Abstract Detail


Spooner, David [1], Ruess, Holly [2], Ellison, Shelby [3], Senalik, Douglas [4], Simon, Philipp [4].

Consensus and discordance in next-generation phylogenetic analyses of Daucus.

High throughput (next-generation) DNA sequencing has removed barriers to data quantity and quality and produces phylogenies with high statistical support. Such data are useful to address phylogenetic congruence among individual genes. 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, three reported before: (1) the entire plastid genome, (2) 47 mitochondrial genes, (3), 94 conserved nuclear orthologs. Here, we report a fourth dataset, (4) 564,895 nuclear SNPs. There are areas of discordance in all four results using the same accessions analyzed with maximum parsimony, maximum likelihood, and with the nuclear data coalescent analyses. The latter two nuclear results show significant areas of discordance that were especially unexpected because these studies used the same DNA samples, the nuclear studies were generated from large and high-quality data sets with the SNPs distributed on all nine linkage groups of D. carota, and the results were supported by high bootstrap values. These results raise questions of the best data and analytical methods to reconstruct and understand the ‘truth’ of a phylogeny.

1 - USDA Agricultural Research Service, 1575 Linden Drive, 1575 Linden Drive, Madison, WI, 53706, United States
2 - University of Texas Southwestern Medical Center, Bioinformatics Core Facility, Dallas, TX, USA
3 - University of Wisconsin, Horticulture, 1575 Linden Drive, Madison, WI, 53706
4 - USDA ARS; University of Wisconsin, Horticulture, 1575 Linden Drive, Madison, WI, 53706

phylogenetic discordance.

Presentation Type: Oral Paper
Session: PHYL1, Phylogenomics I
Location: Virtual/Virtual
Date: Monday, July 27th, 2020
Time: 1:00 PM
Number: PHYL1003
Abstract ID:143
Candidate for Awards:None

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