title: Revisiting phylogenetic signal; strong or negligible impacts of polytomies and branch length information?
abstract: Inaccurate estimates of phylogenetic signal may mislead interpretations of many ecological and evolutionary processes, and hence understanding where potential sources of uncertainty may lay has become a priority for comparative studies. ﻿﻿﻿﻿Importantly, the sensitivity of phylogenetic signal indices and their associated statistical tests to incompletely resolved phylogenies and suboptimal branch-length information has been only partially investigated.﻿﻿﻿ METHODS: ﻿﻿﻿Here, we use simulations of trait evolution along phylogenetic trees to assess whether incompletely resolved phylogenies (polytomic chronograms) and phylogenies with suboptimal branch-length information (pseudo-chronograms) could produce directional biases in significance tests (p-values) associated with Blomberg et al.'s K and Pagel's lambda (λ) statistics, two of the most widely used indices to measure and test phylogenetic signal. Specifically, we conducted pairwise comparisons between the p-values resulted from the use of "true" chronograms and their degraded counterparts (i.e. polytomic chronograms and pseudo-chronograms), and computed the frequency with which the null hypothesis of no phylogenetic signal was accepted using "true" chronograms but rejected when using their degraded counterparts (type I bias) and vice versa (type II bias).
  
  
  
  We found that the use of polytomic chronograms in combination with Blomberg et al.'s K resulted in both, clearly inflated estimates of phylogenetic signal and moderate levels of type I and II biases. More importantly, pseudo-chronograms led to high rates of type I biases. In contrast, Pagel's λ was strongly robust to either incompletely resolved phylogenies and suboptimal branch-length information.
  
  
  
  Our results suggest that pseudo-chronograms can lead to strong overestimation of phylogenetic signal when using Blomberg et al.'s K (i.e. high rates of type I biases), while polytomies may be a minor concern given other sources of uncertainty. In contrast, Pagel's λ seems strongly robust to either incompletely resolved phylogenies and suboptimal branch-length information. Hence, Pagel's λ may be a more appropriate alternative over Blomberg et al.'s K to measure and test phylogenetic signal in most ecologically relevant traits when phylogenetic information is incomplete.
authors.affiliation: Departamento de Ciencias de la Vida, Universidad de Alcalá, 28805, Alcalá de Henares, Madrid, Spain. rmolina@us.es.
authors.forename: Rafael
authors.initials: R
authors.lastname: Molina-Venegas
authors.affiliation: Departamento de Ciencias de la Vida, Universidad de Alcalá, 28805, Alcalá de Henares, Madrid, Spain.
authors.forename: Miguel Á
authors.initials: MÁ
authors.lastname: Rodríguez
mesh_terms: D005075:Biological Evolution; D008957:Models, Genetic; D010802:Phylogeny
keywords: BLADJ; Blomberg’s K; Pagel’s lambda; Phylogenetic resolution; Phylogeny calibration; Pseudo-chronograms