ArticleMolecular biology and evolution2019
Polymorphism-Aware Species Trees with Advanced Mutation Models, Bootstrap, and Rate Heterogeneity.
Article in Molecular biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- The rights and wrongs of rescaling in population genetics simulations.PLoS genetics · 2026Review
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- Scaling up orphan crop research: genebank genetics highlight geographic structure in cultivated cowpea from 10 617 global accessions.The Plant journal : for cell and molecular biology · 2026Article
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- Homoploid hybrid speciation and recurrent hybridization along the northwestern Iberian mountain chains.Annals of botany · 2025Article
- Genome sequencing of 'Fuji' apple clonal varieties reveals genetic mechanism of the spur-type morphology.Nature communications · 2024Article
- Polymorphism-Aware Models in RevBayes: Species Trees, Disentangling Balancing Selection, and GC-Biased Gene Conversion.Molecular biology and evolution · 2024Article
- Genetic characterization of the first Deltacoronavirus from wild birds around Qinghai Lake.Frontiers in microbiology · 2024Article
- ncOrtho: efficient and reliable identification of miRNA orthologs.Nucleic acids research · 2023Article
- Phylogenomic comparative methods: Accurate evolutionary inferences in the presence of gene tree discordance.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Range-wide population genomics of common seadragons shows secondary contact over a former barrier and insights on illegal capture.BMC biology · 2023Article
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- Rapid radiation in a highly diverse marine environment.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Nucleotide Usage Biases Distort Inferences of the Species Tree.Genome biology and evolution · 2022Article
- Taxonomy notes on Vandeae (Orchidaceae) from China: Five new species and two new records.Plant diversity · 2021Article
- Genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world's most threatened primates.Scientific reports · 2021Article
- Article
- The amylase gene cluster in house mice (Mus musculus) was subject to repeated introgression including the rescue of a pseudogene.BMC evolutionary biology · 2020Article
- IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era.Molecular biology and evolution · 2020Article
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4 authors.
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Abstract
Molecular phylogenetics has neglected polymorphisms within present and ancestral populations for a long time. Recently, multispecies coalescent based methods have increased in popularity, however, their application is limited to a small number of species and individuals. We introduced a polymorphism-aware phylogenetic model (PoMo), which overcomes this limitation and scales well with the increasing amount of sequence data whereas accounting for present and ancestral polymorphisms. PoMo circumvents handling of gene trees and directly infers species trees from allele frequency data. Here, we extend the PoMo implementation in IQ-TREE and integrate search for the statistically best-fit mutation model, the ability to infer mutation rate variation across sites, and assessment of branch support values. We exemplify an analysis of a hundred species with ten haploid individuals each, showing that PoMo can perform inference on large data sets. While PoMo is more accurate than standard substitution models applied to concatenated alignments, it is almost as fast. We also provide bmm-simulate, a software package that allows simulation of sequences evolving under PoMo. The new options consolidate the value of PoMo for phylogenetic analyses with population data.
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