Palm phylogenomics

NAISS 2023/5-428


NAISS Medium Compute

Principal Investigator:

Christine Bacon


Göteborgs universitet

Start Date:


End Date:


Primary Classification:

10615: Evolutionary Biology

Secondary Classification:

10607: Botany




Palms are a very diverse group of plants typical of tropical environments globally, in particular in the most diverse tropical area in the world – the American tropics (neotropics). Because of their diversity, palms are a powerful group for studying tropical systems in general. The aim of our project is to produce a phylogeny characterizing the relationships of the palms of the neotropics based on genetic data from Illumina short-read sequencing. This technology works by fragmenting the genome into small pieces which are read by a machine. Reassembling the short reads that are output by the machine are very computationally heavy, as are the downstream steps in going from assembled genomic data to aligning them between species, making gene trees from inferring the distance between genes in different species and finally producing a species tree by synthesizing the often discrepant relationships between genes. Such phylogenetic trees contain information about not only relationships between species, but also the different rates of formation of new species (speciation) along the different branches. The tips of the trees represent living species, which have known distribution data. By defining broad geographical areas based on habitat differences deemed biologically distinct, and then binning living species into these based on their distribution, we can perform analyses important for understanding evolution in the neotropics. It has previously been shown that the Amazon rainforest bioregion is a net supplier of species, meaning more species move out of Amazon than into it. This net outflow of species from the Amazon coupled with the high species richness within could be explained by higher diversification rates in the Amazon. It could also be explained by relative age of the species within, the climastic stability of the Amazon allowing species to accumulate over time, leading to a more species rich system. In our project, using the phylogeny we crate, we will estimate diversification of lineages within the amazon compared to adjacent regions, and the relative age of lineages within vs. outside the Amazon. This will lead to greater understanding of why some areas of the world are more species rich than others, and whether higher diversification or ability to persist in stable environments are more important for making more species rich environments.