“…When studying the demographic history of humans, aDNA has been shown to be an irreplaceable source of information. aDNA studies have revealed large-scale population movements and genetic turnover events in Western Eurasia [17][18][19][20] that were otherwise impossible to recover from human genetic data of modern-day populations. Studies of the uniparentally inherited markers of ancient individuals have also yielded otherwise undetectable results, e.g.…”
mentioning
confidence: 99%
“…Studies of the uniparentally inherited markers of ancient individuals have also yielded otherwise undetectable results, e.g. the loss of European mtDNA diversity following the repeopling of Europe after the last glacial maximum 10 , or the decrease in and partial replacement of diversity of hunter-gatherer Y-chromosome lineages in eastern and central Europe following the Neolithic expansion [21][22][23][24] , followed by the loss of diversity of Neolithic Y-chromosomes lineages with the arrival of Steppe-like ancestry at the beginning of the 3 rd millennium BCE 15,[18][19][20] .…”
Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture assays such as the 1240 k, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240 k capture, YMCA significantly improves the mean coverage and number of sites covered on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe.
“…When studying the demographic history of humans, aDNA has been shown to be an irreplaceable source of information. aDNA studies have revealed large-scale population movements and genetic turnover events in Western Eurasia [17][18][19][20] that were otherwise impossible to recover from human genetic data of modern-day populations. Studies of the uniparentally inherited markers of ancient individuals have also yielded otherwise undetectable results, e.g.…”
mentioning
confidence: 99%
“…Studies of the uniparentally inherited markers of ancient individuals have also yielded otherwise undetectable results, e.g. the loss of European mtDNA diversity following the repeopling of Europe after the last glacial maximum 10 , or the decrease in and partial replacement of diversity of hunter-gatherer Y-chromosome lineages in eastern and central Europe following the Neolithic expansion [21][22][23][24] , followed by the loss of diversity of Neolithic Y-chromosomes lineages with the arrival of Steppe-like ancestry at the beginning of the 3 rd millennium BCE 15,[18][19][20] .…”
Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture assays such as the 1240 k, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240 k capture, YMCA significantly improves the mean coverage and number of sites covered on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe.
“…18 reported a HV haplotype in one sample from Serbia dating from 5800 BCE. Moreover, haplogroup HV was observed in Copper Age specimens from Scotland, Hungary and Germany 25 and in Hungarian and Israeli samples from the Chalcolithic period 26,27 Figure 2Median Joining Network representing the phylogenetic relationships between the new Thracian samples (highlighted in red labels) and the ancient reference dataset. Major mitochondrial lineages and sub-lineages are indicated by different colors as specified in the legend at the top-left.…”
Section: Resultsmentioning
confidence: 99%
“…Nowadays the highest observed European frequency of the lineage K is in Bulgaria (13.3%) 28 and K1c is particularly common in Slavic-speaking countries. In ancient populations, the haplogroup K1c has been identified in six hunter-gatherers dated before the arrival of farming (one in Romania, three in Serbia 18 and two in Greece 29 ), in two Bronze-Age individuals from Hungary and Bulgaria 18,30,31 and in two Central-Europe farmers associated with the Bell-Beaker culture 25,32,33 . The phylogenetic network analysis (Fig.…”
One of the best documented Indo-European civilizations that inhabited Bulgaria is the Thracians, who lasted for more than five millennia and whose origin and relationships with other past and present-day populations are debated among researchers. Here we report 25 new complete mitochondrial genomes of ancient individuals coming from three necropolises located in different regions of Bulgaria – Shekerdja mogila, Gabrova mogila and Bereketska mogila – dated to II-III millennium BC. The identified mtDNA haplogroup composition reflects the mitochondrial variability of Western Eurasia. In particular, within the ancient Eurasian genetic landscape, Thracians locate in an intermediate position between Early Neolithic farmers and Late Neolithic-Bronze Age steppe pastoralists, supporting the scenario that the Balkan region has been a link between Eastern Europe and the Mediterranean since the prehistoric time. Spatial Principal Component Analysis (sPCA) performed on Thracian and modern mtDNA sequences, confirms the pattern highlighted on ancient populations, overall indicating that the maternal gene pool of Thracians reflects their central geographical position at the gateway of Europe.
“…To assess links between diet and cultural evolution on the GHP, stable isotope and ancient DNA (aDNA) research has been conducted on samples from the Neolithic through Iron Age 42 , 58 – 61 . Previous carbon and nitrogen stable isotope analyses of human and faunal osteological samples from this region have focused primarily on Neolithic and Copper Age populations, reporting a transformation in subsistence strategies during the Late Neolithic and Copper Age towards increased consumption of animal protein compared to the previous subperiods 58 , 62 – 65 .…”
The Great Hungarian Plain (GHP) served as a geographic funnel for population mobility throughout prehistory. Genomic and isotopic research demonstrates non-linear genetic turnover and technological shifts between the Copper and Iron Ages of the GHP, which influenced the dietary strategies of numerous cultures that intermixed and overlapped through time. Given the complexities of these prehistoric cultural and demographic processes, this study aims to identify and elucidate diachronic and culture-specific dietary signatures. We report on stable carbon and nitrogen isotope ratios from 74 individuals from nineteen sites in the GHP dating to a ~ 3000-year time span between the Early Bronze and Early Iron Ages. The samples broadly indicate a terrestrial C3 diet with nuanced differences amongst populations and through time, suggesting exogenous influences that manifested in subsistence strategies. Slightly elevated δ15N values for Bronze Age samples imply higher reliance on protein than in the Iron Age. Interestingly, the Füzesabony have carbon values typical of C4 vegetation indicating millet consumption, or that of a grain with comparable δ13C ratios, which corroborates evidence from outside the GHP for its early cultivation during the Middle Bronze Age. Finally, our results also suggest locally diverse subsistence economies for GHP Scythians.
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