The current structure of plant populations reflects not only the present patterns of genetic exchange within and between populations, but also historical gene flow, lineage isolation, and maintenance of ancestral polymorphisms. Phylogeography is a field study interested in the reconstruction of history of species to understand their origins and responses to climatic and other environmental changes in the past that may have influenced their geographical distributions. Several biogeographical hypotheses have been raised to explain the origins of the high biodiversity found in the Amazon. The present study examined the distribution patterns of the genetic variability and the phylogeography of Pseudombobax munguba (Mart. & Zucc.) Dugand, a tree species of the Malvaceae family that occurs exclusively in the Amazonian seasonally flooded forests. For the genetic analyses, 162 individuals from 11 populations of P. munguba distributed in the Brazilian Amazon were sampled using eight microsatellite loci of the cloroplast genome, and 35 individuals belonging to nine populations of P. munguba were analysed based on variation of DNA sequences of the non-coding region trnS/trnG of the chloroplast genome. The microsatellite analysis found two to five alleles per locus and a total of 35 haplotypes over all eight loci. Three populations (Beruri, Catalão e Caxiuanã), located in the Middle and Lower Amazon river, showed no polymorhisms at all. The Nei genetic diversity indexes varied from 0.0 to 0.433. The mean genetic diversity was 0.240 for all populations analysed together and 0.301 considering only the polymorphic populations. An analysis of molecular variance (AMOVA) over all populations showed that the majority of the genetic variation was found within populations (59%). If only polymorphic populations have been considered, this value was 66%. The Mantel test, which correlates genetic and geographical distances between pairs of populations, indicated no isolation by distance between P. munguba populations in the Brazilian Amazon. The trnS/trnG non-coding sequences of the cpDNA contained 10 nucleotide substitutions and three haplotypes were identified in the nine populations of P. munguba. One haplotype was the most frequent (88.6%) and widely distributed in the Brazilian Amazon. The other two were restricted to the Cruzeiro do Sul – AC and Caracaraí – RR populations. The results suggest very restricted maternal gene flow among the P. munguba populations. The low variation found in the microstellites and DNA sequences of the chloroplast genome indicates a recent history of colonization of P. munguba in the Brazilian Amazon and that the colonization in the Central and Lower course of the Amazon river represents a founder effect from a single haplotype. In contrast, the high variation found in the populations located at more elevated areas above sea level suggests that these P. munguba populations are the most ancient ones in the Brazilian Amazon. The data from both microssatelites and DNA sequences from the chloroplast genome of P. munguba suggest that variations in sea level probably occurring in the late Pliocen and early Pleistocen strongly affected the patterns of distribution of the haplotypic diversity in this species. The results corroborate the Amazonian Lake biogeographical hypothesis as a determinant of the genetic structuring of populations in tree species of the seasonally flooded forests in the region.
