What is truth: consensus and discordance in next-generation phylogenetic analyses of Daucus

Authors: Spooner, David; RUESS, HOLLY - Former ARS Employee; Ellison, Shelby; Senalik, Douglas; Simon, Philipp

Submitted to: Journal of Systematics and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/20/2020
Publication Date: 8/25/2020
Citation: Spooner, D.M., Ruess, H., Ellison, S.L., Senalik, D.A., Simon, P.W. 2020. What is truth: consensus and discordance in next-generation phylogenetic analyses of Daucus. Journal of Systematics and Evolution. 58(6):1059-1070. https://doi.org/10.1111/jse.12678.
DOI: https://doi.org/10.1111/jse.12678

Interpretive Summary: Wild and cultivated carrots, technically classified in the genus Daucus, traditionally have contained about 20-25 species worldwide, but a recent molecular-based classification raised the number of Daucus species to about 40, and includes representatives from other traditionally defined genera. This work is part of a broad-range study to better understand the species boundaries and generic limits in Daucus, using massive deoxyribonucleic acid (DNA) data sets gathered by new technologies, by studying the three components of the DNA compartments of the plant, technically referred to as the chloroplast, nucleus, and mitochondria. The trees of interrelationships generated by these techniques are sometimes quite different, even within one of the three genomic compartments, depending on how the data were generated and analyzed. The degree of these differences was unexpected, especially within individual genomes, as we demonstrate by analyzing nuclear DNA from the same carrot species with nuclear fractions and different analytical methods. This study is useful to those studying carrot phylogenies and indeed phylogenies from other plants because it clearly demonstrates this result using a well-studied plant group (the genus Daucus), with different next-generation DNA data sets, and with different analytical methods.

Technical Abstract: High throughput (next-generation) DNA sequencing has revolutionized plant molecular systematics by removing barriers to data quantity and quality. Systematic studies now routinely are conducted with tens to hundreds of thousands of high-quality DNA characters, and often generate phylogenetic trees with high levels of statistical support. Taxonomic incongruence among individual genes or genic regions has long been appreciated and next generation sequencing provides opportunities to explore and quantify its extent. Concatenated analyses of unlinked genes often produce well-resolved phylogenetic trees with bootstrap support on major nodes at or approaching 100%, but have been criticized for providing incorrect phylogenies for various reasons to include a history of hybridization, introgression, and incomplete lineage sorting. The present study compares next-generation sequencing results of the same accessions of Daucus with different genomic regions (94 conserved nuclear orthologs, resequencing data of exonic and intronic regions, and resequencing data of the entire plastid genome), using different analytical methods (maximum parsimony, maximum likelihood, coalescent analyses). The results show significant areas of discordance across both data sets and analytical methods that raise questions of the best data and analytical methods to reconstruct and understand the “truth” of a phylogeny.