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- Bergström, Anders, et al.
(författare)
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Grey wolf genomic history reveals a dual ancestry of dogs
- 2022
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 607:7918, s. 313-320
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Tidskriftsartikel (refereegranskat)abstract
- The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.
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- Anghel,, et al.
(författare)
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Electromagnetic radiation detectors based on Josephson junctions: Effective Hamiltonian
- 2020
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Ingår i: Physical Review B. - 2469-9969 .- 2469-9950. ; 101:2
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Tidskriftsartikel (refereegranskat)abstract
- We theoretically analyze two setups of low-energy single-photon counters based on Josephson junctions (JJs). For this, we propose two simple and general models based on the macroscopic quantum tunneling formalism (MQT). The first setup is similar to the photon counter based on the "cold-electron bolometer" (CEB), where the JJ replaces the CEB in the center of the superconducting antenna. In the second setup, the JJ is capacitively coupled to the antenna. We derive the Hamiltonians for the two setups, and we write the Schrodinger equations, taking into account both the antenna and the JJ. The quantum particles of the MQT models move in two-dimensional potential landscapes, which are parabolic along one direction and may have the form of a washboard potential along another direction. Such a potential landscape has a series of local minima, separated by saddle points. If the particle is prepared in the initial state in the metastable "ground state" of a local minimum, then the photon absorption causes it to jump into an excited state. If the excitation energy is bigger than the potential barrier seen by the quantum particle (the difference between the ground state and the saddle point), the photon is detected. The models are simple and allow us to do mostly analytical calculations. We show that the two setups are equivalent from the MQT point of view since one Hamiltonian can be transformed into the other by changes in variables. For typical values of the JJ and antenna parameters, the setups may work as counters of photons of wavelengths up to at least 1 cm. Dark count rates due to the phase particle tunneling directly from the ground state into the running state have also been evaluated.
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- Chesnokov, A., et al.
(författare)
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The local atomic structure and thermoelectric properties of Ir-doped ZnO : hybrid DFT calculations and XAS experiments
- 2021
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Ingår i: Journal of Materials Chemistry C. - : Royal Society of Chemistry. - 2050-7526 .- 2050-7534. ; 9:14, s. 4948-4960
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Tidskriftsartikel (refereegranskat)abstract
- We combined the hybrid density functional theory (DFT) calculations and X-ray absorption spectroscopy (XAS) experiments in the study of the local atomic structure around Ir ions in ZnO thin films with different iridium content. This was then used in the first principles analysis of the thermoelectric properties of material. The emphasis has been put on the conditions for a positive Seebeck coefficient and p-type electrical conductivity as the functions of the Fermi level. We studied both computationally and experimentally several possible IrOxpolyhedra (complexes) with a different number of surrounding oxygens and Ir oxidation states, including those with the formation of peroxide ions (O22−). In particular, octahedral coordination of iridium ions was identified by reverse Monte Carlo (RMC) simulations of the Ir L3-edge EXAFS spectra of ZnO:Ir thin films as the predominant complex, which is supported by the calculated lowest interstitial oxygen incorporation energies. All the calculated IrOx(x= 4, 5, 6) complexes, regardless of Ir the oxidation state, demonstrate potential for p-type conduction if the Fermi level (μF) falls in the range of 0-0.8 eV from the valence band maximum (VBM) and the Ir concentration is high enough (12.5% in the present DFT calculations). Even though the corresponding calculated Seebeck coefficient (S) around 80-89 μV K−1slightly exceeds the experimental values, we emphasise the presence of an important plateau in the dependence ofSonμFin this range for two complexes with the formation of peroxide ions (O22−). We predicted also that peroxide ions O22−are characterized by the calculated phonon frequencies of 810-942 cm−1in agreement with our previous Raman experimental results. In this light, we discuss the high sensitivity of calculatedS(μF) dependences to the atomic and electronic structure.
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- Purans, J., et al.
(författare)
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Local electronic structure rearrangements and strong anharmonicity in YH3 under pressures up to 180 GPa
- 2021
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- The discovery of superconductivity above 250 K at high pressure in LaH10 and the prediction of overcoming the room temperature threshold for superconductivity in YH10 urge for a better understanding of hydrogen interaction mechanisms with the heavy atom sublattice in metal hydrides under high pressure at the atomic scale. Here we use locally sensitive X-ray absorption fine structure spectroscopy (XAFS) to get insight into the nature of phase transitions and the rearrangements of local electronic and crystal structure in archetypal metal hydride YH3 under pressure up to 180 GPa. The combination of the experimental methods allowed us to implement a multiscale length study of YH3: XAFS (short-range), Raman scattering (medium-range) and XRD (long-range). XANES data evidence a strong effect of hydrogen on the density of 4d yttrium states that increases with pressure and EXAFS data evidence a strong anharmonicity, manifested as yttrium atom vibrations in a double-well potential.
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- Putintseva, Yuliya A., et al.
(författare)
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Siberian larch (Larix sibirica Ledeb.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome
- 2020
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Ingår i: BMC Genomics. - : BMC. - 1471-2164. ; 21:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Plant mitochondrial genomes (mitogenomes) can be structurally complex while their size can vary from similar to 222 Kbp inBrassica napusto 11.3 Mbp inSilene conica. To date, in comparison with the number of plant species, only a few plant mitogenomes have been sequenced and released, particularly for conifers (the Pinaceae family). Conifers cover an ancient group of land plants that includes about 600 species, and which are of great ecological and economical value. Among them, Siberian larch (Larix sibiricaLedeb.) represents one of the keystone species in Siberian boreal forests. Yet, despite its importance for evolutionary and population studies, the mitogenome of Siberian larch has not yet been assembled and studied. Results: Two sources of DNA sequences were used to search for mitochondrial DNA (mtDNA) sequences: mtDNA enriched samples and nucleotide reads generated in the de novo whole genome sequencing project, respectively. The assembly of the Siberian larch mitogenome contained nine contigs, with the shortest and the largest contigs being 24,767 bp and 4,008,762 bp, respectively. The total size of the genome was estimated at 11.7 Mbp. In total, 40 protein-coding, 34 tRNA, and 3 rRNA genes and numerous repetitive elements (REs) were annotated in this mitogenome. In total, 864 C-to-U RNA editing sites were found for 38 out of 40 protein-coding genes. The immense size of this genome, currently the largest reported, can be partly explained by variable numbers of mobile genetic elements, and introns, but unlikely by plasmid-related sequences. We found few plasmid-like insertions representing only 0.11% of the entire Siberian larch mitogenome. Conclusions: Our study showed that the size of the Siberian larch mitogenome is much larger than in other so far studied Gymnosperms, and in the same range as for the annual flowering plantSilene conica(11.3 Mbp). Similar to other species, the Siberian larch mitogenome contains relatively few genes, and despite its huge size, the repeated and low complexity regions cover only 14.46% of the mitogenome sequence.
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- Richtman Feuerborn, Tatiana, et al.
(författare)
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Modern Siberian dog ancestry was shaped by several thousand years of Eurasian-wide trade and human dispersal
- 2021
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 118:39
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Tidskriftsartikel (refereegranskat)abstract
- Dogs have been essential to life in the Siberian Arctic for over 9,500 y, and this tight link between people and dogs continues in Siberian communities. Although Arctic Siberian groups such as the Nenets received limited gene flow from neighboring groups, archaeological evidence suggests that metallurgy and new subsistence strategies emerged in Northwest Siberia around 2,000 y ago. It is unclear if the Siberian Arctic dog population was as continuous as the people of the region or if instead admixture occurred, possibly in relation to the influx of material culture from other parts of Eurasia. To address this question, we sequenced and analyzed the genomes of 20 ancient and historical Siberian and Eurasian Steppe dogs. Our analyses indicate that while Siberian dogs were genetically homogenous between 9,500 to 7,000 y ago, later introduction of dogs from the Eurasian Steppe and Europe led to substantial admixture. This is clearly the case in the Iamal-Nenets region (Northwestern Siberia) where dogs from the Iron Age period (∼2,000 y ago) possess substantially less ancestry related to European and Steppe dogs than dogs from the medieval period (∼1,000 y ago). Combined with findings of nonlocal materials recovered from these archaeological sites, including glass beads and metal items, these results indicate that Northwest Siberian communities were connected to a larger trade network through which they acquired genetically distinctive dogs from other regions. These exchanges were part of a series of major societal changes, including the rise of large-scale reindeer pastoralism ∼800 y ago.
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