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July 30, 2025

The Impact of Sequencing and Genotyping Errors on Bayesian Analysis of Genomic Data under the Multispecies Coalescent Model.

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Authors

JJJiayi JiDalian Ocean UniversityPKPaschalia KapliUniversity of ViennaTFTomáš FlouriUniversity College London

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Overview

Simulation reveals genotyping errors can bias Bayesian analysis of species trees and population metrics.

Key Points

  • Genotyping errors significantly bias estimates of population sizes and species divergence times, reducing analytic power.
  • At low base-calling error rates, species tree estimation remains precise even with low sequencing depth of ~3×.
  • Using computer simulation to assess the influence of genotyping errors in phylogenomic data allows for better inference.
  • Precision increases when sequencing fewer samples at high depths versus many samples at lower depths.

Cite This Study

Ji et al. (2025) studied this question.

synapsesocial.com/papers/68af474ead7bf08b1ead3bfehttps://doi.org/10.1093/molbev/msaf184
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Also Consider

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  1. 1The impact of incomplete taxon sampling on inference of gene flow by Bayesian and summary methods using genomic sequence data2026
  2. 2On the robustness of Bayesian inference of gene flow to intragenic recombination and natural selection2025
  3. 3Bayesian Inference Under the Multispecies Coalescent with Ancient DNA Sequences2024 · 1 citations
  4. 4Two-step Species Tree Inference under the Multispecies Coalescent Using Full-Likelihood2025
  5. 5Estimating waiting distances between genealogy changes under a Multi-Species Extension of the Sequentially Markov Coalescent.2025