Universal Artifacts Affect the Branching of Phylogenetic Trees, Not Universal Scaling Laws

Abstract

BackgroundThe superficial resemblance of phylogenetic trees to other branching structures allows searching for macroevolutionary patterns. However, such trees are just statistical inferences of particular historical events. Recent meta-analyses report finding regularities in the branching pattern of phylogenetic trees. But is this supported by evidence, or are such regularities just methodological artifacts? If so, is there any signal in a phylogeny?MethodologyIn order to evaluate the impact of polytomies and imbalance on tree shape, the distribution of all binary and polytomic trees of up to 7 taxa was assessed in tree-shape space. The relationship between the proportion of outgroups and the amount of imbalance introduced with them was assessed applying four different tree-building methods to 100 combinations from a set of 10 ingroup and 9 outgroup species, and performing covariance analyses. The relevance of this analysis was explored taking 61 published phylogenies, based on nucleic acid sequences and involving various taxa, taxonomic levels, and tree-building methods.Principal FindingsAll methods of phylogenetic inference are quite sensitive to the artifacts introduced by outgroups. However, published phylogenies appear to be subject to a rather effective, albeit rather intuitive control against such artifacts. The data and methods used to build phylogenetic trees are varied, so any meta-analysis is subject to pitfalls due to their uneven intrinsic merits, which translate into artifacts in tree shape. The binary branching pattern is an imposition of methods, and seldom reflects true relationships in intraspecific analyses, yielding artifactual polytomies in short trees. Above the species level, the departure of real trees from simplistic random models is caused at least by two natural factors –uneven speciation and extinction rates; and artifacts such as choice of taxa included in the analysis, and imbalance introduced by outgroups and basal paraphyletic taxa. This artifactual imbalance accounts for tree shape convergence of large trees.SignificanceThere is no evidence for any universal scaling in the tree of life. Instead, there is a need for improved methods of tree analysis that can be used to discriminate the noise due to outgroups from the phylogenetic signal within the taxon of interest, and to evaluate realistic models of evolution, correcting the retrospective perspective and explicitly recognizing extinction as a driving force. Artifacts are pervasive, and can only be overcome through understanding the structure and biological meaning of phylogenetic trees.Catalan Abstract in Translation S1.

Phylogenetic relationships within the superfamily Desmodoroidea (Nematoda: Desmodorida), with descriptions of two new and one known species

“…Likewise, one sequence of Robbea hypermnestra (KJ414467; Ott et al ., ) is located amongst other Stilbonematinae sequences, whereas another sequence of the same species identified by the same laboratory (Y16921; Kampfer, Sturmbauer & Ott, ) is grouped with species of Spiriniinae. The anomalous placement of the latter species is unlikely to be a result of misidentification, and may be the result of inherent artefacts in phylogenetic tree routines (Altaba, ). Therefore, our interpretation is that the family Draconematidae is a sister taxon to the Desmodorinae and Spiriniinae, with the Draconematidae forming a monophyletic crown group characterized by clear morphological synapomorphies (swollen pharyngeal body regions and mid‐posterior body regions with specialized setae) whereas the Desmodorinae and Spiriniinae comprise a paraphyletic stem group without morphological synapomorphies (Lorenzen, ; Fig.…”

A Synoptical Classification of the Bivalvia (Mollusca)

“…However, this reduction in rank merely shifted paraphyly from Cardioidea to its subfamily Cerastodermatinae, the ancestral stock group for Tridacninae. Building a taxonomy that includes living and extinct taxa presents a dilemma: choosing between explicitly recognizing paraphyletic taxa or multiplying supraspecific taxa beyond reasonable bounds (Cela-Conde & Altaba, 2002;Altaba, 2009). We favor an evolutionary classification that, being based upon cladistic analysis, does not dismiss evidence and reflects ancestor-descendant relationships.…”

Thinking in continua: beyond the “adaptive radiation” metaphor

“…However, the task of evolutionary biology is to explain the entire range of tree shapes, from highly symmetrical to maximally unbalanced, a task that is awkward or impossible from the adaptive radiation perspective. Happily, recent methods for exploring imbalance on continuous scales open the door to the study of the full range of imbalance and its causes 64–69. For example, Holman70 used an index of clade imbalance that varies continuously from 0 to 164, 66 to assess the relationship between imbalance and the number of species found at a given node.…”