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Discovering Fragile Clades and Causal Sequences in Phylogenomics by Evolutionary Sparse Learning
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Journal article
Date
2024-06-25
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Biology
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https://doi.org/10.1093/molbev/msae131
Abstract
Phylogenomic analyses of long sequences, consisting of many genes and genomic segments, reconstruct organismal relationships with high statistical confidence. But, inferred relationships can be sensitive to excluding just a few sequences. Currently, there is no direct way to identify fragile relationships and the associated individual gene sequences in species. Here, we introduce novel metrics for gene-species sequence concordance and clade probability derived from evolutionary sparse learning models. We validated these metrics using fungi, plant, and animal phylogenomic datasets, highlighting the ability of the new metrics to pinpoint fragile clades and the sequences responsible. The new approach does not necessitate the investigation of alternative phylogenetic hypotheses, substitution models, or repeated data subset analyses. Our methodology offers a streamlined approach to evaluating major inferred clades and identifying sequences that may distort reconstructed phylogenies using large datasets.
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Sudip Sharma, Sudhir Kumar, Discovering Fragile Clades and Causal Sequences in Phylogenomics by Evolutionary Sparse Learning, Molecular Biology and Evolution, Volume 41, Issue 7, July 2024, msae131, https://doi.org/10.1093/molbev/msae131
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Oxford University Press
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Molecular Biology and Evolution, Vol. 41, Iss. 7
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