Results 111 to 120 of about 280,348 (263)

Three-Way Alignment Improves Multiple Sequence Alignment of Highly Diverged Sequences

Algorithms
The standard approach for constructing a phylogenetic tree from a set of sequences consists of two key stages. First, a multiple sequence alignment (MSA) of the sequences is computed.
Mahbubeh Askari Rad, Alibek Kruglikov, Xuhua Xia   +2 more
doaj   +1 more source

Exploring the lichenization continuum through the marine tripartite symbiosis of Collemopsidium pelvetiae

American Journal of Botany, EarlyView.
Abstract Premise Symbioses between lichen‐forming fungi and brown algae (phaeophytes) are extremely rare. We investigated the interactions between the marine fungus Collemopsidium pelvetiae and its two photosynthetic partners, the brown alga Pelvetia canaliculata and a cyanobacterial symbiont to address questions on symbiosis biology, lichenization ...
Sergio Pérez‐Ortega, Rúdiger Ortiz‐Álvarez, Jacek Wierzchos, Miguel Blázquez, Alain Gérault, Asunción de los Ríos   +5 more
wiley   +1 more source

Evidence of introgression amid phylogenetic conflict in Brachyotum, a plant radiation from the Tropical Andes

American Journal of Botany, EarlyView.
Abstract Premise The species‐rich flora of Tropical Andes underwent multiple rapid and recent diversifications, yet resolving their evolutionary histories remains challenging despite increasing phylogenomic data. Here, we examined phylogenomic conflict in Brachyotum (Melastomataceae) to identify sources preventing its resolution.
Diego Paredes‐Burneo, Ana M. Bedoya, Fabián A. Michelangeli, Lucas C. Majure, Carmen Ulloa Ulloa, Laura P. Lagomarsino   +5 more
wiley   +1 more source

Two decades of resurrection studies: What have we learned about contemporary evolution of plant species?

American Journal of Botany, EarlyView.
Abstract Premise Global climate change has altered the eco‐evolutionary trajectories of plant species, leading to observed shifts in phenotypes, such as earlier flowering. However, disentangling the contributions of plasticity and adaptation to trait changes remains challenging.
Lillie K. Pennington, Seema N. Sheth, Steven J. Franks, Jill T. Anderson, Elena Hamann   +4 more
wiley   +1 more source

Integrative utilization of genomic resources for improved phylogenetic resolution in Sonerileae (Melastomataceae)

American Journal of Botany, EarlyView.
Abstract Premise Advances in new next‐generation sequencing (NGS) methods have revolutionized phylogenetics, yet challenges remain in effectively utilizing data from a wide range of sources. A well‐resolved and broadly sampled phylogeny for Sonerileae, the second‐largest tribe in Melastomataceae, is still lacking, hindering our understanding of its ...
Luo Chen, Marie Claire Veranso‐Libalah, J. Peter Quakenbush, Ying Liu, Fabián A. Michelangeli, Diego F. Morales‐Briones, Gudrun Kadereit   +6 more
wiley   +1 more source

Molecular mechanism of ischemic postconditioning in promoting diabetic ischemic brain injury repair via the microRNA‐34a–BDNF–SIX3 signaling axis

Animal Models and Experimental Medicine, EarlyView.
Diabetes combined with ischemic stroke (DMIS) exacerbates brain infarct size and neuronal damage compared to nondiabetic ischemic stroke (IS). This study reveals that microRNA‐34a (miR‐34a) plays a key role in DMIS pathogenesis: miR‐34a directly targets and suppresses brain‐derived neurotrophic factor (BDNF) and Sine oculis homeobox 3 (SIX3), promoting
Ling Zhao, Chunlan Zou, Junxian Li, Yang Yang, Yuanyuan Han, Tingyu Ke   +5 more
wiley   +1 more source

Detecting cryptic ghost lineage introgression in four‐taxon genomic datasets

Applications in Plant Sciences, EarlyView.
Abstract Premise Hybridization and introgression are pervasive evolutionary forces that have played fundamental roles in shaping the diversity of wild and domesticated plants. Four‐taxon tests for introgression provide a reliable framework for detecting signatures of ancient introgression from genomic data, which have played an important role in ...
Evan S. Forsythe, Blaine S. Pappa, Darren A. Clavette, Devin Y. Mendoza   +3 more
wiley   +1 more source

Ancient hybridization and phylogenetic discordance: Exploring evolutionary complexity in Asteraceae

Applications in Plant Sciences, EarlyView.
Abstract Premise Conflicting phylogenetic signals are common in plant phylogenomics and often reflect evolutionary histories shaped by processes like hybridization, incomplete lineage sorting, and whole‐genome duplication (WGD). We aimed to identify and assess these complex processes in the hyper‐diverse family Asteraceae to offer insight into the ...
Paige A. Ellestad, Erika R. Moore‐Pollard, Carolina M. Siniscalchi, Ramhari Thapa, Linda E. Watson, J. Mauricio Bonifacino, Jennifer R. Mandel   +6 more
wiley   +1 more source

Fusang: a framework for phylogenetic tree inference via deep learning. [PDF]

Nucleic Acids Res, 2023
Wang Z, Sun J, Gao Y, Xue Y, Zhang Y, Li K, Zhang W, Zhang C, Zu J, Zhang L.   +9 more
europepmc   +1 more source

Phylogeny-informed random forests for human microbiome studies

Microbiology Spectrum
Random Forest is a widely used tree-based ensemble learning algorithm that efficiently captures complex nonlinear relationships and higher-order feature interactions with no distributional assumptions to be satisfied.
Hyunwook Koh
doaj   +1 more source