The Impact of Species Tree Estimation Error on Cophylogenetic Reconstruction

Abstract

AbstractJust as a phylogeny encodes the evolutionary relationships among a group of organisms, a cophylogeny represents the coevolutionary relationships among symbiotic partners. Both are widely used to investigate a range of topics in evolutionary biology and beyond. Both are also primarily reconstructed using computational analysis of biomolecular sequence data as well as other biological character 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 theoretical and experimental 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 estimation error and downstream cophylogenetic estimation accuracy. The study includes performance benchmarking usingin silicomodel-based simulations. Our investigation also includes assessments of cophylogenetic reproducibility using genomic sequence datasets sampled from two important models of symbiosis: soil-associated fungi and their endosymbiotic bacteria, and bobtail squid and their bioluminescent bacterial symbionts. Our findings conclusively demonstrate the major impact that upstream phylogenetic estimation error has on downstream cophylogenetic reconstruction quality.