Ancient Nordic mtDNA (Melchior et al. 2010)

The reduction of mtDNA haplogroup I in modern Scandinavians has been observed before (by the same author). Inferences from the 2 Bell Beaker and 1 Bronze Age samples which belong to U subgroups should be cautious, however these contrast with later groups as well as with the earlier Neolithic Scandinavian TRB samples. Table 5 has haplogroup frequencies in various age-place groups. From the paper:

Table 5 shows the occurrence of haplogroups among ancient Danes and Britons and modern Danes and Scandinavians. Using G-tests, no significant deviations were observed among the extant populations or between the ancient Britons and the ancient Danes, despite the two ancient population samples show a surplus of Hg T and Hg I, respectively. We have previously observed a high frequency of Hg I's among Iron Age villagers (Bøgebjerggård) and individuals from the early Christian cemetery, Kongemarken [16], [17]. This trend was also found for the additional sites reported here, Simonsborg, Galgedil and Riisby. The overall frequency of Hg I among the individuals from the Iron Age to the Medieval Age is 13% (7/53) compared to 2.5% for modern Danes [35]. The higher frequencies of Hg I can not be ascribed to maternal kinship, since only two individuals share the same common motif (K2 and K7 at Kongemarken). Except for Skovgaarde (no Hg I's observed) frequencies range between 9% and 29% and there seems to be no trend in relation to time.

There are two main explanations for the reduction in haplogroup I frequency: (a) negative selection and/or (b) the movement of non-I bearing populations into the region of interest. Unless selection occurred very recently (in the last millennium), the lack of a temporal trend adds some weight in favor of (b) and contra (a).

Of interest:

Several haplogroups which are rare or absent among the extant population of southern Scandinavia were observed. Hg's R0a and U7 have been discussed previously [15], [17]. Here we note the finding of Hg N1a in the Medieval Riisby (Table 3), which seems to be common among early European LBK farmers [10], a rare Hg T2 motif in the Iron Age settlement Simonsborg (Table 2) and Hg U5a and Hg U4 at the Early Bronze Age site Bredtoftegård and Neolithic Damsbo (Table 1).

A recent paper on mtDNA haplogroup R0a.

A main conclusion from this paper is that the mtDNA gene pool does not appear to change "monotonically" with time, as the Neolithic Bell Beaker and Bronze Age groups resemble Mesolithic ones rather than the Neolithic TRB. Thus, it is safe to say that simple one-time admixture scenaria between "Paleolithic" and "Neolithic" gene pools grossly oversimplify reality.

The more we learn about prehistory, the less we can believe in the paradigm of static people changing their subsistence, technology, language from the Paleolithic to the present. Migrationism is overdue for a comeback as an explanatory tool for the plethora of unexpected results that the bones of ancient humans present us with.

The persistence of mtDNA-U gene pools down to the Bronze Age leads the authors to consider the Iron Age as the origin of the modern Scandinavian mtDNA gene pool:

However, the frequency of Hg U4 and U5 declines significantly among our more recent Iron Age and Viking Age Danish population samples to the level observed among the extant Danish population. Our study therefore would point to the Early Iron Age and not the Neolithic Funnel Beaker Culture as suggested by Malmström et al. (2009) [14], as the time period when the mtDNA haplogroup frequency pattern, which is characteristic to the presently living population of Southern Scandinavia, emerged and remained by and large unaltered by the subsequent effects of genetic drift.

I find that a reasonable suggestion, as it was in the Iron Age that the Germanic language group seems to have emerged in southern Scandinavia and northern Germany, and started to experience its demographic expansion that rendered it one of the largest in modern Europe. So, it makes sense that the mtDNA composition of that age would persist down to the present-day inhabitants.

Related:

• Ancient Viking mtDNA from Denmark
• Iron Age, Viking Age, and Eskimo mtDNA
• Ancient mtDNA from Iron Age Denmark
• mtDNA of an early Danish sample
• Modern Scandinavians descended (maybe) from Neolithic TRB but not Mesolithic Pitted Ware ancestors
• Some mtDNA links between Asia and Europe

PLoS ONE 5(7): e11898. doi:10.1371/journal.pone.0011898

Genetic Diversity among Ancient Nordic Populations

Linea Melchior et al.

Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however, the success rate varied substantially between sites; the highest rates were obtained with untouched, freshly excavated material, whereas heavy handling, archeological preservation and storage for many years influenced the ability to obtain authentic endogenic DNA. While the nucleotide diversity at two locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among the ancient Danes (average 13%) than among extant Danes and Scandinavians (~2.5%) as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type “diluted” by later immigration events. Interestingly, the two Neolithic samples (4,200 YBP, Bell Beaker culture) that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,300–3,500 YBP) was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture.

Link

Internal diversification of mtDNA haplogroup R0a

Molecular Biology and Evolution, doi:10.1093/molbev/msq178

Internal diversification of mitochondrial haplogroup R0a reveals post-Last Glacial Maximum demographic expansions in South Arabia

Viktor Černý et al.

Abstract

Widespread interest in the first successful Out of Africa dispersal of modern humans 60 – 80 KYA via a southern migration route has overshadowed the study of later periods of South Arabian prehistory. In this work we show that the post-Last Glacial Maximum period of the past 20,000 years, during which climatic conditions were becoming more hospitable, has been a significant time in the formation of the extant genetic composition and population structure of this region. This conclusion is supported by the internal diversification displayed in the highly resolved phylogenetic tree of 89 whole mitochondrial genomes (71 being newly presented here) for haplogroup R0a – the most frequent and widespread haplogroup in Arabia. Additionally, two geographically specific clades (R0a1a1a and R0a2f1) have been identified in non-Arabic speaking peoples such as the Soqotri and Mahri living in the southern part of the Arabian Peninsula where a past refugium was identified by independent archaeological studies. Estimates of time to the most recent common ancestor of these lineages match the earliest archaeological evidence for seafaring activity in the peninsula in the sixth millennium BC.

Link

mtDNA of Yemeni and Ethiopian Jews

From the paper:

Mitochondrial DNA analysis also revealed a high diversity of sub-Saharan African and Eurasian haplotypes in both the Yemenite and Ethiopian Jewish populations (see Fig. 2). Specifically, common haplotypes (haplotypes present at [5%) in Yemenite Jews include the African haplogroup L3x1 and Eurasian haplogroups R0a (renamed from (preHV)1 (Torroni et al., 2006), HV1, J2a1a [renamed from J1b (Palanichamy et al., 2004)] K, R2, U, and U1, and in Ethiopian Jews include African haplogroups L2a1b2 and L5a1 and Eurasian haplogroups R0a and M1a1 (see Fig. 2). Overall, sub-
Saharan African L haplotypes [hereafter referred to as L(xM,N), i.e., all African haplotypes except M and N, following the nomenclature of Behar et al. (2008)], comprise a large proportion of the genetic variation in both Jewish populations, representing 20% in the Yemenite Jews and 50% in Ethiopian Jews. This high frequency contrasts with other Jewish populations, such as Near Eastern and Ashkenazi Jews, who almost entirely lack L(xM,N) haplogroups (Thomas et al., 2002; Richards et al., 2003).

I think that the authors' conclusion that Yemenite Jews are partially descended from Israeli exiles is premature. Sure, they can exclude large-scale introgression of Yemeni mtDNA, but the universe of possibilities is not limited to either Israeli or Yemenite.

The way I see it, only a large-scale study of all global Jewish populations may uncover verified ancient Jewish lineages for both Y-chromosomes and mtDNA. The recent studies on Jews have uncovered several genetic sub-clusters of Jews, and only lineages that occur in 2 or more of these clusters, and preferably geographically separated ones have a strong claim of representing original Jewish lineages. There is a limit on what can be uncovered about the past from the study of living populations.

American Journal of Physical Anthropology doi: 10.1002/ajpa.21360

Mitochondrial DNA reveals distinct evolutionary histories for Jewish populations in Yemen and Ethiopia

Amy L. Non et al.

Abstract

Southern Arabia and the Horn of Africa are important geographic centers for the study of human population history because a great deal of migration has characterized these regions since the first emergence of humans out of Africa. Analysis of Jewish groups provides a unique opportunity to investigate more recent population histories in this area. Mitochondrial DNA is used to investigate the maternal evolutionary history and can be combined with historical and linguistic data to test various population histories. In this study, we assay mitochondrial control region DNA sequence and diagnostic coding variants in Yemenite (n = 45) and Ethiopian (n = 41) Jewish populations, as well as in neighboring non-Jewish Yemeni (n = 50) and Ethiopian (previously published Semitic speakers) populations. We investigate their population histories through a comparison of haplogroup distributions and phylogenetic networks. A high frequency of sub-Saharan African L haplogroups was found in both Jewish populations, indicating a significant African maternal contribution unlike other Jewish Diaspora populations. However, no identical haplotypes were shared between the Yemenite and Ethiopian Jewish populations, suggesting very little gene flow between the populations and potentially distinct maternal population histories. These new data are also used to investigate alternate population histories in the context of historical and linguistic data. Specifically, Yemenite Jewish mitochondrial diversity reflects potential descent from ancient Israeli exiles and shared African and Middle Eastern ancestry with little evidence for large-scale conversion of local Yemeni. In contrast, the Ethiopian Jewish population appears to be a subset of the larger Ethiopian population suggesting descent primarily through conversion of local women.

Link

Y chromosomes and mtDNA from Soqotra

UPDATE (18/11): see a related post on the age of the new mtDNA lineages [end update]

Soqotra is an island in the Indian Ocean which belongs to Yemen. What is most interesting -to me- about this paper, is that 71.4% of the Y-chromosomes belong to haplogroup J*(xJ1, J2) which is found at trace frequencies elsewhere. Interestingly, haplogroup J2 is not found in this isolated region, while haplogroup J1 is found at a frequency of 14.3%.

The authors write:

For the perspective of the Y-chromosome data, a high
frequency of haplogroup J1 in Soqotra is consistent with
a gradient of this haplogroup in the Arabian Peninsula
(Cadenas et al., 2008). These authors estimated ages for
J1 in Arabia (9.7 +/ 2.4 in Yemen, 7.4 +/- 2.3 in Qatar and
6.4 +/- 1.4 KYBP in UAE), consistent with a Neolithic
expansion from the north (where Y-chromosome STR diversity
is higher). However, we report a much higher frequency
of J* (lack of M267 and M172) in Soqotra. Since
this lineage was not found by Cadenas et al. (2008) in
the Arabian Peninsula, this raises the possibility of an
earlier input for these lineages or more probably very
strong genetic drift of a low frequency Arabian lineage
in the Y-chromosome gene pool of Soqotra.

The early dates from Cadenas et al. are due to the use of an evolutionary mutation rate, and thus need to be downgraded to about ~1,000BC onwards, coinciding (within wide confidence intervals) with the formation of the earliest Arabian kingdoms. It seems probable that J*(xJ1, J2) was commoner in the past, and contributed to the population of Soqotra, but this population was later overwhelmed by the expansion of J1-carriers who dominate the Arabian peninsula to this day.

It is unfortunate that apparently many J2 downstream markers were typed even though there is no J2 on the island, whereas haplogroup E, occurring at a frequency of 9.5% was not further resolved. This underscores the need for a more flexible typing stratgy; at this level it is not clear whether this E came to the island from Africa or from Arabia.

American Journal of Physical Anthropology doi: 10.1002/ajpa.20960

Out of Arabia - The settlement of Island Soqotra as revealed by mitochondrial and Y chromosome genetic diversity

Viktor Cerny et al.

Abstract

The Soqotra archipelago is one of the most isolated landmasses in the world, situated at the mouth of the Gulf of Aden between the Horn of Africa and southern Arabia. The main island of Soqotra lies not far from the proposed southern migration route of anatomically modern humans out of Africa 60,000 years ago (kya), suggesting the island may harbor traces of that first dispersal. Nothing is known about the timing and origin of the first Soqotri settlers. The oldest historical visitors to the island in the 15th century reported only the presence of an ancient population. We collected samples throughout the island and analyzed mitochondrial DNA and Y-chromosomal variation. We found little African influence among the indigenous people of the island. Although the island population likely experienced founder effects, links to the Arabian Peninsula or southwestern Asia can still be found. In comparison with datasets from neighboring regions, the Soqotri population shows evidence of long-term isolation and autochthonous evolution of several mitochondrial haplogroups. Specifically, we identified two high-frequency founder lineages that have not been detected in any other populations and classified them as a new R0a1a1 subclade. Recent expansion of the novel lineages is consistent with a Holocene settlement of the island ~6 kya.

Link

Ancient Thracian mtDNA

The presentation of the results isn't very clear. From a cursory comparison of the results listed in the text with the Genographic project list of motifs, at least the following seem represented in the ancient Thracian individuals:

• 1 individual seems to be 16129A 16223T
• 1 individual seems to be 16145A
• 1 individual seems to be 16186T 16190C (however, this looks like 16189C in Fig. 4, 186T and 189C are found in haplogroup T1)
• 1 individual seems to be 16193T 16283C (16193T is found in J2, which also carries 16069T (beyond the region sequenced) 16126C (in the region sequenced but not found).
• 1 individual seems to be 16311C
• 2 individuals seems to be 16362C which in West Eurasia seems to be found in R0a and R6

Anyway, feel free to comment if you can make better sense of these results.

Rom J Leg Med 12 (4) 239 – 246 (2004)

Paleo-mtDNA analysis and population genetic aspects of old Thracian populations from South-East of Romania

Cardos G. et al.

ABSTRACT: Paleo-mtDNA analysis and population genetic aspects of old Thracian populations from South-East of Romania. We have performed a study of mtDNA polymorphisms (HVR I and HVR II sequences) on the skeletal remains of some old Thracian populations from SE of Romania, dating from the Bronze and Iron Age in order to show their contribution to the foundation of the modern Romanian genetic pool and the degree of their genetic kinships with other old and modern human European populations. For this purpose we have applied and adapted three DNA extraction methods: the phenol/chloroform, the guanidine isotiocianat and silica particles and thirdly the Invisorb Forensic Kit (Invitek)-based DNA extraction method. We amplified by PCR short fragments of HVR I and HVR II and sequenced them by the Sanger method. So far, we have obtained mtDNA from 13 Thracian individuals, which we have compared with several modern mtDNA sequences from 5 European present-day populations. Our results reflect an evident genetic similarity between the old Thracian individuals and the modern populations from SE of Europe.

Link (pdf)

mtDNA macro-haplogroup R0

R0 is ancestral to the very widespread HV, V, and H which are frequent in Europe, as well as R0a which is frequent in the Middle East.

BMC Evol Biol. 2008 Jul 4;8(1):191. [Epub ahead of print]

Timing and deciphering mitochondrial DNA macro-haplogroup R0 variability in Central Europe and Middle East.

Brandstaetter A, Zimmermann B, Wagner J, Goebel T, Roeck AW, Salas A, Carracedo A, Parson W.

ABSTRACT: BACKGROUND: Nearly half of the West Eurasian assemblage of human mitochondrial DNA (mtDNA) is fractioned into numerous sub-lineages of the predominant haplogroup (hg) R0. Several hypotheses have been proposed on the origin and the expansion times of some R0 sub-lineages, which were partially inconsistent with each other. Here we describe the phylogenetic structure and genetic variety of hg R0 in five European populations and one population from the Middle East. RESULTS: Our analysis of 1,350 mtDNA haplotypes belonging to R0, including entire control region sequences and 45 single nucleotide polymorphisms from the coding region, revealed significant differences in the distribution of different sub-hgs even between geographically closely located regions. Estimates of coalescence times that were derived using diverse algorithmic approaches consistently affirmed that the major expansions of the different R0 hgs occurred in the terminal Pleistocene and early Holocene. CONCLUSIONS: Given an estimated coalescence time of the distinct lineages of 10 - 18 kya, the differences in the distributions could hint to either limited maternal gene flow after the last glacial maximum due to the alpine nature of the regions involved or to a stochastic loss of diversity due to environmental events and/or disease episodes occurred at different times and in distinctive regions. Our comparison of two different ways of obtaining the timing of the most recent common ancestor confirms that the time of a sudden expansion can be adequately recovered from control region data with valid confidence intervals. For reliable estimates, both procedures should be applied in order to cross-check the results for validity and soundness.

Link

News on Arabian mtDNA

Not one but two recent paper on Arabian mtDNA, giving us a better idea of its geographical structure. I am not sure what to make of the assertion in the first paper that the Arabian peninsula has been the recipient of genetic input from Australia; well, it's in an open access journal so you can form your own opinions.

BMC Evol Biol. 2008 Feb 12;8(1):45 [Epub ahead of print]

Mitochondrial DNA structure in the Arabian Peninsula.

Abu-Amero KK, Larruga JM, Cabrera VM, Gonzalez AM.

ABSTRACT: BACKGROUND: Two potential migratory routes followed by modern humans to colonize Eurasia from Africa have been proposed. These are the two natural passageways that connect both continents: the northern route through the Sinai Peninsula and the southern route across the Bab al Mandab strait. Recent archaeological and genetic evidence have favored a unique southern coastal route. Under this scenario, the study of the population genetic structure of the Arabian Peninsula, the first step out of Africa, to search for primary genetic links between Africa and Eurasia, is crucial. The haploid and maternally inherited mitochondrial DNA (mtDNA) molecule has been the most used genetic marker to identify and to relate lineages with clear geographic origins, as the African Ls and the Eurasian M and N that have a common root with the Africans L3. RESULTS: To assess the role of the Arabian Peninsula in the southern route, we genetically analyzed 553 Saudi Arabs using partial (546) and complete mtDNA (7) sequencing, and compared the lineages obtained with those present in Africa, the Near East, central, east and southeast Asia and Australasia. The results showed that the Arabian Peninsula has received substantial gene flow from Africa (20%), detected by the presence of L, M1 and U6 lineages; that an 18% of the Arabian Peninsula lineages have a clear eastern provenance, mainly represented by U lineages; but also by Indian M lineages and rare M links with Central Asia, Indonesia and even Australia. However, the bulk (62%) of the Arabian lineages has a Northern source. CONCLUSIONS: Although there is evidence of Neolithic and more recent expansions in the Arabian Peninsula, mainly detected by (preHV)1 and J1b lineages, the lack of primitive autochthonous M and N sequences, suggests that this area has been more a receptor of human migrations, including historic ones, from Africa, India, Indonesia and even Australia, than a demographic expansion center along the proposed southern coastal route.

Link

Am J Phys Anthropol. 2008 Feb 6 [Epub ahead of print]

Regional differences in the distribution of the sub-Saharan, West Eurasian, and South Asian mtDNA lineages in Yemen.

Cerný V et al.

Despite its key location for population movements out of and back into Africa, Yemen has not yet been sampled on a regional level for an investigation of sub-Saharan, West Eurasian, and South Asian genetic contributions. In this study, we present mitochondrial DNA (mtDNA) data for regionally distinct Yemeni populations that reveal different distributions of mtDNA lineages. An extensive database of mtDNA sequences from North and East African, Middle Eastern and Indian populations was analyzed to provide a context for the regional Yemeni mtDNA datasets. The groups of western Yemen appear to be most closely related to Middle Eastern and North African populations, while the eastern Yemeni population from Hadramawt is most closely related to East Africa. Furthermore, haplotype matches with Africa are almost exclusively confined to West Eurasian R0a haplogroup in southwestern Yemen, although more sub-Saharan L-type matches appear in more northern Yemeni populations. In fact, Yemeni populations have the highest frequency of R0a haplotypes detected to date, thus Yemen or southern Arabia may be the site of the initial expansion of this haplogroup. Whereas two variants of the sub-Saharan haplogroup M1 were detected only in southwestern Yemen close to the Bab el-Mandeb Strait, different non-African M haplotypes were detected at low frequencies ( approximately 2%) in western parts of the country and at a higher frequency (7.5%) in the Hadramawt. We conclude that the Yemeni gene pool is highly stratified both regionally and temporally and that it has received West Eurasian, Northeast African, and South Asian gene flow.

Link

Ancient mtDNA from Iron Age Denmark

Am J Phys Anthropol. 2007 Nov 28 [Epub ahead of print]

Rare mtDNA haplogroups and genetic differences in rich and poor Danish Iron-Age villages.

Melchior L, Gilbert MT, Kivisild T, Lynnerup N, Dissing J.

The Roman Iron-Age (0-400 AD) in Southern Scandinavia was a formative period, where the society changed from archaic chiefdoms to a true state formation, and the population composition has likely changed in this period due to immigrants from Middle Scandinavia. We have analyzed mtDNA from 22 individuals from two different types of settlements, Bøgebjerggård and Skovgaarde, in Southern Denmark. Bøgebjerggård (ca. 0 AD) represents the lowest level of free, but poor farmers, whereas Skovgaarde 8 km to the east (ca. 200-270 AD) represents the highest level of the society. Reproducible results were obtained for 18 subjects harboring 17 different haplotypes all compatible (in their character states) with the phylogenetic tree drawn from present day populations of Europe. This indicates that the South Scandinavian Roman Iron-Age population was as diverse as Europeans are today. Several of the haplogroups (R0a, U2, I) observed in Bøgebjerggård are rare in present day Scandinavians. Most significantly, R0a, harbored by a male, is a haplogroup frequent in East Africa and Arabia but virtually absent among modern Northern Europeans. We suggest that this subject was a soldier or a slave, or a descendant of a female slave, from Roman Legions stationed a few hundred kilometers to the south. In contrast, the haplotype distribution in the rich Skovgaarde shows similarity to that observed for modern Scandinavians, and the Bøgebjerggård and Skovgaarde population samples differ significantly (P approximately 0.01). Skovgaarde may represent a new upper-class formed by migrants from Middle Scandinavia bringing with them Scandinavian haplogroups.

Link

mtDNA of Saudi Arabians

BMC Evol Biol. 2007 Mar 1;7(1):32 [Epub ahead of print]

Eurasian and African mitochondrial DNA influences in the Saudi Arabian population.

Abu-Amero KK, Gonzalez AM, Larruga JM, Bosley TM, Cabrera VM.

ABSTRACT: BACKGROUND: Genetic studies of the Arabian Peninsula are scarce even though the region was the center of ancient trade routes and empires and may have been the southern corridor for the earliest human migration from Africa to Asia. A total of 120 mtDNA Saudi Arab lineages were analyzed for HVSI/II sequences and for haplogroup confirmatory coding diagnostic positions. A phylogeny of the most abundant haplogroup (preHV)1 (R0a) was constructed based on 13 whole mtDNA genomes. RESULTS: The Saudi Arabian group showed greatest similarity to other Arabian Peninsula populations (Bedouin from the Negev desert and Yemeni) and to Levantine populations. Nearly all the main western Asia haplogroups were detected in the Saudi sample, including the rare U9 clade. Saudi Arabs had only a minority sub-Saharan Africa component (7%), similar to the specific North-African contribution (5%). In addition, a small Indian influence (3%) was also detected. CONCLUSION: The majority of the Saudi-Arab mitochondrial DNA lineages (85%) have a western Asia provenance. Although the still large confidence intervals, the coalescence and phylogeography of (preHV)1 haplogroup (accounting for 18 % of Saudi Arabian lineages) matches a Neolithic expansion in Saudi Arabia.


Link (pdf)