  Identifying and understanding the large-scale biodiversity patterns in time
and space is vital for conservation and addressing fundamental ecological and
evolutionary questions. Network-based methods have proven useful for
simplifying and highlighting important structures in species distribution data.
However, current network-based biogeography approaches cannot exploit the
evolutionary information available in phylogenetic data. We introduce a method
for incorporating evolutionary relationships into species occurrence networks
to produce more biologically informative and robust bioregions. To keep the
bipartite network structure where bioregions are grid cells indirectly
connected through shared species, we incorporate the phylogenetic tree by
connecting ancestral nodes to the grid cells where their descendant species
occur. To incorporate the whole tree without destroying the spatial signal of
narrowly distributed species or ancestral nodes, we weigh tree nodes by the
geographic information they provide. For a more detailed analysis, we enable
integration of the evolutionary relationships at a specific time in the tree.
By sweeping through the phylogenetic tree in time, our method interpolates
between finding bioregions based only on distributional data and finding
spatially segregated clades, uncovering evolutionarily distinct bioregions at
different time slices. We also introduce a way to segregate the connections
between evolutionary branches at a selected time to enable exploration of
overlapping evolutionarily distinct regions. We have implemented these methods
in Infomap Bioregions, an interactive web application that makes it easy to
explore the possibly hierarchical and fuzzy patterns of biodiversity on
different scales in time and space.
