Abstract Aim To determine spatial and temporal commonalities in patterns of chloroplast DNA (cpDNA) variation in three widespread Neotropical tree species. We examine whether patterns of genetic variation are more consistent with
Pliocene or Pleistocene divergence. Location Central American forests, located in El Salvador, Nicaragua, Costa Rica and Panama. Methods We collected sequences from two cpDNA loci from c. 30 locations for each of three species –Bursera simaruba
(Burseraceae; n =278), Brosimum alicastrum (Moraceae; n =210) and Ficus insipida (Moraceae; n =222) – and additionally sequenced one nuclear locus for Bursera simaruba (n =45).
We used Monmonier’s algorithm to detect genetic barriers between regions. Divergence times between these regions were estimated using coalescent analyses. Results Spatial genetic boundaries were found in similar areas for these species, namely between Costa Rica and Nicaragua
for all three species, and between El Salvador and Nicaragua for two species. These boundaries visually coincide with the spatial delimitations of Pliocene islands and previously hypothesized Pleistocene refugia. Divergence time estimates between regions are more consistent with Pleistocene
divergence in two of the three species. Main conclusions Our results point to strong commonalities in the spatial locations of genetic boundaries in these three species, despite the complex geological and climatological history of this region, and ecological differences between
the species. While spatial genetic boundaries coincide conspicuously with possible Pliocene and Pleistocene barriers to gene flow, we cannot distinguish between the two scenarios because of the strong spatial overlap of both barriers. However, the temporal data tentatively suggest that some
of this divergence occurred in the Pleistocene, although limitations in the analysis cannot confirm Pleistocene divergence without external, corroborating data. While we cannot definitively implicate a single historical process as driving patterns of genetic differentiation in all three species,
our results represent an initial step towards identifying a common history of Central American tree species.