The roles of aridification and sea level changes in the diversification and persistence of freshwater fish lineages

While the influence of Pleistocene climatic changes on divergence and
speciation has been well-documented across the globe, complex spatial
interactions between hydrology and eustatics over longer timeframes may
also determine species evolutionary trajectories. Within the
Australian continent, glacial cycles were not associated with
changes in ice cover and instead largely resulted in fluctuations from
moist to arid conditions across the landscape. Here, we investigate the
role of hydrological and coastal topographic changes brought about by
Plio-Pleistocene climatic changes on the biogeographic history of a small
Australian freshwater fish, the southern pygmy perch Nannoperca australis.
Using 7,958 ddRAD-seq (double digest restriction-site associated DNA) loci
and 45,104 filtered SNPs, we combined phylogenetic, coalescent and species
distribution analyses to investigate the various roles of aridification,
sea level and tectonics and associated biogeographic changes across
southeast Australia. Sea-level changes since the Pliocene and reduction or
disappearance of large waterbodies throughout the Pleistocene were
determining factors in strong divergence across the clade, including the
initial formation and maintenance of a cryptic species, N. ‘flindersi’.
Isolated climatic refugia and fragmentation due to lack of connected
waterways maintained the identity and divergence of inter- and
intraspecific lineages. Our historical findings suggest that predicted
increases in aridification and sea level due to anthropogenic climate
change might result in markedly different demographic impacts, both
spatially and across different landscape types.