Simulating and Summarizing Sources of Gene Tree Incongruence

Abstract

We introduce a gene tree simulator that is designed for use in conjunction with approximate Bayesian computation approaches. We show that it can be used to determine the relative importance of hybrid speciation and introgression compared with incomplete lineage sorting (ILS) in producing patterns of incongruence across gene trees. Important features of the new simulator are (1) a choice of models to capture the decreasing probability of successful hybrid species formation or introgression as a function of genetic distance between potential parent species; (2) the ability for hybrid speciation to result in asymmetrical contributions of genetic material from each parent species; (3) the ability to vary the rates of hybrid speciation, introgression, and divergence speciation in different epochs; and (4) incorporation of the coalescent, so that patterns of incongruence due to ILS can be compared with those due to hybrid evolution. Given a set of gene trees generated by the simulator, we calculate a set of statistics, each measuring in a different way the discordance between the gene trees. We show that these statistics can be used to differentiate whether the gene tree discordance was largely due to hybridization, or only due to lineage sorting.

Transcriptome‐based target‐enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia)

“…Nevertheless, our analyses have recovered a maximally‐supported phylogeny, with a topology congruent with recent broad‐scale phylogenies (Figure 2; Kitahara et al, 2016; Quek & Huang, 2019). We noted a slightly elevated level of gene tree incongruence among members of the “Robust” clade (Figure S1), which could be attributed to factors such as incomplete lineage sorting (Woodhams, Lockhart, & Holland, 2016) and varying phylogenetic signal between clades (Gonçalves, Simpson, Ortiz, Shimizu, & Jansen, 2019). Analyses similar to that of Ying et al (2018) performed at a broader scale would reveal factors driving these differences.…”

Efficient summary statistics for detecting lineage fusion from phylogeographic datasets

“…To address this, we need efficient summary statistics for detecting such events, and the present work is an early attempt. Follow‐up work should explore the utility of gene tree‐based summary statistics (e.g., metrics for shape, Fu & Li, 1993; Pybus & Harvey, 2000, or incongruence, Woodhams, Lockhart, & Holland, 2016), scenarios involving merging of non‐sister populations (Garrick et al., 2014; Kearns et al., 2018) or repeated fission‐fusion cycles (Alcala et al., 2016; Alcala & Vuilleumier, 2014), and assess the impact of simplifying assumptions (e.g., instantaneous fusion, recombination‐free neutral independent loci, or equivalence of cumulative N e between fusion and associated baseline scenarios). Notwithstanding remaining knowledge gaps, the capacity of phylogeographers to explicitly consider lineage fusion, owing to the field's transformation from data‐limited to data‐rich (Edwards, Shultz, & Campbell‐Staton, 2015; Garrick et al., 2015), represents a meaningful advancement.…”

A new fast method for inferring multiple consensus trees using k-medoids

“…During the first step, we randomly generated a species phylogenetic tree (i.e. first consensus tree here) T 1 with n leaves using the HybridSim [ 39 ] program. Then, using the same program, we generated K −1 other consensus trees, T 2 , …, T K with n leaves, each of which differed from T 1 by a specified number of hybridization events (the value of the hybridization rate parameter in the HybridSim program varied from 1 to 4 in our simulation; it was drawn randomly using a uniform distribution).…”

“…The HybridSim program developed by Woodhams et al [ 39 ] allows generation of phylogenies in the presence of hybridization and horizontal gene transfer events. This program can generate trees differing from each other by a specified number of coalescence/incomplete lineage sorting producing patterns of incongruence across gene trees.…”