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Q&A ViewAttendees 15

Systematics, Evolution, and Biodiversity

10-Minute Paper

SysEB: Phylogenetics

No one tree to rule them all? Why phylogenomics of large trees may struggle to provide good resolution at all levels

Sunday, October 31, 2021
2:18 PM – 2:30 PM MT
Location: Colorado Convention Center, Meeting Room 505-507
In-Person
Many phylogenomic studies find that while some relationships are easily resolved and have held up since Sanger sequencing days, many difficult nodes remain so even with genome-scale data. Despite theory predicting that incomplete lineage sorting, introgression, and systematic bias are likely to produce discordant or unreliable phylogenetic estimates within genomes and across species, early phylogenomic work was conducted with the hope that more data will help resolve even the most recalcitrant nodes. With a number of whole-genome studies uncovering discordant relationships now published, the focus is shifting to investigation of sources of discordance within genomes and across the tree of life. Here we analyze a new phylogenomic dataset for ants, sequencing representatives of 179 genera and combining those with publicly available sequences for a total of 280 ant taxa from all subfamilies and 83% of genera, representing over 98% of described species-level diversity. This phylogeny presents examples of both “easy” and “difficult” nodes. We investigate the relative contribution of biological and technical causes behind poorly resolved relationships using simulations and recently developed approaches to measuring phylogenomic support. We find that recalcitrant nodes are expected because simulation shows the shortest branches of the ant tree contain minimal signal even with thousands of loci. Furthermore, current approaches for optimizing resolution at deeper nodes of the tree (e.g. relationships among subfamilies) may compromise resolution towards the tips (e.g. relationships among genera). Therefore, separate analyses targeting different levels of divergence may be necessary for the most accurate picture of relationships.