Results 71 to 80 of about 280,348 (263)

Wald Space for Phylogenetic Trees

, 2021
The recently introduced wald space models phylogenetic trees from an evolutionary perspective. We show that it is a stratified space and propose algorithms to compute geodesics. In application we compute a Frechet mean of three trees of different topologies that is fully resolved, unlike in BHV-space. Both, preliminary results on geodesics and on means
Lueg, Jonas, Garba, Maryam K., Nye, Tom M. W., Huckemann, Stephan F., Nielsen, Frank, Barbaresco, Frédéric   +5 more
openaire   +2 more sources

Hijacking the Host Clock: A Nematode Effector Antagonizes Soybean Circadian Defense and Translation Control

Advanced Science, EarlyView.
Soybean employs its circadian clock, governed by GmCCA1, to rhythmically defend against soybean cyst nematodes. The pathogen retaliates by secreting the effector Hg4E02, which hijacks the clock to suppress defense and co‐opt the host's translation machinery for nutrient acquisition.
Xingwei Wang, Yufeng Xu, Yanfei Hu, Lijun Cao, Ru Jiang, Changtian Chen, Rick Masonbrink, Thomas Maier, Yuchen Tu, Yabo Shi, Enhui Liu, Lingan Kong, Chan Guo, Wei Zhao, Peng Shi, Wenzhen Du, Andrew Severin, Thomas Baum, Deliang Peng, Huan Peng, Mian Zhou, Wei Wang   +21 more
wiley   +1 more source

Diversity of Pharmaceuticals Enhances Antibiotic Resistance in the Invertebrate Gut via Biofilm‐Mediated Mechanisms

Advanced Science, EarlyView.
Pharmaceutical diversity acts as an independent driver of antibiotic resistance in soil invertebrates. While bulk soil remains unaffected, the collembolan gut microbiome exhibits significant resistance gene enrichment under complex chemical exposure and diurnal warming.
Yi‐Fei Wang, Ya‐Ning Wang, Da Lin, Jia‐Yang Xu, Feng‐Yuan Qi, Hui‐Ling Cui, Hui‐Jie Lu, Min Qiao, Edward Topp, Dong Zhu, Matthias C. Rillig, Yong‐Guan Zhu   +11 more
wiley   +1 more source

Visualising very large phylogenetic trees in three dimensional hyperbolic space

BMC Bioinformatics, 2004
Background Common existing phylogenetic tree visualisation tools are not able to display readable trees with more than a few thousand nodes. These existing methodologies are based in two dimensional space.
Liberles David A, Hyun Young, Hughes Timothy   +2 more
doaj   +1 more source

PTree: pattern-based, stochastic search for maximum parsimony phylogenies [PDF]

PeerJ, 2013
Phylogenetic reconstruction is vital to analyzing the evolutionary relationship of genes within and across populations of different species. Nowadays, with next generation sequencing technologies producing sets comprising thousands of sequences, robust ...
Ivan Gregor, Lars Steinbrück, Alice C. McHardy   +2 more
doaj   +2 more sources

Stability analysis of phylogenetic trees [PDF]

Bioinformatics, 2012
Abstract Motivation: Phylogenetics, or reconstructing the evolutionary relationships of organisms, is critical for understanding evolution. A large number of heuristic algorithms for phylogenetics have been developed, some of which enable estimates of trees with tens of thousands of taxa. Such trees may not be robust, as small changes in
Saad I. Sheikh, Tamer Kahveci, Sanjay Ranka, J. Gordon Burleigh   +3 more
openaire   +2 more sources

3D Chromatin Architecture Provides Insights Into Leaf Trait Variation Among Pear Species

Advanced Science, EarlyView.
ABSTRACT Three‐dimensional (3D) chromatin architecture plays a fundamental role in eukaryotic gene regulations, its functional significance in perennial fruit trees remains poorly characterized despite extensive applications in crop genomics. Here, we developed high‐resolution (∼5 kb) Hi‐C maps of Pyrus and compared 3D genomic architecture of three ...
Yueyuan Liu, Chenhui Han, Cheng Xue, Manyi Sun, Bobo Song, Yongsong Xue, Guangyan Yang, Shaozhuo Xu, Wei Wei, Jiaming Li, Runze Wang, Jun Wu   +11 more
wiley   +1 more source

Cotton Duplicated Genes Produced by Polyploidy Show Significantly Elevated and Unbalanced Evolutionary Rates, Overwhelmingly Perturbing Gene Tree Topology

Frontiers in Genetics, 2020
A phylogenetic tree can be used to illustrate the evolutionary relationship between a group of genes, especially duplicated genes, which are sources of genetic innovation and are often a hotspot of research.
Fanbo Meng, Yuxin Pan, Jinpeng Wang, Jigao Yu, Chao Liu, Zhikang Zhang, Chendan Wei, He Guo, Xiyin Wang, Xiyin Wang   +9 more
doaj   +1 more source

Integration of Spatiotemporal Multi‐Omics in Peach Fruit Unravels a Metabolic Niche and the Genetic Basis of Trichome‐Mediated Stress Adaptation

Advanced Science, EarlyView.
This study constructed the first spatiotemporal multi‐omics map of peach fruit and discovered a key candidate gene that synergistically regulates trichome development and drought tolerance through the jasmonic acid signaling pathway, providing insights into the coupling mechanism between development and stress resistance.
Zhixin Liu, Ke Cao, Liping Guan, Aizhi Qin, Yong Li, Zihao Zhao, Yinpeng Zhang, Yaping Zhou, Lirong Wang, Xuwu Sun   +9 more
wiley   +1 more source

Comparison of phylogenetic trees defined on different but mutually overlapping sets of taxa: A review

Ecology and Evolution
Phylogenetic trees represent the evolutionary relationships and ancestry of various species or groups of organisms. Comparing these trees by measuring the distance between them is essential for applications such as tree clustering and the Tree of Life ...
Wanlin Li, Aleksandr Koshkarov, Nadia Tahiri   +2 more
doaj   +1 more source