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Phylogeography of a species complex of lowland Neotropical rain forest trees (Carapa, Meliaceae)

Authors

  • Caroline Scotti-Saintagne,

    Corresponding author
    1. INRA UMR 0745 EcoFoG (‘Ecologie des forêts de Guyane’), Campus Agronomique, BP709 – 97387 Kourou, French Guiana, France
      *Correspondence: Caroline Scotti-Saintagne, INRA UMR 0745 EcoFoG (‘Ecologie des forêts de Guyane’), Campus Agronomique, BP709 – 97387 Kourou, French Guiana, France.
      E-mail: caroline.scotti@ecofog.gf
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  • Christopher W. Dick,

    1. Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    2. Smithsonian Tropical Research Institute, Gamboa, Republic of Panama
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  • Henri Caron,

    1. INRA, Université de Bordeaux, UMR1202 BIOGECO, F-33610 Cestas, France
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  • Giovanni G. Vendramin,

    1. Istituto di Genetica Vegetale, Sezione di Firenze, Consiglio Nazionale delle Ricerche, 50019 Sesto Fiorentino, Firenze, Italy
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  • Erwan Guichoux,

    1. INRA, Université de Bordeaux, UMR1202 BIOGECO, F-33610 Cestas, France
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  • Anna Buonamici,

    1. Istituto di Genetica Vegetale, Sezione di Firenze, Consiglio Nazionale delle Ricerche, 50019 Sesto Fiorentino, Firenze, Italy
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  • Caroline Duret,

    1. INRA UMR 0745 EcoFoG (‘Ecologie des forêts de Guyane’), Campus Agronomique, BP709 – 97387 Kourou, French Guiana, France
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  • Pierre Sire,

    1. INRA UMR 0745 EcoFoG (‘Ecologie des forêts de Guyane’), Campus Agronomique, BP709 – 97387 Kourou, French Guiana, France
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  • Renato Valencia,

    1. Laboratorio de Ecología de Plantas y Herbario QCA, Escuela de Ciencias Biológicas, P. Universidad Católica del Ecuador, Apartado 17-01-2184, Quito, Ecuador
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  • Maristerra R. Lemes,

    1. Laboratório de Genética e Biologia Reprodutiva de Plantas, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936, 69083-000 Manaus, AM, Brazil
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    • Present address: Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rua Pacheco Leão 915, Jardim Botânico, 22460-030, Rio de Janeiro, RJ, Brazil.

  • Rogério Gribel,

    1. Laboratório de Genética e Biologia Reprodutiva de Plantas, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936, 69083-000 Manaus, AM, Brazil
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    • Present address: Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rua Pacheco Leão 915, Jardim Botânico, 22460-030, Rio de Janeiro, RJ, Brazil.

  • Ivan Scotti

    1. INRA UMR 0745 EcoFoG (‘Ecologie des forêts de Guyane’), Campus Agronomique, BP709 – 97387 Kourou, French Guiana, France
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*Correspondence: Caroline Scotti-Saintagne, INRA UMR 0745 EcoFoG (‘Ecologie des forêts de Guyane’), Campus Agronomique, BP709 – 97387 Kourou, French Guiana, France.
E-mail: caroline.scotti@ecofog.gf

Abstract

Aim  Many tropical tree species have poorly delimited taxonomic boundaries and contain undescribed or cryptic species. We examined the genetic structure of a species complex in the tree genus Carapa in the Neotropics in order to evaluate age, geographic patterns of diversity and evolutionary relationships, and to quantify levels of introgression among currently recognized species.

Location  Lowland moist forests in the Guiana Shield, the Central and Western Amazon Basin, Chocó and Central America.

Methods  Genetic structure was analysed using seven nuclear simple sequence repeats (nuSSR), five chloroplast SSRs (cpSSR), and two chloroplast DNA (cpDNA) intergenic sequences (trnH–psbA and trnC–ycf6). Bayesian clustering analysis of the SSR data was used to infer population genetic structure and to assign 324 samples to their most likely genetic cluster. Bayesian coalescence analyses were performed on the two cpDNA markers to estimate evolutionary relationships and divergence times.

Results  Two genetic clusters (nu_guianensis and nu_surinamensis) were detected, which correspond to the Neotropical species C. guianensis (sensu latu) and C. surinamensis. Fourteen cpDNA haplotypes clustered into six haplogroups distributed between the two nuclear genetic clusters. Divergence between the haplogroups was initiated in the Miocene, with some haplotype structure evolving as recently as the Pleistocene. The absence of complete lineage sorting between the nuclear and chloroplast genomes and the presence of hybrid individuals suggest that interspecific reproductive barriers are incomplete. NuSSR diversity was highest in C. guianensis and, within C. guianensis, cpDNA diversity was highest in the Central and Western Amazon Basin. Regional genetic differentiation was strong but did not conform to an isolation-by-distance process or exhibit a phylogeographical signal.

Main conclusions  The biogeographical history of Neotropical Carapa appears to have been influenced by events that took place during the Neogene. Our results point to an Amazonian centre of origin and diversification of Neotropical Carapa, with subsequent migration to the Pacific coast of South America and Central America. Gene flow apparently occurs among species, and introgression events are supported by inconsistencies between chloroplast and nuclear lineage sorting. The absence of phylogeographical structure may be a result of the ineffectiveness of geographical barriers among populations and of reproductive isolation mechanisms among incipient and cryptic species in this species complex.

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