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Current Biology, 2021 The reconstruction of evolutionary relationships among species is fundamental for our understanding of biodiversity. Today, evolutionary relationships are closely related with the depiction of the tree of life, and research on the topic is underpinned by methods in molecular phylogenetics that have grown in popularity since the 1960s.
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Phylogenomics with paralogs [PDF]
Proceedings of the National Academy of Sciences, 2015 Significance We demonstrate that the distribution of paralogs in large gene families contains in itself sufficient phylogenetic signal to infer fully resolved species phylogenies. This source of phylogenetic information is independent of information contained in orthologous sequences and is resilient against horizontal gene transfer.
Hellmuth, Marc +5 more
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Evolutionary Sparse Learning for phylogenomics [PDF]
Molecular Biology and Evolution, 2021 AbstractWe 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, Sudip Sharma
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Phylogenomic analysis restructures the ulvophyceae [PDF]
Journal of Phycology, 2021 Here, we present new transcriptome sequencing data from seven species of Dasycladales (Ulvophyceae) and a phylogenomic analysis of the Chlorophyta with a particular focus on Ulvophyceae. We have focused on a broad selection of green algal groups and carefully selected genes suitable for reconstructing deep eukaryote evolutionary histories.
Øyvind Sætren Gulbrandsen +4 more
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Insect Molecular Biology, 2015 AbstractPhylogenomics, the integration of phylogenetics with genome data, has emerged as a powerful approach to study the evolution and systematics of species. Recently, several studies employing phylogenomic tools have provided better insights into insect evolution.
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Phylogenomic analyses data of the avian phylogenomics project [PDF]
Gigascience, 2015 Abstract Background Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all ...
Jarvis, Erich +26 more
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Next-generation phylogenomics [PDF]
Biology Direct, 2013 Thanks to advances in next-generation technologies, genome sequences are now being generated at breadth (e.g. across environments) and depth (thousands of closely related strains, individuals or samples) unimaginable only a few years ago. Phylogenomics--the study of evolutionary relationships based on comparative analysis of genome-scale data--has so ...
Chan, Cheong Xin, Ragan, Mark A.
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Microbial phylogenomics: Branching out [PDF]
Nature, 2003 Has genomics overturned the family tree of microbial life? Thanks in part to often polarized debate, elements of a new synthesis are emerging.
Charlebois, R. L. +2 more
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FUNYBASE: a FUNgal phYlogenomic dataBASE [PDF]
BMC Bioinformatics, 2008 Abstract Background The increasing availability of fungal genome sequences provides large numbers of proteins for evolutionary and phylogenetic analyses. However the heterogeneity of data, including the quality of genome annotation and the difficulty of retrieving true orthologs, makes such investigations challenging.
Marthey, Sylvain +9 more
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, 2018 Phylogenomics aims to infer the evolutionary relationships of organisms, and their genomes, genes, and proteins, from genomic data. Understanding the evolution of these components can provide clues about their biological functions. Here we describe minimal protocols for inferring families of genes (and the proteins they encode), and using them in ...
Riley, Robert, Nagy, Laszlo
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