ArticlePacific Symposium on Biocomputing. Pacific Symposium on Biocomputing2013
Maximum likelihood phylogenetic reconstruction from high-resolution whole-genome data and a tree of 68 eukaryotes.
Article in Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
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- The first mitogenomic phylogenetic framework of Dorcus sensu lato (Coleoptera: Lucanidae), with an emphasis on generic taxonomy in Eastern Asia.BMC ecology and evolution · 2024Article
- Taxonomic Distribution, Phylogenetic Relationship, and Domain Conservation of CRISPR-Associated Cas Proteins.Bioinformatics and biology insights · 2024Article
- Artificial intelligence and bioinformatics: a journey from traditional techniques to smart approaches.Gastroenterology and hepatology from bed to bench · 2024Review
- Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using Mycobacterium tuberculosis isolates.Bioinformatics (Oxford, England) · 2023Article
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- The bowfin genome illuminates the developmental evolution of ray-finned fishes.Nature genetics · 2021Article
- Whole-genome microsynteny-based phylogeny of angiosperms.Nature communications · 2021Article
- Genomic Analysis ofFrontiers in microbiology · 2021Article
- Phylogenetic Reconstruction Based on Synteny Block and Gene Adjacencies.Molecular biology and evolution · 2020Article
- Ancestral Reconstruction and Investigations of Genomic Recombination on some Pentapetalae Chloroplasts.Journal of integrative bioinformatics · 2019Article
- Article
- Genome Rearrangement Shapes Prochlorococcus Ecological Adaptation.Applied and environmental microbiology · 2018Article
- Reconstructing Yeasts Phylogenies and Ancestors from Whole Genome Data.Scientific reports · 2017Article
- Phylogeny analysis from gene-order data with massive duplications.BMC genomics · 2017Article
- Ancestral Genome Reconstruction on Whole Genome Level.Current genomics · 2017Review
- Plastomes of the green algaePeerJ · 2017Article
- Large-Scale Comparative Analysis Reveals the Mechanisms Driving Plastomic Compaction, Reduction, and Inversions in Conifers II (Cupressophytes).Genome biology and evolution · 2016Article
- Two complete mitochondrial genomes fromZooKeys · 2016Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The rapid accumulation of whole-genome data has renewed interest in the study of the evolution of genomic architecture, under such events as rearrangements, duplications, losses. Comparative genomics, evolutionary biology, and cancer research all require tools to elucidate the mechanisms, history, and consequences of those evolutionary events, while phylogenetics could use whole-genome data to enhance its picture of the Tree of Life. Current approaches in the area of phylogenetic analysis are limited to very small collections of closely related genomes using low-resolution data (typically a few hundred syntenic blocks); moreover, these approaches typically do not include duplication and loss events. We describe a maximum likelihood (ML) approach for phylogenetic analysis that takes into account genome rearrangements as well as duplications, insertions, and losses. Our approach can handle high-resolution genomes (with 40,000 or more markers) and can use in the same analysis genomes with very different numbers of markers. Because our approach uses a standard ML reconstruction program (RAxML), it scales up to large trees. We present the results of extensive testing on both simulated and real data showing that our approach returns very accurate results very quickly. In particular, we analyze a dataset of 68 high-resolution eukaryotic genomes, with from 3,000 to 42,000 genes, from the eGOB database; the analysis, including bootstrapping, takes just 3 hours on a desktop system and returns a tree in agreement with all well supported branches, while also suggesting resolutions for some disputed placements.
Indexed as
Identifiers
23424133PMC3712796What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.