New complete human genome reveals 51 megabases of hidden Neanderthal DNA
Scientists remapped sequencing reads from high-quality Altai Neanderthal and Denisovan genomes onto the T2T-CHM13 reference genome, the first complete human reference that resolved the remaining 8 percent of sequences missing from earlier assemblies. The team applied IBDmix to 2,504 individuals from 26 geographically diverse populations and found approximately 51 megabases of Neanderthal sequences that were invisible when using the older GRCh38 reference. These newly detected introgressed segments appeared predominantly in regions where GRCh38 and T2T-CHM13 assemblies diverge. The analysis uncovered population-specific archaic introgression spanning genes involved in metabolism, olfaction, and ion channel function. The researchers integrated their findings into a visualization database called ASH at www.arcseqhub.com. T2T-CHM13 significantly improved read mapping quality in archaic samples compared to GRCh37, though the team noted that commonly used pre-phasing filtering strategies in public datasets substantially influence archaic ancestry determination.
The complete T2T-CHM13 reference genome corrects assembly errors and exposes archaic genetic variation that previous references missed, offering a fuller picture of how Neanderthal interbreeding left functional traces in living human populations.
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