The Impact of Species Tree Estimation Error on Cophylogenetic Reconstruction

Kevin J. Liu

Abstract:

Just as a phylogeny encodes the evolutionary relationships among a group of organisms, a cophylogeny represents the coevolutionary relationships among symbiotic partners. Both are primarily recon- structed using computational analysis of biomolecular sequence data. The most widely used cophylogenetic reconstruction methods utilize an important simplifying assumption: species phylogenies for each set of coevolved taxa are required as input and assumed to be correct. Many studies have shown that this assumption is rarely – if ever – satisfied, and the consequences for cophylogenetic studies are poorly understood.
To address this gap, we conduct a comprehensive performance study that quantifies the relationship between species tree estima- tion error and downstream cophylogenetic estimation accuracy. We study the performance of state-of-the-art methods for cophy- logenetic reconstruction using in silico model-based simulations. Our investigation also includes assessments of cophylogenetic re- producibility using genomic sequence datasets sampled from two important models of symbiosis: soil-associated fungi and their en- dosymbiotic bacteria, and bobtail squid and their bioluminescent bacterial symbionts.
Our findings conclusively demonstrate the major impact that upstream phylogenetic estimation error has on downstream co- phylogenetic reconstruction quality. Relative to other experimental factors such as cophylogenetic estimation method choice and coevo- lutionary event costs, phylogenetic estimation error ranked highest in importance based on a random forest-based variable importance assessment. We conclude with practical guidance and future re- search directions. In particular, among the many considerations needed for accurate cophylogenetic reconstruction – choice of co- phylogenetic reconstruction method and method settings, sampling design, and others – just as much attention must be paid to careful species phylogeny estimation using modern best practices.