  This article evaluates bias in one class of methods used to estimate archaic
admixture in modern humans. These methods study the pattern of allele sharing
among modern and archaic genomes. They are sensitive to "ghost" admixture,
which occurs when a population receives archaic DNA from sources not
acknowledged by the statistical model. The effect of ghost admixture depends on
two factors: branch-length bias and population-size bias. Branch-length bias
occurs because a given amount of admixture has a larger effect if the two
populations have been separated for a long time. Population-size bias occurs
because differences in population size distort branch lengths in the gene
genealogy. In the absence of ghost admixture, these effects are small. They
become important, however, in the presence of ghost admixture. Estimators
differ in the pattern of response. Increasing a given parameter may inflate one
estimator but deflate another. For this reason, comparisons among estimators
are informative. Using such comparisons, this article supports previous
findings that the archaic population was small and that Europeans received
little gene flow from archaic populations other than Neanderthals. It also
identifies an inconsistency in estimates of archaic admixture into Melanesia.
