The Evolutionary Puzzle: Charting the Challenges of Phylogenomic Incongruence
Incongruence in the phylogenomics era
The study of phylogenetics plays a crucial role in deciphering the evolutionary history of organisms, genes, and biological traits. By reconstructing the Tree of Life, valuable insights have been gained into the history of life on Earth. In recent years, phylogenomics (phylogenetic analysis of genome-scale data) has emerged as the gold standard for determining life’s history. While it has brought newfound clarity to many branches of the Tree of Life, there are still unresolved branches that have a significant impact on our understanding of key evolutionary events, such as early animal evolution. In this article, we chart the cadre of biological and analytical factors contributing to conflicting phylogenetic hypotheses, known as incongruence.
Biological Factors: When Locus History Differs from Organismal History
Several biological factors contribute to the incongruence. Incomplete lineage sorting is one such factor, occurring when locus lineages do not neatly align with speciation events, leading to discrepancies between locus trees and species trees. Horizontal gene transfer involves the transfer of genetic material between organisms without sexual reproduction and is a non-vertical mode of evolution. Hybridization/introgression, another non-vertical mode of evolution, refers to the interbreeding of distinct species or lineages, resulting in the transfer of genetic material and hybrid lineages. Recombination, the shuffling of genetic material during meiosis, can result in new combinations of alleles and chimeric loci with distinct evolutionary histories. Finally, convergent molecular evolution occurs when sequences independently evolve in different lineages, potentially leading to the inference of incorrect evolutionary relationships.
Analytical Factors: The Challenges of Data Analysis
Analytical factors also contribute to incongruence in phylogenomic studies. Stochastic errors arising from random variation in data can affect the accuracy of phylogenetic inference. These errors include sampling error, measurement error, and model misspecification. Systematic errors, on the other hand, are non-random biases in data that impact the accuracy of phylogenetic inference. These biases can stem from long-branch attraction, compositional heterogeneity, or saturation. Treatment errors encompass the mistakes that can arise from the choice of analytical methods or software, such as substitution models, partitioning schemes, or alignment trimming and tree search algorithms. Correcting these errors can greatly improve the accuracy of phylogenomic inference.
Detecting Incongruence: Where is the Tree Unstable?
There are various methods to detect incongruence in phylogenomic data sets. One such method involves subsampling smaller subsets of loci with a robust phylogenetic signal and re-inferring the species phylogeny—this is termed phylogenomic subsampling. Single-locus phylogenetic tree topologies and information content can also shed light on incongruence. Quartet sampling, where the relationships between four taxa are analyzed, is another effective approach. These methods are essential for identifying and addressing incongruence to enhance the accuracy of phylogenomic inference.
Future Directions: The Path Ahead
The field of phylogenomics holds numerous avenues for future research:
• Which factors matter and when? Developing pipelines to account for diverse sources of error will remain a key component to phylogenomic research.
• More (high-quality) taxa, more (high-quality) genes. Obtaining high-quality data will improve all processes in a phylogenomic workflow.
• The forest grows: how can tree space be efficiently examined? As datasets continue to grow, so does the number of possible topologies. Efficiently searching for the ‘best’ tree is a statistical challenge.
• Green computing. Phylogenomics can take a massive amount of computation. The carbon footprint of such computing cannot be overlooked.
These research directions underscore the need for innovation and collaboration in phylogenomics. With continued advancements and interdisciplinary efforts, we can further transform our understanding of the Tree of Life, unravel the mysteries of biodiversity, and gain profound insights into the evolution of life on our planet.
Conclusion
Although phylogenomics has greatly advanced our understanding of the Tree of Life, incongruence persists due to biological and analytical factors. This article has explored these factors, discusses methods to identify and address incongruence, and outlined future research avenues. Correcting incongruence is crucial for improving the accuracy of phylogenomic inference. As innovation and collaboration thrive in the field, we can anticipate a continued transformation in our understanding of the Tree of Life and the intricate tapestry of biodiversity it represents.
Reference
Steenwyk, J.L., Li, Y., Zhou, X. et al. Incongruence in the phylogenomics era. Nat Rev Genet (2023). https://www.nature.com/articles/s41576-023-00620-x