The lower frequency of archaic ancestry on the X chromosome and near testis-expressed genes suggests that first-generation hybrids had high levels of infertility. Additionally, loci associated with neurological and psychiatric disorders have higher levels of archaic haplotypes, suggesting deleterious effects of archaic admixture.
Some results of archaic admixture were positive--including genes associated with skin pigmentation and metabolism. These alleles would have allowed ancient humans to adapt to different climatic regions more rapidly. Some Neanderthal alleles related to immune function have also led to positive adaptations in humans.
Zac Truesdell - Journal update - Genome Biology - 2
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1920-z
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