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Phylogenomics of the carrot genus (Daucus, Apiaceae)

Carlos Arbizu, Holly Ruess, Douglas Senalik, Philipp W. Simon, David M. Spooner
American journal of botany 2014 v.101 no.10 pp. 1666-1685
monophyly, Daucus, carrots, alleles, germplasm conservation, data collection, topology, nucleotide sequences, DNA
Molecular phylogenetics of genome-scale data sets (phylogenomics) often produces phylogenetic trees with unprecedented resolution. We here explore the utility of multiple nuclear orthologs for the taxonomic resolution of a wide variety of Daucus species and outgroups. We studied the phylogeny of 89 accessions of 13 species and two subspecies of Daucus, and an additional ten accessions of related genera (Ammi, Astrodaucus, Caucalis, Margotia, Oenanthe, Orlaya, Pseudorlaya, Torilis, Turgenia) with DNA sequences of 94 nuclear orthologs of average aligned length of 1180 bp, with a concatenated database length of 111,166 bp. We analyzed our data with maximum parsimony (MP), maximum likelihood (ML), and concordance analysis. Reiterative analyses examined data of both alleles using ambiguity codes or a single allele with the highest coverage, trimmed vs. untrimmed homopolymers, pure exonic vs. pure intronic data and the use of all 94 markers vs. reduced subset of markers. Our MP and ML trees are highly resolved, with 100% bootstrap support for most of the external and many of the internal clades. They grouped multiple accessions of many different species as monophyletic with strong support, but failed to support others such as 1) the subspecies of D. carota and D. capillifolius, 2) D. sahariensis and D. syrticus, and 3) D. broteri and D. guttatus. These taxa also are hard to distinguish with morphological characters. The single allele analysis gave slightly better topological resolution in some clades, and is a logically more defendable analysis. Trimming homopolymers provided potentially more reliable data, but was time consuming failed to increase taxonomic resolution. The exonic data, as expected, had fewer parsimony-informative characters in the intronic regions as a proportion of the total characters. Similar phylogenetic results of the dominant topology can be obtained with many fewer markers. Our research highlights some difficult species groups in Daucus, and discovered misidentifications in germplasm collections. It highlights a useful subset of markers and methodological approaches for future studies of a dominant topologies in Daucus, saving time and funds. The entire database is useful for future workers wishing to explore causes of discordance in Daucus.