ArticleScience (New York, N.Y.)2025
CASTER: Direct species tree inference from whole-genome alignments.
Article in Science (New York, N.Y.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Article
- Genomic diversification between aposematic and cryptic phenotypes of Oophaga granulifera (Anura: Dendrobatidae).Scientific reports · 2026Article
- Reticulated adaptive radiation and phylogenomic diversity loss in the Hawaiian honeycreepers.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Atlantic forest origins and Amazon connections: the evolutionary history of Adenocalymma.Annals of botany · 2026Article
- Chemical distance outweighs phylogeny in VOC-mediated cross-species plant defense communication.Science China. Life sciences · 2026Article
- Pre-divergence hybridization and adaptive introgression shaped the genetic architecture of East Asian domestic pigs.Science China. Life sciences · 2026Article
- Genome-wide SNVs revealed reticulate evolutionary history of a Eurasian-African songbird radiation (Zoological research · 2026Article
- Phlag: scalable detection of genomics regions with unexplained phylogenetic heterogeneity.Bioinformatics (Oxford, England) · 2026Article
- Morphological and molecular evidence clarifies the taxonomic position of Indosasa solearis and reveals the hybrid origin of Sinobambusa (Poaceae: Bambusoideae: Arundinarieae).BMC plant biology · 2026Article
- Global approaches to infectious disease surveillance and modeling.Nature medicine · 2026Review
- WASTER: Practical de novo Phylogenomics from Low-coverage Short Reads.Molecular biology and evolution · 2026Article
- Pan-genome analysis of wax apple (Frontiers in plant science · 2026Article
- Admixture in a butterfly species complex creates a genomic mosaic of ancestry with distinct histories for different chromosomes.bioRxiv : the preprint server for biology · 2025Article
- Speciation Genomics in the Tiger Whiptail Lizards (Aspidoscelis tigris Complex).Genome biology and evolution · 2025Article
- HAlign-G: rapid and low-memory multiple-genome aligner for large-scale closely related genomes.Genome biology · 2025Article
- Linking phenotype to genotype using comprehensive genomic comparisons.Current opinion in genetics & development · 2025Review
- Reticulate allopolyploidy and subsequent dysploidy drive evolution and diversification in the cotton family.Nature communications · 2025Article
- The Impact of Sequencing and Genotyping Errors on Bayesian Analysis of Genomic Data under the Multispecies Coalescent Model.Molecular biology and evolution · 2025Article
- ASTER: A Package for Large-Scale Phylogenomic Reconstructions.Molecular biology and evolution · 2025Article
- Construction of the graph genomes of Takifugu provides novel insights into the genomic mechanisms of population structure and migratory traits.BMC biology · 2025Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Genomes contain mosaics of discordant evolutionary histories, challenging the accurate inference of the tree of life. Although genome-wide data are routinely used for discordance-aware phylogenomic analyses, because of modeling and scalability limitations, the current practice leaves out large chunks of genomes. As more high-quality genomes become available, we urgently need discordance-aware methods to infer the tree directly from a multiple genome alignment. In this study, we introduce Coalescence-Aware Alignment-Based Species Tree Estimator (CASTER), a theoretically justified site-based method that eliminates the need to predefine recombination-free loci. CASTER is scalable to hundreds of mammalian whole genomes. We demonstrate the accuracy and scalability of CASTER in simulations that include recombination and apply CASTER to several biological datasets, showing that its per-site scores can reveal both biological and artifactual patterns of discordance across the genome.
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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.