Identifying Bird Remains Using Ancient DNA Barcoding.

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

Range shifts or extinction? Ancient DNA and distribution modelling reveal past and future responses to climate warming in cold-adapted birds.

Global warming is predicted to cause substantial habitat rearrangements, with the most severe effects expected to occur in high-latitude biomes. However, one major uncertainty is whether species will be able to shift their ranges to keep pace with climate-driven environmental changes. Many recent studies on mammals have shown that past range contractions have been associated with local extinctions rather than survival by habitat tracking. Here, we have used an interdisciplinary approach that combines ancient DNA techniques, coalescent simulations and species distribution modelling, to investigate how two common cold-adapted bird species, willow and rock ptarmigan (Lagopus lagopus and Lagopus muta), respond to long-term climate warming. Contrary to previous findings in mammals, we demonstrate a genetic continuity in Europe over the last 20 millennia. Results from back-casted species distribution models suggest that this continuity may have been facilitated by uninterrupted habitat availability and potentially also the greater dispersal ability of birds. However, our predictions show that in the near future, some isolated regions will have little suitable habitat left, implying a future decrease in local populations at a scale unprecedented since the last glacial maximum

Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes

The social organization of the first fully sedentary societies that emerged during the Neolithic period in Southwest Asia remains enigmatic, mainly because material culture studies provide limited insight into this issue. However, because Neolithic Anatolian communities often buried their dead beneath domestic buildings, household composition and social structure can be studied through these human remains. Here, we describe genetic relatedness among co-burials associated with domestic buildings in Neolithic Anatolia using 59 ancient genomes, including 22 new genomes from Aşıklı Höyük and Çatalhöyük. We infer pedigree relationships by simultaneously analyzing multiple types of information, including autosomal and X chromosome kinship coefficients, maternal markers, and radiocarbon dating. In two early Neolithic villages dating to the 9th and 8th millennia BCE, Aşıklı Höyük and Boncuklu, we discover that siblings and parent-offspring pairings were frequent within domestic structures, which provides the first direct indication of close genetic relationships among co-burials. In contrast, in the 7th millennium BCE sites of Çatalhöyük and Barcın, where we study subadults interred within and around houses, we find close genetic relatives to be rare. Hence, genetic relatedness may not have played a major role in the choice of burial location at these latter two sites, at least for subadults. This supports the hypothesis that in Çatalhöyük, and possibly in some other Neolithic communities, domestic structures may have served as burial location for social units incorporating biologically unrelated individuals. Our results underscore the diversity of kin structures in Neolithic communities during this important phase of sociocultural development.Additional co-authors: Hasan Can Gemici, Arda Sevkar, Nihan Dilşad Dağtaş, Gülşah Merve Kılınç, Donovan Adams, Arielle R. Munters, Ekin Sağlıcan, Marco Milella, Eline M.J. Schotsmans, Erinç Yurtman, Mehmet Çetin, Sevgi Yorulmaz, N. Ezgi Altınışık, Ayshin Ghalichi, Anna Juras, C. Can Bilgin, Torsten Günther, Jan Storå, Mattias Jakobsson, Maurice de Kleijn, Gökhan Mustafaoğlu, Andrew Fairbairn, Jessica Pearson, İnci Togan, Nurcan Kayacan, Arkadiusz Marciniak, Clark Spencer Larsen, Ian Hodder, Çiğdem Atakuman, Marin Pilloud, Elif Sürer, Fokke Gerritsen, Rana Özbal, Douglas Baird, Yılmaz Selim Erdal, Güneş Duru, Mihriban Özbaşaran, Scott D. Haddow, Christopher J. Knüsel, Anders Götherström, Füsun Özer, Mehmet Some

Nonreceding hare lines: genetic continuity since the Late Pleistocene in European mountain hares (Lepus timidus)

Throughout time, climate changes have caused substantial rearrangements of habitats which have alternately promoted and disfavoured different types of taxa. At first glance, the mountain hare (Lepus timidus) shows the typical hallmarks of a cold-adapted species that has retreated to refugia since the onset of the current Holocene interglacial. In contrary to expectations, however, the species has a high contemporary genetic diversity with no clear differentiation between geographically isolated populations. In order to clarify the phylogeographic history of European mountain hares, we here analysed ancient DNA from the glacial populations that inhabited the previous midlatitude European tundra region. Our results reveal that the Ice Age hares had similar levels of genetic variation and lack of geographic structure as observed today, and the ancient samples were intermingled with modern individuals throughout the reconstructed evolutionary tree. This suggest a temporal genetic continuity in Europe, where the mountain hares were able to keep pace with the rapid changes at the last glacial/interglacial transition, and successfully track their shifting habitat to northern and alpine regions. Further, the temporal demographic analyses showed that the species’ population size in Europe appear to have been tightly linked with palaeoclimatic fluctuations, with increases and declines occurring during periods of global cooling and warming, respectively. Taken together, our results suggest that neither habitat shifts nor demographic fluctuations have had any substantial impact on the genetic diversity of European mountain hares. This remarkable resilience, which contrasts to a majority of previously investigated cold-adapted species, is likely due to its generalist nature which makes it less vulnerable to environmental changes

A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition

Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked innovations in symbolism, technology, and foodways. We present thirteen ancient genomes (c.8500-7500 calBCE) 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 a mixed ancestry from western and eastern Fertile Crescent, and that the community received immigrants. Our results further suggest that the community was organised along biological family lines. We document bodily interventions such as head-shaping and cauterization among the individuals examined, reflecting Çayönü's cultural ingenuity. Finally, we identify Upper Mesopotamia as the likely source of eastern gene flow into Neolithic Anatolia, in line with material culture evidence. We hypothesise 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

The genetic history of Scandinavia from the Roman Iron Age to the present

The authors acknowledge support from the National Genomics Infrastructure in Stockholm funded by Science for Life Laboratory, the Knut and Alice Wallenberg Foundation and the Swedish Research Council, and SNIC/Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. We used resources from projects SNIC 2022/23-132, SNIC 2022/22-117, SNIC 2022/23-163, SNIC 2022/22-299, and SNIC 2021-2-17. This research was supported by the Swedish Research Council project ID 2019-00849_VR and ATLAS (Riksbankens Jubileumsfond). Part of the modern dataset was supported by a research grant from Science Foundation Ireland (SFI), grant number 16/RC/3948, and co-funded under the European Regional Development Fund and by FutureNeuro industry partners.Peer reviewedPublisher PD

Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean

We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of complex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 present-day published genomes, we found that genetic diversity within each region steadily increased through the Holocene. We further observed that the inferred sources of gene flow shifted in time. In the first half of the Holocene, Southwest Asian and the East Mediterranean populations homogenized among themselves. Starting with the Bronze Age, however, regional populations diverged from each other, most likely driven by gene flow from external sources, which we term “the expanding mobility model.” Interestingly, this increase in inter-regional divergence can be captured by outgroup-f$_3$-based genetic distances, but not by the commonly used F$_{ST}$ statistic, due to the sensitivity of F$_{ST}$, but not outgroup-f$_3$, to within-population diversity. Finally, we report a temporal trend of increasing male bias in admixture events through the Holocene

Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication

Yurtman, ozer, Yuncu et al. provide an ancient DNA data set to demonstrate the impact of human activity on the demographic history of domestic sheep. The authors demonstrate that there may have been multiple domestication events with notable changes to the gene pool of European and Anatolian sheep since the Neolithic. 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

Animal movement on short and long time scales and the effect on genetic diversity in cold-adapted species

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.</p