After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and ...microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data.
Here we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses.
We propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.
Ancient DNA (aDNA) obtained from human remains is typically fragmented and present in relatively low amounts. Here we investigate a set of optimal methods for producing aDNA data by comparing ...silica-based DNA extraction and aDNA library preparation protocols. We also test the efficiency of whole-genome enrichment (WGC) on ancient human samples by modifying a number of parameter combinations. We find that the Dabney extraction protocol performs significantly better than alternatives. We further observed a positive trend with the BEST library protocol indicating lower clonality. Notably, our results suggest that WGC is effective at retrieving endogenous DNA, particularly from poorly-preserved human samples, by increasing human endogenous proportions by 5x. Thus, aDNA studies will be most likely to benefit from our results.
We studied a set of methods used to generate ancient genome data from archaeological human samples from different sites and periods, and with varying levels of preservation. In these experiments we compared two sample preparation techniques, two silica-based DNA extraction protocols, and two aDNA library preparation protocols. Finally, we explored the efficiency of whole-genome capture (WGC) on aDNA libraries with different characteristics by comparing a set of protocol modifications.
Rapid and cost-effective retrieval of endogenous DNA from ancient specimens remains a limiting factor in palaeogenomic research. Many methods have been developed to increase ancient DNA yield, but ...modifications to existing protocols are often based on personal experience rather than systematic testing. Here, we present a new silica column-based extraction protocol, where optimizations were tested in controlled experiments. Using relatively well-preserved permafrost samples, we tested the efficiency of pretreatment of bone and tooth powder with a bleach wash and a predigestion step. We also tested the recovery efficiency of MinElute and QIAquick columns, as well as Vivaspin columns with two molecular weight cut-off values. Finally, we tested the effect of uracil-treatment with two different USER enzyme concentrations. We find that neither bleach wash combined with a predigestion step, nor predigestion by itself, significantly increased sequencing efficiency. Initial results, however, suggest that MinElute columns are more efficient for ancient DNA extractions than QIAquick columns, whereas different molecular weight cut-off values in centrifugal concentrator columns did not have an effect. Uracil treatments are effective at removing DNA damage even at concentrations of 0.15 U/µL (as compared to 0.3 U/µL) of ancient DNA extracts.
Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked innovations in symbolism, technology, and diet. We present 13 ancient genomes (c. 8500 to 7500 cal ...BCE) from Pre-Pottery Neolithic Çayönü in the Tigris basin together with bioarchaeological and material culture data. Our findings reveal that Çayönü was a genetically diverse population, carrying mixed ancestry from western and eastern Fertile Crescent, and that the community received immigrants. Our results further suggest that the community was organized along biological family lines. We document bodily interventions such as head shaping and cauterization among the individuals examined, reflecting Çayönü’s cultural ingenuity. Last, we identify Upper Mesopotamia as the likely source of eastern gene flow into Neolithic Anatolia, in line with material culture evidence. We hypothesize that Upper Mesopotamia’s cultural dynamism during the Neolithic Transition was the product not only of its fertile lands but also of its interregional demographic connections.
Neolithic Upper Mesopotamia was a center of cultural innovation; ancient genomes now reveal that it was also a migration hub.
In 2016, archaeological excavations undertaken by the Ephorate of Antiquities of West Attica, Piraeus and Islands 3.8 km south-west of Athens, Greece, revealed mass burials of 79 skeletons in three ...rows. The burials are dated to the 7th century BC. The anthropological field documentation was undertaken by The Swedish Institute of Athens, and followed established bioarchaeological protocols regarding taphonomic processes, age, sex, injuries, and pathological changes. The descriptions and interpretations should be regarded as preliminary field observations. A majority of the individuals were young adult or juvenile males, most of them without signs of active disease and with a generally good oral health status, but with corroded iron shackles around their wrists. Cause of death could not be determined although extensive and likely perimortem fractures were observed. The only object related to injury and/or possible cause of death was an arrowhead found in the chest of one of the skeletons. Why and where the individuals were killed is a matter of conjecture; the observations from the field documentation neither validate, nor disprove the hypothesis that these individuals were captives and victims of the socalled "Cylonian conspiracy" in the 7th century BC.
Sheep were among the first domesticated animals, but their demographic history is little understood. Here we analyzed nuclear polymorphism and mitochondrial data (mtDNA) from ancient central and west ...Anatolian sheep dating from Epipaleolithic to late Neolithic, comparatively with modern-day breeds and central Asian Neolithic/Bronze Age sheep (OBI). Analyzing ancient nuclear data, we found that Anatolian Neolithic sheep (ANS) are genetically closest to present-day European breeds relative to Asian breeds, a conclusion supported by mtDNA haplogroup frequencies. In contrast, OBI showed higher genetic affinity to present-day Asian breeds. These results suggest that the east-west genetic structure observed in present-day breeds had already emerged by 6000 BCE, hinting at multiple sheep domestication episodes or early wild introgression in southwest Asia. Furthermore, we found that ANS are genetically distinct from all modern breeds. Our results suggest that European and Anatolian domestic sheep gene pools have been strongly remolded since the Neolithic.
Bird remains that are difficult to identify taxonomically using morphological methods, are common in the palaeontological record. Other types of challenging avian material include artefacts and food ...items from endangered taxa, as well as remains from aircraft strikes. We here present a DNA-based method that enables taxonomic identification of bird remains, even from material where the DNA is heavily degraded. The method is based on the amplification and sequencing of two short variable parts of the 16S region in the mitochondrial genome. To demonstrate the applicability of this approach, we evaluated the method on a set of Holocene and Late Pleistocene postcranial bird bones from several palaeontological and archaeological sites in Europe with good success.
In 2016, archaeological excavations undertaken by the Ephorate of Antiquities of West Attica, Piraeus and Islands 3.8 km south-west of Athens, Greece, revealed mass burials of 79 skeletons in three ...rows. The burials are dated to the 7th century BC. The anthropological field documentation was undertaken by The Swedish Institute of Athens, and followed established bioarchaeological protocols regarding taphonomic processes, age, sex, injuries, and pathological changes. The descriptions and interpretations should be regarded as preliminary field observations. A majority of the individuals were young adult or juvenile males, most of them without signs of active disease and with a generally good oral health status, but with corroded iron shackles around their wrists. Cause of death could not be determined although extensive and likely perimortem fractures were observed. The only object related to injury and/or possible cause of death was an arrowhead found in the chest of one of the skeletons. Why and where the individuals were killed is a matter of conjecture; the observations from the field documentation neither validate, nor disprove the hypothesis that these individuals were captives and victims of the so-called “Cylonian conspiracy” in the 7th century BC.
The genetic diversity in modern species is strongly affected by contemporary gene flow between populations, which in turn is governed by individual dispersal capacities and barriers in the landscape. ...However, current patterns of variation have also been shaped by movement over longer time-scales, such as the successive shifts in species distributions that have occurred during past climate changes. This thesis is focused on cold-adapted species, and one parameter that has greatly influenced their current genetic diversity is how they coped with climate warming at the last glacial/interglacial transition, ca 11.7 thousand years ago. I examined this in three different small herbivore taxa; true lemmings (Lemmus), ptarmigan (Lagopus) and hares (Lepus), whose modern distributions stretch from the exposed tundra to the subarctic moorlands and taiga. In the first paper, I investigated contemporary genetic structure in the cyclic Norwegian lemming (Lemmus lemmus) and proposed that mass movements during peak years act as pulses of gene flow between mountain areas, which homogenise the gene pool over surprisingly vast geographic distances. However, when I used ancient DNA to analyse the lemmings’ ability for long-term directional movement, I found that the Ice Age populations that inhabited the former midlatitude European tundra-steppe appear to have been incapable of shifting their distribution northwards following post-glacial climate warming. Instead, the results suggest that the endemic Norwegian lemming descends from an isolated population that survived the last glacial maximum in situ in a restricted ice free refugium. In contrast to the glacial lemmings, as well the majority of previously studied mammals, the ptarmigan (L. lagopus and L. muta) and hare (L. timidus) analyses revealed a long-term genetic continuity in Europe, where the midlatitude populations were able to keep pace with the rapidly changing climate at the last glacial/interglacial transition, enabling them to shift their ranges to northern and high-alpine regions. These different outcomes might be explained by ptarmigans’ flight capability that allows a less restricted dispersal across fragmented landscapes, and that the generalist nature of mountain hares makes them less vulnerable to habitat alterations. Species distribution modelling, however, indicated that continued climate warming will make some isolated regions unsuitable in the future, thereby forcing populations to adapt the new environmental conditions in order to avoid local extinctions.
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Manuscript. Paper 3: Manuscript. Paper 4: Manuscript.
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