Fig. 3: Benchmarks.
From: EdgeHOG: a method for fine-grained ancestral gene order inference at large scale
a, The simulated genome evolution benchmark. Each dot represents one of the 99 ancestral levels in a species tree with 100 extant genomes. The x axis gives the relative evolutionary divergence44 from root of an ancestral node (0 for the root, near to 1 close to the leaves). The top row’s y axis gives the precision of each algorithmic step of edgeHOG and of Agora at each ancestral level, measuring the proportion of predicted edges that are true edges in the simulated ancestral genome. The bottom row’s y axis shows recall, that is, the proportion of true edges predicted by each method. b, The YGOB benchmark. The species tree depicts the phylogeny of the 20 yeast genomes in YGOB. The star indicates a whole genome duplication (WGD) event in the last common ancestor of 12 yeasts. The pink circle indicates the tree root, where YGOB-curated ancestral gene order is available. This curated order is compared with predictions by edgeHOG and AGORA, allowing evaluation of precision and recall. c, The masked extant gene orders benchmark. The species tree on the left shows the phylogeny of 50 vertebrate genomes from the OMA database, sampled to represent clade diversity. The ten coloured extant genomes correspond to those whose gene order is masked (and is to be inferred). The ten coloured internal levels correspond to the most direct ancestor of each masked species. Scatterplots compare edgeHOG and AGORA in inferring masked edges using a projection of each edge between two ancestral genes at the parental level onto their corresponding single-copy descendant genes in the extant masked species. Note the near 0% recall for Salmo trutta due to a whole gene duplication on its terminal branch, leaving no information to ‘phase’ the duplicated genes. Panel c silhouettes adapted from PhyloPic under Creative Commons licenses: Anguilla anguilla, Ingo Braasch (CC0 1.0); Salmo trutta, Carlos Cano-Barbacil (CC0 1.0); Cirripectes variolosus, Mykle Hoban (CC BY-SA 3.0); Latimeria chalumnae, Chuanixn Yu (CC0 1.0); Podarcis muralis, Titouan Montessuit (Attribution 4.0 International); Crocodylus, Becky Barnes (CC0 1.0); Nestor notabilis, Matías Muñoz (CC0 1.0); Tachyglossus aculeatus, Becky Barnes (PDM 1.0); Manis culionensis, Steven Traver (CC0 1.0); Tupaia javanica, Margot Michaud (CC0 1.0).
