Phylogeny and biogeography of Ceiba Mill. (Malvaceae, Bombacoideae)

The Neotropics is the most species-rich area in the world, and the mechanisms that generated and maintain its biodiversity are still debated. This paper contributes to the debate by investigating the evolutionary and biogeographic history of the genus Ceiba Mill. (Malvaceae, Bombacoideae). Ceiba comprises 18 mostly Neotropical species, largely endemic to two major biomes, seasonally dry tropical forests (SDTFs) and rain forests. Its species are among the most characteristic elements of Neotropical SDTF, one of the most threatened biomes in the tropics. Phylogenetic analyses of DNA sequence data (from the nuclear ribosomal internal transcribed spacers [nrITS] for 30 accessions representing 14 species of Ceiba) recovered the genus as monophyletic. The phylogeny showed geographic and ecological structure in three main clades: (i) a rain forest lineage of nine accessions of C. pentandra sister to the remaining species; (ii) a highly supported clade composed of C. schottii and C. aesculifolia from Central American and Mexican SDTF, plus two accessions of C. samauma from semi-humid, inter Andean valleys in Peru; and (iii) a highly supported South American SDTF clade including 10 species showing little sequence variation. Within this South American SDTF clade, no species represented by multiple accessions were resolved as monophyletic. We demonstrate that the patterns of species age, monophyly, and geographic structure previously reported for SDTF species within the Leguminosae family are not shared by Ceiba, suggesting that further phylogenetic studies of unrelated groups are required to understand general patterns

Chemocoding as an identification tool where morphological- and DNA-based methods fall short:Inga as a case study

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this recordThe need for species identification and taxonomic discovery has led to the development of innovative technologies for large‐scale plant identification. DNA barcoding has been useful, but fails to distinguish among many species in species‐rich plant genera, particularly in tropical regions. Here, we show that chemical fingerprinting, or ‘chemocoding’, has great potential for plant identification in challenging tropical biomes. Using untargeted metabolomics in combination with multivariate analysis, we constructed species‐level fingerprints, which we define as chemocoding. We evaluated the utility of chemocoding with species that were defined morphologically and subject to next‐generation DNA sequencing in the diverse and recently radiated neotropical genus Inga (Leguminosae), both at single study sites and across broad geographic scales. Our results show that chemocoding is a robust method for distinguishing morphologically similar species at a single site and for identifying widespread species across continental‐scale ranges. Given that species are the fundamental unit of analysis for conservation and biodiversity research, the development of accurate identification methods is essential. We suggest that chemocoding will be a valuable additional source of data for a quick identification of plants, especially for groups where other methods fall short

The origin of the legumes is a complex paleopolyploid phylogenomic tangle closely associated with the cretaceous-paleogene (K-Pg) mass extinction event

This is the final version. Available from Oxford University Press via the DOI in this record. The consequences of the Cretaceous-Paleogene (K-Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian or early Paleocene and that, apart from the Detarioideae WGD, paleopolyploidy occurred close to the KPB. We conclude that the early evolution of the legumes followed a complex history, in which multiple auto- and/or allopolyploidy events coincided with rapid diversification and in association with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic.Swiss National Science FoundationUniversity of ZurichNatural Sciences and Engineering Research Council of CanadaNational Environment Research CouncilFonds de la Recherche Scientifique of Belgiu

Macroevolutionary patterns in overexpression of tyrosine:An anti‐herbivore defence in a speciose tropical tree genus, Inga (Fabaceae)

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this record.1.Plant secondary metabolites are a key defence against herbivores, and their evolutionary origin is likely from primary metabolites. Yet for this to occur, an intermediate step of overexpression of primary metabolites would need to confer some advantage to the plant. Here, we examine the evolution of overexpression of the essential amino acid, L‐tyrosine and its role as a defence against herbivores. 2.We examined overexpression of tyrosine in 97 species of Inga (Fabaceae), a genus of tropical trees, at five sites throughout the Neotropics. We predicted that tyrosine could act as an anti‐herbivore defence because concentrations of 4% tyrosine in artificial diets halved larval growth rates. We also collected insect herbivores to determine if tyrosine and its derivatives influenced host associations. 3.Overexpression of tyrosine was only present in a single lineage comprising 21 species, with concentrations ranging from 5% to 20% of the leaf dry weight. Overexpression was pronounced in expanding but not in mature leaves. Despite laboratory studies showing toxicity of L‐tyrosine, Inga species with tyrosine suffered higher levels of herbivory. We therefore hypothesize that overexpression is only favoured in species with less effective secondary metabolites. Some tyrosine‐producing species also contained secondary metabolites that are derived from tyrosine: tyrosine‐gallates, tyramine‐gallates and DOPA‐gallates. Elevated levels of transcripts of prephenate dehydrogenase, an enzyme in the tyrosine biosynthetic pathway that is insensitive to negative feedback from tyrosine, were found only in species that overexpress tyrosine or related gallates. Different lineages of herbivores showed contrasting responses to the overexpression of tyrosine and its derived secondary metabolites in their host plants. 4.Synthesis. We propose that overexpression of some primary metabolites can serve as a chemical defence against herbivores, and are most likely to be selected for in species suffering high herbivory due to less effective secondary metabolites. Overexpression may be the first evolutionary step in the transition to the production of more derived secondary metabolites. Presumably, derived compounds would be more effective and less costly than free tyrosine as anti‐herbivore defences.National Science Foundatio