation in Jordanians

Mitochondrial DNA variation in Jordanians and their genetic relationship to other Middle East populations.

González AM, Karadsheh N, Maca-Meyer N, Flores C, Cabrera VM, Larruga JM.

BACKGROUND: The Levant is a crucial region in understanding human migrations between Africa and Eurasia. Although some mitochondrial DNA (mtDNA) studies have been carried out in this region, they have not included the Jordan area. This paper deals with the mtDNA composition of two Jordan populations. AIM: The main objectives of this article are: first, to report mtDNA sequences of an urban and an isolate sample from Jordan and, second, to compare them with each other and with other nearby populations.

SUBJECTS AND METHODS: The analyses are based on HVSI and HVSII mtDNA sequences and diagnostic RFLPs to unequivocally classify into haplogroups 101 Amman and 44 Dead Sea unrelated individuals from Jordan.

RESULTS: Statistical analysis revealed that, whereas the sample from Amman did not significantly differ from their Levantine neighbours, the Dead Sea sample clearly behaved as a genetic outlier in the region. Its outstanding Eurasian haplogroup U3 frequency (39%) and its south-Saharan Africa lineages (19%) are the highest in the Middle East. On the contrary, the lack ((preHV)1) or comparatively low frequency (J and T) of Neolithic lineages is also striking. Although strong drift by geographic isolation could explain the anomalous mtDNA pool of the Dead Sea sample, the fact that its mtDNA lineage composition mirrors, in geographic origin and haplogroup frequencies, its Y-chromosome pool, points to founder effect as the main cause. Ancestral M1 lineages detected in Jordan that have affinities with those recently found in Northwest but not East Africa question the African origin of the M1 haplogroup.

CONCLUSION: Results are in agreement with an old human settlement in the Jordan region. However, in spite of the attested migratory spreads, genetically divergent populations, such as that of the Dead Sea, still exist in the area.

If I ever find the full text for this I’ll link to it. I’m guessing the Jordan area could be a possible origin ppoint for M1

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)..

m1-dist21

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.

 em781

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.

Tracing European founder lineages in the Near Eastern mtDNA pool

Tracing European founder lineages in the Near Eastern mtDNA pool

Founder analysis is a method for analysis of nonrecombining DNA sequence data, with the aim of identification and dating of migrations into new territory. The method picks out founder sequence types in potential source populations and dates lineage clusters deriving from them in the settlement zone of interest. Here, using mtDNA, we apply the approach to the colonization of Europe, to estimate the proportion of modern lineages whose ancestors arrived during each major phase of settlement. To estimate the Palaeolithic and Neolithic contributions to European mtDNA diversity more accurately than was previously achievable, we have now extended the Near Eastern, European, and northern-Caucasus databases to 1,234, 2, 804, and 208 samples, respectively. Both back-migration into the source population and recurrent mutation in the source and derived populations represent major obstacles to this approach. We have developed phylogenetic criteria to take account of both these factors, and we suggest a way to account for multiple dispersals of common sequence types. We conclude that (i) there has been substantial back-migration into the Near East, (ii) the majority of extant mtDNA lineages entered Europe in several waves during the Upper Palaeolithic, (iii) there was a founder effect or bottleneck associated with the Last Glacial Maximum, 20,000 years ago, from which derives the largest fraction of surviving lineages, and (iv) the immigrant Neolithic component is likely to comprise less than one-quarter of the mtDNA pool of modern Europeans.

euromtdna1

Extensive female-mediated gene flow from sub-Saharan Africa into near eastern Arab populations

Extensive female-mediated gene flow from sub-Saharan Africa into near eastern Arab populations.

We have analyzed and compared mitochondrial DNA variation of populations from the Near East and Africa and found a very high frequency of African lineages present in the Yemen Hadramawt: more than a third were of clear sub-Saharan origin. Other Arab populations carried ~10% lineages of sub-Saharan origin, whereas non-Arab Near Eastern populations, by contrast, carried few or no such lineages, suggesting that gene flow has been preferentially into Arab populations. Several lines of evidence suggest that most of this gene flow probably occurred within the past ~2,500 years. In contrast, there is little evidence for male-mediated gene flow from sub-Saharan Africa in Y-chromosome haplotypes in Arab populations, including the Hadramawt. Taken together, these results are consistent with substantial migration from eastern Africa into Arabia, at least in part as a result of the Arab slave trade, and mainly female assimilation into the Arabian population as a result of miscegenation and manumission.

This study appears to show the genetic legacy in Arabia of the Arab slave trade in black Africans, with the contribtion from African males being virtually non existant. It’s estimated that Arab slavery brought roughly 15 million African slaves into North Africa and the Saudi peninsula.

Dingoes arrived in Australia about 6,000 years ago, from China.

The dingo may have been introduced on a single occasion to Australia

Dingo, APA genetic analysis of the Australian dingo suggests the dogs tagged along on an epic expansion of people out of southern China around 6,000 years ago.
An international team claims dingoes descend from a small group that could have been introduced to Australia in a “single chance event” from Asia.

Evidence from mitochondrial DNA suggests that the wild dogs arrived on the continent around 5,000 years ago.

The work appears in Proceedings of the National Academy of Sciences.

Peter Savolainen of the Royal Institute of Technology in Stockholm, Sweden, and colleagues think the introduction of the dogs may be associated with the spread of seafaring Austronesian-speaking people throughout South-East Asia.

The Austronesian culture had its origins in south China, expanding from Taiwan via the Philippines to Indonesia.

Although dingoes are now wild, they descend from domestic dogs that accompanied these Austronesians on their voyages.

Family tree

The new data comes from an analysis of dingo, dog and wolf mitochondrial DNA (mtDNA) types. This is the DNA found in the cell’s “power houses”, and it is passed down from parent to offspring on the maternal side only.

On a family tree of mtDNA types in different members of the dog family, dingoes sit on a major branch alongside 70% of domestic dog sequences.

All the dingo mtDNA types either belonged to or showed great similarity to a single type called A29.

DNA links dingoes to an expansion out of southern China
Studies of dingo physiques suggest they are very similar to Indian pariah dogs and wolves. This has led some researchers to propose that seafaring peoples from India may have introduced them to Australia.

But among domestic dogs, A29 is found only in East Asia, suggesting the dogs’ origins lie here, rather than on the Indian subcontinent. The researchers analysed mtDNA sequences in 211 dingoes and compared them to a world-wide sample of 676 dogs.

When Europeans arrived in Australia, the dingo was widespread, living mostly as a wild animal. However, some Aboriginal groups kept them as pets or as hunting dogs.

And the DNA study for more detail

A detailed picture of the origin of the Australian dingo, obtained from the study of mitochondrial DNA
Peter Savolainen*,†, Thomas Leitner‡, Alan N. Wilton§, Elizabeth Matisoo-Smith¶, and Joakim Lundeberg*
+Author Affiliations 

Abstract
To determine the origin and time of arrival to Australia of the dingo, 582 bp of the mtDNA control region were analyzed in 211 Australian dingoes sampled in all states of Australia, 676 dogs from all continents, and 38 Eurasian wolves, and 263 bp were analyzed in 19 pre-European archaeological dog samples from Polynesia. We found that all mtDNA sequences among dingoes were either identical to or differing by a single substitution from a single mtDNA type, A29. This mtDNA type, which was present in >50% of the dingoes, was found also among domestic dogs, but only in dogs from East Asia and Arctic America, whereas 18 of the 19 other types were unique to dingoes. The mean genetic distance to A29 among the dingo mtDNA sequences indicates an origin ≈5,000 years ago. From these results a detailed scenario of the origin and history of the dingo can be derived: dingoes have an origin from domesticated dogs coming from East Asia, possibly in connection with the Austronesian expansion into Island Southeast Asia. They were introduced from a small population of dogs, possibly at a single occasion, and have since lived isolated from other dog populations

Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis

Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis
Georgi Hudjashova, Toomas Kivisilda,b,c, Peter A. Underhilld, Phillip Endicotte, Juan J. Sanchezf, Alice A. Lind, Peidong Sheng, Peter Oefnerh, Colin Renfrewc,i, Richard Villemsa, and Peter Forsterj, 2007.

Published and new samples of Aboriginal Australians and Melanesians were analyzed for mtDNA (n = 172) and Y variation (n = 522), and the resulting profiles were compared with the branches known so far within the global mtDNA and the Y chromosome tree. (i) All Australian lineages are confirmed to fall within the mitochondrial founder branches M and N and the Y chromosomal founders C and F, which are associated with the exodus of modern humans from Africa ≈50–70,000 years ago. The analysis reveals no evidence for any archaic maternal or paternal lineages in Australians, despite some suggestively robust features in the Australian fossil record, thus weakening the argument for continuity with any earlier Homo erectus populations in Southeast Asia. (ii) The tree of complete mtDNA sequences shows that Aboriginal Australians are most closely related to the autochthonous populations of New Guinea/Melanesia, indicating that prehistoric Australia and New Guinea were occupied initially by one and the same Palaeolithic colonization event ≈50,000 years ago, in agreement with current archaeological evidence. (iii) The deep mtDNA and Y chromosomal branching patterns between Australia and most other populations around the Indian Ocean point to a considerable isolation after the initial arrival. (iv) We detect only minor secondary gene flow into Australia, and this could have taken place before the land bridge between Australia and New Guinea was submerged ≈8,000 years ago, thus calling into question that certain significant developments in later Australian prehistory (the emergence of a backed-blade lithic industry, and the linguistic dichotomy) were externally motivated.

Conclusions
The mitochondrial and Y chromosomal results presented here point toward one early founder group settling both Australia and NG soon after the exodus from Africa ≈50–70,000 years ago, at a time when the lowered sea levels joined the two islands into one land mass, necessitating sea travel only across narrow straits such as Wallace’s Line. The deep and specific phylogenetic lineages today within this former landmass indicate a small founding population size and subsequent isolation of Australia and, to a lesser extent, of NG, from the rest of the world. These founder events and the lack of contact could underlie the divergent morphological development seen in the Australian human fossil record and could also help explain the remarkably restricted range of Pleistocene Australian lithic industries and bone artifacts compared with contemporaneous cultures elsewhere in the world (55).

Estimated dates for mtDNA:

Region Hg N ρ SE Age, yr
Aus/Mel M 50 7,9 1,1 53,400 ± 7,500
Aus/Mel Q’M29 27 6,6 1,4 44,300 ± 9,800
Aus/Mel Q 22 4,7 1,0 32,000 ± 6,500
Mel Q1 11 3,2 0,9 21,500 ± 6,100
Aus/Mel Q2 4 4,5 1,4 30,400 ± 9,300
Mel Q3 7 3,1 0,8 21,300 ± 5,500
Mel M29 5 2,8 1,2 18,900 ± 8,300
Mel M27 7 5,9 1,4 39,600 ± 9,800
Mel M28 8 3,0 1,0 20,300 ± 6,500
Mel M28a 6 1,7 0,7 11,300 ± 4,500
Aus M42 6 6,0 1,3 40,600 ± 9,000
Aus/Mel N 51 7,9 1,1 53,200 ± 7,300
Aus N12 4 2,5 1,1 16,900 ± 7,200
Aus S 12 3,8 0,8 25,400 ± 5,200
Aus S1 4 3,3 1,1 22,000 ± 7,700
Aus S2 4 2,3 0,8 15,200 ± 5,100
Aus/Mel R 33 8,6 1,2 58,400 ± 8,400
Aus/Mel P 31 7,6 0,9 51,700 ± 5,800
Mel P1 6 4,5 1,0 30,400 ± 6,500
Mel P2 7 1,9 0,6 12,600 ± 4,000
Aus/Mel P3 5 5,8 1,2 39,200 ± 8,200
Aus/Mel P4 8 9,8 1,9 65,900 ± 13,200
Aus P4b 3 7,0 1,7 47,300 ± 11,700
Mel P4a 5 3,8 1,1 25,700 ± 7,500

Y chromosomes in PNG and Aborigines.

Fig. 3.