Data and code from: Spatially heterogeneous gene flow may hinder linking phylogeographic data to macroevolutionary patterns

Biogeography relies on estimates of phylogeny and gene flow to test
hypotheses. Established theory posits (1) gene flow varies non-randomly
with respect to geography and (2) gene flow can mislead phylogenetic
inference. These findings, often viewed in isolation, together suggest
that spatial impacts on gene flow could bias biogeographic inference. For
example, whenever a “peripheral” population is isolated and inferred as
sister to a “core” clade of adjacent populations that exchange migrants,
it might reflect elevated gene flow of “core” populations rather than
macroevolutionary processes (e.g., direction of colonization). Given this
ubiquitous but often unacknowledged biogeographic setting, it remains
unknown how spatial influences on gene flow impact metrics used to assess
biogeographic hypotheses (e.g., branch length or monophyly). We simulate
gene flow that varies nonrandomly regarding geography and found that
relatively low levels of gene flow lead to monophyly of adjacent
populations, with longer branches for peripheral populations, regardless
of true divergence history. We highlight an empirical example wherein
antbirds (Thamnophilidae) are young in Amazonia, but older at Amazonia’s
periphery. Although it is unclear if the simulated bias applies to
antbirds, our results suggest a distinguishability problem for any nodes
stemming from radiations in geographically heterogeneous environments.