Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms

The gene tree delusion

“…12). The striking difference between ASTRAL and MP-EST may be explained by MP-EST's reliance on rooted gene trees whereas the input for ASTRAL is unrooted quartets (Simmons and Gatesy, 2015). ASTRAL bootstrap support for Perissodactyla + Carnivora (67%) based on 413 genes is also much lower than Song et al's (2012) reported support values of 96% and 98% for this controversial clade based on MP-EST and STAR, respectively (Fig.…”

“…Song et al (2012) reported bootstrap trees for both MP-EST and STAR in their figure S1 for 447 genes, but did not show optimal trees based on these methods. We performed shortcut coalescence analyses with the 447 gene trees from Song et al (2012) to determine the optimal species tree(s) with MP-EST, STAR, and also ASTRAL that is less prone to misrooting artifacts (Simmons and Gatesy, 2015). The optimal MP-EST tree ( Fig.…”

Inferring rooted species trees from unrooted gene trees using approximate Bayesian computation

“…Simmons and Gatesy (2015) argue that the anomaly zone, in which the most probable gene tree has a different topology from that of the species tree, does not apply to the rooting of the angiosperms because there is only one short branch leading to the Amborella-Nuphar clade, whereas the anomaly zone typically occurs when there are two consecutive branches on a path from the root to the tips (Degnan, 2013; Rosenberg, 2013). Although this is typical of species trees in the anomaly zone, a species tree with only one short branch can still be in the anomaly zone if the less basal branch can be indefinitely long if the more basal branch is sufficiently short (Degnan and Rosenberg, 2006).…”

Response to Comment on “Statistical binning enables an accurate coalescent-based estimation of the avian tree”

“…Thus, the research community needs species tree estimation methods that are highly accurate for large taxon data sets with gene tree estimation error. Although there is progress in the development of summary methods with good accuracy under these conditions (5), all current summary methods are affected by gene tree estimation error (1,(5)(6)(7)(8)(9)(10)(11). Hence, WSB provides a useful tool for species tree estimation in modern phylogenomic analysis.…”

“…However, all current proofs of statistical consistency for standard coalescent-based summary methods assume error-free gene trees. Furthermore, concatenated analyses can be more accurate than summary methods in the presence of substantial gene tree estimation error resulting from low phylogenetic signal (1,(5)(6)(7)(8)(9)(10)(11), a problem that confronted the Avian Phylogenomics Consortium (12). Because simulations showed that species trees computed with statistical binning followed by the summary method maximum pseudolikelihood estimation of species trees (MP-EST) (4) "produced more accurate estimated species trees compared to MP-EST applied to unbinned gene data sets that have low phylogenetic signal" (12), the Avian Phylogenomics Consortium (which included Liu and Edwards) decided to use statistical binning with MP-EST to compute a coalescentbased avian species tree (12).…”