Results 271 to 280 of about 15,172 (305)

Incongruence in the phylogenomics era

Nature Reviews Genetics, 2023
Genome-scale data and the development of novel statistical phylogenetic approaches have greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its branches. However, incongruence - the inference of conflicting evolutionary histories - remains pervasive in phylogenomic data, hampering our ability to reconstruct and ...
Jacob L. Steenwyk, Yuanning Li, Xiaofan Zhou, Xing-Xing Shen, Antonis Rokas   +4 more
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Evolutionary Sparse Learning for Phylogenomics [PDF]

Molecular Biology and Evolution, 2021
A bstract We introduce a supervised machine learning approach with sparsity constraints for phylogenomics, referred to as evolutionary sparse learning (ESL). ESL builds models with genomic loci—such as genes, proteins, genomic segments, and positions—as parameters.
Sudhir Kumar, Greg Gibson, Sudhir Kumar
exaly   +4 more sources

Phylogenomics of the Liquorilactobacillus Genus

Current Microbiology, 2023
The genus Liquorilactobacillus is a new genus commonly found in wine and plants. Despite its significance, previous studies on Liquorilactobacillus are primarily focused on phenotypic experiments, with limited genome-level studies. This study used comparative genomics to analyze 24 genomes from the genus Liquorilactobacillus, including two novel ...
Xu, Liu, Weicheng, Li, Zhihong, Sun, Zhi, Zhong, Tiansong, Sun   +4 more
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Phylogenomic networks

Trends in Microbiology, 2011
Phylogenomics is aimed at studying functional and evolutionary aspects of genome biology using phylogenetic analysis of whole genomes. Current approaches to genome phylogenies are commonly founded in terms of phylogenetic trees. However, several evolutionary processes are non tree-like in nature, including recombination and lateral gene transfer (LGT).
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Mitochondrial phylogenomics of the Hymenoptera

Molecular Phylogenetics and Evolution, 2019
The insect order Hymenoptera presents marvelous morphological and ecological diversity. Higher-level hymenopteran relationships remain controversial, even after recent phylogenomic analyses, as their taxon sampling was limited. To shed light on the origin and diversification of Hymenoptera, in particular the poorly studied Parasitica, we undertook ...
Pu, Tang, Jia-Chen, Zhu, Bo-Yin, Zheng, Shu-Jun, Wei, Michael, Sharkey, Xue-Xin, Chen, Alfried P, Vogler   +6 more
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Phylogenomic analysis of chromoviruses

Cytogenetic and Genome Research, 2005
Genome sequences of model organisms provide a unique opportunity to obtain insight into the complete diversity of any transposable element (TE) group. A limited number of chromoviruses, the chromodomain containing genus of Metaviridae, is known from plant, fungal and vertebrate genomes.
B, Gorinsek, F, Gubensek, D, Kordis
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A phylogenomic analysis of the Ascomycota

Fungal Genetics and Biology, 2006
An automated procedure was developed to extract orthologous sequences from fungal genomes and incorporate them into phylogenomic analyses in a timely and efficient manner. This approach involves parsing an all versus all BLASTP search of 17 proteomes and creating a similarity matrix from e-values, which is then used to cluster proteins into related ...
Barbara, Robbertse, John B, Reeves, Conrad L, Schoch, Joseph W, Spatafora   +3 more
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A phylogenomic analysis of turtles

Molecular Phylogenetics and Evolution, 2015
Molecular analyses of turtle relationships have overturned prevailing morphological hypotheses and prompted the development of a new taxonomy. Here we provide the first genome-scale analysis of turtle phylogeny. We sequenced 2381 ultraconserved element (UCE) loci representing a total of 1,718,154bp of aligned sequence.
Nicholas G, Crawford, James F, Parham, Anna B, Sellas, Brant C, Faircloth, Travis C, Glenn, Theodore J, Papenfuss, James B, Henderson, Madison H, Hansen, W Brian, Simison   +8 more
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Phylogenomics of African guenons

Chromosome Research, 2008
The karyotypes of 28 specimens belonging to 26 species of Cercopithecinae have been compared with each other and with human karyotype by chromosome banding and, for some of them, by Zoo-FISH (human painting probes) techniques. The study includes the first description of the karyotypes of four species and a synonym of Cercopithecus nictitans.
Sibyle, Moulin, Michèle, Gerbault-Seureau, Bernard, Dutrillaux, Florence Anne, Richard   +3 more
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Phylogenomics

2015
In der Evolutionsbiologie wurde in den letzten Jahren durch Aufkommen der Phylogenomik ein neues Kapitel aufgeschlagen. Mit Hilfe genomweiter Analysen wird es zunehmend möglich, schwierige Fragestellungen zur Evolutionsgeschichten zu untersuchen, doch diese neuen Perspektiven sind gleichzeitig verbunden mit erhöhter Komplexität und anderen ...
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