Phylogeny of the Neotropical sages (Salvia subg. Calosphace; Lamiaceae) and insights into pollinator and area shifts

Salvia subg. Calosphace (Lamiaceae, Lamiales) is a highly diverse clade endemic to the New World. The phylogenetic relationships of Calosphace have been previously investigated using DNA sequences of nuclear ITS region and plastid psbA–trnH intergenic spacer, but the resulting trees lack resolution and support for many clades. The present paper reassesses the phylogenetic relationships of subgenus Calosphace, including a broader taxon sampling, with a special focus on representing previously unsampled sections, and using an additional plastid marker (trnL–trnF region). Our results show increased resolution and overall patterns of support, recovering ten main clades. Within core Calosphace, the most inclusive of these main clades, 17 new subclades were identified. Of the 42 sections for which more than one species was analysed, only 12 are monophyletic. Our biogeographical analysis identified at least twelve migrations to South America from Mexican and Central American lineages, in agreement with previous suggestions of multiple origins of South American Calosphace diversity. This analysis also confirmed a colonization of the Antilles by Andean lineages. The reconstruction of ancestral states of pollination syndromes showed multiple shifts to ornithophily from melittophily and one reversal to the latter.Fil: Fragoso-Martínez, Itzi. Universidad Nacional Autónoma de México; MéxicoFil: Martínez-Gordillo, Martha. Universidad Nacional Autónoma de México; MéxicoFil: Salazar, Gerardo A.. Universidad Nacional Autónoma de México; MéxicoFil: Sazatornil, Federico David. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Jenks, Aaron A.. Berkeley University; Estados UnidosFil: García Peña, María del Rosario. Universidad Nacional Autónoma de México; MéxicoFil: Barrera-Aveleida, Giovanna. Universidad Nacional Autónoma de México; MéxicoFil: Benitez Vieyra, Santiago Miguel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Magallón, Susana. Universidad Nacional Autónoma de México; MéxicoFil: Cornejo-Tenorio, Guadalupe. Universidad Nacional Autónoma de México; MéxicoFil: Granados Mendoza, Carolina. Universidad Nacional Autónoma de México; Méxic

Population Genomics of Organelle Genomes in Crop Plants

Chloroplast and mitochondria are specialized structure located in the cytoplasm of plant cells which possess their own genomes and are usually transmitted by one parent only. Organelle DNA markers have been widely used for phylogeny and population genetics studies because theirlow evolutionary rates allow to look further back in the past than nuclear data. This low evolutionary rate, however, was also a drawback because the diversity revealed by traditional methods (Sanger sequencing, microsatellites, RFLP, etc.) was low and was not necessarily discriminatoryenough to study genetic structure and genetic relationships. Nowadays, the fast development of next-generation sequencing methods has changed the way organelle genomes sequences are obtained. It is now easy to get whole organelle genome sequences, even for an orphan species.Because the quantity of data and the amount of diversity generated by these new methods have strongly increased, the way organelle genetic data can be used has also changed. This chapter provides a review on how to retrieve organelle genomic polymorphism from next-generationsequencing technology, with an emphasis on the specificity of organelles compared to nuclear data: how to efficiently sequence this highly repeated DNA resulting from multiple copies of the organelle genome within a cell, how to deal with the intra-individual diversity generated,and how to reconstruct a whole organelle genome sequence. This chapter will then review how next-generation sequencing technology has changed the main fields of organelle population genomics, i.e. population genetics, phylogeny, phylogeography and DNA barcoding.These new possibilities will be analysed in the light of the new drawbacks going along with the ?big data?