Annals of Botany Page 1 of 15 doi:10.1093/aob/mcv005, available online at www.aob.oxfordjournals.org Phylogenetic analysis in Myrcia section Aulomyrcia and inferences on plant diversity in the Atlantic rainforest Vanessa Graziele Staggemeier1,2,*, Jose´Alexandre Felizola Diniz-Filho1,Fe´lix Forest2 and Eve Lucas2,3 1Departamento de Ecologia, Laborato´rio de Ecologia Teo´rica e Sı´ntese, ICB, Universidade Federal de Goia´s, 74001-970, Goiaˆnia, GO, Brazil, 2Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK and 3Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK * For correspondence. E-mail
[email protected] Received: 21 June 2014 Returned for revision: 31 July 2014 Accepted: 23 December 2014 Downloaded from Background and Aims Myrcia section Aulomyrcia includes 120 species that are endemic to the Neotropics and disjunctly distributed in the moist Amazon and Atlantic coastal forests of Brazil. This paper presents the first comprehensive phylogenetic study of this group and this phylogeny is used as a basis to evaluate recent classifica- tion systems and to test alternative hypotheses associated with the history of this clade. http://aob.oxfordjournals.org/ Methods Fifty-three taxa were sampled out of the 120 species currently recognized, plus 40 outgroup taxa, for one nuclear marker (ribosomal internal transcribed spacer) and four plastid markers (psbA-trnH, trnL-trnF, trnQ-rpS16 and ndhF). The relationships were reconstructed based on Bayesian and maximum likelihood analyses. Additionally, a likelihood approach, ‘geographic state speciation and extinction’, was used to estimate region- dependent rates of speciation, extinction and dispersal, comparing historically climatic stable areas (refugia) and unstable areas.