Molecular phylogeny and evolution of inflorescence types in Eperua

The Amazonian hyperdominant genus Eperua (Fabaceae) currently holds 18 described species and has two strongly different inflorescence and flower types, with corresponding different pollination syndrome. The evolution of these vastly different inflorescence types within this genus was unknown and the main topic in this study.

We constructed a molecular phylogeny, based on the full nuclear ribosomal DNA and partial plastome, using Bayesian inference and maximum likelihood methods, to test whether the genus is monophyletic, whether all species are monophyletic and if the shift from bat to bee pollination (or vice versa) occurred once in this genus.

All but two species are well supported by the nuclear ribosomal phylogeny. The plastome phylogeny, however, shows a strong geographic signal suggesting strong local hybridization or chloroplast capture, rendering chloroplast barcodes meaningless in this genus.

With our data, we cannot fully resolve the backbone of the tree to clarify sister genera relationships and confirm monophyly of the genus Eperua. Within the genus the shift from bat to bee and bee to bat pollination has occurred several times but, in the latter, not always leading to a pendant inflorescence.

Methods
The data was obtained by genome skims of Eperua species (150 bp reads). We used Illumina HiSeq and NovaSeq sequencing and made de-novo assemblies of nuclear ribosomal DNA (NRb) and the full plastome. For those accessions where de-novo assembly did not work, we mapped the reads on those that were successful. For the plastome, we extracted the coding DNA sequences (CDS). NRb and CDS sequences were aligned with MAFFT. 

See Molecular phylogeny and evolution of inflorescence types in Eperua, American Journal of Botany for full methods.