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March 15, 2026Molecular Biology and EvolutionOpen Access

Comparing Neanderthal introgression maps reveals core agreement but substantial heterogeneity

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Authors

YCYaen ChenKVKeila Velázquez-ArcelayJCJohn A. Capra

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Overview

Genome-wide comparisons reveal core Neanderthal ancestry regions, suggesting substantial method-driven variability.

Key Points

  • This research aims to evaluate the accuracy and variability of various Neanderthal introgression detection algorithms.
  • Compared 14 genome-wide introgression maps across 11 detection algorithms.
  • Algorithms include admixfrog, ArchaicSeeker2, and other statistical methods.
  • Evaluated input types: archaic, modern, and simulated genomes.
  • Identified core regions predicted consistently by nearly all methods.
  • Observed substantial heterogeneity in introgression maps at the individual genome level.
  • Different algorithms may lead to varying conclusions in downstream analyses.

Cite This Study

Chen et al. (2026) studied this question.

synapsesocial.com/papers/69b606c483145bc643d1d046https://doi.org/10.1093/molbev/msag064
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Also Consider

Synapse has enriched 5 closely related papers on similar clinical questions. Consider them for comparative context:

  1. 1Comparing Neanderthal introgression maps reveals core agreement but substantial heterogeneity2025
  2. 2A Refined Analysis of Neanderthal-Introgressed Sequences in Modern Humans with a Complete Reference Genome2024
  3. 3Archaic ancestry inference in imputed ancient human genomes2025 · 1 citations
  4. 4Recurrent gene flow between Neanderthals and modern humans over the past 200,000 years2024 · 27 citations
  5. 5The evolutionary fate of Neanderthal DNA in 30,780 admixed genomes with recent African-like ancestry2024