ArticleSystematic biology2015
PoMo: An Allele Frequency-Based Approach for Species Tree Estimation.
Article in Systematic biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- How Does Transcription-Associated Mutagenesis Shape tRNA Microevolution?Genome biology and evolution · 2026Article
- Homoploid hybrid speciation and recurrent hybridization along the northwestern Iberian mountain chains.Annals of botany · 2025Article
- Stochastic Character Mapping: An Under-Exploited Approach to the Study of Molecular Evolution.Journal of molecular evolution · 2025Article
- Sex-biased Migration and Demographic History of the Big European Firefly Lampyris noctiluca.Molecular biology and evolution · 2025Article
- Mitochondrial genomes of the European sardine (Sardina pilchardus) reveal Pliocene diversification, extensive gene flow and pervasive purifying selection.Scientific reports · 2024Article
- Polymorphism-Aware Models in RevBayes: Species Trees, Disentangling Balancing Selection, and GC-Biased Gene Conversion.Molecular biology and evolution · 2024Article
- Multiple introductions of divergent lineages and admixture conferred the high invasiveness in a widespread weed (Evolutionary applications · 2024Article
- Conceptual and empirical bridges between micro- and macroevolution.Nature ecology & evolution · 2023Review
- Not out of the Mediterranean: Atlantic populations of the gorgonianEcology and evolution · 2023Article
- Article
- A Mutation-Selection Model of Protein Evolution under Persistent Positive Selection.Molecular biology and evolution · 2022Article
- Nucleotide Usage Biases Distort Inferences of the Species Tree.Genome biology and evolution · 2022Article
- Parallel introgression, not recurrent emergence, explains apparent elevational ecotypes of polyploid Himalayan snowtrout.Royal Society open science · 2021Article
- Taxonomic Uncertainty and the Anomaly Zone: Phylogenomics Disentangle a Rapid Radiation to Resolve Contentious Species (Gila robusta Complex) in the Colorado River.Genome biology and evolution · 2021Article
- Genome-wide association study identifies new loci associated with risk of HBV infection and disease progression.BMC medical genomics · 2021Article
- Ambiguity Coding Allows Accurate Inference of Evolutionary Parameters from Alignments in an Aggregated State-Space.Systematic biology · 2021Article
- Multi-level patterns of genetic structure and isolation by distance in the widespread plant Mimulus guttatus.Heredity · 2020Article
- Efficiently inferring the demographic history of many populations with allele count data.Journal of the American Statistical Association · 2020Article
- The transition distribution of a sample from a Wright-Fisher diffusion with general small mutation rates.Journal of mathematical biology · 2019Article
- Quantifying GC-Biased Gene Conversion in Great Ape Genomes Using Polymorphism-Aware Models.Genetics · 2019Article
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3 authors.
Funding
Abstract
Incomplete lineage sorting can cause incongruencies of the overall species-level phylogenetic tree with the phylogenetic trees for individual genes or genomic segments. If these incongruencies are not accounted for, it is possible to incur several biases in species tree estimation. Here, we present a simple maximum likelihood approach that accounts for ancestral variation and incomplete lineage sorting. We use a POlymorphisms-aware phylogenetic MOdel (PoMo) that we have recently shown to efficiently estimate mutation rates and fixation biases from within and between-species variation data. We extend this model to perform efficient estimation of species trees. We test the performance of PoMo in several different scenarios of incomplete lineage sorting using simulations and compare it with existing methods both in accuracy and computational speed. In contrast to other approaches, our model does not use coalescent theory but is allele frequency based. We show that PoMo is well suited for genome-wide species tree estimation and that on such data it is more accurate than previous approaches.
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