Ancient introgression in mouse lemurs (Microcebus:Cheirogaleidae) explains 20 years of phylogenetic uncertainty

Mouse lemurs (genus Microcebus) are a clade of approximately 26 named
species of small, nocturnal primates endemic to Madagascar. The genus
radiated one and ten million years ago and is morphologically cryptic,
with most species having been named within the past 20 years largely based
on phylogenetic analysis of short fragments of mitochondrial data. More
recent work has been focused on revisiting species designations with
autosomal nuclear data using more sophisticated statistical approaches.
The order of speciation events in Microcebus remains contentious,
particularly with regard to the placement of the M. ravelobensis clade. We
investigated support for previous phylogenetic hypotheses based on
available whole-genome assemblies from six species and an outgroup. We
recovered over 4,000 one-to-one orthologs from these assemblies and used
concatenation and coalescent species tree methods to evaluate if
differences between previous studies were due to methodological
differences or to limitations from too few loci. Observed gene tree
discordance was high with patterns inconsistent with incomplete lineage
sorting alone. Therefore, we estimated phylogenetic networks to
investigate ancient introgression events that may explain observed gene
tree distributions and previous phylogenetic conflicts. A network model,
invoking some role for introgressive hybridization in the early evolution
of Microcebus, better characterizes phylogenetic relationships than does
any binary species tree. Our results provide insights into the
biogeographic history of a threatened and diverse group of primates while
also highlighting an important role for phylogenetic network methods in
resolving cases of phylogenetic uncertainty.