| 1. |
- Allentoft, Morten E., et al.
(författare)
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100 ancient genomes show repeated population turnovers in Neolithic Denmark
- 2024
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Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 625, s. 329-337
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Tidskriftsartikel (refereegranskat)abstract
- Major migration events in Holocene Eurasia have been characterized genetically at broad regional scales1–4. However, insights into the population dynamics in the contact zones are hampered by a lack of ancient genomic data sampled at high spatiotemporal resolution5–7. Here, to address this, we analysed shotgun-sequenced genomes from 100 skeletons spanning 7,300 years of the Mesolithic period, Neolithic period and Early Bronze Age in Denmark and integrated these with proxies for diet (13C and 15N content), mobility (87Sr/86Sr ratio) and vegetation cover (pollen). We observe that Danish Mesolithic individuals of the Maglemose, Kongemose and Ertebølle cultures form a distinct genetic cluster related to other Western European hunter-gatherers. Despite shifts in material culture they displayed genetic homogeneity from around 10,500 to 5,900 calibrated years before present, when Neolithic farmers with Anatolian-derived ancestry arrived. Although the Neolithic transition was delayed by more than a millennium relative to Central Europe, it was very abrupt and resulted in a population turnover with limited genetic contribution from local hunter-gatherers. The succeeding Neolithic population, associated with the Funnel Beaker culture, persisted for only about 1,000 years before immigrants with eastern Steppe-derived ancestry arrived. This second and equally rapid population replacement gave rise to the Single Grave culture with an ancestry profile more similar to present-day Danes. In our multiproxy dataset, these major demographic events are manifested as parallel shifts in genotype, phenotype, diet and land use.
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| 2. |
- Allentoft, Morten E., et al.
(författare)
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Population genomics of post-glacial western Eurasia
- 2024
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Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 625:7994, s. 301-311
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Tidskriftsartikel (refereegranskat)abstract
- Western Eurasia witnessed several large-scale human migrations during the Holocene1–5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes—mainly from the Mesolithic and Neolithic periods—from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a ‘great divide’ genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 bp, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 bp, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a ‘Neolithic steppe’ cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.
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| 3. |
- Jensen, Theis Zetner Trolle, et al.
(författare)
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An integrated analysis of Maglemose bone points reframes the Early Mesolithic of Southern Scandinavia
- 2020
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- The extensive peat bogs of Southern Scandinavia have yielded rich Mesolithic archaeological assemblages, with one of the most iconic artefacts being the bone point. Although great in number they remain understudied. Here we present a combined investigation of the typology, protein-based species composition, and absolute chronology of Maglemosian bone points. The majority of the bone points are made from cervids and bovines. However, changes both in species composition and barb morphology can be directly linked to a paucity of finds lasting nearly 600 years in Southern Scandinavia around 10,300 cal BP. We hypothesize that this hiatus was climate-driven and forced hunter-gatherers to abandon the lakes. Furthermore, the marked change in bone points coincides with a change in lithic technology. We, therefore, propose that the Maglemose culture in Southern Scandinavia is fundamentally divided into an Early Complex and a Late Complex.
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| 4. |
- Aurbakken, Einar, et al.
(författare)
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Transient spectroscopy from time-dependent electronic-structure theory without multipole expansions
- 2024
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Ingår i: Physical Review A: covering atomic, molecular, and optical physics and quantum information. - : American Physical Society. - 2469-9926 .- 2469-9934. ; 109:1
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Tidskriftsartikel (refereegranskat)abstract
- Based on the work done by an electromagnetic field on an atomic or molecular electronic system, a general gauge-invariant formulation of transient absorption spectroscopy is presented within the semiclassical approximation. Avoiding multipole expansions, a computationally viable expression for the spectral response function is derived from the minimal-coupling Hamiltonian of an electronic system interacting with one or more laser pulses described by a source-free, enveloped electromagnetic vector potential. With a fixed-basis expansion of the electronic wave function, the computational cost of simulations of laser-driven electron dynamics beyond the dipole approximation is the same as simulations adopting the dipole approximation. We illustrate the theory by time-dependent configuration interaction and coupled-cluster simulations of core-level absorption and circular dichroism spectra.
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| 5. |
- Delcey, Mickael G, et al.
(författare)
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Efficient calculations of a large number of highly excited states for multiconfigurational wavefunctions
- 2019
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Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 40:19, s. 1789-1799
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Tidskriftsartikel (refereegranskat)abstract
- Electronically excited states play important roles in many chemical reactions and spectroscopic techniques. In quantum chemistry, a common technique to solve excited states is the multiroot Davidson algorithm, but it is not designed for processes like X-ray spectroscopy that involves hundreds of highly excited states. We show how the use of a restricted active space wavefunction together with a projection operator to remove low-lying electronic states offers an efficient way to reach single and double-core-hole states. Additionally, several improvements to the stability and efficiency of the configuration interaction (CI) algorithm for a large number of states are suggested. When applied to a series of transition metal complexes the new CI algorithm does not only resolve divergence issues but also leads to typical reduction in computational time by 70%, with the largest savings for small molecules and large active spaces. Together, the projection operator and the improved CI algorithm now make it possible to simulate a wide range of single- and two-photon spectroscopies.
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| 6. |
- Delcey, Mickael G., et al.
(författare)
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Exact semi-classical light-matter interaction operator applied to two-photon processes with strong relativistic effects
- 2020
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Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 153:2
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Tidskriftsartikel (refereegranskat)abstract
- X-ray processes involve interactions with high-energy photons. For these short wavelengths, the perturbing field cannot be treated as constant, and there is a need to go beyond the electric-dipole approximation. The exact semi-classical light-matter interaction operator offers several advantages compared to the multipole expansion such as improved stability and ease of implementation. Here, the exact operator is used to model x-ray scattering in metal K pre-edges. This is a relativistic two-photon process where absorption is dominated by electric-dipole forbidden transitions. With the restricted active space state-interaction approach, spectra can be calculated even for the multiconfigurational wavefunctions including second-order perturbation. However, as the operator itself depends on the transition energy, the cost for evaluating integrals for hundreds of thousands unique transitions becomes a bottleneck. Here, this is solved by calculating the integrals in a molecular-orbital basis that only runs over the active space, combined with a grouping scheme where the operator is the same for close-lying transitions. This speeds up the calculations of single-photon processes and is critical for the modeling of two-photon scattering processes. The new scheme is used to model Kα resonant inelastic x-ray scattering of iron-porphyrin complexes with relevance to studies of heme enzymes, for which the total computational time is reduced by several orders of magnitude with an effect on transition intensities of 0.1% or less.
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| 7. |
- Egfjord, Anne Friis Holm, et al.
(författare)
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Genomic Steppe ancestry in skeletons from the Neolithic Single Grave Culture in Denmark
- 2021
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 16
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Tidskriftsartikel (refereegranskat)abstract
- The Gjerrild burial provides the largest and best-preserved assemblage of human skeletal material presently known from the Single Grave Culture (SGC) in Denmark. For generations it has been debated among archaeologists if the appearance of this archaeological complex represents a continuation of the previous Neolithic communities, or was facilitated by incoming migrants. We sampled and analysed five skeletons from the Gjerrild cist, buried over a period of c. 300 years, 2600/2500–2200 cal BCE. Despite poor DNA preservation, we managed to sequence the genome (>1X) of one individual and the partial genomes (0.007X and 0.02X) of another two individuals. Our genetic data document a female (Gjerrild 1) and two males (Gjerrild 5 + 8), harbouring typical Neolithic K2a and HV0 mtDNA haplogroups, but also a rare basal variant of the R1b1 Y-chromosomal haplogroup. Genome-wide analyses demonstrate that these people had a significant Yamnaya-derived (i.e. steppe) ancestry component and a close genetic resemblance to the Corded Ware (and related) groups that were present in large parts of Northern and Central Europe at the time. Assuming that the Gjerrild skeletons are genetically representative of the population of the SGC in broader terms, the transition from the local Neolithic Funnel Beaker Culture (TRB) to SGC is not characterized by demographic continuity. Rather, the emergence of SGC in Denmark was part of the Late Neolithic and Early Bronze Age population expansion that swept across the European continent in the 3rd millennium BCE, resulting in various degrees of genetic replacement and admixture processes with previous Neolithic populations.
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| 8. |
- Ertan, Emelie, et al.
(författare)
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Setting the stage for theoretical x-ray spectra of the H2S molecule with multi-configurational quantum chemical calculations of the energy landscape
- 2020
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 152:9
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Tidskriftsartikel (refereegranskat)abstract
- In the H2S molecule, the interplay between different core levels can be investigated in great detail in relation to x-ray spectroscopy, which requires a theory for interpretation. Hence, valence and core excitations into the two antibonding molecular orbitals of the H2S molecule have been calculated within a multi-configurational wave function framework. Scanning along the S-H stretching coordinates, we derive potential energy surfaces and transition dipole moments involving the ground state and core and valence excited states. Both valence excitations and the S1s(-1) and S2p(-1) core excitations show pairs of dissociative and bound electronic states. These pairs of states are nearly degenerate in H2S at the ground state geometry. The close degeneracy together with conical intersections makes H2S an interesting target for x-ray spectroscopy involving ultra-fast dissociation influenced by non-adiabatic transitions and interference. For future investigations with x-ray absorption spectroscopy (XAS) and resonant inelastic x-ray scattering (RIXS), it is valuable to compare H2S with the water molecule, which exhibits state-selective gating to different vibrational modes [R. C. Couto et al., Nat. Commun. 8, 14165 (2017)] in its well-separated O1s(-1) core excited states. The dense manifolds of the S2p(-1) core excited states will complicate the analysis of K-alpha edge RIXS, but dynamical effects could be evaluated through detuning and by comparing with L edge XAS. In L edge RIXS, the dynamical effects will be more pronounced due to the longer lifetime of the S2p(-1) core excited states compared to the S1s(-1) core excited states.
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| 9. |
- Ertan, Emelie, et al.
(författare)
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Setting the stage for theoretical X-ray spectra of the H2S molecule with RASPT2 calculations of the energy landscape
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Electronic valence- and core-excitations into the anti-bonding orbitals of the H2S molecule have been calculated within a multi-configurational wave-function framework (RASPT2). Potential energy surfaces and transition dipole moments have been derived in two dimensions for the S-H stretching coordinates. The |S1s-1, 6a11> and |S1s-1, 3b21> core-excited states in H2S are nearly degenerate along the symmetric stretching coordinate, for which we have identified two conical intersections. The small energy splitting of the S1s-1 core-excited states at equilibrium geometry arise from an avoided crossing at broken symmetry. Compared to the water molecule, which exhibit state-selective gating to different vibrational modes [Nat. Commun. 8 14165 (2017)] in its well-separated O1s-1 core-excited states, we expect a strong coupling between the close-lying |S1s-1, 6a11> and |S1s-1, 3b21> states. This could lead to dissociative dynamics observable in K-edge RIXS. The S2p-1 core-excited states form two dense manifolds of spin-orbit coupled states, which can be schematically characterised as bound |S2p-1,3b21> and dissociative |S2p-1,6a11> states. We identify three conical intersections in the singlet and triplet states along the symmetric stretching coordinate. Mapping the molecular singlet and triplet states to the atomic dissociation limit reveals a symmetry selection rule, leading to an off-set of the 1|3a1-1,6a11> state relative to the other S2p-1 core-excited states. The dense manifolds of S2p-1 core-excited states will complicate the analysis of Kα-edge RIXS, but dynamical effects could be evaluated through detuning and in comparison to L-edge XAS. In L-edge RIXS, the dynamical effects well be more pronounced due to a longer life-time of the S2p-1 core-excited states compared to the S1s-1 core-excited states.
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| 10. |
- Farnelid, Hanna, et al.
(författare)
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Nitrogenase Gene Amplicons from Global Marine Surface Waters Are Dominated by Genes of Non-Cyanobacteria
- 2011
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:4, s. e19223-
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Tidskriftsartikel (refereegranskat)abstract
- Cyanobacteria are thought to be the main N-2-fixing organisms (diazotrophs) in marine pelagic waters, but recent molecular analyses indicate that non-cyanobacterial diazotrophs are also present and active. Existing data are, however, restricted geographically and by limited sequencing depths. Our analysis of 79,090 nitrogenase (nifH) PCR amplicons encoding 7,468 unique proteins from surface samples (ten DNA samples and two RNA samples) collected at ten marine locations worldwide provides the first in-depth survey of a functional bacterial gene and yield insights into the composition and diversity of the nifH gene pool in marine waters. Great divergence in nifH composition was observed between sites. Cyanobacteria-like genes were most frequent among amplicons from the warmest waters, but overall the data set was dominated by nifH sequences most closely related to non-cyanobacteria. Clusters related to Alpha-, Beta-, Gamma-, and Delta-Proteobacteria were most common and showed distinct geographic distributions. Sequences related to anaerobic bacteria (nifH Cluster III) were generally rare, but preponderant in cold waters, especially in the Arctic. Although the two transcript samples were dominated by unicellular cyanobacteria, 42% of the identified non-cyanobacterial nifH clusters from the corresponding DNA samples were also detected in cDNA. The study indicates that non-cyanobacteria account for a substantial part of the nifH gene pool in marine surface waters and that these genes are at least occasionally expressed. The contribution of non-cyanobacterial diazotrophs to the global N-2 fixation budget cannot be inferred from sequence data alone, but the prevalence of non-cyanobacterial nifH genes and transcripts suggest that these bacteria are ecologically significant.
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