| 11. |
- Pereira, Ricardo J., et al.
(författare)
-
Mind the numt : Finding informative mitochondrial markers in a giant grasshopper genome
- 2021
-
Ingår i: Journal of Zoological Systematics and Evolutionary Research. - : John Wiley & Sons. - 0947-5745 .- 1439-0469. ; 59:3, s. 635-645
-
Tidskriftsartikel (refereegranskat)abstract
- The barcoding of the mitochondrial COX1 gene has been instrumental in cataloguing the tree of life, and in providing insights in the phylogeographic history of species. Yet, this strategy has encountered difficulties in major clades characterized by large genomes, which contain a high frequency of nuclear pseudogenes originating from the mitochondrial genome (numts). Here, we use the meadow grasshopper (Chorthippus parallelus), which possesses a giant genome of similar to 13 Gb, to identify mitochondrial genes that are underrepresented as numts, and test their use as informative phylogeographic markers. We recover the same full mitochondrial sequence using both whole genome and transcriptome sequencing, including functional protein-coding genes and tRNAs. We show that a region of the mitogenome containing the COX1 gene, typically used in DNA barcoding, has disproportionally higher diversity and coverage than the rest of the mitogenome, consistent with multiple insertions of that region into the nuclear genome. By designing new markers in regions of less elevated diversity and coverage, we identify two mitochondrial genes that are less likely to be duplicated as numts. We show that, while these markers show high levels of incomplete lineage sorting between subspecies, as expected for mitochondrial genes, genetic variation reflects their phylogeographic history accurately. These findings allow us to identify useful mitochondrial markers for future studies in C. parallelus, an important biological system for evolutionary biology. More generally, this study exemplifies how non-PCR-based methods using next-generation sequencing can be used to avoid numts in species characterized by large genomes, which have remained challenging to study in taxonomy and evolution.
|
|
| 12. |
- van der Valk, Tom, et al.
(författare)
-
Million-year-old DNA sheds light on the genomic history of mammoths
- 2021
-
Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 591:7849, s. 265-269
-
Tidskriftsartikel (refereegranskat)abstract
- Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far are from a horse specimen dated to 780–560 thousand years ago2. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.
|
|
| 13. |
- Ye, Mingliang, et al.
(författare)
-
Preparation and properties of situ-sintered SiC ceramics aided by ZnO-Al2O3-CaO
- 2022
-
Ingår i: Journal of Alloys and Compounds. - : Elsevier. - 0925-8388 .- 1873-4669. ; 890
-
Tidskriftsartikel (refereegranskat)abstract
- The safe treatment and disposal of radioactive graphite waste is becoming an important issue worldwide. The objective of this paper is to prepare the SiC-ZAC (ZAC: ZnO-Al2O3-CaO) composite ceramic for immobilizing radioactive graphite, where ZAC is as sintering additives. The effects of the sintering system and ZAC content on the phase compositions, microstructure, and properties of SiC-ZAC composite ceramic are studied by XRD, SEM-EDS, TEM-EDS, linear shrinkage, Vickers hardness, and thermal conductivity. By vacuum hot pressing sintering at 1600 degrees C for 1 h, the results show that the S-35-160 0 (65 wt% SiC, 10.5 wt% ZnO, 15.72 wt% Al2O3, 8.78 wt% CaO) sample is the potentially applicable formula composition due to its better performance, in which the Vickers hardness and the thermal conductivity are 165.2 HV10, 14.6 W m(-1) k(-1) respectively, and the normalized elemental mass loss of Si, Al and Ca are 0.0064-0.0108 g/m(2), 21.4784-24.7837 g/m(2), 56.9108-67.5637 g/m(2) after 42 days at pH = 5/7/9 solution, respectively. Importantly, ZAC sintering additives can form the bond phases of CaAl4O7, CaAl2O4, Ca3Al2(OH)(12), and Ca2Al2SiO7 under relatively low temperatures to reduce the sintering temperature for SiC ceramics. Meanwhile, the existing form of the Zn element is revealed: one part of the Zn forms glass phase, and the other part volatilized by carbothermic reduction.
|
|
| 14. |
- Zhao, Xiaofeng, et al.
(författare)
-
Exploring the relationship between Ln leaching and Ln-O binding energy in monazite (Nd, Sm, Eu)
- 2022
-
Ingår i: Journal of The American Ceramic Society. - : John Wiley & Sons. - 0002-7820 .- 1551-2916. ; 105:1, s. 553-563
-
Tidskriftsartikel (refereegranskat)abstract
- Understanding the chemical durability of waste forms is important for the long-term deep geological disposal of actinides. However, in-depth investigations on the leaching mechanism of monazite ceramic waste forms remain to be poorly understand. Inspired by the degradation process of Ce-monazite controlled by the fracture of Ce-O bond of (010) surface under the action of permeable water molecules, the relationship between Ln leaching and Ln-O binding energy in LnPO(4) (Ln = Nd, Sm, Eu) monazites is investigated by combining dissolution experiments and first-principles calculations. The dissolution experiments are performed in 0.001 mol/L HCl solutions at 363 K. Before and after leaching, the phase compositions of specimens are carefully investigated by refined XRD and GIXRD, and the results confirm that the dissolved phases in contact with the leachate are LnPO(4) monazite. Some specific issues are discussed in detail by first-principles calculations, such as the bond length, charge transfer, electron localization function, and chemical bond properties. Moreover, the boundary conditions of crystal-growing of LnPO(4) monazite are investigated to define the chemical potential that is used to calculate the defect formation energy (Ef) of Ln vacancy in (010) surface. Importantly, the Ef results show the difficulty order of forming a vacancy defect of Ln on (010) surface is Eu > Sm > Nd, which is consistent with the leaching stability of Ln in LnPO(4) (Ln = Nd, Sm, Eu) monazite.
|
|
