Results 1 to 10 of about 17,196 (119)
BMC Plant Biology, 2020 Background Plastome-scale data have been prevalent in reconstructing the plant Tree of Life. However, phylogenomic studies currently based on plastomes rely primarily on maximum likelihood inference of concatenated alignments of plastid genes, and thus ...
Xu Zhang, Yanxia Sun, Jacob B Landis
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VBCG: 20 validated bacterial core genes for phylogenomic analysis with high fidelity and resolution
Microbiome, 2023 Background Phylogenomic analysis has become an inseparable part of studies of bacterial diversity and evolution, and many different bacterial core genes have been collated and used for phylogenomic tree reconstruction.
Renmao Tian, Behzad Imanian
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Frontiers in Plant Science, 2022 A major challenge in phylogenetics and -genomics is to resolve young rapidly radiating groups. The fast succession of species increases the probability of incomplete lineage sorting (ILS), and different topologies of the gene trees are expected, leading ...
Martha Kandziora +5 more
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So many genes, so little time: A practical approach to divergence-time estimation in the genomic era. [PDF]
PLoS ONE, 2018 Phylogenomic datasets have been successfully used to address questions involving evolutionary relationships, patterns of genome structure, signatures of selection, and gene and genome duplications.
Stephen A Smith +2 more
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Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: yeasts revisited. [PDF]
PLoS ONE, 2011 Phylogenomic approaches to the resolution of inter-species relationships have become well established in recent years. Often these involve concatenation of many orthologous genes found in the respective genomes followed by analysis using standard ...
Jaqueline Hess, Nick Goldman
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PhyloFisher: A phylogenomic package for resolving eukaryotic relationships.
PLoS Biology, 2021 Phylogenomic analyses of hundreds of protein-coding genes aimed at resolving phylogenetic relationships is now a common practice. However, no software currently exists that includes tools for dataset construction and subsequent analysis with diverse ...
Alexander K Tice +14 more
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Congruence Amidst Discordance between Sequence and Protein-Content Based Phylogenies of Fungi
Journal of Fungi, 2020 Amid the genomic data explosion, phylogenomic analysis has resolved the tree of life of different organisms, including fungi. Genome-wide clustering has also been conducted based on gene content data that can lighten the issue of the unequal evolutionary
Guohua Xiao, Guirong Tang, Chengshu Wang
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Phylogenomic assessment of the role of hybridization and introgression in trait evolution.
PLoS Genetics, 2021 Trait evolution among a set of species-a central theme in evolutionary biology-has long been understood and analyzed with respect to a species tree. However, the field of phylogenomics, which has been propelled by advances in sequencing technologies, has
Yaxuan Wang +3 more
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The complete mitochondrial genome of Orthaga achatina (Lepidoptera: Pyralidae)
Mitochondrial DNA. Part B. Resources, 2021 Orthaga achatina Butler is an important pest of camphor trees in Asia. The complete mitochondrial genome of O. achatina was sequenced in this study, which was 15,150 bp in size and comprised of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal ...
Bing Liu +3 more
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Phylogenomics with incomplete taxon coverage: the limits to inference
BMC Evolutionary Biology, 2010 Background Phylogenomic studies based on multi-locus sequence data sets are usually characterized by partial taxon coverage, in which sequences for some loci are missing for some taxa.
McMahon Michelle M +2 more
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