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Post by Admin on Dec 5, 2018 7:02:07 GMT
The Tyrolean Iceman is an extraordinarily well-preserved natural that lived south of the Alpine ridge ~5,200 years before present (ybp), during the Copper Age. Despite studies that have investigated his genetic profile, the relation of the Iceman´s maternal lineage with present-day mitochondrial variation remains elusive. Studies of the Iceman have shown that his mitochondrial DNA (mtDNA) belongs to a novel lineage of haplogroup K1 (K1f) not found in extant populations. We analyzed the complete mtDNA sequences of 42 haplogroup K bearing individuals from populations of the Eastern Italian Alps – putatively in genetic continuity with the Tyrolean Iceman—and compared his mitogenome with a large dataset of worldwide K1 sequences. Our results allow a re-definition of the K1 phylogeny, and indicate that the K1f haplogroup is absent or rare in present-day populations. We suggest that mtDNA Iceman´s lineage could have disappeared during demographic events starting in Europe from ~5,000 ybp. Based on the comparison of our results with published data, we propose a scenario that could explain the apparent contrast between the phylogeographic features of maternal and paternal lineages of the Tyrolean Iceman within the context of the demographic dynamics happening in Europe from 8,000 ybp. The Tyrolean Iceman has also been extensively characterized genetically. Whole genome sequencing data indicate that the Iceman was blood group 0, lactose intolerant and genetically predisposed to cardiovascular diseases6. Moreover, Keller and colleagues6 showed that the Iceman belongs to the Y-chromosome haplogroup G2a-L91. Comparing the Iceman’s genomic data to the human reference genome (UCSC hg19) specified the Iceman´s lineage into one of the four sub-branches of G2a L-91 (G2a2a1a2a1a-FGC5672) following the latest version of the Y-DNA Haplogroup Tree7. Comparative analysis based on informative autosomal SNPs and Y-chromosome data showed a clear link with genetic diversity of extant populations further supported by recent whole genome-data analysis8. However, an important question regarding the Iceman genetic heritage remains unanswered. In fact, despite the mitochondrial DNA (mtDNA) of the Iceman being well characterised9,10,11,12, the relation of his lineage with present-day mitochondrial diversity remains elusive. The first study on the complete mtDNA of the Iceman11 showed that the ancient mitogenome was a novel lineage of mtDNA haplogroup K1 (named K1f), not yet detected in extant populations. Ermini et al.11 proposed that the Iceman’s haplogroup may remain undetected simply due to inadequate sampling. This hypothesis should be considered due to the paucity of data regarding K1 haplogroups available at the time of the study, especially from alpine populations, which are putatively in genetic continuity with the Iceman. Alternatively, the K1f haplogroup and its closest neighbors may have been lost during repeated demographic and population events occurring in the Alps since the Neolithic. Reich et al. (2016) found mtDNA haplogroup K1a along with Y-DNA haplogroup G1a among ancient samples from Iran (Chalcolithic). One individual from Neolithic Iran (I1671) had Y-DNA haplogroup G1a1 and mtDNA haplogroup K1a, which closely matches the Tyrolian Iceman's gentic profile. Ötzi was likely to be one of the Near Eastern farmers who migrated to Western Europe from the Neolithic to the Bronze Age as G1a is the genetic signature of Near Eastern farmer ancestry. Haplogroup K was found in approximately 15% of the Neolithic samples from Europe and their main paternal lineage was Y-DNA haplogroup G2a. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those of Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia. After the OCA2 and HERC2 genes associated with iris colour were analysed, it was confirmed that Ötzi had brown eyes. The most strongly associated variant, rs12913832 in the Iceman's genome, is associated with brown eye colour in over 80% of cases (keller et al. 2012).
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Post by Admin on Dec 5, 2018 18:02:12 GMT
The Iceman mitochondrial genetic heritage The mitogenomes of 42 haplogroup K individuals from Eastern Italian Alps were analyzed (Table S1). The most frequently observed K1 Alpine haplogroups were K1a4 and K1a1, similar to the worldwide K1 distribution (Fig. 1) and K1a + 195 (Table S2). Rare haplogroups were also observed in this study such as K1a19 and K1a24, and K1e1, which was represented in our dataset by a novel haplotype defined by a specific transition in the coding region (transition A15244G; sample #111Gm in the Fig. S2). Neither the Iceman’s lineage nor any other intermediate haplotypes of K1f were detected. Figure 1: Main skeleton of haplogroup K1 and its branches based on all of the mitogenomes. Next, we analyzed all K1 mitogenomes available in the literature, scanning databases, in combination with our dataset (n = 1077; Table S2). The whole K1 tree was updated and the Iceman’s sequence was added to the phylogeny (Fig. 1). This tree was compared with the one presented by Ermini and collaborators11 that used in total 115 K sequences (85 of which were K1 mitogenomes). The Iceman’s mitogenome falls within a cluster defined by transition T16362C (K1 + 16362) that includes K1d (5.6 thousand years [kya]; standard error: 0.6–10.7) and K1e (13.8 kya; standard error: 6.5–21.4) haplogroups. The collected data created a clearer and more robust representation of K1 + 16362 cluster despite being defined exclusively by an unstable mutation on the rapidly mutating mtDNA control region. Indeed, only one sequence of unknown origin (EU073969) shared the mutation T16362C with the Iceman´s mitogenome in the tree built by Ermini and colleagues11. Currently, this cluster encompasses 13 other modern sequences mostly derived from individuals of known European ancestry (five sampled in Denmark, one in Scotland, one in the Alps, and six of unknown origin; see Fig. 2). The closest observed haplotype (JQ704724) to the Iceman’s mitogenome is, however, quite distant from K1f, being separated by six mutational steps (five of which are in the coding region). Figure 2: Most parsimonious phylogenetic tree of the K1 + 16362 cluster. Overall, the results indicate that K1f has been lost from present-day populations, rather than being a rare haplotype undetected due to inadequate sampling. With a binomial distribution13,14 given the size of our dataset, we estimated (with a 95% of probability) that the K1f lineage should not occur with a frequency above 0.3%. In addition, the most parsimonious phylogenetic tree showed that there exist no intermediate haplotypes connecting the Tyrolean Iceman’s lineage to the main root of K1 (Fig. 2). Recently, considerable knowledge has been gained on the mtDNA diversity of ancient Europeans15. It appears that the Iceman´s haplogroup may not be the only case of a described mtDNA lineages that has apparently been lost. Two examples include lineages from haplogroup H (H46b and H88) that have been detected in two Linear Pottery culture individuals (LBK, 5450-4775 BC) in Germany16. However, H46b and H88 haplogroups are only one-step mutation away from the extant ancestral haplogroups (H46 and H*, respectively). This is in contrast to the described phylogeographic features of the K1f haplogroup, suggesting that the entire branch of K1f was lost. Whole mitochondrial DNA sequencing in Alpine populations and the genetic history of the Neolithic Tyrolean Iceman www.researchgate.net/publication/290443135_Whole_mitochondrial_DNA_sequencing_in_Alpine_populations_and_the_genetic_history_of_the_Neolithic_Tyrolean_Iceman
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Post by Admin on Dec 6, 2018 18:10:50 GMT
Reconstructing the genetic history of the Tyrolean Iceman The focused analysis of the Tyrolean Iceman has produced important information on his origin and genetic relations between Iceman and extant European populations. The availability of data on genetic markers with different modes of inheritance and rates of evolution allows to perform comparative analysis that shed further light on the genetic history of the Tyrolean Iceman. Interestingly, there is a contrast between the Iceman´s maternal and paternal genetic heritage. While the branch of mtDNA K1f lineage has probably been lost from present-day populations according to this study, the Y-chromosome branch G2a-L91 is still observed in Europe, and reaches remarkable frequencies ( > 10%) in groups from the Mediterranean area, i.e. Sardinians and Corsicans6,17. How can this pattern be explained? The direct comparison of the evolutionary history of specific female and male lineages can be complicated by differences in their phylogenetic structure and resolution. However, it is likely that the dissimilarity observed in the diachronic patterns of the Iceman’s genetic lineages are due mainly to the distributions of K1f and G2a in Europe prior to 5,000 ybp and later demographic events that shaped the European genetic structure. Recent ancient DNA studies suggest that both mtDNA haplogroup K1 and Y-chromosome G2a reached the European continent around 8,000 ybp by migrations of Early Neolithic people from the Near East through continental and Mediterranean routes15,18,19,20 (see Fig. 3A). Subsequently, these haplogroups spread across the continent, as shown by the distribution of K1 and G2a from several Europeans specimens dated > 5,000 ybp (see Fig. 3B and its legend for references and details). At that time, the K1 haplogroup was present in West, South, East, and North Europe with its main branches (K1a, K1b) and rarer branch like K1e, whereas K1f was virtually restricted to the Alps since it has not been observed outside this region. On the other hand, G2a was the predominant Y-chromosome lineage observed in the European Neolithic samples analyzed thus far15,19,20,21,22,23. Figure 3 While the Iceman’s Y-chromosome lineage was part of the Early Neolithic genetic substrate, as suggested from current distributions of G2a-L91 (Fig. 3C), the mtDNA K1f lineage developed locally in the Eastern Alps at least from ~5,200 ybp (the time of the Iceman). After 5,000 ybp, population expansion, migrations and admixture occurred throughout the continent, re-shaping the genetic structure of Europeans8,15,21. These events led to the almost complete replacement of the Y-chromosome haplogroup G2a-L91 by other haplogroups (e.g. R1b). However, Sardinians and Corsicans maintained such genetic feature due to geographic isolation, as supported from whole-genome data6,8 (Fig. 3). Conversely, the K1f branch may have been completely replaced by haplogroups that are frequent today (e.g haplogroup H). This process was probably favored by the stationary demographic state of population groups bearing K1 haplotypes in the Alps as suggested by the Bayesian Skyline Plot (BSP) of Fig. S3. This is additionally supported by archaeological data24 that suggests low population density during the Neolithic and the Copper Age (5,450-4,150 ybp) in the Iceman’s territory (Vinschgau valley), while significant demographic growth started ~2,000 years later during the Middle Bronze Age. In conclusion, by combining genetic data from modern-day populations and European Neolithic specimens, we gained new insights into the genetic history of the Tyrolean Iceman. This study demonstrates the continued importance of this unique specimen to shed light on the early migrations in Europe, and marks a first step towards a systematic study of the genetic history of ancient Alpine groups. Scientific Reports volume6, Article number: 18932 (2016)
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Post by Admin on Dec 8, 2018 17:57:32 GMT
“Through analyzing the Iceman’s toolkit from different viewpoints and reconstructing the entire life cycle of each instrument, we were able to gain insights into Ötzi’s cultural background, his individual history, and his last hectic days,” Wierer told Gizmodo. “What we do is to examine tools from the past and reconstruct their life cycle in detail, from their production to their utilization until they were finally discarded. In this way we are able to determine many features of the lifestyle of prehistoric people. In Ötzi’s case we were dealing with the toolkit of a specific person, about whom we already knew a great deal. This made the research all the more exciting.” Previous studies suggested all of Ötzi’s chert—a sedimentary rock that produces sharp edges when flaked, or knapped—came from a single region in Northern Italy known as the Lessini Mountains. But the new analysis suggests the stones in Ötzi’s six tools were imported from at least three different regions in northern Italy, all within 25 to 44 miles (40 to 70 km) from the valley where the Iceman lived. This means that villages were being supplied with chert from different outcrops, and that contacts were maintained over long distances. This is not a new suggestion, as a previous study showed that the metal from Ötzi’s copper axe originated from Southern Tuscany some 350 miles (555 km) from where Ötzi met his fate in the Italian Alps. Wierer and her colleagues also examined the wear and tear on the Iceman’s tools. The distinctive flake patterns show that Ötzi was a right-handed individual, something not known before, and that he wasn’t an expert flintknapper. “The technical skill of flintworking, measurable by the regularity of work, the presence or absence of mistakes, is not excellent but on a medium level,” Wierer told Gizmodo. The tools were of various ages, and as noted, acquired from different regions. Looking at the quality of the edges, Wierer’s team suspects that Ötzi re-sharpened and reshaped some of his tools shortly before he died. He wasn’t working on any of his equipment when he was killed, as all of his tools were found in their respective bags—except the dagger, which was found lying in meltwater next to Ötzi’s mummified body. Interestingly, the dagger had a broken tip, but minimal signs of wear; the authors suggest Ötzi used his small dagger as an ornamental display, wearing it on his belt as a status symbol. By analyzing the pollen contained within the foods consumed by Ötzi, along with other prior evidence, Wierer and her colleagues were able to reconstruct his hectic itinerary in the hours before he died. Roughly 33 hours before his death, the Iceman was up in the mountains at a height of 8,200 feet (2,500 meters) above sea level. From there, he made a descent along the southern slope of the alpine ridge, reaching a location where he spent some time before making another ascent up the mountains. He climbed to a height of 9,800 feet (3,000 meters) about four to five hours before his death. Ötzi managed to eat three meals during this 33-hour period, including a final meal about two hours before he was killed. It has been hypothesized that Ötzi was involved in three conflicts in the hours before he died, the first of which is based on circumstantial evidence, namely the absence of a bow and set of arrows to match his arrowheads. It’s possible Ötzi was attacked, and his bow and arrow damaged, stolen, or discarded in haste—though no evidence exists to support this assertion aside from the conspicuous absence of this equipment. But the other two conflicts are on firmer footing, as evidenced by injuries observed on the Iceman’s body. After Ötzi made his descent to the valley below, he was attacked. “The second conflict is shown by several injuries on the body of the , the most evident of which is a deep wound on the right hand in a position which is characteristic for self-defense,” Wierer told Gizmodo. “Due to the healing process which had already started, researchers know that the cut happened at least 24 hours before his death.”
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Post by Admin on Dec 9, 2018 18:11:18 GMT
In September 1991, two hikers discovered a human corpse (Fig. 1), partially covered by snow and ice, on the Tisenjoch Pass in the Italian part of the Ötztal Alps. The Tyrolean Iceman, a 5,300-year-old Copper age individual, is now conserved at the Archaeological Museum in Bolzano, Italy, together with an array of accompanying artefacts. An arrowhead lodged within the soft tissue of the left shoulder, having caused substantial damage to the left subclavian artery, indicated a violent death1. Speculations on his origin, his life habits and the circumstances surrounding his demise initiated a variety of morphological, biochemical and molecular analyses. Studies of the Iceman's mitochondrial genome began 3 years after his discovery with an analysis of the HVS1 region2 and led to the sequence analysis of the entire mitochondrial genome3,4. Figure 1: The Tyrolean Iceman. Although these mitochondrial DNA (mtDNA) studies yielded conclusive data, no successful amplification of nuclear DNA from the Iceman has been reported to date. As cold environments often provide for good biomolecular preservation and as methods for ancient DNA analysis have recently improved, a whole-genome sequencing study was initiated in 2010. A 0.1-g bone biopsy was taken from the Iceman's left ilium under sterile conditions in the Iceman's preservation cell at the South Tyrol Archaeological Museum in Bolzano, Italy, DNA was extracted at the Institute of Human Genetics in Tübingen, Germany and a sequencing library was generated at febit GmbH in Heidelberg, Germany. Paired-end high-throughput sequencing on the SOLiD 4 platform was performed at Life Technologies facilities, Beverly, MA, USA. We found indication for recent common ancestry between the Iceman and present-day inhabitants of the Tyrrhenian Sea (particularly Corsica and Sardinia), that the Iceman probably had brown eyes, belonged to blood group O and was probably lactose intolerant. We further found a genetic predisposition for an increased risk for coronary heart disease (CHD), which may have contributed to the development of previously reported vascular calcifications. In addition, we found sequences corresponding to ∼60% of the genome of B. burgdorferi that are indicative of the earliest human case of infection with the pathogen for Lyme borreliosis. Figure 2: Analysis of DNA damage patterns. The average nucleotide composition around the ends of the analysed reads shows the typical pattern expected for ancient DNA fragmentation (Fig. 2a and b). A sharp increase in the frequency of purines (A and G) is observed at the first base upstream of the forward reads, accompanied by a complementary increase of pyrimidines (C and T) just downstream of the reverse reads. Additionally, substitution rates for each of the possible nucleotide mismatches along the sequencing read also show the expected pattern. While substitution rates are generally low (<0.25%) for most mismatch types, C to T transitions show an increased overall rate, in particular towards the end of the reads (up to 3.5% at the first nucleotide). As above, the increase in C to T transitions for the forward reads are accompanied by the complementary increase in G to A transitions observed for the reverse reads. Overall, these results are comparable to other ancient human genomes recently published, such as the Saqqaq5 and the Australian Aboriginal genome8,9, and therefore provide additional indication that the sequences are indeed ancient. Figure 3: Autosomal and Y-chromosome evidence of the Iceman's origin. As a next step we analysed the genetic ancestry of the Iceman. As the Iceman's mtDNA haplotype has not yet been detected among thousands of sampled contemporary individuals, it has been difficult to assess his genetic ancestry with high accuracy. The first analysis was to determine if the Iceman's autosomal DNA shows an affinity to any specific population or if he remains an outlier among contemporary samples. We intersected genotype calls of greater than ×6 coverage from his genome with the population reference sample consisting of more than 1,300 Europeans genotyped for SNPs on the Affymetrix 500K array11,12, 125 individuals from seven North African populations ranging from Egypt to Morocco on the Affymetrix 6.0 array and 20 Qatari samples from the Arabian Peninsula13. When plotting the Iceman's genotype along the first two major axes of variation in Principal Component space (PC1 versus PC2), PC1 is driven by a north-to-south gradient differentiating North Africans from Europeans, and PC2 aligns individuals along north-to-south gradient within Europe (Fig. 3a). The Iceman clusters nearest to southern European samples, suggesting no greater genetic affinity with the North African or Middle Eastern components of variation than present day southern Europeans (Fig. 3a). When considering only European populations, however, we observe that the Iceman clusters closest with five outlier contemporary samples from south-western Europe. In particular, the Iceman abuts the Italian samples originating from geographically isolated regions such as Sardinia (Fig. 3b). Analysis of a larger set of samples, including Sardinians from HGDP across a smaller subset of SNPs, further supports the clustering of the Iceman with samples from Sardinia based on autosomal SNPs (Fig. 3f). New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing www.nature.com/articles/ncomms1701
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