Abstract Detail

Phylogenomics

Lee, Aaron [1], Gilman, Ian S. [2], Srivastav, Mansa [3], Lerner, Ariel [4], Donoghue, Michael [5], Clement, Wendy [6].

Targeted enrichment of Angiosperms353 in the Dipsacales highlights nodes of conflict and clarity.

Phylogenetic relationships in the Dipsacales are generally well resolved, but largely based on plastid data. The remaining areas of poor resolution, including the placement of Heptacodium and Zabelia, and relationships within the Caprifolieae and Linnaeeae, hinder our interpretation of morphological evolution. In this first nuclear phylogenomic study of relationships among Dipsacales lineages, we sample a significant number of nuclear loci from the Angiosperms353 probe set using targeted enrichment. To compare the utility of these loci across taxonomic depths, we sampled 94 taxa both broadly across 43 of the 44 commonly recognized genera, and densely in three species-rich genera. Here, we present our data analysis pipeline and phylogenetic findings. We used a two-step approach in assembling the target loci in HybPiper, first using the original probe set, then “spiking” the target file with representative assembled loci from each major clade in Dipsacales. Paralog calls from 256 loci were visually assessed, of which 224 were retained. We then used Ward clustering of mean exon lengths to identify suitable loci and taxa, and tree-based methods to filter and clean locus alignments. Of the targeted 353 loci, we retained 313 exon-only and 308 exon+flanking region (supercontig) loci. We also assembled plastid genomes using mapping-based assembly from off-target reads. Our nuclear and plastid analyses largely resolved backbone and within-clade relationships, and we now confidently place Heptacodium sister to Caprifolieae at a well-supported node of clarity. However, the major clades Zabelia, Linnaeeae, and Morinoideae resisted resolution due to cytonuclear discordance and topological differences between exon-only and exon+flanking region alignments. Concordance analysis of gene trees at these nodes suggests that the flanking regions provide additional signal towards phylogenetic resolution. Furthermore, relationships between Linnaeeae genera are complicated by cytonuclear discordance, and species-level relationships in densely sampled clades (Viburnum and Caprifolieae) remain poorly supported despite high recovery. Ultimately, we favor reconstructing this first-pass nuclear phylogenomic Dipsacales tree with flanking regions due to their contributed sequence variation. However, our final trees were sensitive to filtering parameters of input phylogenomic data due to low variability across the target loci, particularly in exonic regions and woody lineages. At nodes of conflict, discordance between gene trees and cellular compartments indicate complex evolutionary histories; identifying their sources will require close investigation of incomplete lineage sorting, introgression, and hybridization.

1 - University of Minnesota, Twin Cities, Department of Plant and Microbial Biology, 712 Biological Sciences, 1445 Gortner Avenue, Saint Paul, MN, 55108, USA
2 - Yale University, Ecology and Evolutionary Biology, 165 Prospect St, Osborn Memorial Labs, New Haven, CT, 06511, USA
3 - Yale University, Ecology And Evolutionary Biology, 420 Temple Street, Helen Hadley Hall, Environmental Science Center, Room Number 356, New Haven, CT, 06511, United States
4 - The College of New Jersey, Department of Biology, 2000 Pennington Road, Ewing, NJ, 08628, USA
5 - Yale University, Department Of Ecology And Evolutionary Biology, 21 Sachem St., New Haven, CT, 06511, United States
6 - The College Of New Jersery, Dept. Of Biology, 2000 Pennington Road, Ewing, NJ, 08628, United States

Keywords:
Zabelia
Heptacodium
Angiosperms353
gene tree conflict
cytonuclear discordance.

Presentation Type: Oral Paper
Session: PHYLOIII, Phylogenomics III
Location: Virtual/Virtual
Date: Thursday, July 22nd, 2021
Time: 11:15 AM(EDT)
Number: PHYLOIII006
Abstract ID:602
Candidate for Awards:None