Speciation in coastal basins driven by staggered headwater captures: Dispersal of a species complex, Leporinus bahiensis, as revealed by genome-wide SNP data

Past sea level changes and geological instability along watershed
boundaries have largely influenced fish distribution across coastal
basins, either by dispersal via palaeodrainages now submerged or by
headwater captures, respectively. Accordingly, the South American Atlantic
coast encompasses several small and isolated drainages that share a
similar species composition, representing a suitable model to infer
historical processes. Leporinus bahiensis is a freshwater fish species
widespread along adjacent coastal basins over narrow continental shelf
with no evidence of palaeodrainage connections at low sea level periods.
Therefore, this study aimed to reconstruct its evolutionary history to
infer the role of headwater captures in the dispersal process. To
accomplish this, we employed molecular-level phylogenetic and population
structure analyses based on Sanger sequences (5 genes) and genome-wide SNP
data. Phylogenetic trees based on Sanger data were inconclusive, but SNPs
data did support the monophyletic status of L. bahiensis. Both COI and SNP
data revealed structured populations according to each hydrographic basin.
Species delimitation analyses revealed from 3 (COI) to 5 (multilocus
approach) MOTUs, corresponding to the sampled basins. An intricate
biogeographic scenario was inferred and supported by Approximate Bayesian
Computation (ABC) analysis. Specifically, a staggered pattern was revealed
and characterized by sequential headwater captures from basins adjacent to
upland drainages into small coastal basins at different periods. These
headwater captures resulted in dispersal throughout contiguous coastal
basins, followed by deep genetic divergence among lineages. To decipher
such recent divergences, as herein represented by L. bahiensis
populations, we used genome-wide SNPs data. Indeed, the combined use of
genome-wide SNPs data and ABC method allowed us to reconstruct the
evolutionary history and speciation of L. bahiensis. This framework might
be useful in disentangling the diversification process in other
neotropical fishes subject to a reticulate geological history.