| 1. |
- Ma, Tao, et al.
(författare)
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Genomic insights into salt adaptation in a desert poplar
- 2013
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 4, s. 2797-
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Tidskriftsartikel (refereegranskat)abstract
- Despite the high economic and ecological importance of forests, our knowledge of the genomic evolution of trees under salt stress remains very limited. Here we report the genome sequence of the desert poplar, Populus euphratica, which exhibits high tolerance to salt stress. Its genome is very similar and collinear to that of the closely related mesophytic congener, P. trichocarpa. However, we find that several gene families likely to be involved in tolerance to salt stress contain significantly more gene copies within the P. euphratica lineage. Furthermore, genes showing evidence of positive selection are significantly enriched in functional categories related to salt stress. Some of these genes, and others within the same categories, are significantly upregulated under salt stress relative to their expression in another salt-sensitive poplar. Our results provide an important background for understanding tree adaptation to salt stress and facilitating the genetic improvement of cultivated poplars for saline soils.
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| 2. |
- Liu, Shuyu, et al.
(författare)
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Demographic History and Natural Selection Shape Patterns of Deleterious Mutation Load and Barriers to Introgression across Populus Genome
- 2022
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Ingår i: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 39:2
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Tidskriftsartikel (refereegranskat)abstract
- Hybridization and resulting introgression are important processes shaping the tree of life and appear to be far more common than previously thought. However, how the genome evolution was shaped by various genetic and evolutionary forces after hybridization remains unresolved. Here we used whole-genome resequencing data of 227 individuals from multiple widespread Populus species to characterize their contemporary patterns of hybridization and to quantify genomic signatures of past introgression. We observe a high frequency of contemporary hybridization and confirm that multiple previously ambiguous species are in fact F1 hybrids. Seven species were identified, which experienced different demographic histories that resulted in strikingly varied efficacy of selection and burdens of deleterious mutations. Frequent past introgression has been found to be a pervasive feature throughout the speciation of these Populus species. The retained introgressed regions, more generally, tend to contain reduced genetic load and to be located in regions of high recombination. We also find that in pairs of species with substantial differences in effective population size, introgressed regions are inferred to have undergone selective sweeps at greater than expected frequencies in the species with lower effective population size, suggesting that introgression likely have higher potential to provide beneficial variation for species with small populations. Our results, therefore, illustrate that demography and recombination have interplayed with both positive and negative selection in determining the genomic evolution after hybridization.
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| 3. |
- Miehe, Georg, et al.
(författare)
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The Kobresia pygmaea ecosystem of the Tibetan highlands – Origin, functioning and degradation of the world's largest pastoral alpine ecosystem: Kobresia pastures of Tibet
- 2019
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697. ; 648, s. 754-771
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Tidskriftsartikel (refereegranskat)abstract
- With 450,000 km2 Kobresia (syn. Carex) pygmaea dominated pastures in the eastern Tibetan highlands are the world's largest pastoral alpine ecosystem forming a durable turf cover at 3000–6000 m a.s.l. Kobresia's resilience and competitiveness is based on dwarf habit, predominantly below-ground allocation of photo assimilates, mixture of seed production and clonal growth, and high genetic diversity. Kobresia growth is co-limited by livestock-mediated nutrient withdrawal and, in the drier parts of the plateau, low rainfall during the short and cold growing season. Overstocking has caused pasture degradation and soil deterioration over most parts of the Tibetan highlands and is the basis for this man-made ecosystem. Natural autocyclic processes of turf destruction and soil erosion are initiated through polygonal turf cover cracking, and accelerated by soil-dwelling endemic small mammals in the absence of predators. The major consequences of vegetation cover deterioration include the release of large amounts of C, earlier diurnal formation of clouds, and decreased surface temperatures. These effects decrease the recovery potential of Kobresia pastures and make them more vulnerable to anthropogenic pressure and climate change. Traditional migratory rangeland management was sustainable over millennia, and possibly still offers the best strategy to conserve and possibly increase C stocks in the Kobresia turf.
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| 4. |
- Shi, Tingting, et al.
(författare)
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The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees
- 2024
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Ingår i: Molecular Plant. - : Elsevier. - 1674-2052 .- 1752-9867. ; 17:5, s. 725-746
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180-bp presence/absence variant affecting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.
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| 5. |
- Wang, Zhaofeng, et al.
(författare)
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Phylogeographical analyses of domestic and wild yaks based on mitochondrial DNA : new data and reappraisal
- 2010
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Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 37:12, s. 2332-2344
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Tidskriftsartikel (refereegranskat)abstract
- Aim We aimed to examine the phylogeographical structure and demographic history of domestic and wild yaks (Bos grunniens) based on a wide range of samples and complete mitochondrial genomic sequences. Location The Qinghai-Tibetan Plateau (QTP) of western China. Methods All available D-loop sequences for 405 domesticated yaks and 47 wild yaks were examined, including new sequences from 96 domestic and 34 wild yaks. We further sequenced the complete mitochondrial genomes of 48 domesticated and 21 wild yaks. Phylogeographical analyses were performed using the mitochondrial D-loop and the total genome datasets. Results We recovered a total of 123 haplotypes based on the D-loop sequences in wild and domestic yaks. Phylogenetic analyses of this dataset and the mitochondrial genome data suggested three well-supported and divergent lineages. Two lineages with six D-loop haplogroups were recovered for all morphological breeds of domestic yaks across their distributions in the QTP, while one more lineage and more endemic haplogroups or haplotypes were found for wild yaks. Based on the mitochondrial genome data, the divergences of the three lineages were estimated to have occurred around 420,000 and 580,000 years ago, consistent with the geological records of two large glaciation events experienced in the QTP. Main conclusions There are distinct phylogeographical differences between wild and domestic yaks. However, there is no apparent geographical correlation between identified haplogroups and distributions of domestic yaks. Three differentiated lineages of yaks probably evolved allopatrically in different regions during the Pleistocene glaciation events, then reunited into a single gene pool during post-glacial population expansion and migrations before the start of the domestication of yaks in the Holocene.
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| 6. |
- Xu, L., et al.
(författare)
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Silver-Catalyzed Controlled Intermolecular Cross-Coupling of Silyl Enol Ethers : Scalable Access to 1,4-Diketones
- 2022
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Ingår i: Organic Letters. - : American Chemical Society (ACS). - 1523-7060 .- 1523-7052. ; 24:25, s. 4513-4518
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Tidskriftsartikel (refereegranskat)abstract
- A protocol for silver-catalyzed controlled intermolecular cross-coupling of silyl enolates is disclosed. The protocol displays good functional group tolerance and allows efficient preparation of a series of synthetically useful 1,4-diketones. Preliminary mechanistic investigations suggest that the reaction proceeds through a one-electron process involving free radical species in which PhBr acts as the oxidant.
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| 7. |
- Chai, Gaoda, et al.
(författare)
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Deciphering the Role of Chalcogen-Containing Heterocycles in Nonfullerene Acceptors for Organic Solar Cells
- 2020
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Ingår i: ACS Energy Letters. - : AMER CHEMICAL SOC. - 2380-8195. ; 5:11, s. 3415-3425
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Tidskriftsartikel (refereegranskat)abstract
- The field of organic solar cells has experienced paradigm-shifting changes in recent years because of the emergence of nonfullerene acceptors (NFAs). It is critically important to gain more insight into the structure-property relationship of the emerging A-DAD-A-type NFAs. In this Letter, a family of NFAs named BPF-4F, BPT-4F, and BPS-4F incorporating various chalcogen-containing heterocycles, i.e., furan, thiophene, and selenophene, respectively, was designed and synthesized. These NFAs exhibited dramatic differences in their photovoltaic performances with device efficiencies of 16.8% achieved by the thiophene-based cells, which was much higher than the furan-based ones (12.6%). In addition, the selenophene-based NFA showed a red-shifted absorption relative to the furan- and thiophene-based ones and obtained a decent efficiency of 16.3% owing to an improved J(SC). The reasons why these NFAs performed differently are systematically studied by comparing their optoelectronic properties and film morphology, which provides new understandings of the molecular design of high-performance NFAs.
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| 8. |
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| 9. |
- Chen, Yan, et al.
(författare)
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Silver-Promoted (4+1) Annulation of Isocyanoacetates with Alkylpyridinium Salts : Divergent Regioselective Synthesis of 1,2-Disubstituted Indolizines
- 2021
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Ingår i: Organic Letters. - : American Chemical Society (ACS). - 1523-7060 .- 1523-7052. ; 23:19, s. 7555-7560
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Tidskriftsartikel (refereegranskat)abstract
- An unprecedented silver-promoted regioselective (4 + 1) annulation of isocyanoacetates with pyridinium salts is reported. The established protocol provides controlled, facile, and modular access to a range of synthetically useful N-fused heterocyclic scaffolds containing indolizines, pyrrolo[1,2-a]quinolines, pyrrolo[2,1-a]isoquinolines, and 1H-imidazo[4,5-a]indolizin-2(3H)-ones. A mechanistic pathway involving nucleophilic addition/protonation/elimination/cydoisomerization is proposed.
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| 10. |
- Chen, Zeyuan, et al.
(författare)
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Survival in the Tropics despite isolation, inbreeding and asexual reproduction : insights from the genome of the world's southernmost poplar (Populus ilicifolia)
- 2020
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Ingår i: The Plant Journal. - : Wiley. - 0960-7412 .- 1365-313X. ; 103:1, s. 430-442
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Tidskriftsartikel (refereegranskat)abstract
- Species are becoming extinct at unprecedented rates as a consequence of human activity. Hence it is important to understand the evolutionary dynamics of species with already small population sizes. Populus ilicifolia is a vulnerable poplar species that is isolated from other poplar species and is uniquely adapted to the Tropics. It has a very limited size, reproduces partly clonally and is therefore an excellent case study for conservation genomics. We present here the first annotated draft genome of P. ilicifolia, characterize genome-wide patterns of polymorphisms and compare those to other poplar species with larger natural ranges. P. ilicifolia experienced a more prolonged and severe decline of effective population size (Ne) and signs of genetic erosion than any other poplar species with which it was compared. At present, the species has the lowest genome-wide genetic diversity, the highest abundance of long runs of homozygosity, high inbreeding levels as well as a high overall accumulation of deleterious variants. However, more effective purging of severely deleterious variants and adaptation to the Tropics may have contributed to its survival. Hence, in spite of its limited genetic variation, it is certainly worth pursuing the conservation efforts of this unique species.
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| 11. |
- Geng, Xin, et al.
(författare)
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Construction of Phenanthridinone Skeletons through Palladium-Catalyzed Annulation
- 2023
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Ingår i: Journal of Organic Chemistry. - : American Chemical Society (ACS). - 0022-3263 .- 1520-6904. ; 88:17, s. 12738-12743
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Tidskriftsartikel (refereegranskat)abstract
- Herein, a straightforward synthetic approach for the construction of phenanthridin-6(5H)-one skeletons is disclosed. The developed protocol relies on palladium catalysis, providing controlled access to a range of functionalized phenanthridin-6(5H)-ones in 59-88% yields. Furthermore, plausible reaction pathways are proposed based on mechanistic experiments.
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| 12. |
- Geng, Xin, et al.
(författare)
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Tandem Palladium/Copper-Catalyzed Decarboxylative Approach to Benzoimidazo- and Imidazophenanthridine Skeletons
- 2022
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Ingår i: Organic Letters. - : American Chemical Society (ACS). - 1523-7060 .- 1523-7052. ; 24:50, s. 9194-9199
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Tidskriftsartikel (refereegranskat)abstract
- A protocol for a tandem Pd/Cu-catalyzed intermolecular cross-coupling cascade between o-bromobenzoic acids and 2-(2-bromoaryl)-1H-benzo[d]imidazoles or the corresponding imidazoles is presented. The protocol provides conceptually novel and controlled access to synthetically useful N-fused (benzo)imidazophenanthridine scaffolds with high efficiency, a broad substrate scope, and excellent functional group compatibility.
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| 13. |
- Guo, Songchang, et al.
(författare)
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Origin of mitochondrial DNA diversity of domestic yaks
- 2006
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Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Background: The domestication of plants and animals was extremely important anthropologically. Previous studies have revealed a general tendency for populations of livestock species to include deeply divergent maternal lineages, indicating that they were domesticated in multiple, independent events from genetically discrete wild populations. However, in water buffalo, there are suggestions that a similar deep maternal bifurcation may have originated from a single population. These hypotheses have rarely been rigorously tested because of a lack of sufficient wild samples. To investigate the origin of the domestic yak (Poephagus grunnies), we analyzed 637 bp of maternal inherited mtDNA from 13 wild yaks (including eight wild yaks from a small population in west Qinghai) and 250 domesticated yaks from major herding regions. Results: The domestic yak populations had two deeply divergent phylogenetic groups with a divergence time of > 100,000 yrs BP. We here show that haplotypes clustering with two deeply divergent maternal lineages in domesticated yaks occur in a single, small, wild population. This finding suggests that all domestic yaks are derived from a single wild gene pool. However, there is no clear correlation of the mtDNA phylogenetic clades and the 10 morphological types of sampled yaks indicating that the latter diversified recently. Relatively high diversity was found in Qinghai and Tibet around the current wild distribution, in accordance with previous suggestions that the earliest domestications occurred in this region. Conventional molecular clock estimation led to an unrealistic early dating of the start of the domestication. However, Bayesian estimation of the coalescence time allowing a relaxation of the mutation rate Conclusion: The information gathered here and the previous studies of other animals show that the demographic histories of domestication of livestock species were highly diverse despite the common general feature of deeply divergent maternal lineages. The results further suggest that domestication of local wild prey ungulate animals was a common occurrence during the development of human civilization following the postglacial colonization in different locations of the world, including the high, arid Qinghai-Tibetan Plateau.
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| 14. |
- Huang, M. -Q, et al.
(författare)
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Switchable Copper-Catalyzed Approach to Benzodithiole, Benzothiaselenole, and Dibenzodithiocine Skeletons
- 2020
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Ingår i: Organic Letters. - : American Chemical Society (ACS). - 1523-7060 .- 1523-7052. ; 22:9, s. 3454-3459
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Tidskriftsartikel (refereegranskat)abstract
- A copper-catalyzed reaction between 2-bromo-benzothioamides and S8 or Se involving sulfur rearrangement is reported, enabling access to benzodithioles 2 and benzothiaselenoles 6 in the presence of Cs2CO3. In the absence of S8 or Se, the reaction affords dibenzodithiocines 7 via two consecutive C(sp2)-S Ullmann couplings.
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| 15. |
- Li, Jianquan, et al.
(författare)
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Can Language Models Make Fun? A Case Study in Chinese Comical Crosstalk
- 2023
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Ingår i: Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). - Stroudsburg, PA : Association for Computational Linguistics. - 9781959429722 ; , s. 7581-7596
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Konferensbidrag (refereegranskat)abstract
- Language is the principal tool for human communication, in which humor is one of the most attractive parts. Producing natural language like humans using computers, a.k.a, Natural Language Generation (NLG), has been widely used for dialogue systems, chatbots, text summarization, as well as AI-Generated Content (AIGC), e.g., idea generation, and scriptwriting. However, the humor aspect of natural language is relatively under-investigated, especially in the age of pre-trained language models. In this work, we aim to preliminarily test whether NLG can generate humor as humans do. We build the largest dataset consisting of numerous Chinese Comical Crosstalk scripts (called C3 in short), which is for a popular Chinese performing art called 'Xiangsheng' or '相声' since 1800s. We benchmark various generation approaches including training-from-scratch Seq2seq, fine-tuned middle-scale PLMs, and large-scale PLMs with and without fine-tuning. Moreover, we also conduct a human assessment, showing that 1) large-scale pretraining largely improves crosstalk generation quality; and 2) even the scripts generated from the best PLM is far from what we expect. We conclude humor generation could be largely improved using large-scale PLMs, but it is still in its infancy. The data and benchmarking code are publicly available in https://github.com/anonNo2/crosstalk-generation. © 2023 Association for Computational Linguistics.
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| 16. |
- Li, Yuan, et al.
(författare)
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Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci
- 2010
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 27:5, s. 1001-1014
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Tidskriftsartikel (refereegranskat)abstract
- Nucleotide variation at 12 to 16 nuclear loci was studied in three spruce species from the Qinghai-Tibetan Plateau (QTP), Picea likiangensis, P. wilsonii and P. purpurea, and one species from the Tian Shan mountain range, P. schrenkiana. Silent nucleotide diversity was limited in P. schrenkiana and high in the three species from the QTP, with values higher than in boreal spruce species, despite their much more restricted distributions compared to that of the boreal species. In contrast to European boreal species that have experienced severe bottlenecks in the past, coalescent-based analysis suggests that DNA polymorphism in the species from the QTP and adjacent areas is compatible with the standard neutral model (P. likiangensis, P. wilsonii, P. schrenkiana) or with population growth (P. purpurea). In order to test if P. purpurea is a diploid hybrid of P. likiangensis and P. wilsonii, we used a combination of approaches, including model based inference of population structure, Isolation-with-Migration models and recent theoretical results on the effect of introgression on the geographic distribution of diversity. In contrast to the three other species, each of which was predominantly assigned to a single cluster in the Structure analysis, P. purpurea individuals were scattered over the three main clusters and not, as we had expected, confined to the P. likiangensis and P. wilsonii clusters. Furthermore the contribution of P. schrenkiana was by far the largest one. In agreement with this, the divergence between P. purpurea and P. schrenkiana was lower than the divergence of either P. likiangensis or P. wilsonii from P. schrenkiana. These results, together with previous ones showing that P. purpurea and P. wilsonii share the same haplotypes at both chloroplast and mitochondrial markers, suggest that P. purpurea has a complex origin, possibly involving additional species.
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| 17. |
- Li, Zhonghu, et al.
(författare)
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Population Genetic Evidence for Complex Evolutionary Histories of Four High Altitude Juniper Species in the Qinghai-Tibetan Plateau
- 2012
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Ingår i: Evolution. - : Wiley. - 0014-3820 .- 1558-5646. ; 66:3, s. 831-845
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Tidskriftsartikel (refereegranskat)abstract
- Population genetics data based on multiple nuclear loci provide invaluable information to understand demographic, selective, and divergence histories of the current species. We studied nucleotide variation at 13 nuclear loci in 53 populations distributed among four closely related, but morphologically distinct juniper species of the QinghaiTibetan Plateau (QTP). We used a novel approach combining Approximate Bayesian Computation and a recently developed neutrality test based on the maximum frequency of derived mutations to examine the demographic and selective histories of individual species, and isolation-with-migration analyses to study the joint history of the species and detect gene flow between them. We found that (1) the four species, which diverged in response to the extensive QTP uplifts, have different demographic histories; (2) two loci, Pgi and CC0822, depart significantly from neutrality in one species and Pgi, is also marginally significant in another; and (3) shared polymorphisms are common, indicating both incomplete lineage sorting and gene flow after species divergence. In addition, the detected unidirectional gene flow provides indirect support for the theoretical prediction that introgression should mostly take place from local to invading species. Our results, together with previous studies, underscore complex evolutionary histories of plant diversification in the biodiversity-hotspot QTP.
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| 18. |
- Li, Zhonghu, et al.
(författare)
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The Pleistocene demography of an alpine juniper of the Qinghai-Tibetan Plateau : tabula rasa, cryptic refugia or something else?
- 2011
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Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 38:1, s. 31-43
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Tidskriftsartikel (refereegranskat)abstract
- Aim Numerous palaeoecological and genetic studies have shown that different tree species responded in very different ways to Pleistocene climatic oscillations. Some were forced into small refugia far from their current range, while others were able to survive in small refugia close to, or even within, their current natural range. In this study we examine the Pleistocene demography of a juniper species (Juniperus przewalskii, Cupressaceae) from the Qinghai-Tibetan Plateau. Location The Qinghai-Tibetan Plateau (QTP). Methods Eight nuclear loci were sequenced in 141 individuals from 20 natural populations distributed across the entire natural range of J. przewalskii, and coalescent analysis was used to test demographic hypotheses. Results The overall nucleotide diversity in the sample was low (pi(sil) = 0.0029), with few rare alleles and pronounced population genetic structure (F-ST = 0.181). We detected a division previously found using chloroplast DNA markers: all segregating sites in populations from the central part of the QTP appear to be a subset of those found around the edge of the plateau, confirming the relatively young age of the former. In contrast to the middle Pleistocene bottlenecks detected in boreal tree species, the coalescent-based analyses failed to reject the standard neutral model for the juniper species considered here. Main conclusions Juniperus przewalskii did not undergo marked changes in population sizes during the Pleistocene, although this species seems to have experienced recent, post-glacial expansion. This finding is largely consistent with the limited number of previous studies on conifer species of the QTP, but contradicts findings of studies on boreal species. These findings have wide implications for understanding plant species' responses to past climatic oscillations on the high-elevation QTP.
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| 19. |
- Liu, Jianquan, et al.
(författare)
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Closing the radical gap in chemical synthesis
- 2020
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 368:6497, s. 1312-1313
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Unstable radical intermediates are harnessed in a microfluidic electrochemical cell
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| 20. |
- Lockwood, Jared, et al.
(författare)
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A new phylogeny for the genus Picea from plastid, mitochondrial adn nuclear sequences
- 2013
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 69:3, s. 717-727
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Tidskriftsartikel (refereegranskat)abstract
- Studies over the past ten years have shown that the crown groups of most conifer genera are only about 15–25 Ma old. The genus Picea (spruces, Pinaceae), with around 35 species, appears to be no exception. In addition, molecular studies of co-existing spruce species have demonstrated frequent introgression. Per- haps not surprisingly therefore previous phylogenetic studies of species relationships in Picea, based mostly on plastid sequences, suffered from poor statistical support. We therefore generated mitochon- drial, nuclear, and further plastid DNA sequences from carefully sourced material, striking a balance between alignability with outgroups and phylogenetic signal content. Motif duplications in mitochon- drial introns were treated as characters in a stochastic Dollo model; molecular clock models were cali- brated with fossils; and ancestral ranges were inferred under maximum likelihood. In agreement with previous findings, Picea diverged from its sister clade 180 million years ago (Ma), and the most recent common ancestor of today’s spruces dates to 28 Ma. Different from previous analyses though, we find a large Asian clade, an American clade, and a Eurasian clade. Two expansions occurred from Asia to North America and several between Asia and Europe. Chinese P. brachytyla, American P. engelmannii, and Nor- way spruce, P. abies, are not monophyletic, and North America has ten, not eight species. Divergence times imply that Pleistocene refugia are unlikely to be the full explanation for the relationships between the European species and their East Asian relatives. Thus, northern Norway spruce may be part of an Asian species complex that diverged from the southern Norway spruce lineage in the Upper Miocene, some 6 Ma, which can explain the deep genetic gap noted in phylogeographic studies of Norway spruce. The large effective population sizes of spruces, and incomplete lineage sorting during speciation, mean that the interspecific relationships within each of the geographic clades require further studies, especially based on genomic information and population genetic data.
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| 21. |
- Ma, Tao, et al.
(författare)
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Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex
- 2018
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : NATL ACAD SCIENCES. - 0027-8424 .- 1091-6490. ; 115:2, s. E236-E243
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Tidskriftsartikel (refereegranskat)abstract
- How genome divergence eventually leads to speciation is a topic of prime evolutionary interest. Genomic islands of elevated divergence are frequently reported between diverging lineages, and their size is expected to increase with time and gene flow under the speciation-with-gene-flow model. However, such islands can also result from divergent sorting of ancient polymorphisms, recent ecological selection regardless of gene flow, and/or recurrent background selection and selective sweeps in low-recombination regions. It is challenging to disentangle these nonexclusive alternatives, but here we attempt to do this in an analysis of what drove genomic divergence between four lineages comprising a species complex of desert poplar trees. Within this complex we found that two morphologically delimited species, Populus euphratica and Populus pruinosa, were paraphyletic while the four lineages exhibited contrasting levels of gene flow and divergence times, providing a good system for testing hypotheses on the origin of divergence islands. We show that the size and number of genomic islands that distinguish lineages are not associated with either rate of recent gene flow or time of divergence. Instead, they are most likely derived from divergent sorting of ancient polymorphisms and divergence hitchhiking. We found that highly diverged genes under lineage-specific selection and putatively involved in ecological and morphological divergence occur both within and outside these islands. Our results highlight the need to incorporate demography, absolute divergence measurement, and gene flow rate to explain the formation of genomic islands and to identify potential genomic regions involved in speciation.
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| 22. |
- Peng, Yanling, et al.
(författare)
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Phylogeographic analysis of the fir species in southern China suggests complex origin and genetic admixture
- 2012
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Ingår i: Annals of Forest Science. - 1286-4560 .- 1297-966X. ; 69:3, s. 409-416
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Tidskriftsartikel (refereegranskat)abstract
- ContextFir species are mainly distributed across the high latitudes, preferring cold climates. The phylogeographic origins of those subtropical fir species that occur in low latitudes in southern China remain elusive, as does the nature of any inter-lineage hybridization.AimsIn fir species, mitochondrial DNA (mtDNA) is mater- nally inherited and chloroplast DNA (cpDNA) is paternally inherited, and the genetic variations in the two make them particularly useful for examining species’ hybridizations and evolutionary histories.Materialsand methods We sequenced four DNA frag- ments: two of mtDNA and two of cpDNA for 161 individuals from four subtropical endangered fir species (Abies beshan- zuensis, Abies ziyuanensis, Abies yuanbaoshanensis, and Abies fanjingshanensis) and two more northerly distributed ones (Abies recurvata and Abies fargesii) from central and southwest China.ResultsThree mitotypes and four chlorotypes were recov- ered from the four southern species. In most populations, individuals share a single fixed mitotype and chlorotype. Three mitotypes clustered into two distinct clades, each associated with one of the northern species examined. For four chlorotypes, one occurred in A. ziyuanensis, A. beshan- zuensis, A. fargesii, and A. recurvata, another in A. ziyua- nensis and A. recurvata, the remaining two differed from others by two mutations exclusively in A. fanjingshanenis and A. yuanbaoshanensis.ConclusionPhylogeographic origins of the subtropical fir species are complex, and genetic admixtures occurred dur- ing the evolutionary history of A. ziyuanensis. The geno- typed populations further provide basic frames for genetic delimitation and effective conservation of these endangered species in the future.
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| 23. |
- Peng, Yanling, et al.
(författare)
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Range expansion during the Pleistocene drove morphological radiation of the fir genus (Abies, Pinaceae) in the Qinghai-Tibet Plateau and Himalayas
- 2015
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Ingår i: Botanical journal of the Linnean Society. - : Wiley-Blackwell. - 0024-4074 .- 1095-8339. ; 179:3, s. 444-453
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Tidskriftsartikel (refereegranskat)abstract
- Range expansion caused by climate oscillations in the past probably promoted morphological radiation in a few plant groups. In this study, we aim to test this hypothesis through phylogeographical analysis of the cold-tolerant fir genus (Abies) in the Qinghai-Tibet Plateau (QTP) and Himalayas, where it comprises 12 described species. We examined sequence variation in two maternally inherited mitochondrial (mt) DNA fragments (nad5-4 and nad7-1) and two paternally inherited plastid DNA fragments (trnS-G and trnL-F) for 733 individuals from 75 populations of the species in a monophyletic group. Only six mtDNA haplotypes were recovered, but five were shared between multiple species and one occurred at a high frequency, providing strong evidence of range expansion. Forty-three plastid DNA haplotypes were detected, 19 of which were shared between species and three occurred at high frequency. Network, mismatch and Bayesian skyline plot analyses of all plastid DNA haplotypes from this clade clearly suggested range expansion. This expansion was dated as having occurred during the longest and most extensive glaciation in the Pleistocene. Our results therefore supported the range expansion hypothesis for this clade of Abies during the Pleistocene; expansion probably drove the morphological radiation of the clade in the QTP and Himalayas, although it remains unclear whether the different morphotypes should be acknowledged as independent, reproductively isolated species.
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| 24. |
- Shatskiy, Andrey, et al.
(författare)
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Back cover
- 2021
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Ingår i: Chemical Science. - : Royal Society of Chemistry (RSC). - 2041-6520 .- 2041-6539. ; 12:15, s. 5430-5437
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Tidskriftsartikel (refereegranskat)
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| 25. |
- Shatskiy, Andrey, et al.
(författare)
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Controlling Radical Relay Processes with Visible Light
- 2021
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Ingår i: Chem. - : Cell Press. - 2451-9308 .- 2451-9294. ; 7:2, s. 283-285
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Harnessing free radical intermediates for selective functionalization of organic compounds has been widely demonstrated under photocatalytic conditions requiring a distinct photocatalyst. In this issue of Chem, Seo, Chang, and co-workers demonstrate an alternative photocatalyst- free light-mediated approach that allows efficient amidation of aldehydes via N-centered radical intermediate.
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| 26. |
- Shatskiy, Andrey, et al.
(författare)
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Electrifying catalytic aerobic oxidation
- 2021
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Ingår i: NATURE CATALYSIS. - : Springer Nature. - 2520-1158. ; 4:2, s. 96-97
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 27. |
- Shatskiy, Andrey, 1989-, et al.
(författare)
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Stereoselective synthesis of unnatural α-amino acid derivatives through photoredox catalysis
- 2021
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Ingår i: Chemical Science. - : Royal Society of Chemistry. - 2041-6520 .- 2041-6539. ; 12:15, s. 5430-5437
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Tidskriftsartikel (refereegranskat)abstract
- A protocol for stereoselective C-radical addition to a chiral glyoxylate-derived N-sulfinyl imine was developed through visible light-promoted photoredox catalysis, providing a convenient method for the synthesis of unnatural α-amino acids. The developed protocol allows the use of ubiquitous carboxylic acids as radical precursors without prior derivatization. The protocol utilizes near-stoichiometric amounts of the imine and the acid radical precursor in combination with a catalytic amount of an organic acridinium-based photocatalyst. Alternative mechanisms for the developed transformation are discussed and corroborated by experimental and computational studies.
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| 28. |
- Shen, Xuanyu, et al.
(författare)
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Silver-Assisted [3+2] Annulation of Nitrones with Isocyanides : Synthesis of 2,3,4-Trisubstituted 1,2,4-Oxadiazolidin-5-ones
- 2020
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Ingår i: Journal of Organic Chemistry. - : AMER CHEMICAL SOC. - 0022-3263 .- 1520-6904. ; 85:5, s. 3560-3567
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Tidskriftsartikel (refereegranskat)abstract
- A silver-assisted method for [3 + 2] annulation of nitrones with isocyanides has been developed. The developed protocol allows access to a variety of 2,3,4-trisubstituted 1,2,4-oxadiazolidin-S-one derivatives as single diastereomers in good to excellent yields using silver oxide as the catalyst and molecular oxygen as the terminal oxidant. A plausible mechanism involving a nucleophilic addition/cyclization/protodeargentation/oxidation pathway is proposed on the basis of experimental results.
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| 29. |
- Wang, Jing, et al.
(författare)
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Evidence for widespread selection in shaping the genomic landscape during speciation of Populus
- 2020
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Ingår i: Molecular Ecology. - : Wiley-Blackwell. - 0962-1083 .- 1365-294X. ; 29:6, s. 1120-1136
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Tidskriftsartikel (refereegranskat)abstract
- Increasing our understanding of how evolutionary processes drive the genomic landscape of variation is fundamental to a better understanding of the genomic consequences of speciation. However, genome-wide patterns of within- and between- species variation have not been fully investigated in most forest tree species despite their global ecological and economic importance. Here, we use whole-genome resequencing data from four Populus species spanning the speciation continuum to reconstruct their demographic histories and investigate patterns of diversity and divergence within and between species. Using Populus trichocarpa as an outgroup species, we further infer the genealogical relationships and estimate the extent of ancient introgression among the three aspen species (Populus tremula, Populus davidiana and Populus tremuloides) throughout the genome. Our results show substantial variation in these patterns along the genomes with this variation being strongly predicted by local recombination rates and the density of functional elements. This implies that the interaction between recurrent selection and intrinsic genomic features has dramatically sculpted the genomic landscape over long periods of time. In addition, our findings provide evidence that, apart from background selection, recent positive selection and long-term balancing selection have also been crucial components in shaping patterns of genome-wide variation during the speciation process.
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| 30. |
- Wang, Juan, et al.
(författare)
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Genetic Differentiation and Delimitation between Ecologically Diverged Populus euphratica and P. pruinosa
- 2011
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:10, s. e26530-
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Tidskriftsartikel (refereegranskat)abstract
- Background: The fixed genetic differences between ecologically divergent species were found to change greatly depending on the markers examined. With such species it is difficult to differentiate between shared ancestral polymorphisms and past introgressions between the diverging species. In order to disentangle these possibilities and provide a further case for DNA barcoding of plants, we examine genetic differentiation between two ecologically divergent poplar species, Populus euphratica Oliver and P. pruinosa Schrenk using three different types of genetic marker. Methodology/Principal Findings: We genotyped 290 individuals from 29 allopatric and sympatric populations, using chloroplast (cp) DNA, nuclear (nr) ITS sequences and eight simple sequence repeat (SSR) loci. Three major cpDNA haplotypes were widely shared between the two species and between-species cpDNA differentiation (FCT) was very low, even lower than among single species populations. The average SSR FCT values were higher. Bayesian clustering analysis of all loci allowed a clear delineation of the two species. Gene flow, determined by examining all SSR loci, was obvious but only slightly asymmetrical. However, the two species were almost fixed for two different nrITS genotypes that had the highest FCT, although a few introgressed individuals were detected both in allopatric and sympatric populations. Conclusions: The two species shared numerous ancestral polymorphisms at cpDNA and a few SSR loci. Both ITS and a combination of nuclear SSR data could be used to differentiate between the two species. Introgressions and gene flow were obvious between the two species either during or after their divergence. Our findings underscore the complex genetic differentiations between ecologically diverged species and highlight the importance of nuclear DNA (especially ITS) differentiation for delimiting closely related plant species.
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| 31. |
- Wang, Jing, 1989-, et al.
(författare)
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Increased genetic divergence between two closely related fir species in areas of range overlap
- 2014
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 4:7, s. 1019-1029
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Tidskriftsartikel (refereegranskat)abstract
- Because of introgressive hybridization, closely related species can be more similar to each other in areas of range overlap (parapatry or sympatry) than in areas where they are geographically isolated from each other (allopatry). Here, we report the reverse situation based on nuclear genetic divergence between two fir species, Abies chensiensis and Abies fargesii, in China, at sites where they are parapatric relative to where they are allopatric. We examined genetic divergence across 126 amplified fragment length polymorphism (AFLP) markers in a set of 172 individuals sampled from both allopatric and parapatric populations of the two species. Our analyses demonstrated that AFLP divergence was much greater between the species when comparisons were made between parapatric populations than between allopatric populations. We suggest that selection in parapatry may have largely contributed to this increased divergence.
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| 32. |
- Wang, Jing, et al.
(författare)
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Species delimitation and biogeography of two fir species (Abies) in central China : cytoplasmic DNA variation
- 2011
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Ingår i: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 107:4, s. 362-370
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Tidskriftsartikel (refereegranskat)abstract
- It remains unclear how speciation history might contribute to species-specific variation and affect species delimitation. We examined concordance between cytoplasmic genetic variation and morphological taxonomy in two fir species, Abies chensiensis and A. fargesii, with overlapping distributions in central China. Range-wide genetic variation was investigated using mitochondrial (mt) and plastid (pt) DNA sequences, which contrast in their rates of gene flow. Four mtDNA haplotypes were recovered and showed no obvious species' bias in terms of relative frequency. In contrast, a high level of ptDNA variation was recorded in both species with 3 common ptDNA haplotypes shared between them and 21 rare ptDNA haplotypes specific to one or other species. We argue that the lack of concordance between morphological and molecular variation between the two fir species most likely reflects extensive ancestral polymorphism sharing for both forms of cytoplasmic DNA variation. It is feasible that a relatively fast mutation rate for ptDNA contributed to the production of many species-specific ptDNA haplotypes, which remained rare due to insufficient time passing for their spread and fixation in either species, despite high levels of intraspecific ptDNA gene flow. Our phylogeographic analyses further suggest that polymorphisms in both organelle genomes most likely originated during and following glacial intervals preceding the last glacial maximum, when species distributions became fragmented into several refugia and then expanded in range across central China.
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| 33. |
- Wang, Y. -C, et al.
(författare)
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Copper-assisted Wittig-type olefination of aldehydes with p-toluenesulfonylmethyl isocyanide
- 2022
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Ingår i: Organic Chemistry Frontiers. - : Royal Society of Chemistry (RSC). - 2052-4110 .- 2052-4129. ; 9:15, s. 4158-4163
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Tidskriftsartikel (refereegranskat)abstract
- The Wittig reaction is a valuable and powerful tool in organic synthesis, providing a convenient route from aldehydes and ketones to alkenes. Herein, a novel copper-assisted Wittig-type olefination of aldehydes with p-toluenesulfonylmethyl isocyanide (TosMIC) is disclosed, providing a direct and operationally simple approach to (E)-vinyl sulfones under mild conditions, compatible with a multitude of common functional groups. Experimental and computational investigations imply that the reaction proceeds through an intriguing electronically-controlled (3 + 2)/retro-(3 + 2) cycloaddition pathway.
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| 34. |
- Wu, H., et al.
(författare)
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Modular synthesis of 3-substituted isocoumarinsviasilver-catalyzed aerobic oxidation/6-endoheterocyclization ofortho-alkynylbenzaldehydes
- 2021
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Ingår i: Organic and biomolecular chemistry. - : Royal Society of Chemistry (RSC). - 1477-0520 .- 1477-0539. ; 19:30, s. 6657-6664
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Tidskriftsartikel (refereegranskat)abstract
- A method involving silver-catalyzed aerobic oxidation/6-endoheterocyclization ofortho-alkynylbenzaldehydes to yield 3-substituted isocoumarins is described. The developed protocol allows convenient access to a range of synthetically useful 3-substituted isocoumarins and related fused heterocyclolactones in good to high yields, using silver tetrafluoroborate as the catalyst, and atmospheric oxygen as the terminal oxidant and the source of endocyclic oxygen. Mechanistic studies suggest the involvement of a free-radical pathway.
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| 35. |
- Zhang, Jian, et al.
(författare)
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Rapidly Evolving Genes and Stress Adaptation of Two Desert Poplars, Populus euphratica and P. pruinosa
- 2013
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:6, s. e66370-
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Tidskriftsartikel (refereegranskat)abstract
- Understanding which genes have evolved rapidly with the recent tree speciation in arid habitats can provide valuable insights into different adaptation mechanisms. We employed a comparative evolutionary analysis of expressed sequence tags (ESTs) from two desert poplars, Populus pruinosa and P. euphratica, which diverged in the recent past. Following an approach taken previously with P. euphratica, we conducted a deep transcriptomic analysis of P. pruinosa. To maximize representation of conditional transcripts, mRNA was obtained from living tissues of two types of callus and desert-grown trees. De novo assembly generated 114,866 high-quality unique sequences using Solexa sequence data. Following assembly we were able to identify, with high confidence, 2859 orthologous sequence pairs between the two species. Based on the ratio of nonsynonymous (Ka) to synonymous (Ks) substitutions, we identified a total of 84 (2.9%) ortholog pairs exhibiting rapid evolution with signs of strong selection (Ka/Ks>1). Genes homologous to these ortholog pairs in model species are mainly involved in 'responses to stress', 'ubiquitin-dependent protein catabolic processes', and 'biological regulation'. Finally, we examined the expression patterns of candidate genes with rapid evolution in response to salt stress. Only one pair of orthologs up-regulated their expression in both species while three and four genes were found to up-regulated in P. pruinosa and in P. euphratica respectively. Our findings together suggest that the genes at the same category or network but with differentiated expressions or functions may have evolved rapidly during adaptive divergence of the two species to differentiated salty desert habitats.
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