Molecular Ecology (2003) 12, 105–115 © 2003 Blackwell Publishing Ltd Blackwell Science, Ltd Evidences for multiple maternal lineages of Caryocar brasiliense populations in the Brazilian Cerrado based on the analysis of chloroplast DNA sequences and microsatellite haplotype variation ROSANE G. COLLEVATTI, *‡ DARIO GRATTAPAGLIA *† and JOHN. D. HAY ‡ *Pós-Graduação em Ciências Genômicas, Universidade Católica de Brasília, SGAN 916, Mod. B, Brasília, DF. Brasil 70790 –160, †Laboratório de Genética de Plantas, EMBRAPA Recursos Genéticos e Biotecnologia, C.P.02372, Brasília, D.F. Brasil, 70770 – 900, ‡Departamento de Ecologia, Universidade de Brasília, Brasília, D.F. Brasil, 70910 – 900 Abstract In this work we report on the phylogeography of the endangered tree species Caryocar brasiliense based on variability in two classes of maternally inherited chloroplast DNA sequences with different rates of molecular evolution. Eleven sequence haplotypes of a noncoding region between the genes trnT and trnF and 21 distinct 10-locus microsatellite haplotypes could be identified in a total of 160 individuals, collected in 10 widespread populations of C. brasiliense. An AMOVA indicated that most of the variation can be attributed to differences among populations, both for DNA sequence (87.51%) and microsatellites (84.38%). Phylogeography based on a median-joining network analysis of the noncoding region showed a sharp difference from the analysis of microsatellite haplotypes. Neverthe- less, both analyses indicated that multiple lineages may have contributed to the origin of C. brasiliense populations in Brazilian Cerrado. Incongruences in the microsatellite haplo- types network suggest that homoplasy, which emerged from recurrent and independent mutations, greatly influenced the evolution of the C. brasiliense chloroplast genome. We hypothesize that our results may show the outcome of the restriction of ancient relic populations to moist refugias during extended droughts coinciding with glaciation in the northern hemisphere. The subsequent spread to favourable areas throughout Central Brazil may have caused contact between different lineages during the interglacial periods. The extinction of megafauna dispersers in the last glaciation may have caused a restriction in seed movement and currently, gene flow has been occurring mainly by pollen movement. Keywords: Caryocar brasiliense, Caryocaraceae, cpDNA, microsatellites, phylogeography, tropical tree Received 23 May 2002; revision received 23 August 2002; accepted 30 August 2002 Introduction Species that undergo long–term biogeographic barriers to gene flow may be composed of geographical populations that belong to different gene genealogies and are correlated to geographical boundaries (Avise et al . 1987; Avise 1994). Phylogeography is based on the spatial distribution of gene genealogies, and provides a means of detecting the correlation between geographical distribution of haplotypes and their genealogical relationships (Avise et al . 1987). This area of study relies on the variability at more conserved cytoplasmic genomes with uniparental inheritance, low levels of mutation rate and no recom- bination, such as the chloroplast for plants (cpDNA), and the mitochondrial genome (mtDNA) for animals (Birky 1988; Avise 1994). Additionally, because of the haploid nature and mode of inheritance, the effective population size for the chloroplast genome is expected to be one-half that for the nuclear genome, leading to a stronger effect of Correspondence: Rosane Garcia Collevatti, Pós-Graduação em Ciências Genômicas, Universidade Católica de Brasília, SGAN 916, Mod. B, Asa Norte, Brasília, DF 70790 –160. Fax: + 55613405550; E-mail: rosanegc@pos.ucb.br