ArticleSystematic biology2022
Excluding Loci With Substitution Saturation Improves Inferences From Phylogenomic Data.
Article in Systematic biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 55 citations in OpenAlex.
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- PickMe: Sample Selection for Species Tree Reconstruction using Coalescent Weighted Quartets.Systematic biology · 2025Article
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- When the Past Fades: Detecting Phylogenetic Signal with SatuTe.Molecular biology and evolution · 2025Article
- Dating in the Dark: Elevated Substitution Rates in Cave Cockroaches (Blattodea: Nocticolidae) Have Negative Impacts on Molecular Date Estimates.Systematic biology · 2024Article
- Reliable estimation of tree branch lengths using deep neural networks.PLoS computational biology · 2024Article
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- The Neotropical endemic liverwort subfamily Micropterygioideae had circum-Antarctic links to the rest of the Lepidoziaceae during the early Cretaceous.Ecology and evolution · 2024Article
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- Identifying and addressing methodological incongruence in phylogenomics: A review.Evolutionary applications · 2023Review
- Mito-nuclear discordance within Anthozoa, with notes on unique properties of their mitochondrial genomes.Scientific reports · 2023Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The historical signal in nucleotide sequences becomes eroded over time by substitutions occurring repeatedly at the same sites. This phenomenon, known as substitution saturation, is recognized as one of the primary obstacles to deep-time phylogenetic inference using genome-scale data sets. We present a new test of substitution saturation and demonstrate its performance in simulated and empirical data. For some of the 36 empirical phylogenomic data sets that we examined, we detect substitution saturation in around 50% of loci. We found that saturation tends to be flagged as problematic in loci with highly discordant phylogenetic signals across sites. Within each data set, the loci with smaller numbers of informative sites are more likely to be flagged as containing problematic levels of saturation. The entropy saturation test proposed here is sensitive to high evolutionary rates relative to the evolutionary timeframe, while also being sensitive to several factors known to mislead phylogenetic inference, including short internal branches relative to external branches, short nucleotide sequences, and tree imbalance. Our study demonstrates that excluding loci with substitution saturation can be an effective means of mitigating the negative impact of multiple substitutions on phylogenetic inferences. [Phylogenetic model performance; phylogenomics; substitution model; substitution saturation; test statistics.].
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