Phenotypic Legacy of Archaic Admixture

What is the estimated decline of Neanderthal ancestry oertime?

from 4.3-5.7% from a time shortly after introgression to 1.1-2.2% in Eurasians today

Why might have Neanderthal alleles been removed from the modern human genome?

consequences of harmful epistatic interactions between human and Neanderthal alleles

What does it mean if a non-african individual carries a derived allele seen in Neanderthals but absent from the west-Africa Yoruba?

it it likely to originate from Neanderthals

How does divergence help to search for Neanderthal haplotypes in modern human genomes?

high sequence divergence of the non-African haplotype to all YRI haplotypes but low divergence to Neanderthal

How does haplotype length help to search for Neanderthal haplotypes in modern human genomes?

haplotype length consistent with interbreeding 37-86 thousand years ago

Does the X or Y chromosome have higher Neanderthal ancestry?

the X

What do important genomic regions tend to have?

less Neanderthal ancestry

What evidence suggests that Neanderthal alleles caused decreased fertility in males when moved to a modern human genetic background?

genes that are specific to testes were enriched in regions of low Neanderthal ancestry, X chromosome to be especially dense in male hybrid sterility genes

How much introgressed sequence in found in each individual on average?

23 Mb

Where are Neanderthal alleles located on average?

far away from genes

Why are Neanderthal alleles located far away from genes?

under less negative selection because they are less likely to affect genes

What happen to the Neanderthal/Denisovan genes in the modern human gene pools?

increased frequency under positive selection, removed by negative selection

How would one look at if ancient humans had aneuploidy?

look at abundance of genes associated with X and Y chromosomes

Did ancient humans have aneuploidy?

yes