title: Phylogenetic analysis in Myrcia section Aulomyrcia and inferences on plant diversity in the Atlantic rainforest.
abstract: OBJECTIVE
  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 classification systems and to test alternative hypotheses associated with the history of this clade.
  
  
  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.
  
  
  RESULTS
  Maximum likelihood and Bayesian inferences indicate that Myrcia and Marlierea are polyphyletic, and the internal groupings recovered are characterized by combinations of morphological characters. Phylogenetic relationships support a link between Amazonian and north-eastern species and between north-eastern and south-eastern species. Lower extinction rates within glacial refugia suggest that these areas were important in maintaining diversity in the Atlantic forest biodiversity hotspot.
  
  
  CONCLUSIONS
  This study provides a robust phylogenetic framework to address important ecological questions for Myrcia s.l. within an evolutionary context, and supports the need to unite taxonomically the two traditional genera Myrcia and Marlierea in an expanded Myrcia s.l. Furthermore, this study offers valuable insights into the diversification of plant species in the highly impacted Atlantic forest of South America; evidence is presented that the lowest extinction rates are found inside refugia and that range expansion from unstable areas contributes to the highest levels of plant diversity in the Bahian refugium.
authors.affiliation: Departamento de Ecologia, Laboratório de Ecologia Teórica e Síntese, ICB, Universidade Federal de Goiás, 74001-970, Goiânia, GO, Brazil, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK and Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK Departamento de Ecologia, Laboratório de Ecologia Teórica e Síntese, ICB, Universidade Federal de Goiás, 74001-970, Goiânia, GO, Brazil, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK and Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK v.staggemeier@gmail.com.
authors.forename: Vanessa Graziele
authors.initials: VG
authors.lastname: Staggemeier
authors.affiliation: Departamento de Ecologia, Laboratório de Ecologia Teórica e Síntese, ICB, Universidade Federal de Goiás, 74001-970, Goiânia, GO, Brazil, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK and Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK.
authors.forename: José Alexandre Felizola
authors.initials: JA
authors.lastname: Diniz-Filho
authors.affiliation: Departamento de Ecologia, Laboratório de Ecologia Teórica e Síntese, ICB, Universidade Federal de Goiás, 74001-970, Goiânia, GO, Brazil, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK and Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK.
authors.forename: Félix
authors.initials: F
authors.lastname: Forest
authors.affiliation: Departamento de Ecologia, Laboratório de Ecologia Teórica e Síntese, ICB, Universidade Federal de Goiás, 74001-970, Goiânia, GO, Brazil, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK and Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK Departamento de Ecologia, Laboratório de Ecologia Teórica e Síntese, ICB, Universidade Federal de Goiás, 74001-970, Goiânia, GO, Brazil, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK and Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK.
authors.forename: Eve
authors.initials: E
authors.lastname: Lucas
mesh_terms: D001483:Base Sequence; D001499:Bayes Theorem; D044822:Biodiversity; D005075:Biological Evolution; D001938:Brazil; D018744:DNA, Plant / Q000235:genetics; D005843:Geography; D016013:Likelihood Functions; D008969:Molecular Sequence Data; D027822:Myrtaceae / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D018087:Plastids / Q000235:genetics; D065947:Rainforest; D017422:Sequence Analysis, DNA; D013020:South America
chemical_list: D018744:DNA, Plant
keywords: Atlantic forest; Aulomyrcia; GeoSSE; Marlierea; Myrcia; Myrtaceae; diversification rates; diversity patterns; extinction; speciation