Tag Archives: Mitochondrial DNA.

Using ancient DNA to examine genetic continuity at the Mesolithic-Neolithic transition in Portugal

Using ancient DNA to examine genetic continuity at the Mesolithic-Neolithic transition in Portugal

Two main mechanisms for the introduction of agriculture at the transition from the Mesolithic to the Neolithic in Portugal have been proposed: indigenous adoption and colonisation. Distinguishing between these mechanisms can be regarded as a question of genetic continuity or discontinuity at the transition. A genetic comparison of late Mesolithic and early Neolithic populations at the transition using ancient DNA is described here. Mitochondrial DNA (mtDNA) was extracted from human remains collected in several Mesolithic sites of the Sado estuary and from Neolithic cave sites. Phylogenetic analysis, based on the mitochondrial hypervariable region 1 (HVSI), and comparison with DNA from modern European populations was performed. The absence of mtDNA haplogroup J in the ancient Portuguese Neolithic sample suggests that this population was not derived directly from Near Eastern farmers. The Mesolithic and Neolithic groups show genetic discontinuity implying colonisation at the Neolithic transition in Portugal.

A study of Mesolithic and Neolithic Mt DNA from sites inPortugal.

mesoneoportugal1

J shows iself to be absent from the Mesolithic and Neolithic samples, and there was some loss of diversity in less common Hg’s. There’s a fair difference between the Mesolithic and Neolithic samples, suggestin population discontinuity-probably a large amount of immgration at the start of the neolithic, although the lack of J suggests this wasn’t from the near East

mesodna

old-dna-port

It also mentions isotope studies on the bones show a very abrupt change from the Meolithic Maritime diet to the land based Neolithic diet, the same as in Britain.

Deep common ancestry of Indian and western-Eurasian mitochondrial DNA lineages

mtdna1

Deep common ancestry of Indian and western-Eurasian mitochondrial DNA lineages

About a fifth of the human gene pool belongs largely either to Indo-European or Dravidic speaking people inhabiting the Indian peninsula. The ‘Caucasoid share’ in their gene pool is thought to be related predominantly to the Indo-European speakers. A commonly held hypothesis, albeit not the only one, suggests a massive Indo-Aryan invasion to India some 4,000 years ago [1]. Recent limited analysis of maternally inherited mitochondrial DNA (mtDNA) of Indian populations has been interpreted as supporting this concept [2,3]. Here, this interpretation is questioned. We found an extensive deep late Pleistocene genetic link between contemporary Europeans and Indians, provided by the mtDNA haplogroup U, which encompasses roughly a fifth of mtDNA lineages of both populations. Our estimate for this split is close to the suggested time for the peopling of Asia and the first expansion of anatomically modern humans in Eurasia [4–8] and likely pre-dates their spread to Europe. Only a small fraction of the ‘Caucasoid-specific’ mtDNA lineages found in Indian populations can be ascribed to a relatively recent admixture.

Not that I support an Indo European invasion at that date, anyway.

The Making of the African mtDNA Landscape

The Making of the African mtDNA Landscape

Africa presents the most complex genetic picture of any continent, with a time depth for mitochondrial DNA
(mtDNA) lineages 1100,000 years. The most recent widespread demographic shift within the continent was most probably the Bantu dispersals, which archaeological and linguistic evidence suggest originated in West Africa 3,000–4,000 years ago, spreading both east and south. Here, we have carried out a thorough phylogeographic analysis of mtDNA variation in a total of 2,847 samples from throughout the continent, including 307 new sequences from southeast African Bantu speakers. The results suggest that the southeast Bantu speakers have a composite origin on the maternal line of descent, with ~44% of lineages deriving from West Africa, ~21% from either West or Central Africa, ~30% from East Africa, and ~5% from southern African Khoisan-speaking groups. The ages of the major founder types of both West and East African origin are consistent with the likely timing of Bantu dispersals, with those from the west somewhat predating those from the east. Despite this composite picture, the southeastern African Bantu groups are indistinguishable from each other with respect to their mtDNA, suggesting that they either had a common origin at the point of entry into southeastern Africa or have undergone very extensive gene flow since.

An old paper from 2002 that I’m posting for reference while I’m hunting down info on L3a.

Paragroup L3A
We here define two previously unlabeled subclades of L3A, L3f, and L3g. The lineages remaining within L3* represent ~20% of all L3A types in Africa. Although they are distributed throughout the continent, they reach the highest frequencies in East Africa, where they account for about half of all types from this region. This frequency profile suggests an origin for L3 in East Africa (Watson et al. 1997). This is supported by the evidence that the out-of-Africa migration, which took place from a source in East Africa 60,000–80,000 years ago, gave rise only to L3 lineages outside Africa.

mtDNA Variation in the South African Kung and Khwe—and Their Genetic Relationships to Other African Populations

mtDNA Variation in the South African Kung and Khwe—and Their Genetic Relationships to Other African Populations

The mtDNA variation of 74 Khoisan-speaking individuals (Kung and Khwe) from Schmidtsdrift, in the Northern Cape Province of South Africa, was examined by high-resolution RFLP analysis and control region (CR) sequencing. The resulting data were combined with published RFLP haplotype and CR sequence data from sub-Saharan African populations and then were subjected to phylogenetic analysis to deduce the evolutionary relationships among them. More than 77% of the Kung and Khwe mtDNA samples were found to belong to the major mtDNA lineage, macrohaplogroup L* (defined by a HpaI site at nucleotide position 3592), which is prevalent in sub-Saharan African populations. Additional sets of RFLPs subdivided macrohaplogroup L* into two extended haplogroups—L1 and L2—both of which appeared in the Kung and Khwe. Besides revealing the significant substructure of macrohaplogroup L* in African populations, these data showed that the Biaka Pygmies have one of the most ancient RFLP sublineages observed in African mtDNA and, thus, that they could represent one of the oldest human populations. In addition, the Kung exhibited a set of related haplotypes that were positioned closest to the root of the human mtDNA phylogeny, suggesting that they, too, represent one of the most ancient African populations. Comparison of Kung and Khwe CR sequences with those from other African populations confirmed the genetic association of the Kung with other Khoisan-speaking peoples, whereas the Khwe were more closely linked to non–Khoisan-speaking (Bantu) populations. Finally, the overall sequence divergence of 214 African RFLP haplotypes defined in both this and an earlier study was 0.364%, giving an estimated age, for all African mtDNAs, of 125,500–165,500 years before the present, a date that is concordant with all previous estimates derived from mtDNA and other genetic data, for the time of origin of modern humans in Africa.

I’m going through a lot of DNA studies atthe moment looking for evidence of M1 and M. Apparently one  HG, L3a, seems closely related to it, as L3a is the precursor to M.

The Asian mtDNA phylogeny is subdivided into two macrohaplogroups, one of which is M. M is delineated by a DdeI site at np 10394 and an AluI site of np 10397. The only African mtDNA found to have both of these sites is the Senegalese haplotype AF24. This haplotype branches off African subhaplogroup L3a (figs.2 and3), suggesting that haplogroup M mtDNAs might have been derived from this African mtDNA lineage; however, it is also possible that this particular haplotype is present in Africa because of back-migration from Asia.

I was entertained to see someone was using this to claim M1 was African in origin on another site.. leaving out the inconvenient back-migration from Asia at the end of the quote. Since M itself seems absent in Africa, and M1 traces the path of U in North and East Africa pretty closely, it’s now pretty much a done deal that M1 arrived in North Africa from West Asia. The real mystery is the lack of L3 and M in India, but the Toba eruption could easily have caused a wipe out across India that erased the first immigrants there. I’d like to observe that this L3a seems to have followed the North African population movements that curved southwards down into the West coast of Africa, so I think that its from the back migration may be possible, or at least dating to the expansion from upper Egypt about 24k ago with a origin from the Nile area. I shall have a dig into L3a distribution, something I should have done a while ago.

Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans

Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans

Recent advances in the understanding of the maternal and paternal heritage of southand southwest Asian populations have highlighted their role in the colonization of Eurasia byanatomically modern humans. Further understanding requires a deeper insight into the topology ofthe branches of the Indian mtDNA phylogenetic tree, which should be contextualized within thephylogeography of the neighboring regional mtDNA variation. Accordingly, we have analyzedmtDNA control and coding region variation in 796 Indian (including both tribal and castepopulations from different parts of India) and 436 Iranian mtDNAs.

 The results were integratedand analyzed together with published data from South, Southeast Asia and West Eurasia.Results: Four new Indian-specific haplogroup M sub-clades were defined. These, in combinationwith two previously described haplogroups, encompass approximately one third of the haplogroupM mtDNAs in India. Their phylogeography and spread among different linguistic phyla and socialstrata was investigated in detail. Furthermore, the analysis of the Iranian mtDNA pool revealedpatterns of limited reciprocal gene flow between Iran and the Indian sub-continent and allowed theidentification of different assemblies of shared mtDNA sub-clades.

Conclusions: Since the initial peopling of South and West Asia by anatomically modern humans,when this region may well have provided the initial settlers who colonized much of the rest ofEurasia, the gene flow in and out of India of the maternally transmitted mtDNA has been surprisingly limited. Specifically, our analysis of the mtDNA haplogroups, which are shared betweenIndian and Iranian populations and exhibit coalescence ages corresponding to around the earlyUpper Paleolithic, indicates that they are present in India largely as Indian-specific sub-lineages. Incontrast, other ancient Indian-specific variants of M and R are very rare outside the sub-continent

mt-dna-india m-maps u-map-india 

Click to enlarge all images.

The quest for finding the origin of haplogroup M and a plausible scenario for the peopling of Eurasia.

Based on the high frequency and diversity of haplogroupM in India and elsewhere in Asia, some authors have suggested (versus [3]) that M may have arisen in SouthwestAsia [16,17,31]. Finding M1 or a lineage ancestral to M1 in India, could help to explain the presence of M1 inAfrica as a result of a back migration from India. Yet, to date this has not been achieved [15], this study). Therefore, one cannot rule out the still most parsimonious scenario that haplogroup M arose in East Africa [3].Furthermore, the lack of L3 lineages other than M and N(indeed, L3M and L3N) in India is more consistent withthe African launch of haplogroup M. On the other hand,one also observes that: i) M1 is the only variant of haplo-group M found in Africa; ii) M1 has a fairly restricted phy-logeography in Africa, barely penetrating into sub-Saharan populations, being found predominantly inassociation with the Afro-Asiatic linguistic phylum – afinding that appears to be inconsistent with the distribu-tion of sub-clades of haplogroups L3 and L2 that havesimilar time depths. That, plus the presence of M1 without accompanying L lineages in the Caucasus [32] and [ourunpublished data], leaves the question about the origin of haplogroup M still open.

The paper gives the age of M2 at about 70k, with 21k either way.  Reading through it there seems to be more of a case for M appearing in the Arabian area, the same for the later M1 and U. Call me mad but I think the absence of M in general could be down to the Toba eruption, which must have had some serious impact in South Asia as it put down ash 2m thick all over India.

A study of the L1c haplogroup of the mitochondrial DNA

A study of the L1c haplogroup of the mitochondrial DNA.
page 7

In this communication, we present a study of the human mitochondrial haplogroup L1c which has been carried out on a total of 455 individuals from 27 African and American populations using both hypervariable regions 1 and 2. The results obtained lead us to draw three main conclusions. First, the time to the L1c most recent common ancestor (TMRCA) has been estimated as 90,000 ± 13,000 YBP, substantially older than the previous estimate (59,650 ± 11,800) and in agreement with archaeological dating. Second, we observed that L1c frequencies reach very high values in Western Pygmies populations (from 86% to 98%), hunter-gatherers supposed to be the most ancient inhabitants of this area. Third and finally, the median networks built using our dataset change the phylogeny of the entire haplogroup. In fact, we present a substantially modified structure for the sub-haplogroups L1c1 and L1c3 and identify a new clade, L1c4 which contains mostly sequences from Pygmies.

Taking into consideration the L1c phylogeographic features together with archaeological knowledge, we propose that the hunter-gatherers communities living in Central Africa at least 40,000 YBP could be the ancestors of both Bantu and Western Pygmy populations. These two groups could have separated later on, because of the cycles of expansion and fragmentation of the forest environment occurred till 12,000 YBP. As the next step of this research, we will sequence the complete mtDNA genome in order to test the robustness of the new phylogeny.

Nice to see an older date for this.

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.