| 61. |
- Liu, Yan-Jing, et al.
(författare)
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De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China
- 2019
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Ingår i: Science China Life Sciences. - : Springer Science and Business Media LLC. - 1674-7305 .- 1869-1889. ; 62:5, s. 609-618
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Tidskriftsartikel (refereegranskat)abstract
- The white poplar (Populus alba) is widely distributed in Central Asia and Europe. There are natural populations of white poplar in Irtysh River basin in China. It also can be cultivated and grown well in northern China. In this study, we sequenced the genome of P. alba by single-molecule real-time technology. De novo assembly of P. alba had a genome size of 415.99 Mb with a contig N50 of 1.18 Mb. A total of 32,963 protein-coding genes were identified. 45.16% of the genome was annotated as repetitive elements. Genome evolution analysis revealed that divergence between P. alba and Populus trichocarpa (black cottonwood) occurred similar to 5.0 Mya (3.0, 7.1). Fourfold synonymous third-codon transversion (4DTV) and synonymous substitution rate (ks) distributions supported the occurrence of the salicoid WGD event (similar to 65 Mya). Twelve natural populations of P. alba in the Irtysh River basin in China were sequenced to explore the genetic diversity. Average pooled heterozygosity value of P. alba populations was 0.170 +/- 0.014, which was lower than that in Italy (0.271 +/- 0.051) and Hungary (0.264 +/- 0.054). Tajima's D values showed a negative distribution, which might signify an excess of low frequency polymorphisms and a bottleneck with later expansion of P. alba populations examined.
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| 62. |
- Mao, Jian-Feng, et al.
(författare)
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Distinct niche divergence characterizes the homoploid hybrid speciation of Pinus densata on the Tibetan Plateau
- 2011
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Ingår i: American Naturalist. - : University of Chicago Press. - 0003-0147 .- 1537-5323. ; 177:4, s. 424-439
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Tidskriftsartikel (refereegranskat)abstract
- Ecological divergence and selection for novel adaptations to new habitats have been theoretically proposed to play important roles in promoting homoploid hybrid speciation (HHS). The successful establishment of Pinus densata on the Tibetan Plateau is one of the few known examples of HHS. In this study, we carried out extensive field expeditions to obtain representative coverage of occurrence sites of P. densata and its two putative parents. We then applied a series of geographic information system-based analyses to define the patterns of environmental variation within and among the three pine species, to remove potentially confounding effects of spatial autocorrelation in the environmental data due to allopatric ranges, and to build species distribution models. All results consistently indicated that the ecological preferences of P. densata and its parental species have diverged, and they identified candidate ecological factors associated with habitat-specific adaptation. Projections from niche modeling indicated that P. densata could extend across a vast range along the parallel valley systems of the southeastern Tibetan Plateau. Our findings provide evidence of a distinct niche shift in P. densata and support the hypothesis that local adaptation and geographic isolation help maintain and reinforce between-species differences and reproductive isolation in the species complex.
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| 63. |
- Mao Li, J.-F., et al.
(författare)
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Empirical assessment of the reproductive fitness components of the hybrid pine Pinus densata on the Tibetan Plateau
- 2009
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Ingår i: Evolutionary Ecology. - : Springer Science and Business Media LLC. - 0269-7653 .- 1573-8477. ; 23:3, s. 447-462
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Tidskriftsartikel (refereegranskat)abstract
- Pinus densata is distributed on the Tibetan Plateau, where it forms extensive forests at high elevations. Genetic studies have provided evidence that P. densata originated through hybridization between P. yunnanensis and P. tabuliformis. To clarify the relationships among these pines, and assess their reproductive fitness in their respective habitats, we conducted a comparative analysis of eight cone and seed morphometric traits and six reproductive traits in them. Among the eight morphometric traits examined, six appeared to be intermediate in P. densata between those of P. yunnanensis and P. tabuliformis. There were significant differences among the three pines in all of the morphometric traits, and P. densata showed greater variability in these traits than the other two pines. In contrast to the morphometric traits, the reproductive traits (including the proportions of filled and empty seeds, ovule abortion rate, seed efficiency, meiotic abnormalities during microsporogenesis and pollen viability) differed little among the three pines, indicating that they have similar overall rates of effective pollination and fertilization in their respective natural environments. Despite their location on the high plateau, natural populations of P. densata appeared to have normal levels of reproductive success, comparable to those of the two parental species in their natural habitats. This study provides empirical data characterizing the reproductive success and adaptation of a stabilized homoploid hybrid in a novel habitat that is ecologically and spatially inaccessible to its parental species.
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| 64. |
- Meng, Jingxiang, et al.
(författare)
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Adaptive Differentiation in Seedling Traits in a Hybrid Pine Species Complex, Pinus densata and Its Parental Species, on the Tibetan Plateau
- 2015
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:3
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Tidskriftsartikel (refereegranskat)abstract
- Evidence from molecular genetics demonstrates that Pinus densata is a natural homoploid hybrid originating from the parent species Pinus tabuliformis and Pinus yunnanensis, and ecological selection may have played a role in the speciation of Pinus densata. However, data on differentiation in adaptive traits in the species complex are scarce. In this study, we performed a common garden test on 16 seedling traits to examine the differences between Pinus densata and its parental species in a high altitude environment. We found that among the 16 analyzed traits, 15 were significantly different among the species. Pinus tabuliformis had much earlier bud set and a relatively higher bud set ratio but poorer seedling growth, and Pinus yunnanensis had opposite responses for the same traits. Pinus densata had the greatest fitness with higher viability and growth rates than the parents. The relatively high genetic contribution of seedling traits among populations suggested that within each species the evolutionary background is complex. The correlations between the seedling traits of a population within a species and the environmental factors indicated different impacts of the environment on species evolution. The winter temperature is among the most important climate factors that affected the fitness of the three pine species. Our investigation provides empirical evidence on adaptive differentiation among this pine species complex at seedling stages.
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| 65. |
- Ninnes, Sofia, 1984-
(författare)
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Molecular analysis of lake-sediment organic matter : long-term dynamics and environmental implications in boreal lakes
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Lake sediment organic matter is material composed of residues from plants, algae, animals, fungi and bacteria. Its molecular composition is dependent on the sources as well as secondary biotic and abiotic transformations, which combined generates a highly complex matrix. Considering that organic matter plays a key role in carbon and nitrogen cycle, and its composition affects many different biogeochemical reactions, paleolimnologic studies have payed proportionately little attention to the organic matter composition compared with the other sediment fractions, even though organic matter makes up 20–60 % of the dry sediment mass in boreal and subarctic lakes. This thesis therefore primarily aims to explore and evaluate two methods; pyrolysis-gas chromatography/mass spectrometry (Pyrolysis-GC/MS) and diffuse reflectance Fourier-transform infrared spectroscopy (DRIFTS) for characterisation of bulk organic matter at the molecular level, both which have been extensively used for soils and peat and which balances the need for cost and time-effective analysis and for analytical detail.With pyrolysis-GC/MS the organic matter composition and long-term dynamics in two neighbouring boreal lakes is explored and compared with the conventional bulk carbon and nitrogen contents and their stable isotopes. Both pyrolysis data and conventional data capture the timing of organic matter compositional changes, but only pyrolysis provides detailed information on how the composition changes, which allows for a deeper understanding of the processes behind the changes. The same two lakes are also analysed with DRIFTS and with this approach information on the major organic compound groups aromatics, lignin, aliphatics, proteins and polysaccharides is extracted. In combination with the rapid analysis time and low cost, DRIFTS emerges as a very useful tool for rapid yet informative organic matter analysis. DRIFTS is then evaluated as a stand-alone tool for sediment characterisation in four mountain lakes. The four lakes all have different sediment composition and as a result of the multi-fraction information obtained with DRIFTS compositional differences can be related and explained in terms of their individual lake and landscape settings. The importance of landscape setting is further highlighted in the synthesis of the long-term dynamics of lake-water quality in seven lakes where development trajectories and responses to different types of disturbances are connected to the extent of peatlands within the lake catchments. This thesis demonstrates the advantages of two different approaches for more detailed lake sediment organic matter characterisation and advances our understanding of the molecular organic matter composition in boreal lakes over the Holocene, and how landscape setting affects both the organic matter composition and the sensitivity of lakes to disturbance.
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| 66. |
- Olajos, Fredrik, et al.
(författare)
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Estimating species colonization dates using DNA in lake sediment
- 2018
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Ingår i: Methods in Ecology and Evolution. - : British Ecological Society. - 2041-210X. ; 9:3, s. 535-543
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Tidskriftsartikel (refereegranskat)abstract
- Detection of DNA in lake sediments holds promise as a tool to study processes like extinction, colonization, adaptation and evolutionary divergence. However, low concentrations make sediment DNA difficult to detect, leading to high false negative rates. Additionally, contamination could potentially lead to high false positive rates. Careful laboratory procedures can reduce false positive and negative rates, but should not be assumed to completely eliminate them. Therefore, methods are needed that identify potential false positive and negative results, and use this information to judge the plausibility of different interpretations of DNA data from natural archives.We developed a Bayesian algorithm to infer the colonization history of a species using records of DNA from lake-sediment cores, explicitly labelling some observations as false positive or false negative. We illustrate the method by analysing DNA of whitefish (Coregonus lavaretus L.) from sediment cores covering the past 10,000 years from two central Swedish lakes. We provide the algorithm as an R-script, and the data from this study as example input files.In one lake, Stora Lögdasjön, where connectivity with the proto-Baltic Sea and the degree of whitefish ecotype differentiation suggested colonization immediately after deglaciation, DNA was indeed successfully recovered and amplified throughout the post-glacial sediment. For this lake, we found no loss of detection probability over time, but a high false negative rate. In the other lake, Hotagen, where connectivity and ecotype differentiation suggested colonization long after deglaciation, DNA was amplified only in the upper part of the sediment, and colonization was estimated at 2,200 bp based on the assumption that successful amplicons represent whitefish presence. Here the earliest amplification represents a false positive with a posterior probability of 41%, which increases the uncertainty in the estimated time of colonization.Complementing careful laboratory procedures aimed at preventing contamination, our method estimates contamination rates from the data. By combining these results with estimates of false negative rates, our models facilitate unbiased interpretation of data from natural DNA archives.
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| 67. |
- Peng, Ru, et al.
(författare)
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In-situ Neutron Diffraction Study of the Deformation Behaviour of two High-Manganese Austenitic Steels
- 2011
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Ingår i: Materials Science Forum. - Stafa-Zurich, Switzerland : Trans Tech Publications Inc.. - 0255-5476 .- 1662-9752. ; 681, s. 474-479
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Tidskriftsartikel (refereegranskat)abstract
- In-situ neutron diffraction experiments under tensile loading were carried out to study the micromechanical behaviour of two iron-manganese based steels, a TWIP (twinning induced plasticity) steel with 30 wt% Mn and a TRIP steel (transformation induced plasticity) with 20 wt% Mn. The former was loaded to 31.3% strain and the latter to 20% strain. The 30 wt.% Mn steel had a fully austenitic microstructure which remained stable over the loading range studied, while stress induced austenite to α´- and ε-martensite transformations occur in the 20 wt.% Mn steel which initially contained an α´-martensite in addition to the austenite. The evolution of lattice strains under tensile loading differs between the two steels, reflected their different plastic deformation mechanisms. A stronger grain-orientation dependent behaviour is observed during deformation for the 20 wt.% Mn in contrast to the 30wt.% Mn steel.
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| 68. |
- Schmit, Stephanie L, et al.
(författare)
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Novel Common Genetic Susceptibility Loci for Colorectal Cancer.
- 2019
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 111:2, s. 146-157
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Tidskriftsartikel (refereegranskat)abstract
- Background: Previous genome-wide association studies (GWAS) have identified 42 loci (P < 5 × 10-8) associated with risk of colorectal cancer (CRC). Expanded consortium efforts facilitating the discovery of additional susceptibility loci may capture unexplained familial risk.Methods: We conducted a GWAS in European descent CRC cases and control subjects using a discovery-replication design, followed by examination of novel findings in a multiethnic sample (cumulative n = 163 315). In the discovery stage (36 948 case subjects/30 864 control subjects), we identified genetic variants with a minor allele frequency of 1% or greater associated with risk of CRC using logistic regression followed by a fixed-effects inverse variance weighted meta-analysis. All novel independent variants reaching genome-wide statistical significance (two-sided P < 5 × 10-8) were tested for replication in separate European ancestry samples (12 952 case subjects/48 383 control subjects). Next, we examined the generalizability of discovered variants in East Asians, African Americans, and Hispanics (12 085 case subjects/22 083 control subjects). Finally, we examined the contributions of novel risk variants to familial relative risk and examined the prediction capabilities of a polygenic risk score. All statistical tests were two-sided.Results: The discovery GWAS identified 11 variants associated with CRC at P < 5 × 10-8, of which nine (at 4q22.2/5p15.33/5p13.1/6p21.31/6p12.1/10q11.23/12q24.21/16q24.1/20q13.13) independently replicated at a P value of less than .05. Multiethnic follow-up supported the generalizability of discovery findings. These results demonstrated a 14.7% increase in familial relative risk explained by common risk alleles from 10.3% (95% confidence interval [CI] = 7.9% to 13.7%; known variants) to 11.9% (95% CI = 9.2% to 15.5%; known and novel variants). A polygenic risk score identified 4.3% of the population at an odds ratio for developing CRC of at least 2.0.Conclusions: This study provides insight into the architecture of common genetic variation contributing to CRC etiology and improves risk prediction for individualized screening.
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| 69. |
- Shen, Yong-Feng, et al.
(författare)
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Deformation mechanisms of a 20Mn TWIP steel investigated by in situ neutron diffraction and TEM
- 2013
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Ingår i: Acta Materialia. - : Elsevier. - 1359-6454 .- 1873-2453. ; 61:16, s. 6093-6106
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Tidskriftsartikel (refereegranskat)abstract
- The deformation mechanisms and associated microstructure changes during tensile loading of an annealed twinning-induced plasticity steel with chemical composition Fe-20Mn-3Si-3Al-0.045C (wt.%) were systematically investigated using in situ time-of-flight neutron diffraction in combination with post mortem transmission electron microscopy (TEM). The initial microstructure of the investigated alloy consists of equiaxed gamma grains with the initial alpha'-phase of similar to 7% in volume. In addition to dislocation slip, twinning and two types of martensitic transformations from the austenite to alpha'- and epsilon-martensites were observed as the main deformation modes during the tensile deformation. In situ neutron diffraction provides a powerful tool for establishing the deformation mode map for elucidating the role of different deformation modes in different strain regions. The critical stress is 520 MPa for the martensitic transformation from austenite to alpha'-martensite, whereas a higher stress (>600 MPa) is required for actuating the deformation twin and/or the martensitic transformation from austenite to epsilon-martensite. Both epsilon- and alpha'-martensites act as hard phases, whereas mechanical twinning contributes to both the strength and the ductility of the studied steel. TEM observations confirmed that the twinning process was facilitated by the parent grains oriented with < 1 1 1 > or < 1 1 0 > parallel to the loading direction. The nucleation and growth of twins are attributed to the pole and self-generation formation mechanisms, as well as the stair-rod cross-slip mechanism.
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| 70. |
- Shimono, Ayako, et al.
(författare)
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Spatial variation in local pollen flow and mating success in a Picea abies clone archive and their implications for a novel “breeding without breeding” strategy
- 2011
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Ingår i: Tree Genetics & Genomes. - : Springer. - 1614-2942 .- 1614-2950. ; 7, s. 499-509
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Tidskriftsartikel (refereegranskat)abstract
- Currently, Norway spruce (Picea abies) breeding in Sweden is based on crosses between the best clones followed by clonal testing of the progenies to select for the long-term breeding population. An alternative breeding strategy called “Breeding without Breeding” (BwB) is proposed, which, in principle, relies on the DNA markerbased pedigree reconstruction from wind-pollinated progenies instead of controlled crosses. To test whether the pedigree structure could be established from progenies of clonal trials, we investigated the spatial pattern of local pollen flow and paternity assignment in a clone archive of Norway spruce. The results showed that 42% of the progeny can be assigned to fathers within 30-m distance with high confidence. Effective pollen dispersal decreased rapidly with distance and followed exponential distribution on local scale. The extent of close-neighbor (within 6 m) mating ranged from 0% to 48% among grafts with an average of 13%. Distance explained 25% deviance in mating success, and other factors such as phenology and spatial configuration of the clones should have contributed the rest. The success of parentage assignment in clone archive opens up the possibility to apply BwB in clonal trials of species that are easy to propagate vegetatively. This procedure could substantially shorten the breeding cycle and still give similar gain per year as the conventional breeding.
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