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  • 1
    Online Resource
    Online Resource
    Primulina sichuanensis var. pinnatipartita (Gesneriaceae), a remarkable new variety from Chongqing, China
    Magnolia Press ; 2019
    In:  Phytotaxa Vol. 406, No. 5 ( 2019-06-25), p. 287-293
    Details
    In: Phytotaxa, Magnolia Press, Vol. 406, No. 5 ( 2019-06-25), p. 287-293
    Abstract: Here, we describe and illustrate Primulina sichuanensis var. pinnatipartita, a new variety from southwestern China. This new variety is primarily distinguished from the type variety, P. sichuanensis var. sichuanensis, by its pinnatipartite leaf blade, a rare character in the genus Primulina. We show the morphological features of this new variety with illustrations and photographs.
    Type of Medium: Online Resource
    ISSN: 1179-3163 , 1179-3155
    URL: Issue
    URL: Article
    DOI: 10.11646/phytotaxa.406.5
    DOI: 10.11646/phytotaxa.406.5.4
    Language: Unknown
    Publisher: Magnolia Press
    Publication Date: 2019
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Genomic vulnerability to climate change in Quercus acutissima , a dominant tree species in East Asian deciduous forests
    Wiley ; 2023
    In:  Molecular Ecology Vol. 32, No. 7 ( 2023-04), p. 1639-1655
    Details
    In: Molecular Ecology, Wiley, Vol. 32, No. 7 ( 2023-04), p. 1639-1655
    Abstract: Understanding the evolutionary processes that shape the landscape of genetic variation and influence the response of species to future climate change is critical for biodiversity conservation. Here, we sampled 27 populations across the distribution range of a dominant forest tree, Quercus acutissima , in East Asia, and applied genome‐wide analyses to track the evolutionary history and predict the fate of populations under future climate. We found two genetic groups (East and West) in Q. acutissima that diverged during Pliocene. We also found a heterogeneous landscape of genomic variation in this species, which may have been shaped by population demography and linked selections. Using genotype‐environment association analyses, we identified climate‐associated SNPs in a diverse set of genes and functional categories, indicating a model of polygenic adaptation in Q. acutissima . We further estimated three genetic offset metrics to quantify genomic vulnerability of this species to climate change due to the complex interplay between local adaptation and migration. We found that marginal populations are under higher risk of local extinction because of future climate change, and may not be able to track suitable habitats to maintain the gene–environment relationships observed under the current climate. We also detected higher reverse genetic offsets in northern China, indicating that genetic variation currently present in the whole range of Q. acutissima may not adapt to future climate conditions in this area. Overall, this study illustrates how evolutionary processes have shaped the landscape of genomic variation, and provides a comprehensive genome‐wide view of climate maladaptation in Q. acutissima .
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    URL: Article
    DOI: 10.1111/mec.v32.7
    DOI: 10.1111/mec.16843
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 2020749-9
    detail.hit.zdb_id: 1126687-9
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    Linked selection shapes the landscape of genomic variation in three oak species
    Wiley ; 2022
    In:  New Phytologist Vol. 233, No. 1 ( 2022-01), p. 555-568
    Details
    In: New Phytologist, Wiley, Vol. 233, No. 1 ( 2022-01), p. 555-568
    Abstract: Natural selection shapes genome‐wide patterns of diversity within species and divergence between species. However, quantifying the efficacy of selection and elucidating the relative importance of different types of selection in shaping genomic variation remain challenging. We sequenced whole genomes of 101 individuals of three closely related oak species to track the divergence history, and to dissect the impacts of selective sweeps and background selection on patterns of genomic variation. We estimated that the three species diverged around the late Neogene and experienced a bottleneck during the Pleistocene. We detected genomic regions with elevated relative differentiation (‘ F ST ‐islands’). Population genetic inferences from the site frequency spectrum and ancestral recombination graph indicated that F ST ‐islands were formed by selective sweeps. We also found extensive positive selection; the fixation of adaptive mutations and reduction neutral diversity around substitutions generated a signature of selective sweeps. Prevalent negative selection and background selection have reduced genetic diversity in both genic and intergenic regions, and contributed substantially to the baseline variation in genetic diversity. Our results demonstrate the importance of linked selection in shaping genomic variation, and illustrate how the extent and strength of different selection models vary across the genome.
    Type of Medium: Online Resource
    ISSN: 0028-646X , 1469-8137
    URL: Issue
    URL: Article
    DOI: 10.1111/nph.v233.1
    DOI: 10.1111/nph.17793
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 208885-X
    detail.hit.zdb_id: 1472194-6
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  • 4
    Online Resource
    Online Resource
    Globally Relaxed Selection and Local Adaptation in Boechera stricta
    Oxford University Press (OUP) ; 2022
    In:  Genome Biology and Evolution Vol. 14, No. 4 ( 2022-04-10)
    Details
    In: Genome Biology and Evolution, Oxford University Press (OUP), Vol. 14, No. 4 ( 2022-04-10)
    Abstract: The strength of selection varies among populations and across the genome, but the determinants of efficacy of selection remain unclear. In this study, we used whole-genome sequencing data from 467 Boechera stricta accessions to quantify the strength of selection and characterize the pattern of local adaptation. We found low genetic diversity on 0-fold degenerate sites and conserved non-coding sites, indicating functional constraints on these regions. The estimated distribution of fitness effects and the proportion of fixed substitutions suggest relaxed negative and positive selection in B. stricta. Among the four population groups, the NOR and WES groups have smaller effective population size (Ne), higher proportions of effectively neutral sites, and lower rates of adaptive evolution compared with UTA and COL groups, reflecting the effect of Ne on the efficacy of natural selection. We also found weaker selection on GC-biased sites compared with GC-conservative (unbiased) sites, suggested that GC-biased gene conversion has affected the strength of selection in B. stricta. We found mixed evidence for the role of the recombination rate on the efficacy of selection. The positive and negative selection was stronger in high-recombination regions compared with low-recombination regions in COL but not in other groups. By scanning the genome, we found different subsets of selected genes suggesting differential adaptation among B. stricta groups. These results show that differences in effective population size, nucleotide composition, and recombination rate are important determinants of the efficacy of selection. This study enriches our understanding of the roles of natural selection and local adaptation in shaping genomic variation.
    Type of Medium: Online Resource
    ISSN: 1759-6653
    URL: Article
    DOI: 10.1093/gbe/evac043
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2495328-3
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  • 5
    Online Resource
    Online Resource
    Linked selection, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence in Quercus dentata
    Wiley ; 2022
    In:  Journal of Systematics and Evolution Vol. 60, No. 6 ( 2022-11), p. 1344-1357
    Details
    In: Journal of Systematics and Evolution, Wiley, Vol. 60, No. 6 ( 2022-11), p. 1344-1357
    Abstract: Multiple evolutionary forces contribute to heterogeneous genomic landscapes; however, disentangling their relative contributions is challenging. We sampled nine populations across the distribution of Quercus dentata , a dominant forest tree in East Asia, and used whole‐genome sequencing data to investigate mechanisms underlying divergence. We identified two genetic groups (north and south) that diverged ~1.84 million years ago, consistent with the uplift of the Qinling Mountains during the Pleistocene. The north group experienced a bottleneck during the middle–late Pleistocene and expanded from multiple refugia. The south group experienced a more severe bottleneck and showed high population differentiation, probably due to long‐term isolation and habitat fragmentation. We detected genomic islands with elevated relative differentiation ( F ST ) scattered across the genome. Among these, 65.9% showed reduced absolute divergence ( d XY ) consistent with linked selection, while the remaining (34.1%) showed elevated d XY suggestive of divergent sorting of ancient polymorphisms. The recombination rate in genomic islands was lower than background, suggesting the importance of genome structure in shaping the genomic landscape. We detected 108 single nucleotide polymorphisms significantly associated with environmental factors, 12 of which clustered in a region of ~500 kb. This region showed multiple signals of positive selection in the north group, including the enrichment of XP‐extended haplotype homozygosity scores, an elevated population branch statistic, and an excess of high‐frequency derived alleles. In addition, we found that linkage disequilibrium was low and derived haplotypes declined rapidly in this region, indicating selection on standing variation. Our results clarify the evolutionary processes driving genomic divergence in Q. dentata .
    Type of Medium: Online Resource
    ISSN: 1674-4918 , 1759-6831
    URL: Issue
    URL: Article
    DOI: 10.1111/jse.v60.6
    DOI: 10.1111/jse.12817
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2516638-4
    SSG: 6,25
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere
    Springer Science and Business Media LLC ; 2022
    In:  Nature Communications Vol. 13, No. 1 ( 2022-03-14)
    Details
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 13, No. 1 ( 2022-03-14)
    Abstract: Northern Hemisphere forests changed drastically in the early Eocene with the diversification of the oak family (Fagaceae). Cooling climates over the next 20 million years fostered the spread of temperate biomes that became increasingly dominated by oaks and their chestnut relatives. Here we use phylogenomic analyses of nuclear and plastid genomes to investigate the timing and pattern of major macroevolutionary events and ancient genome-wide signatures of hybridization across Fagaceae. Innovation related to seed dispersal is implicated in triggering waves of continental radiations beginning with the rapid diversification of major lineages and resulting in unparalleled transformation of forest dynamics within 15 million years following the K-Pg extinction. We detect introgression at multiple time scales, including ancient events predating the origination of genus-level diversity. As oak lineages moved into newly available temperate habitats in the early Miocene, secondary contact between previously isolated species occurred. This resulted in adaptive introgression, which may have further amplified the diversification of white oaks across Eurasia.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    URL: Article
    DOI: 10.1038/s41467-022-28917-1
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2553671-0
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  • 7
    Online Resource
    Online Resource
    Linked selection and recombination rate generate both shared and lineage‐specific genomic islands of divergence in two independent Quercus species pairs
    Wiley ; 2023
    In:  Journal of Systematics and Evolution
    Details
    In: Journal of Systematics and Evolution, Wiley
    Abstract: A fundamental question in speciation genomics is how evolutionary processes shape the genomic landscape of differentiation between species. Regions of elevated differentiation, referred to as genomic islands, could be shared among closely related species (shared islands) or specific to a lineage (lineage‐specific islands). Shared islands are typically assumed to result from background selection. However, simulations and empirical studies have suggested that positive selection contributes to both shared and lineage‐specific islands. Here, we utilized comparative population genomics to examine the contributions of different evolutionary processes to patterns of genetic differentiation when gene flow and incomplete lineage sorting are minimal. We used whole‐genome resequencing data for 135 individuals from four oak species, including two independent species pairs, Quercus variabilis  Blume and Quercus acutissima Carruth. in the subgenus Cerris , and Quercus dentata Thunb. and Quercus griffithii Hook.f. & Thomson ex Miq. in the subgenus Quercus . We found that both shared and subgenus‐specific islands were caused by positive selection, including selective sweeps in current populations and in their most recent common ancestors. Moreover, the recombination rate was a better predictor of genomic differentiation than gene density. Overall, our results reveal that recombination and positive selection impacted genomic differentiation considerably and provide a more precise grasp of how genomic islands formed in Quercus .
    Type of Medium: Online Resource
    ISSN: 1674-4918 , 1759-6831
    URL: Article
    DOI: 10.1111/jse.13008
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 2516638-4
    SSG: 6,25
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Genome-Wide Identification and Expression Analysis of Calmodulin-Like Gene Family in Paspalums vaginatium Revealed Their Role in Response to Salt and Cold Stress
    MDPI AG ; 2023
    In:  Current Issues in Molecular Biology Vol. 45, No. 2 ( 2023-02-16), p. 1693-1711
    Details
    In: Current Issues in Molecular Biology, MDPI AG, Vol. 45, No. 2 ( 2023-02-16), p. 1693-1711
    Abstract: The calmodulin-like (CML) family is an important calcium (Ca2+) sensor in plants and plays a pivotal role in the response to abiotic and biotic stresses. As one of the most salt-tolerant grass species, Paspalums vaginatum is resistant to multiple abiotic stresses, such as salt, cold, and drought. However, investigations of PvCML proteins in P. vaginatum have been limited. Based on the recently published P. vaginatum genome, we identified forty-nine PvCMLs and performed a comprehensive bioinformatics analysis of PvCMLs. The main results showed that the PvCMLs were unevenly distributed on all chromosomes and that the expansion of PvCMLs was shaped by tandem and segmental duplications. In addition, cis-acting element analysis, expression profiles, and qRT–PCR analysis revealed that PvCMLs were involved in the response to salt and cold stress. Most interestingly, we found evidence of a tandem gene cluster that independently evolved in P. vaginatum and may participate in cold resistance. In summary, our work provides important insight into how grass species are resistant to abiotic stresses such as salt and cold and could be the basis of further gene function research on CMLs in P. vaginatum.
    Type of Medium: Online Resource
    ISSN: 1467-3045
    URL: Article
    DOI: 10.3390/cimb45020109
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2090836-2
    SSG: 12
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  • 9
    Online Resource
    Online Resource
    Correction to: Actively implementing an evidence-based feeding guideline for critically ill patients (NEED): a multicenter, cluster-randomized, controlled trial
    Springer Science and Business Media LLC ; 2022
    In:  Critical Care Vol. 26, No. 1 ( 2022-12)
    Details
    In: Critical Care, Springer Science and Business Media LLC, Vol. 26, No. 1 ( 2022-12)
    Type of Medium: Online Resource
    ISSN: 1364-8535
    URL: Article
    DOI: 10.1186/s13054-022-03982-6
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2051256-9
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  • 10
    Online Resource
    Online Resource
    Actively implementing an evidence-based feeding guideline for critically ill patients (NEED): a multicenter, cluster-randomized, controlled trial
    Springer Science and Business Media LLC ; 2022
    In:  Critical Care Vol. 26, No. 1 ( 2022-12)
    Details
    In: Critical Care, Springer Science and Business Media LLC, Vol. 26, No. 1 ( 2022-12)
    Abstract: Previous cluster-randomized controlled trials evaluating the impact of implementing evidence-based guidelines for nutrition therapy in critical illness do not consistently demonstrate patient benefits. A large-scale, sufficiently powered study is therefore warranted to ascertain the effects of guideline implementation on patient-centered outcomes. Methods We conducted a multicenter, cluster-randomized, parallel-controlled trial in intensive care units (ICUs) across China. We developed an evidence-based feeding guideline. ICUs randomly allocated to the guideline group formed a local "intervention team", which actively implemented the guideline using standardized educational materials, a graphical feeding protocol, and live online education outreach meetings conducted by members of the study management committee. ICUs assigned to the control group remained unaware of the guideline content. All ICUs enrolled patients who were expected to stay in the ICU longer than seven days. The primary outcome was all-cause mortality within 28 days of enrollment. Results Forty-eight ICUs were randomized to the guideline group and 49 to the control group. From March 2018 to July 2019, the guideline ICUs enrolled 1399 patients, and the control ICUs enrolled 1373 patients. Implementation of the guideline resulted in significantly earlier EN initiation (1.20 vs. 1.55 mean days to initiation of EN; difference − 0.40 [95% CI − 0.71 to − 0.09]; P  = 0.01) and delayed PN initiation (1.29 vs. 0.80 mean days to start of PN; difference 1.06 [95% CI 0.44 to 1.67]; P  = 0.001). There was no significant difference in 28-day mortality (14.2% vs. 15.2%; difference − 1.6% [95% CI − 4.3% to 1.2%]; P  = 0.42) between groups. Conclusions In this large-scale, multicenter trial, active implementation of an evidence-based feeding guideline reduced the time to commencement of EN and overall PN use but did not translate to a reduction in mortality from critical illness. Trial registration: ISRCTN, ISRCTN12233792 . Registered November 20th, 2017.
    Type of Medium: Online Resource
    ISSN: 1364-8535
    URL: Article
    DOI: 10.1186/s13054-022-03921-5
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2051256-9
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