Data from: Species-specific responses to paleoclimatic changes and landscape barriers drive contrasting phylogeography of co-distributed lemur species in northeastern Madagascar

River barriers have long played a central role in diversification models
of tropical regions, including the exceptionally biodiverse island of
Madagascar. Although their role is best understood by integrating
additional factors such as elevation and the ecological niche of a
species, empirical studies integrating these variables remain rare. We
used restriction site-associated DNA sequencing to assess the combined
effect of rivers, topography, climate, and forest cover on the
distributions and diversity of four Microcebus and two Avahi species
(Primates, Lemuriformes) in northeastern Madagascar. We inferred
population structure, gene flow, and genetic diversity, and assessed the
association of these ecogeographic variables and genetic differentiation
using isolation-by-resistance models. Our results show that significant
differences in genetic diversity and connectivity among species can be
explained by species-specific responses to landscape features and
phylogeographic histories. Specifically, rivers present general barriers
to gene flow, but dispersal between inter-river systems is possible via
high-elevation headwater regions. While this led to high connectivity and
genetic diversity in M. lehilahytsara and A. laniger, gene flow among M.
jonahi populations is limited by low climatic niche suitability at higher
elevations. Moreover, the more restricted distributions of M. macarthurii,
M. simmonsi and A. mooreorum likely resulted from refugial dynamics and
sea level fluctuations leading to allopatric divergence and microendemism.
Together, the findings illustrate how ecological differences among species
and temporal landscape dynamics mediate the role of rivers as dispersal
barriers. They also highlight the importance of prioritizing river
headwaters and topographically complex regions, which were shown to
promote connectivity, in conservation efforts.