Amazon diversification and cross‐Andean dispersal of the widespread Neotropical tree species <i>Jacaranda copaia</i> (Bignoniaceae)

Abstract

Abstract Aim The phylogeographical history of Neotropical species can be difficult to reconstruct because of superimposed Neogene and Quaternary histories, and because of taxonomic uncertainty. We analysed range‐wide genetic diversity in a widespread pioneer tree species, Jacaranda copaia (Aubl.) D. Don, to characterize phylogeographical structure, date the evolutionary relationships among lineages, and evaluate the role of dispersal and vicariance in establishing the present geographical range. Location Guiana Shield; central, southern and western Amazon Basin; Chocó region; Central America. Methods We analysed nine nuclear simple sequence repeat loci (nu SSR ), eight chloroplast SSR s (cp SSR ), and two cp DNA intergenic sequences in 341 adult trees. Genetic differentiation at nu SSR s was inferred using Bayesian clustering. Dating of chloroplast lineage divergence was obtained using a range of published mutation rates and Bayesian coalescence analyses. Population divergence dating was performed using an isolation‐with‐migration model for eight loci (one cp sequence and seven nu SSR s). Results Nuclear SSR variation identified three geographically overlapping clusters ( nu‐ 1, nu‐ 2, nu‐ 3). Twelve cp DNA haplotypes were clustered into two haplogroups ( cp‐ 1, cp‐ 2) with the central Amazon harbouring the highest diversity. Molecular dating analysis suggests that cp DNA haplotype diversification started around the end of the Pliocene (2.61 Ma on average), whereas population divergence was more recent and occurred during the mid‐Quaternary (point estimates between 357 and 436 ka). Main conclusions The genetic variation of J. copaia in the Neotropics was shaped mainly by Pleistocene events. Chloroplast diversity did not display the expected cis / trans Andean disjunction, indicating recent dispersal. Nuclear variation revealed that separate regions share a recent history, with a centre of diversity in the central Amazon Basin. The geographical pattern of diversity is congruent with the distribution of the two subspecies, J . copaia copaia and J. copaia spectabilis , and evidence of nu SSR admixture between the two taxa supports their classification as subspecies.