| 1. |
- Gao, Jie, et al.
(författare)
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Demography and speciation history of the homoploid hybrid pine Pinus densata on the Tibetan Plateau
- 2012
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Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 21:19, s. 4811-4827
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Tidskriftsartikel (refereegranskat)abstract
- Pinus densata is an ecologically successful homoploid hybrid that inhabits vast areas of heterogeneous terrain on the south-eastern Tibetan Plateau as a result of multiple waves of colonization. Its region of origin, route of colonization onto the plateau and the directions of introgression with its parental species have previously been defined, but little is known about the isolation and divergence history of its populations. In this study, we surveyed nucleotide polymorphism over eight nuclear loci in 19 representative populations of P. densata and its parental species. Using this information and coalescence simulations, we assessed the historical changes in its population size, gene flow and divergence in time and space. The results indicate a late Miocene origin for P. densata associated with the recent uplift of south-eastern Tibet. The subsequent differentiation between geographical regions of this species began in the late Pliocene and was induced by regional topographical changes and Pleistocene glaciations. The ancestral P. densata population had a large effective population size but the central and western populations were established by limited founders, suggesting that there were severe bottlenecks during the westward migration out of the ancestral hybrid zone. After separating from their ancestral populations, population expansion occurred in all geographical regions especially in the western range. Gene flow in P. densata was restricted to geographically neighbouring populations, resulting in significant differentiation between regional groups. The new information on the divergence and demographic history of P. densata reported herein enhances our understanding of its speciation process on the Tibetan Plateau.
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| 2. |
- Gao, Jie, et al.
(författare)
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Phylogeography and introgression between Pinus kesiya and Pinus yunnanensis in Southeast Asia
- 2024
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Ingår i: Journal of Systematics and Evolution. - : John Wiley & Sons. - 1674-4918 .- 1759-6831. ; 62:1, s. 120-134
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Tidskriftsartikel (refereegranskat)abstract
- Southeast Asia (SEA) has seen strong climatic oscillations and fluctuations in sea levels during the Quaternary. The impact of past climate changes on the evolution and distribution of local flora in SEA is still poorly understood. Here we aim to infer how the Quaternary climate change affects the evolutionary process and range shifts in two pine species. We investigated the population genetic structure and diversity using cytoplasmic DNA markers, and performed ecological niche modeling to reconstruct the species past distribution and to project range shift under future climates. We found substantial gene flow across the continuous distribution of the subtropical Pinus yunnanensis. In contrast, the tropical Pinus kesiya showed a strong population structure in accordance with its disjunct distribution across montane islands in Indochina and the Philippines. A broad hybrid zone of the two species occurs in southern Yunnan. Asymmetric introgression from the two species was detected in this zone with dominant mitochondrial gene flow from P. yunnanensis and chloroplast gene flow from P. kesiya. The observed population structure suggests a typical postglaciation expansion in P. yunnanensis, and a glacial expansion and interglacial contraction in P. kesiya. Ecological niche modeling supports the inferred demographic history and predicts a decrease in range size for P. kesiya under future climates. Our results suggest that tropical pine species in SEA have undergone evolutionary trajectories different from high latitude species related to their Quaternary climate histories. We also illustrate the need for urgent conservation actions in this fragmented landscape.
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| 3. |
- Guo, Jing-Fang, et al.
(författare)
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Low genetic diversity and population connectivity fuel vulnerability to climate change for the Tertiary relict pine Pinus bungeana
- 2023
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Ingår i: Journal of Systematics and Evolution. - : John Wiley & Sons. - 1674-4918 .- 1759-6831. ; 61:1, s. 143-156
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Tidskriftsartikel (refereegranskat)abstract
- Endemic species are important components of regional biodiversity and hold the key to understanding local adaptation and evolutionary processes that shape species distributions. This study investigated the biogeographic history of a relict conifer Pinus bungeana Zucc. ex Endl. confined to central China. We examined genetic diversity in P. bungeana using genotyping-by-sequencing and chloroplast and mitochondrial DNA markers. We performed spatial and temporal inference of recent genetic and demographic changes, and dissected the impacts of geography and environmental gradients on population differentiation. We then projected P. bungeana's risk of decline under future climates. We found extremely low nucleotide diversity (average π 0.0014), and strong population structure (global FST 0.234) even at regional scales, reflecting long-term isolation in small populations. The species experienced severe bottlenecks in the early Pliocene and continued to decline in the Pleistocene in the western distribution, whereas the east expanded recently. Local adaptation played a small (8%) but significant role in population diversity. Low genetic diversity in fragmented populations makes the species highly vulnerable to climate change, particularly in marginal and relict populations. We suggest that conservation efforts should focus on enhancing gene pool and population growth through assisted migration within each genetic cluster to reduce the risk of further genetic drift and extinction.
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| 4. |
- Pan, Jin, et al.
(författare)
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Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers
- 2015
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 15:4, s. 711-722
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Tidskriftsartikel (refereegranskat)abstract
- Flexibility and low cost make genotyping-by-sequencing (GBS) an ideal tool for population genomic studies of nonmodel species. However, to utilize the potential of the method fully, many parameters affecting library quality and single nucleotide polymorphism (SNP) discovery require optimization, especially for conifer genomes with a high repetitive DNA content. In this study, we explored strategies for effective GBS analysis in pine species. We constructed GBS libraries using HpaII, PstI and EcoRI-MseI digestions with different multiplexing levels and examined the effect of restriction enzymes on library complexity and the impact of sequencing depth and size selection of restriction fragments on sequence coverage bias. We tested and compared UNEAK, Stacks and GATK pipelines for the GBS data, and then developed a reference-free SNP calling strategy for haploid pine genomes. Our GBS procedure proved to be effective in SNP discovery, producing 7000-11000 and 14751 SNPs within and among three pine species, respectively, from a PstI library. This investigation provides guidance for the design and analysis of GBS experiments, particularly for organisms for which genomic information is lacking.
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| 5. |
- Wang, Baosheng, 1983-, et al.
(författare)
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Colonization of the Tibetan Plateau by the homoploid hybrid pine Pinus densata
- 2011
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Ingår i: Molecular Ecology. - Leicester : Blackwell Scientific Publications. - 0962-1083 .- 1365-294X. ; 20:18, s. 3796-3811
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Tidskriftsartikel (refereegranskat)abstract
- Pinus densata is an intriguingly successful homoploid hybrid species that occupies vast areas of the southeastern Tibetan Plateau in which neither of its parental species are present, but the colonization processes involved are poorly understood. To shed light on how this species colonized and became established on the plateau, we surveyed paternally inherited chloroplast (cp) and maternally inherited mitochondrial (mt) DNA variation within and among 54 populations of P. densata and its putative parental species throughout their respective ranges. Strong spatial genetic structure of both cp and mtDNA were detected in P. densata populations. Mitotypes specific to P. densata were likely generated by complex recombination events. A putative ancestral hybrid zone in the northeastern periphery of P. densata was identified, and we propose that the species then colonized the plateau by migrating westwards. Along the colonization route, consecutive bottlenecks and surfing of rare alleles caused a significant reduction in genetic diversity and strong population differentiation. The direction and intensity of introgression from parental species varied among geographic regions. In western parts of its range, the species seems to have been isolated from seed and pollen flow from its parent species for a long time. The observed spatial distribution of genetic diversity in P. densata also appears to reflect the persistence of this species on the plateau during the last glaciation. Our results indicate that both ancient and contemporary population dynamics have contributed to the spatial distribution of genetic diversity in P. densata, which accordingly reflects its evolutionary history.
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| 6. |
- Wang, Baosheng, et al.
(författare)
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Extremely low nucleotide polymorphism in Pinus krempfii Lecomte, a unique flat needle pine endemic to Vietnam
- 2014
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 4:11, s. 2228-2238
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Tidskriftsartikel (refereegranskat)abstract
- Pinus krempfii Lecomte is a morphologically and ecologically unique pine, endemic to Vietnam. It is regarded as vulnerable species with distribution limited to just two provinces: Khanh Hoa and Lam Dong. Although a few phylogenetic studies have included this species, almost nothing is known about its genetic features. In particular, there are no studies addressing the levels and patterns of genetic variation in natural populations of P.krempfii. In this study, we sampled 57 individuals from six natural populations of P.krempfii and analyzed their sequence variation in ten nuclear gene regions (approximately 9kb) and 14 mitochondrial (mt) DNA regions (approximately 10kb). We also analyzed variation at seven chloroplast (cp) microsatellite (SSR) loci. We found very low haplotype and nucleotide diversity at nuclear loci compared with other pine species. Furthermore, all investigated populations were monomorphic across all mitochondrial DNA (mtDNA) regions included in our study, which are polymorphic in other pine species. Population differentiation at nuclear loci was low (5.2%) but significant. However, structure analysis of nuclear loci did not detect genetically differentiated groups of populations. Approximate Bayesian computation (ABC) using nuclear sequence data and mismatch distribution analysis for cpSSR loci suggested recent expansion of the species. The implications of these findings for the management and conservation of P.krempfii genetic resources were discussed.
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| 7. |
- Wang, Baosheng, 1983-
(författare)
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Hybridization and Evolution in the Genus Pinus
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Gene flow and hybridization are pervasive in nature, and can lead to different evolutionary outcomes. They can either accelerate divergence and promote speciation or reverse differentiation. The process of divergence and speciation are strongly influenced by both neutral and selective forces. Disentangling the interplay between these processes in natural systems is important for understanding the general importance of interspecific gene flow in generating novel biodiversity in plants. This thesis first examines the importance of introgressive hybridization in the evolution of the genus Pinus as a whole, and then focusing on specific pine species, investigates the role of geographical, environmental and demographical factors in driving divergence and adaptation.By examining the distribution of cytoplasmic DNA variation across the wide biogeographic range of the genus Pinus, I revealed historical introgression and mtDNA capture events in several groups of different pine species. This finding suggests that introgressive hybridization was common during past species’ range contractions and expansions and thus has played an important role in the evolution of the genus. To understand the cause and process of hybrid speciation, I focused on the significant case of hybrid speciation in Pinus densata. I established the hybridization, colonization and differentiation processes that defined the origin of this species. I found P. densata originated via multiple hybridization events in the late Miocene. The direction and intensity of introgression with two parental species varied among geographic regions of this species. During the colonization on Tibetan Plateau from the ancestral hybrid zone, consecutive bottlenecks and surfing of rare alleles caused a significant reduction in genetic diversity and strong population differentiation. Divergence within P. densata started from the late Pliocene onwards, induced by regional topographic changes and Pleistocene glaciations. To address the role of neutral and selective forces on genetic divergence, I examined the association of ecological and geographical distance with genetic distance in Pinus yunnanensis populations. I found both neutral and selective forces have contributed to population structure and differentiation in P. yunnanensis, but their relative contributions varied across the complex landscape. Finally, I evaluated genetic diversity in the Vietnamese endemic Pinus krempfii. I found extremely low genetic diversity in this species, which is explained by a small ancestral population, short-term population expansion and recent population decline and habitat fragmentation.These findings highlight the role of hybridization in generating novel genetic diversity and the different mechanisms driving divergence and adaptation in the genus Pinus.
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| 8. |
- Wang, Baosheng, 1983-, et al.
(författare)
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Impact of Geography and Climate on the Genetic Differentiation of the Subtropical Pine Pinus yunnanensis
- 2013
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Ingår i: PLOS ONE. - : plosone. - 1932-6203. ; 8:6, s. e67345-
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Tidskriftsartikel (refereegranskat)abstract
- Southwest China is a biodiversity hotspot characterized by complex topography, heterogeneous regional climates and rich flora. The processes and driving factors underlying this hotspot remain to be explicitly tested across taxa to gain a general understanding of the evolution of biodiversity and speciation in the region. In this study, we examined the role played by historically neutral processes, geography and environment in producing the current genetic diversity of the subtropical pine Pinus yunnanensis. We used genetic and ecological methods to investigate the patterns of genetic differentiation and ecological niche divergence across the distribution range of this species. We found both continuous genetic differentiation over the majority of its range, and discrete isolated local clusters. The discrete differentiation between two genetic groups in the west and east peripheries is consistent with niche divergence and geographical isolation of these groups. In the central area of the species' range, population structure was shaped mainly by neutral processes and geography rather than by ecological selection. These results show that geographical and environmental factors together created stronger and more discrete genetic differentiation than isolation by distance alone, and illustrate the importance of ecological factors in forming or maintaining genetic divergence across a complex landscape. Our findings differ from other phylogenetic studies that identified the historical drainage system in the region as the primary factor shaping population structure, and highlight the heterogeneous contributions that geography and environment have made to genetic diversity among taxa in southwest China.
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| 9. |
- Wang, Baosheng, et al.
(författare)
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Mitochondrial DNA capture and divergence in Pinus provide new insights into the evolution of the genus
- 2014
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 80, s. 20-30
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Tidskriftsartikel (refereegranskat)abstract
- The evolution of the mitochondrial (mt) genome is far from being fully understood. Systematic investigations into the modes of inheritance, rates and patterns of recombination, nucleotide substitution, and structural changes in the mt genome are still lacking in many groups of plants. In this study, we sequenced >11 kbp mtDNA segments from multiple accessions of 36 pine species to characterize the evolutionary patterns of mtDNA in the genus Pious. We found extremely low substitution rates and complex repetitive sequences scattered across different genome regions, as well as chimeric structures that were probably generated by multiple intergenomic recombinations. The mtDNA-based phylogeny of the genus differed from that based on chloroplast and nuclear DNA in the placement of several groups of species. Such discordances suggest a series of mtDNA capture events during past range shifts of the pine species and that both vertical and horizontal inheritance are implicated in the evolution of mtDNA in Pinus. MtDNA dating revealed that most extant lineages of the genus originated during Oligocene-Miocene radiation and subgenus Strobus diversified earlier than subgenus Pinus. Our findings illustrate a reticular evolutionary pathway for the mt genome through capture and recombination in the genus Pinus, and provide new insights into the evolution of the genus.
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| 10. |
- Wang, Siyun, et al.
(författare)
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Environmental impacts from conventional and shale gas and oil development in China considering regional differences and well depth
- 2021
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Ingår i: Resources, Conservation and Recycling. - : Elsevier. - 0921-3449 .- 1879-0658. ; 167
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Tidskriftsartikel (refereegranskat)abstract
- China has stepped up its oil and gas development including unconventional resources as foreign dependence for oil and gas increased. Environmental impacts from the development phase has also caused widespread concern. To better understand environment impacts from current oil and gas development in China, a hybrid life cycle analysis (H-LCA) model was used to estimate the impact of six fields at the development stage based on data from 2017. The full environmental impact and full impact intensity (i.e., full environmental impact per unit of output by calorific value) of shale gas, conventional natural gas and oil development in China was compared and analyzed by eliminating well depth. Shale gas has 12.5% more environmental impact than conventional natural gas. Environmental impact of natural gas development is roughly 1.5 to 2 times that of conventional oil. Development of gas in Sichuan Basin have the greatest environmental impact, following southeast coast, Song Liao Basin, and Junggar Basin. However, the full impact intensity of shale gas development is more than five times that of conventional natural gas, but natural gas is still greener than conventional oil. The greatest full impact intensity is found in Junggar Basin, following Song Liao Basin and southeastern coast. From the comparison of full environmental impact and full impact intensity under per well depth, it's found that both of these are not positively correlated with reservoir depth and well depth even in the same basin. More attention should be paid to driving effects of specific reservoir developments and geological conditions.
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| 11. |
- Xia, Hanhan, et al.
(författare)
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Combining mitochondrial and nuclear genome analyses to dissect the effects of colonization, environment, and geography on population structure in Pinus tabuliformis
- 2018
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Ingår i: Evolutionary Applications. - : John Wiley & Sons. - 1752-4571. ; 11:10, s. 1931-1945
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Tidskriftsartikel (refereegranskat)abstract
- The phylogeographic histories of plants in East Asia are complex and shaped by both past large‐scale climatic oscillations and dramatic tectonic events. The impact of these historic events, as well as ecological adaptation, on the distribution of biodiversity remains to be elucidated. Pinus tabuliformis is the dominant coniferous tree in northern China, with a large distribution across wide environmental gradients. We examined genetic variation in this species using genotyping‐by‐sequencing and mitochondrial (mt) DNA markers. We found population structure on both nuclear and mt genomes with a geographic pattern that corresponds well with the landscape of northern China. To understand the contributions of environment, geography, and colonization history to the observed population structure, we performed ecological niche modeling and partitioned the among‐population genomic variance into isolation by environment (IBE), isolation by distance (IBD), and isolation by colonization (IBC). We used mtDNA, which is transmitted by seeds in pine, to reflect colonization. We found little impact of IBE, IBD, and IBC on variation in neutral SNPs, but significant impact of IBE on a group of outlier loci. The lack of IBC illustrates that the maternal history can be quickly eroded from the nuclear genome by high rates of gene flow. Our results suggest that genomic variation in P. tabuliformis is largely affected by neutral and stochastic processes, and the signature of local adaptation is visible only at robust outlier loci. This study enriches our understanding on the complex evolutionary forces that shape the distribution of genetic variation in plant taxa in northern China, and guides breeding, conservation, and reforestation programs for P. tabuliformis.
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| 12. |
- Xia, Hanhan, et al.
(författare)
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Microhomologies Are Associated with Tandem Duplications and Structural Variation in Plant Mitochondrial Genomes
- 2020
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Ingår i: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653. ; 12:11, s. 1965-1974
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Tidskriftsartikel (refereegranskat)abstract
- Short tandem repeats (STRs) contribute to structural variation in plant mitochondrial genomes, but the mechanisms underlying their formation and expansion are unclear. In this study, we detected high polymorphism in the nad7-1 region of the Pinus tabuliformis mitogenome caused by the rapid accumulation of STRs and rearrangements over a few million years ago. The STRs in nad7-1 have a 7-bp microhomology (TAG7) flanking the repeat array. We then scanned the mitogenomes of 136 seed plants to understand the role of microhomology in the formation of STR and mitogenome evolution. A total of 13,170 STRs were identified, and almost half of them were associated with microhomologies. A substantial amount (1,197) of microhomologies was long enough to mediate structural variation, and the length of microhomology is positively correlated with the length of tandem repeat unit. These results suggest that microhomology may be involved in the formation of tandem repeat via microhomology-mediated pathway, and the formation of longer duplicates required greater length of microhomology. We examined the abundance of these 1,197 microhomologies, and found 75% of them were enriched in the plant mitogenomes. Further analyses of the 400 prevalent microhomologies revealed that 175 of them showed differential enrichment between angiosperms and gymnosperms and 186 differed between angiosperms and conifers, indicating lineage-specific usage and expansion of microhomologies. Our study sheds light on the sources of structural variation in plant mitochondrial genomes and highlights the importance of microhomology in mitochondrial genome evolution.
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| 13. |
- Zhao, Wei, et al.
(författare)
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Weak Crossability Barrier but Strong Juvenile Selection Supports Ecological Speciation of the Hybrid Pine Pinus Densata on the Tibetan Plateau
- 2014
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Ingår i: Evolution. - : John Wiley & Sons. - 0014-3820 .- 1558-5646. ; 68:11, s. 3120-3133
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Tidskriftsartikel (refereegranskat)abstract
- Determining how a new hybrid lineage can achieve reproductive isolation is a key to understanding the process and mechanisms of homoploid hybrid speciation. Here, we evaluated the degree and nature of reproductive isolation between the ecologically successful hybrid species Pinus densata and its parental species P. tabuliformis and P. yunnanensis. We performed interspecific crosses among the three species to assess their crossability. We then conducted reciprocal transplantation experiments to evaluate their fitness differentiation, and to examine how natural populations representing different directions of introgression differ in adaptation. The crossing experiments revealed weak genetic barriers among the species. The transplantation trials showed manifest evidence of local adaptation as the three species all performed best in their native habitats. Pinus densata populations from the western edge of its distribution have evolved a strong local adaptation to the specific habitat in that range; populations representing different directions of introgressants with the two parental species all showed fitness disadvantages in this P. densata habitat. These observations illustrate that premating isolation through selection against immigrants from other habitat types or postzygotic isolation through selection against backcrosses between the three species is strong. Thus, ecological selection in combination with endogenous components and geographic isolation has likely played a significant role in the speciation of P. densata.
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| 14. |
- Lee, Cheng-Ruei, et al.
(författare)
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Young inversion with multiple linked QTLs under selection in a hybrid zone
- 2017
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Ingår i: NATURE ECOLOGY & EVOLUTION. - : Springer Science and Business Media LLC. - 2397-334X. ; 1:5
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Tidskriftsartikel (refereegranskat)abstract
- Fixed chromosomal inversions can reduce gene flow and promote speciation in two ways: by suppressing recombination and by carrying locally favoured alleles at multiple loci. However, it is unknown whether favoured mutations slowly accumulate on older inversions or if young inversions spread because they capture pre-existing adaptive quantitative trait loci (QTLs). By genetic mapping, chromosome painting and genome sequencing, we have identified a major inversion controlling ecologically important traits in Boechera stricta. The inversion arose since the last glaciation and subsequently reached local high frequency in a hybrid speciation zone. Furthermore, the inversion shows signs of positive directional selection. To test whether the inversion could have captured existing, linked QTLs, we crossed standard, collinear haplotypes from the hybrid zone and found multiple linked phenology QTLs within the inversion region. These findings provide the first direct evidence that linked, locally adapted QTLs may be captured by young inversions during incipient speciation.
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| 15. |
- Sun, Jing, et al.
(författare)
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Development and characterization of 10 microsatellite loci in paeonia lactiflora (paeoniaceae)
- 2011
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Ingår i: American Journal of Botany. - Lancaster, Pa. : Published in cooperation with the Botanical Society of America by the Brooklyn Botanic Gardens. - 0002-9122 .- 1537-2197. ; 98:9, s. E242-E243
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Tidskriftsartikel (refereegranskat)abstract
- Premise of the study: Microsatellite primers were developed in Paeonia lactiflora for further population genetic studies. Methods and Results: Ten dinucleotide microsatellite markers were developed using an enriched genomic library. They were identified in 58 individuals, and nine markers were also amplified in its cultivars. The number of alleles per locus ranged from three to 11, with a mean of six. The observed and expected heterozygosities ranged from 0.1662 to 0.9140 and from 0.0841 to 0.8157, respectively. Conclusions: These microsatellite markers will facilitate further studies on population genetics variation and genetic structure of P. lactiflora.
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| 16. |
- Wang, Wenhuan, et al.
(författare)
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Energy savings in China's energy sectors and contributions to air pollution reduction in the 12th Five Year Plan
- 2018
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Ingår i: Journal of Cleaner Production. - : Elsevier BV. - 0959-6526 .- 1879-1786. ; 200, s. 305-317
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Tidskriftsartikel (refereegranskat)abstract
- Energy efficiency and air pollution mitigation are critical issues for future development of the Chinese economy. Energy savings and their contribution to reduced air pollution from energy sectors during the 12th Five Year Plan are assessed using input-output analysis. A new dynamic quantitative method was developed to explore key sectors and identify critical paths for efficient emission reductions from energy industries. All the energy intensive key sectors, including Metal, Power, Chemical Products, Nonmetal are used to determine critical paths for emission reductions. Results indicate that the Coal Sector failed to achieve significant energy savings and did not contribute to direct and overall emissions reductions. The Oil Sector only achieved co-effects for reduction of overall waste gas, SO2, and particulates, while the Power Sector achieved emission reductions of all air pollutants. The results suggest that Chinese government should enact four main measures to achieve effective targets for energy savings and emission reductions: (1) Strengthen energy conservation in Coal and Oil Sectors, particularly the Coal Sector. (2) Promote energy conservation and emission reductions in highly energy intensive sectors to help emission reductions from other sectors. (3) Promote synergy effects of energy savings and emission reductions to enterprises. (4) Set lowest emission reduction targets for each department combined with targets for energy savings.
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