Incongruence in the phylogenomics era

Abstract

Genome-scale data and the development of novel statistical phylogenetic approaches have greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its branches. However, incongruence - the inference of conflicting evolutionary histories - remains pervasive in phylogenomic data, hampering our ability to reconstruct and interpret the tree of life. Biological factors, such as incomplete lineage sorting, horizontal gene transfer, hybridization, introgression, recombination and convergent molecular evolution, can lead to gene phylogenies that differ from the species tree. In addition, analytical factors, including stochastic, systematic and treatment errors, can drive incongruence. Here, we review these factors, discuss methodological advances to identify and handle incongruence, and highlight avenues for future research.

Figure 1 |. Incongruence at different levels of genomic organization.

a | The topology shown in blue supports a sister group relationship of taxa A and B, whereas the orange topology supports a sister group relationship of taxa A and C. The inference of such conflicting topologies defines incongruence. Incongruence can occur at different levels in the genome, such as among c | whole chromosomes (e.g., analyses of one chromosome support the blue topology but analyses of another support the orange topology), d | regions of a chromosome (dark grey regions represent lack of homology), e | genes (or loci), f | within a gene or locus (e.g., different domains support different topologies), and g | among sites in a multiple sequence alignment. Note that incongruence is also prevalent in other types of data (e.g., behavioral or morphological traits) and can occur at all evolutionary depths.

Figure 2 |. Major biological factors that contribute to incongruence.

Incomplete lineage sorting can lead to to gene trees that differ from the species phylogeny due to variation in the sorting of ancestral polymorphisms. Horizontal gene transfer, hybridization, and introgression can all lead to gene phylogenies that differ from the species tree. Recombination can result in loci with chimeric evolutionary histories. Duplication and loss can lead to hidden paralogy. Independently evolved traits in different phylogenetic lineages can be associated with convergent molecular evolution (green), contributing to incongruence.

Figure 3 |. Analytical factors can contribute to incongruence at every step in a phylogenomic workflow.

a | Taxon sampling can impact all downstream analyses in phylogenomic studies. b | During orthology inference, biases (e.g., sequence length biases) and analytical errors (e.g., erroneous orthology inferences) can contribute to incongruence. Each color corresponds to a unique ortholog present in each of the four taxa. c | Misalignment and excessive trimming of individual groups of orthologous genes can further decrease the accuracy of phylogenetic inferences. An example of erroneous ortholog inclusion is depicted using red font. d | Species tree inference via concatenation (left) or coalescence (right) is susceptible to multiple additional sources of error—complexity of model space, model misspecification, and inadequate model complexity, to name just a few.