Mitogenomes from the middle of the Merovingian period in the Lorraine region

herange-burial

Investigating the kinship between individuals deposited in exceptional Merovingian multiple burials through aDNA analysis: The case of Hérange burial 41 (Northeast France), by Deguilloux et al. Journal of Archaeological Science: Reports (2018) 20:784-790.

Interesting excerpts (emphasis mine):

The Merovingian period in Northeast France (developing from 440/450 to 700/710 CE; Legoux et al., 2004) represents [a case of multiple burial], where a large majority of the types of deposits encountered consists of individual burials. In this context, whereas hundreds of individual burials are known, the syntheses recently conducted have enabled the inventory of only six multiple burials (Lefebvre and Lafosse, 2016). These observations naturally raised questions about the exceptional circumstances that led the members of the community to set up such unusual burials. The archaeological site of Hérange, excavated in 2014 (Lorraine, Grand Est region; Fig. S1), holds a key position in the debate surrounding the interpretation of multiple burials during the Merovingian period since it contains one of these rare multiple burials: burial 41, which was dated through archaeological material to the period 530–640 CE.

(…) The biological analysis of the human remains recovered in the second burial (“burial 41”) enabled the demonstration of the combined presence of a woman of approximately 40 years old (A) and three immature individuals, including a 4–5-year-old child (B), a 14–16-year-old teenager (C) and a 2,5–3-month-old infant (D) (Lefebvre and Lafosse, 2016) (Fig. 1). Since rare multiple burials described for the Merovingian period in Northeast France mainly contained two or rarely three deceased, the discovery of a burial grouping four individuals reinforced its exceptional nature. (…) Intriguingly, great care was observed in the treatment of the dead, as illustrated through a special arrangement of the deceased in the grave (Fig. 1). Indeed, the woman A occupied a central position in the grave, with her left arm covering part of the body of child D, her right arm covering the torso of child B and her right hand covering the legs of children B and C. Several arguments, such as the close contact or the imbrication of the bones of individuals A, B and C, have attested to the simultaneity of their deposits in the burial (Lefebvre and Lafosse, 2016).

mitochondrial-distribution-merovingian
Geographic distribution of the extant European individuals sharing mitochondrial haplotypes with the Hérange human remains.

Interestingly, studies have demonstrated an important chronological homogeneity for the rare multiple burials discovered for the Merovingian period in the Lorraine region (Lefebvre and Lafosse, 2016). The collected data support the existence of an epiphenomenon arisen around the middle of the Merovingian period and that may have linked the multiple burials to (i) a funerary “fashion trend” for a special group of the community, (ii) an increase in cases of violence or (iii) an epidemic crisis linked to infectious disease. In other Lorraine sites, none of the available indices permitted the specification of the cause of death for the individuals recovered in these specific burials. The deceased could well have died of natural causes, violent acts or infectious diseases that had left no visible evidence on the skeletal.

merovingian-y-chromosome
Nuclear data (Y chromosome SNPs and nuclear STRs) typed on the four Hérange human remains (STRs alleles shown in grey were not fully replicated).

The aDNA analyses conducted on the four individuals discovered in the exceptional multiple burial 41 from Hérange (Lorraine) have demonstrated strong biological links between three individuals. Notably, we could propose that the woman A was the mother of the two immatures B and D deposited just besides her whereas she was not genetically closely related to the teenager C deposited along her legs. Consequently, we propose that the special arrangement of the deceased in the grave clearly reflected the degree of biological links between the deposited individuals. In Hérange, the bereaved were well aware of kinship among the deceased, wanted to express this close linkage through their relative location within the burial, and intentionally arranged body positions consequently. In conclusion, the collected archaeological, archaeo-anthropological and genetic data suggest that the special setup of the multiple burial 41 in the Hérange necropolis and the great care in the treatment of the dead, could be explained by the contemporaneous death of the four related individuals. Data gathered for other archaeological sites from the region or in Germany suggested an epidemic crisis (plague epidemic?) during the middle of the Merovingian period that may explain the contemporaneous death of related individuals living in close contact and easily sharing pathogens.

mitogenomes-merovingian

Reported mtDNA haplogroups include U* for samples A, B, and D, and H for sample C.

Related:

Recent Africa origin with hybridization, and back to Africa 70,000 years ago

mtdna-l-out-of-africa-expansion

Open access Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago, by Cabrera et al. BMC Evol Biol (2018) 18(98).

Abstract (emphasis mine):

Background

The main unequivocal conclusion after three decades of phylogeographic mtDNA studies is the African origin of all extant modern humans. In addition, a southern coastal route has been argued for to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, the out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion and, consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basal L3 lineages around 70 kya.

Results

The coalescence ages of all Eurasian (M,N) and African (L3 ) lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. An Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. This correlation rather seems to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers.

Conclusions

These results are congruent with a model proposing an out-of-Africa migration into Asia, following a northern route, of early anatomically modern humans carrying pre-L3 mtDNA lineages around 125 kya, subsequent diversification of pre-L3 into the basal lineages of L3, a return to Africa of Eurasian fully modern humans around 70 kya carrying the basal L3 lineages and the subsequent diversification of Eurasian-remaining L3 lineages into the M and N lineages in the outside-of-Africa context, and a second Eurasian global expansion by 60 kya, most probably, out of southeast Asia. Climatic conditions and the presence of Neanderthals and other hominins might have played significant roles in these human movements. Moreover, recent studies based on ancient DNA and whole-genome sequencing are also compatible with this hypothesis.

homo-sapiens-neandertal-denisovan

You can also read the recent interesting open access review How did Homo sapiens evolve? by Julia Galway-Witham, Chris Stringer, Science (2018) 360:6395 1296-1298.

Related:

Bantu distinguished from Khoe by uniparental markers, not genome-wide autosomal admixture

bantu-expansion

The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola, by Oliveira et al. bioRxiv (2018).

Interesting excerpts (emphasis mine):

The origins of NRY diversity in SW Angola

In accordance with our previous mtDNA study9, the present NRY analysis reveals a major division between the Kx’a-speaking !Xun and the Bantu-speaking groups, whose paternal genetic ancestry does not display any old remnant lineages, or a clear link to pre-Bantu eastern African migrants introducing Khoe-Kwadi languages and pastoralism into southern Africa (cf. 15). This is especially evident in the distribution of the eastern African subhaplogroup E1b1b1b2b29, which reaches the highest frequency in the !Xun (25%) and not in the formerly Kwadi-speaking Kwepe (7%). This observation, together with recent genome-wide estimates of 9-22% of eastern African ancestry in other Kx’a and Tuu-speaking groups35, suggests that eastern African admixture was not restricted to present-day Khoe-Kwadi speakers. Alternatively, it is likely that the dispersal of pastoralism and Khoe-Kwadi languages involved a series of punctuated contacts that led to a wide variety of cultural, genetic and linguistic outcomes, including possible shifts to Khoe-Kwadi by originally Bantu-speaking peoples36.

Although traces of an ancestral pre-Bantu population may yet be found in autosomal genome-wide studies, the extant variation in both uniparental markers strongly supports a scenario in which all groups of the Angolan Namib share most of their genetic ancestry with other Bantu groups but became increasingly differentiated within the highly stratified social context of SW African pastoral societies11.

bantu-pastoralists
Y chromosome phylogeny, haplogroup distribution and map of the sampling locations. The phylogenetic tree was reconstructed in BEAST based on 2,379 SNPs and is in accordance with the known Y chromosome topology. Main haplogroup clades and their labels are shown with different colors. Age estimates are reported in italics near each node, with the TMRCA of main haplogroups shown with their corresponding color. A map of the sampling locations, re-used with permission from Oliveira et al. (2018) 9, is shown on the bottom left, and the haplogroup distribution per population is shown on the bottom right, with color-coding corresponding to the phylogenetic tree.

The influence of socio-cultural behaviors on the diversity of NRY and mtDNA

A comparison of the NRY variation with previous mtDNA results for the same groups 9 identifies three main sex-specific patterns. First, gene flow from the Bantu into the !Xun is much higher for male than for female lineages (31% NRY vs. 3% mtDNA), similar to the reported male-biased patterns of gene flow from Bantu to Khoisan-speaking groups33, and from non-Pygmies to Pygmies in Central Africa 37. A comparable trend, involving exclusive introgression of NRY eastern African lineages into the !Xun (25%) was also found. (…)

Secondly, the levels of intrapopulation diversity in the Bantu-speaking peoples from the Namib were found to be consistently higher for mtDNA than for the NRY, reflecting the marked association between the Bantu expansion and the relatively young NRY E1b1a1a1 haplogroup, which has no parallel in mtDNA25,39. (…)

In the context of the Bantu expansions, these patterns have been mostly interpreted as the result of polygyny and/or higher levels of assimilation of females from resident forager communities38,40. However, most groups from the Angolan Namib are only mildly polygynous11 and ethnographic data suggest that the actual rates of polygyny in many populations may be insufficient to significantly reduce Nem2,41. In addition, the finding of a large Nef/ Nem ratio in the Himba (Fig. S5), who have almost no Khoisan-related mtDNA lineages9, indicates that female biased introgression cannot fully explain the observed patterns.

An alternative explanation may be sought in the prevailing matrilineal descent rules, which might have created a sex-specific structuring effect, similar to that proposed for patrilineal groups from Central Asia (…)

bantu-xun-plot
Bayesian skyline plots (BSP) of effective population size change through time, based on mtDNA (red) and the NRY (black). Thick lines show the mean estimates and dashed lines show the 95% HPD intervals. The vertical line highlights the 2 ky before present mark. Effective sizes are plotted on a log scale. Generation times of 25 and 31 years were assumed for mtDNA and the NRY, respectively32.

The third important sex-specific pattern observed in this study is the much lower amount of between-group differentiation for NRY than for mtDNA among Bantu-speaking populations (4.4% NRY vs. 20.2% mtDNA), in spite of the patrilocal residence patterns of all ethnic groups (Table S5). This difference can hardly be explained by unequal levels of introgression of “Khoisan” mtDNA lineages into the Bantu, since the percentage of mtDNA variation remains high (18.8%) when the Kuvale, who have high frequencies of “Khoisan”-related mtDNA, are excluded from the comparisons. It therefore seems more plausible that differentiation is higher in the mtDNA simply because there is more ancestral mtDNA than NRY variation that can be sorted among different populations (see 45). Moreover, due to the matriclanic organization of all Bantu-speaking communities, factors enhancing inter-group differentiation, like kin-structured migration and kin-structured founder effects46, would have been restricted to mtDNA. Finally, it is also likely that the discrepancy between among-group divergence of mtDNA and NRY might have been influenced by higher migration rates in males than females. In fact, although all Bantu-speaking populations have patrilocal residence patterns, the observance of endogamy rules severely constrains the between-group mobility of females. In this context, the children from extramarital unions involving members from different populations tend to be raised in the mother’s group, effectively increasing male versus female migration rates. Moreover, it is likely that, in the highly hierarchized setting of the Namib, most intergroup extramarital unions would involve men from dominant groups and women from peripatetic communities. This hypothesis is indirectly supported by the finding that in NRY-based clusters (but not in mtDNA) pastoralist populations are grouped together with peripatetic communities that share their cultural traits (Figs. S6 and 3b), suggesting that migration of NRY lineages follows a path that is similar to horizontally transmitted cultural features.

Related:

Native American genetic continuity and oldest mtDNA hg A2ah in the Andean region

Native American gene continuity to the modern admixed population from the Colombian Andes: Implication for biomedical, population and forensic studies by Criollo-Rayo et al., Forensic Sci Int Genet (2018), in press, corrected proof.

Abstract (emphasis mine):

Andean populations have variable degrees of Native American and European ancestry, representing an opportunity to study admixture dynamics in the populations from Latin America (also known as Hispanics). We characterized the genetic structure of two indigenous (Nasa and Pijao) and three admixed (Ibagué, Ortega and Planadas) groups from Tolima, in the Colombian Andes. DNA samples from 348 individuals were genotyped for six mitochondrial DNA (mtDNA), seven non-recombining Y-chromosome (NRY) region and 100 autosomal ancestry informative markers. Nasa and Pijao had a predominant Native American ancestry at the autosomal (92%), maternal (97%) and paternal (70%) level. The admixed groups had a predominant Native American mtDNA ancestry (90%), a substantial frequency of European NRY haplotypes (72%) and similar autosomal contributions from Europeans (51%) and Amerindians (45%). Pijao and nearby Ortega were indistinguishable at the mtDNA and autosomal level, suggesting a genetic continuity between them. Comparisons with multiple Native American populations throughout the Americas revealed that Pijao, had close similarities with Carib-speakers from distant parts of the continent, suggesting an ancient correlation between language and genes. In summary, our study aimed to understand Hispanic patterns of migration, settlement and admixture, supporting an extensive contribution of local Amerindian women to the gene pool of admixed groups and consistent with previous reports of European-male driven admixture in Colombia.

andean-y-dna-mtdna
Ancestral uniparental haplogroups and diversity in Tolima. Geography of sampling locations. The
top and middle sections show the frequency of Native American mtDNA haplogroups and NRY lineages for all
populations. Gene diversity is shown below their respective pie chart. The lower part depicts the geography of the
region where the sampling sites of Ortega and Pijao are closely located in Tolima’s Magdalena river valley and
Ibague, Planadas and Nasa located in the Andes cordilleras (additional geographic details are shown in SF1).

Highlights from the paper:

  • MtDNA suggest a pre/post Columbian genetic continuity in the Colombian Andes.
  • Y-chromosome diversity follows a clinal gradient in the studied region.
  • Sex-biased/male-driven admixture process, involving Pijao women with European men.
  • Admixed closer to Indigenous resguardos have a higher Native American ancestry.

Also interesting is the recent paper Mitochondrial lineage A2ah found in a pre‐Hispanic individual from the Andean region, by Russo et al., in American Journal of Human Biology (2018), with an interesting sample from the Regional Developments II period (540 ± 60 BP).

phylogeny-a2ah-mtdna
Phylogeny of the A2ah mitochondrial lineage based on HVR I sequences. Both MaximumParsimony andMaximumLikelihood reconstructions led to the same typology. The tree was rooted with the RSRS. Sample ID: Cueva: Pukara de La Cueva, STACRUZ: Santa Cruz, BNI: Beni, BR: South-eastern Brazil, TobaChA: TobaGranChaco

Related:

Canid Y-chromosome phylogeny reveals distinct haplogroups among Neolithic European dogs

dog-phylogeny

Open access Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs, by Oetjens et al., BMC Genomics (2018) 19:350.

Interesting excerpts (modified for clarity, emphasis mine):

Introduction

Canid mitochondrial phylogenies show that dogs and wolves are not reciprocally monophyletic. The mitochondrial tree contains four deeply rooted clades encompassing dogs and many grey wolf groups. These four clades form the basis of dog mitochondrial haplogroup assignment, known as haplogroups A-D. The time of the most recent common ancestor (TMRCA) of haplogroups A-D significantly predates estimates for domestication based on archeological and genetic evidence. Instead, these clades may represent variation present among the founding population of the dog lineage or the results of wolf introgressions into dog populations. The relative frequencies of mitochondria haplogroups are not stable over time, with changes reflecting processes such as drift, migration, and population growth. Although the mitochondria A and B haplogroups are most common in contemporary European dogs, surveys of ancient samples indicate that the majority of ancient European dogs carried the C or D mitochondrial haplotype. This apparent turnover in mitochondrial haplogroups may reflect the migration of a distinct dog population into Europe over the past 15,000 years.

canid-phylogeny
Maximum likelihood phylogeny of 118 candid Y-chromosomes A Y-chromosome haplogroup tree produced by RAxML (8.1.13) using the GTR+ I model is depicted. Clades in the tree have been collapsed by haplogroup assignment. The number of samples within each collapsed node is indicated in parentheses next to the haplogroup assignment. For each node, percent bootstrap support out of 1000 iterations is indicated above the branch. The locations of three ancient samples, based on the presence of diagnostic mutations, are indicated in red

Discussion

Using the variation discovered from sequence data, we applied a Bayesian MCMC approach to estimate TMRCAs for each haplotype group. Our estimated Y-chromosome mutation rate (3.07 × 10− 10 substitutions per site per year, relaxed clock model) falls within the range of a previous estimate by Ding et al. who used a similar calibration and estimate 1.35 × 10− 10– 4.31 × 10− 10 substitutions per site per year. The TMRCAs we estimated are substantially older than mitochondria phylogenies calibrated with tip dates of ancient samples, which report clade-specific TMRCAs < 25,000 years ago. We note that our Y-chromosome TMRCA estimates are extremely sensitive to our assumptions about the age of the root of the tree and should be interpreted with caution due to the uncertainty in this single calibration point. However, the relative ages of the branches and the chronological order of haplogroup divergences are more robust than the absolute estimated dates.

In general, the relationships between Y-chromosome haplogroups and autosomal ancestry we report are very similar to the relationships described in Shannon et al. As noted earlier, our dataset includes a subset of wolves with Y-chromosomes assigned to a dog Y-haplogroup. However, ADMIXTURE analysis does not indicate substantial recent dog ancestry in these samples, suggesting that their placement on the Y-chromosome phylogeny reflects variation in Y-chromosome haplotypes that was present in the ancestral population and therefore predates the domestication process or is the result of ancient introgression events whose signature of autosomal ancestry has been diluted.

y-chromosome-admixture-dogs
The relationship between autosomal ancestry and Y-chromosome haplogroups Major groupings of canine ancestry are shown based on a principal components analysis of autosomal markers from 499 village dogs from Shannon et al. a. The geographic origin of each sample is indicated by color. The 104 male dogs used in this study are projected onto the resulting principal components and colored based on haplogroup (b). Village dogs from (a) are shown as transparent dots in (b)

Conclusions

Using sequencing data, we find that the estimated TMRCA of dog Y haplogroups predates dog domestication. We further reveal the placement of several wolf Y-chromosomes within deep branches of dog haplogroup clades. Using an expanded set of mutations diagnostic for each haplogroup, we find that distinct Y haplogroups were present in Europe during the Neolithic and that CTC, a ~ 4700 year old ancient dog from Germany has a Y-chromosome that shares diagnostic alleles with wolves found in India.

Other studies

On the same subject, you can read another recent study, bioRxiv preprint New Evidence of the Earliest Domestic Dogs in the Americas, by Perri et al. (2018); and also a recent, open access paper (see above featured image) Ancient European dog genomes reveal continuity since the Early Neolithic, by Botigué et al., Science Communications (2017).

While Proto-Indo-European- and Proto-Uralic-speakers had a close relationship with dogs (revealed in their reconstructed language and attributed archaeological cultures), I think it will be very difficult to ascertain any population movement based on them, unless there is a clear, well-established archaeological relationship between a specific culture and dog-breeding.

Nevertheless, I would say that this kind of studies are more likely to give some information related to these and other cultures than, for example, the study of honeybees in honey-hunting vs. beekeeping cultures (see e.g. The Complex Demographic History and Evolutionary Origin of the Western Honey Bee, Apis Mellifera, by Cridland, Tsutsui, and Ramírez GBE 2017), which was also related to the development of both PIE and PU cultures.

See also:

Male-biased expansions and migrations also observed in Northwestern Amazonia

Open access preprint Cultural Innovations influence patterns of genetic diversity in Northwestern Amazonia, by Arias et al., bioRxiv (2018).

Abstract (emphasis mine):

Human populations often exhibit contrasting patterns of genetic diversity in the mtDNA and the non-recombining portion of the Y-chromosome (NRY), which reflect sex-specific cultural behaviors and population histories. Here, we sequenced 2.3 Mb of the NRY from 284 individuals representing more than 30 Native-American groups from Northwestern Amazonia (NWA) and compared these data to previously generated mtDNA genomes from the same groups, to investigate the impact of cultural practices on genetic diversity and gain new insights about NWA population history. Relevant cultural practices in NWA include postmarital residential rules and linguistic-exogamy, a marital practice in which men are required to marry women speaking a different language. We identified 2,969 SNPs in the NRY sequences; only 925 SNPs were previously described. The NRY and mtDNA data showed that males and females experienced different demographic histories: the female effective population size has been larger than that of males through time, and both markers show an increase in lineage diversification beginning ~5,000 years ago, with a male-specific expansion occurring ~3,500 years ago. These dates are too recent to be associated with agriculture, therefore we propose that they reflect technological innovations and the expansion of regional trade networks documented in the archaeological evidence. Furthermore, our study provides evidence of the impact of postmarital residence rules and linguistic exogamy on genetic diversity patterns. Finally, we highlight the importance of analyzing high-resolution mtDNA and NRY sequences to reconstruct demographic history, since this can differ considerably between males and females.

y-dna-mtdna-amazonia
MDS plots for mtDNA and NRY. Stress values (within parentheses) are indicated in percentages.

Looking more precisely at the different groups (even with the resampling approach), there are no significant differences between matrilocal and patrilocal groups. At best, as the study proposes, “this is just one of the factors at play in structuring the observed genetic variation”.

Interesting excerpts:

(…) we found evidence that the patterns of genetic differentiation depend on the geographical scale of the study. The magnitude of between-population differentiation in the NRY compared to the mtDNA is smaller when looking at the continental scale than in NWA (Figure 6). This is in agreement with the findings of Wilkins and Marlowe (2006), who showed that the excess of between-population differentiation for the NRY in comparison to the mtDNA decreases when comparing more geographically distant populations. Heyer et al. (2012) and Wilkins and Marlowe (2006) have proposed that at a local scale the patterns of genetic diversity reflect cultural practices over a relatively small number of generations, whereas at a larger geographic scale the genetic diversity reflects old migration and/or old common ancestry patterns(Heyer et al. 2012; Wilkins and Marlowe 2006).

y-dna-mtdna-amazon
BSPs for the mtDNA and NRY sequences from NWA. The dotted lines indicate the 95% HPD intervals. Ne was corrected for generation time according to (Fenner 2005), using 26 years for mtDNA and 31 years for NRY.

The BSP plots and the diversity statistics indicate that overall the Ne of males has been smaller than that of females. One tentative explanation for this difference is that it reflects larger differences in reproductive success among males than among females. Some support for this explanation comes from the shape of the phylogenies (Supplementary Figures 1 and 6), since differences in reproductive success and the cultural transmission of fertility lead to imbalance phylogenies (Blum et al. 2006; Heyer et al. 2015). We estimated a common index of tree imbalance (Colless index) and calculated whether the mtDNA and NRY trees were more unbalanced than 1000 simulated trees generated under a Yule process (Bortolussi et al. 2006) (i.e. a simple pure birth process that assumes that the birth rate of new lineages is the same along the tree). We found that the NRY tree is more unbalanced than predicted by the Yule model (p-value=0.001), whereas the mtDNA tree is not significantly different from trees generated by the Yule model (p-value=0.628). It has been suggested that highly mobile hunter-gatherer societies, such as those typical of most of human prehistory, were polygynous bands (Dupanloup et al. 2003); similarly, nomadic horticulturalist Amazonian societies exhibit strong differences in reproductive success due to the common practice of polygyny, especially among community chiefs, whose offspring also enjoy a high fertility (Neel 1970; 1980; Neel and Weiss 1975).

Furthermore, a more recent expansion can be observed in the BSP based on the NRY, but not in the mtDNA BSP (Figure 5), indicating an expansion specifically in the paternal line. The reasons behind this recent male-biased population expansion, which starts ~3.5 kya, are as yet unclear. However, similar male-biased expansions have been observed in other studies using high-resolution NRY sequences (Batini et al. 2017; Karmin et al. 2015).

Related:

North Asian mitogenomes hint at the arrival of pastoralists from West to East ca. 2800-1000 BC

north-asia-mitogenomes

Open access Investigating Holocene human population history in North Asia using ancient mitogenomes, by Kılınç et al., Scientific Reports (2018) 8: 8969.

Abstract (emphasis mine):

Archaeogenomic studies have largely elucidated human population history in West Eurasia during the Stone Age. However, despite being a broad geographical region of significant cultural and linguistic diversity, little is known about the population history in North Asia. We present complete mitochondrial genome sequences together with stable isotope data for 41 serially sampled ancient individuals from North Asia, dated between c.13,790 BP and c.1,380 BP extending from the Palaeolithic to the Iron Age. Analyses of mitochondrial DNA sequences and haplogroup data of these individuals revealed the highest genetic affinity to present-day North Asian populations of the same geographical region suggesting a possible long-term maternal genetic continuity in the region. We observed a decrease in genetic diversity over time and a reduction of maternal effective population size (Ne) approximately seven thousand years before present. Coalescent simulations were consistent with genetic continuity between present day individuals and individuals dating to 7,000 BP, 4,800 BP or 3,000 BP. Meanwhile, genetic differences observed between 7,000 BP and 3,000 BP as well as between 4,800 BP and 3,000 BP were inconsistent with genetic drift alone, suggesting gene flow into the region from distant gene pools or structure within the population. These results indicate that despite some level of continuity between ancient groups and present-day populations, the region exhibits a complex demographic history during the Holocene.

north-asians-mtdna-haplogroup-frequency
Relationship between ancient North Asians and other populations based on haplogroup frequencies. Ancient North Asians as a single group (SIB, n = 41) and as divided into three different regional groups including Cis-Baikal (CISB, n = 23), Trans-Baikal (TRAB, n = 7) and Yakutia (YAK, n = 9) or as divided into three temporal groups including Early (7,000 BP, n = 11), Middle (4800 BP, n = 16) and Late (3000 BP, n = 11). Two individuals from Krasnoyarsk and Blagoveshensk are not included in regional groups due to their distinct geographical locations. (a) Barplot showing haplogroup frequencies on a dataset of 1,780 individuals. PCA plot based on haplogroup frequencies calculated using (b) 291 individuals with full mitochondrial sequences. Ancient North Asians are included as a single population. (c) 1,780 individuals. Ancient North Asians are included as three different regional groups in the analysis. See also Supplementary Tables S1, S4–S12 and Fig. S3a and b in Supplementary Information.

Interesting excerpts:

Although highly dependent on sample size and thus prone to generalization, haplotype sharing analysis between three spatial groups and other modern and ancient populations (Supplementary Table S15) revealed that the TRAB group shared most lineages with ancient Kazakh Altai (KA) and modern Nganasan (NGN)39,40,41,42. The CISB group shared most lineages with Tubalar39,42, KA43 and Early Bronze Age groups of Russia (BO)12, which might reflect the Siberian roots of BO, consistent with MDS based on Fst (Fig. 3b). The YAK group shared most lineages with the CISB, BO and Tubalar groups. These results showed that despite being from different sides of the Lake Baikal, the CISB and YAK groups shared most lineages with the Tubalar and also both of them were to a certain degree affiliated to the BO of the Cis-Baikal region, thus, reflecting a shared common ancestry. Furthermore, the CISB and YAK groups share lineages supporting the hypothesis of a lasting continuity in this large geographical territory. However, the TRAB group may have different legacy with affinities to ancient Kazakh Altai and modern Nganasan groups (that, actually, may have relocated from the Trans-Baikal region in times post-dating our sample).

north-asian-mtdna-plot
Relationship between ancient North Asians and other ancient and present-day populations based on Slatkin’s linearized pairwise FST. MDS plot based on Slatkin’s linearized pairwise FST calculated using (a) full mitochondrial DNA sequences. (b) HVRI sequences. See also Fig. S3c and d in Supplementary Information, Supplementary Tables S13–S15.

Two findings, however, were intriguing. One was the discovery of only weak support for a single regional population in comparisons between Early vs. Late as well as Middle vs. Late groups in the region. This may be explained by population structure, as the Late group comprised geographically very distant individuals, such as individuals from Krasnoyarsk Krai and Amur Oblast, not represented in the other diachronic groups (Table S9). Another explanation for rejecting the null hypothesis of continuity between the Middle and Late (4,800–3,000 BP) groups might be due to an interruption and the arrival of pastoralists at the beginning of the Iron Age between 3,670 to 2,760  BP as suggested by the archaeological record32. Thus, the introduction of the new lifeways, technologies and material culture expressions might also here be associated to an increased mobility into the area.

The second point was the estimated reduction in maternal effective population size and haplotype diversity around 7,000 BP. Intriguingly, climate modelling and radiocarbon dating studies53 suggest that climatic change and a collapse of the riverine ecosystems might have affected the human populations in Cis Baikal between 7,000–6,000 BP in line with our results. This finding was further supported by archaeological studies pointing to a possible hiatus38,54,55.

Although our results provide a first glimpse into population structure and diversity in North Asia during the Holocene which link to trend in the archaeological record, complete genome sequences will provide a higher resolution of more complex demographic events in the region.

Yet another hint at the west-east (and not east-west) population movement in Eurasia after the Corded Ware and Yamna expansions, without any significant change in the other direction until the Iron Age (as we know from Fennoscandian samples), which leaves still less space to propose incoming Uralic-speaking groups from Asia…

Related:

Hungarian mitogenomes similar to East and West Slavs, but genetic substratum predates their historic contacts

middle-age-hungarian

Whole mitochondrial genome diversity in two Hungarian populations, Malyarchuk et al. Mol Genet Genomics (2018).

Abstract:

Complete mitochondrial genomics is an effective tool for studying the demographic history of human populations, but there is still a deficit of mitogenomic data in European populations. In this paper, we present results of study of variability of 80 complete mitochondrial genomes in two Hungarian populations from eastern part of Hungary (Szeged and Debrecen areas). The genetic diversity of Hungarian mitogenomes is remarkably high, reaching 99.9% in a combined sample. According to the analysis of molecular variance (AMOVA), European populations showed a low, but statistically significant level of between-population differentiation (Fst = 0.61%, p = 0), and two Hungarian populations demonstrate lack of between-population differences. Phylogeographic analysis allowed us to identify 71 different mtDNA sub-clades in Hungarians, sixteen of which are novel. Analysis of ancestry-informative mtDNA sub-clades revealed a complex genetic structure associated with the genetic impact of populations from different parts of Eurasia, though the contribution from European populations is the most pronounced. At least 8% of ancestry-informative haplotypes found in Hungarians demonstrate similarity with East and West Slavic populations (sub-clades H1c23a, H2a1c1, J2b1a6, T2b25a1, U4a2e, K1c1j, and I1a1c), while the influence of Siberian populations is not so noticeable (sub-clades A12a, C4a1a, and probably U4b1a4).

Interesting excerpt:

Our analysis of ancestry-informative mtDNA sub-clades revealed a complex genetic structure associated with the genetic impact of populations from different parts of Europe. At least 8% of ancestry-informative haplotypes found in Hungarians demonstrate similarity with East (Russians and Ukrainians) and West (Poles and Slovaks) Slavic populations (sub-clades H1c23a, H2a1c1, J2b1a6, T2b25a1, U4a2e, K1c1j, and I1a1c). This observation is consistent with the results of mtDNA studies of medieval populations living in the Hungarian-Slavic contact zone of the Carpathian Basin in the 9th–12th centuries AD (Csákyová et al. 2016). Taken together, these data confirm earlier historical and archaeological reports on mixed populations of medieval Slavs and Magyars, based on the research into cemeteries discovered in Central Europe (Csősz et al. 2016; Csákyová et al. 2016). On the other hand, we cannot confirm the Hungarian-Slavic contacts using molecular dating of the identified mtDNA sub-clades, since their age exceeds the estimated time of the contact period and varies from 1.3 kya (for K1c1j) to 5.2 kya (for T2b25a1) (Figure S1). One of an issue may be sample size problem, because some haplotypes may be missed in the sampling, and this can lead to an overestimate of the age of the mtDNA sub-clade (Richards et al. 2000).

hungarian-mtdna-haplogroup-j
Figure S1. MDS plot based on Fst values calculated from complete mtDNA sequences for population samples from Europe. Stress value = 0.00078

However, it is known that the evolutionary ages of most mtDNA lineages specific to Eastern and Central Europeans correspond to approximately 4 kya (from 2.3 to 5.9 kya) (Malyarchuk et al. 2008, 2017; Mielnik-Sikorska et al. 2013; Översti et al. 2017), thus coinciding with the time of the Bronze Age expansion of Eastern Europeans in accordance with the Kurgan model established by archaeologists and paleogeneticists (Gimbutas 1971; Allentoft et al. 2015; Haak et al. 2015). Thus, similar haplotypes among Hungarians and Slavs and other European ethnic groups can be a reflection of the common genetic substratum which predates the formation of the most modern European populations. Therefore, mtDNA sub-clades H5a1m, T2a1c, and W3a1d1 (with the ages varying from 2.6 to 3.9 kya, based on complete mtDNA mutation rate), which are shared by Hungarians and Finno-Ugric peoples, such as Estonians and Finns, may testify these pan-European relationships (Figure S1). Another example is the sub-clade J2b1a6, which unites the mtDNA haplotypes of the ancient and modern population of Eastern and Central Europe from the Iron Age to the present (Figure S1).

Related:

Domesticated horse population structure, selection, and mtDNA geographic patterns

przewalski-hutai

Open access Detecting the Population Structure and Scanning for Signatures of Selection in Horses (Equus caballus) From Whole-Genome Sequencing Data, by Zhang et al, Evolutionary Bioinformatics (2018) 14:1–9.

Abstract (emphasis mine):

Animal domestication gives rise to gradual changes at the genomic level through selection in populations. Selective sweeps have been traced in the genomes of many animal species, including humans, cattle, and dogs. However, little is known regarding positional candidate genes and genomic regions that exhibit signatures of selection in domestic horses. In addition, an understanding of the genetic processes underlying horse domestication, especially the origin of Chinese native populations, is still lacking. In our study, we generated whole genome sequences from 4 Chinese native horses and combined them with 48 publicly available full genome sequences, from which 15 341 213 high-quality unique single-nucleotide polymorphism variants were identified. Kazakh and Lichuan horses are 2 typical Asian native breeds that were formed in Kazakh or Northwest China and South China, respectively. We detected 1390 loss-of-function (LoF) variants in protein-coding genes, and gene ontology (GO) enrichment analysis revealed that some LoF-affected genes were overrepresented in GO terms related to the immune response. Bayesian clustering, distance analysis, and principal component analysis demonstrated that the population structure of these breeds largely reflected weak geographic patterns. Kazakh and Lichuan horses were assigned to the same lineage with other Asian native breeds, in agreement with previous studies on the genetic origin of Chinese domestic horses. We applied the composite likelihood ratio method to scan for genomic regions showing signals of recent selection in the horse genome. A total of 1052 genomic windows of 10 kB, corresponding to 933 distinct core regions, significantly exceeded neutral simulations. The GO enrichment analysis revealed that the genes under selective sweeps were overrepresented with GO terms, including “negative regulation of canonical Wnt signaling pathway,” “muscle contraction,” and “axon guidance.” Frequent exercise training in domestic horses may have resulted in changes in the expression of genes related to metabolism, muscle structure, and the nervous system.

horse-admixture
Bayesian clustering output for 5 K values from K = 2 to K = 8 in 45 domestic horses. Each individual is represented by a vertical line, which is partitioned into colored segments that represent the proportion of the inferred K clusters.

Interesting excerpts:

Admixture proportions were assessed without user-defined population information to infer the presence of distinct populations among the samples (Figure 2). At K = 3 or K = 4, Franches-Montagnes and Arabian forms one unique cluster; at K = 5, Jeju pony forms one unique cluster. For other breeds, comparatively strong population structure exists among breeds, and they can be assigned to 2 (or 3) alternate clusters from K = 3 to K = 5 including group A (Duelmener, Fjord, Icelandic, Kazakh, Lichuan, and Mongolian) and group B (Hanoverian, Morgan, Quarter, Sorraia, and Standardbred). For group A, geographically this was unexpected, where Nordic breeds (Norwegian Fjord, Icelandic, and Duelmener) clustered with Asian breeds including the Mongolian. Previous results of mitochondrial DNA have revealed links between the Mongolian horse and breeds in Iceland, Scandinavia, Central Europe, and the British Isles. The Mongol horses are believed to have been originally imported from Russia subsequently became the basis for the Norwegian Fjord horse.31 At K = 6, Sorraia forms one unique cluster. The Sorraia horse has no long history as a domestic breed but is considered to be of a nearly ancestral type in the southern part of the Iberian Peninsula.32 However, our result did not support Sorraia as an independent ancestral type based on result from K = 2 to K = 5, and the unique cluster in K = 6 may be explained by the small population size and recently inbreeding programs. Genetic admixture of Morgan reveals that these breeds are currently or traditionally continually crossed with other breeds from K = 2 to K = 8. The Morgan horse has been a largely closed breed for 200 years or more but there has been some unreported crossbreeding in recent times.33

horse-pca
Principal component analysis results of all 48 horses. The x-axis denotes the value of PC1, whereas the y-axis denotes the value of PC2. Each dot in the figure represents one individual.

Bayesian clustering and PCA demonstrated the relationships among the horse breeds with weak geographic patterns. The tight grouping within most native breeds and looser grouping of individuals in admixed breeds have been reported previously in modern horses using data from a 54K SNP chip.33,34 Cluster analysis reveals that Arabian or Franches-Montagnes forms one unique cluster with relatively low K value, which is consistent with former study using 50K SNP chip 33,34 Interestingly, Standardbred forms a unique cluster with relatively high K value in this study, different from previous study.33 To date, no footprints are available to describe how the earliest domestic horses spread into China in ancient times. Our study found that Kazakh and Lichuan were assigned to the same lineage as other native Asian breeds, in agreement with previous studies on the origin of Chinese domestic horses.4,5,35,36 The strong genetic relationship between Asian native breeds and European native breeds have made it more difficult to understand the population history of the horse across Eurasia. Low levels of population differentiation observed between breeds might be explained by historical admixture. Unlike the domestic pig in China,8  we suggest that in China, Northern/Southern distinct groups could not be used to genetically distinct native Chinese horse breeds. We consider that during domestication process of horse, gene flow continued among Chinese-domesticated horses.


Open access Some maternal lineages of domestic horses may have origins in East Asia revealed with further evidence of mitochondrial genomes and HVR-1 sequences, by Ma et al., PeerJ (2018).

Abstract:

Objectives
There are large populations of indigenous horse (Equus caballus) in China and some other parts of East Asia. However, their matrilineal genetic diversity and origin remained poorly understood. Using a combination of mitochondrial DNA (mtDNA) and hypervariable region (HVR-1) sequences, we aim to investigate the origin of matrilineal inheritance in these domestic horses.

Methods
To investigate patterns of matrilineal inheritance in domestic horses, we conducted a phylogenetic study using 31 de novo mtDNA genomes together with 317 others from the GenBank. In terms of the updated phylogeny, a total of 5,180 horse mitochondrial HVR-1 sequences were analyzed.

Results
Eighteen haplogroups (Aw-Rw) were uncovered from the analysis of the whole mitochondrial genomes. Most of which have a divergence time before the earliest domestication of wild horses (about 5,800 years ago) and during the Upper Paleolithic (35–10 KYA). The distribution of some haplogroups shows geographic patterns. The Lw haplogroup contained a significantly higher proportion of European horses than the horses from other regions, while haplogroups Jw, Rw, and some maternal lineages of Cw, have a higher frequency in the horses from East Asia. The 5,180 sequences of horse mitochondrial HVR-1 form nine major haplogroups (A-I). We revealed a corresponding relationship between the haplotypes of HVR-1 and those of whole mitochondrial DNA sequences. The data of the HVR-1 sequences also suggests that Jw, Rw, and some haplotypes of Cw may have originated in East Asia while Lw probably formed in Europe.

Conclusions
Our study supports the hypothesis of the multiple origins of the maternal lineage of domestic horses and some maternal lineages of domestic horses may have originated from East Asia.

horse-mtdna
Median joining network constructed based on the 247- bp HVR-1 sequences. Circles are proportional to the number of horses represented and a scale indicator (for node sizes) was provided. The length of lines represents the number of variants that separate nodes (some manual adjustment was made for visually good). In the circles, the colors of solid pie slices indicate studied horse populations: Orange, European horses; Blue, horses of West Asia; Light Green, horses from East Asia; Grey, ancient horses; Purper, Przewalskii horses.

Geographic distributions of horse mtDNA haplogroups

The analysis of geographic distribution of the mitochondrial genome haplogroups showed that horse populations in Europe or East Asia included all haplogroups defined from the mtDNA genome sequences. The lineage Fw comprised entirely of Przewalskii horses. The two haplogroups Iw and Lw displayed frequency peaks in Europe (14.08% and 37.32%, respectively) and a decline to the east (9.33% and 8.00% in the West Asia, and 6.45% and 12.90% in East Asia, respectively), especially for Lw, which contained the largest number of European horses (Table 2). However, an opposite distribution pattern was observed for haplogroups Aw, Hw, Jw, and Rw, which were harbored by more horses from East Asia than those from other regions. The proportions of horses from East Asia for the four haplogroups were 38%, 88%, 62%, and 54%, respectively.

horse-mtdna-tree
Schematic phylogeny of mtDNAs genome from modern horses. This tree includes 348 sequences
and was rooted at a donkey (E. asinus) mitochondrial genome (not displayed). The topology was inferred by a beast approach, whereas a time divergence scale (based on rate substitutions) is shown on the bottom (age estimates were indicated with thousand years (KY)). The percentages on each branch represent Bayesian posterior credibility and the alphabets on the right represent the names of haplogroups. Additional details concerning ages were given in Tables S3 and S6.

Related:

A multidisciplinary approach to Neolithic life reconstruction

france-neolithic

Open access A Multidisciplinary Approach to Neolithic Life Reconstruction, by Goude et al. J Archaeol Method Th (2018).

Abstract (emphasis mine):

The expansion of Neolithic stable isotope studies in France now allows distinct regional population-scale food patterns to be linked to both local environment influences and specific economic choices. Carbon and nitrogen isotope values of more than 500 humans and of animal samples also permit hypotheses on sex-biased human provenance. To advance population scale research, we here present the first study that draws together carbon (C), nitrogen (N), sulphur (S) and strontium (Sr), dental calculus, aDNA, and palaeoparasitology analysis to infer intra-population patterns of diet and provenance in a Middle Neolithic population from Le Vigneau 2 (human = 40; fauna = 12; 4720–4350 cal. BC) from north-western France. The data of the different studies, such as palaeoparasitology to detect diet and hygiene, CNS isotopes and dental calculus analysis to examine dietary staples, Sr and S isotopes to discriminate non-locals, and aDNA to detect maternal (mtDNA) versus paternal lineages (Y chromosome), were compared to anthropological information of sex and age. Collagen isotope data suggest a similar diet for all individuals except for one child. The provenance isotopic studies suggest no clear differences between sexes, suggesting both males and females used the territory in a similar pattern and had access to foods from the same environments.

internal-external-burials
Radiogenic strontium isotope ratios from human teeth

Relevant excerpt:

With regard to aDNA analysis and the information this reveals on genetic provenance, Table 1 presents the mitochondrial haplogroups (SNPs typing) retrieved from the human remains. SNPs typing made it possible to assign one individual (LVH3, male < 60 years old) to maternal lineage K (or derivatives), and another individual (LVH12) to lineage H (or derivatives), whereas the low number of SNPs recovered for the last sample (LVH26) did not make it possible to assign any haplogroup. No Y chromosome SNP, as well as no reproducible result for HVR-I sequences, could be obtained for any Le Vigneau 2 individual. Unfortunately, major DNA degradation prevents precise identification of the maternal and paternal lineages, and these two mitochondrial haplogroups do not allow any assessment about female mobility. However, we can note that maternal lineages characterized in the Le Vigneau 2 site are quite common in Neolithic farmer groups and fit within the French Middle Neolithic variability (from 14 to 25.5% for haplogroup K and from 7.9 to 40.9% for haplogroup H; Beau et al. 2017), including farmers from the Paris Basin (35% of H and 18.33% of K for the Gurgy site; Rivollat et al. 2015).