Testing species relationships and delimitation in the Amazonian hyperdominant Astrocaryum section Huicungo (Arecaceae) using chloroplast data from genome skimming

Hyperdominant trees in Amazonia account for half of the individual trees (>10 cm dbh) in the forest, and thus play a crucial role in ecosystem dynamics. However, several of these widespread hyperdominant species may be complexes hiding cryptic diversity that can affect species richness estimates and conservation priorities. Here, we study the intraspecific variation of Astrocaryum murumuru (Arecaceae), a keystone and hyperdominant species in Amazonia, also known as Astrocaryum sect. Huicungo, a complex of 15 understory to subcanopy palm species. Using chloroplast DNA from genome skimming (>66 kbp alignment) in a Bayesian framework, we present evidence that A. sect. Huicungo represents three separately evolving lineages, suggesting that the section is not a single hyperdominant species, and that the 15 morphology-based species may be an over-representation. Genome skimming chloroplast data did not fully resolve the species-level phylogenetic relationships in A. sect. Huicungo mostly because of gene discordance and the paraphyly of most species. Contrary to a previous nuclear-based phylogenetic analysis, the chloroplast genomic data did not recover A. sect. Huicungo monophyletic, but yielded monophyly in an increased number of species (six) in the complex. Interspecific phylogenetic relationships showed a geographic pattern, and the traditional morphology-based classification was not supported. Our phylogenomic results are discussed in light of earlier phylogeographical studies using Sanger sequencing. Our findings show the utility of genome skimming data in species delimitation analyses to uncover intraspecific variation of hyperdominant species in Amazonia, the largest evergreen tropical forest.