Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology.

Abstract

Taxonomic congruence and total evidence are competing paradigms in phylogenetic inference. Taxonomic congruence focuses on deriving a consensus from the results obtained from separately analyzed data sets, whereas total evidence uses character congruence in the search for the best-fitting hypothesis for all of the available character evidence. Explicit or implicit use of taxonomic congruence is usually employed when an investigator either has both molecular and morphological data sets or has different gene-, rRNA-, or protein-sequence data sets available. Indeed, a taxonomic congruence rationale is frequently used as the basis for exploring classes of data, thus allowing comparison between the phylogenetic signal emerging from a particular data set and those of other such classes. Problematic aspects of employing the taxonomic congruence approach include the potentially misleading and arbitrary choices of both a consensus method and the division of characters into subsets. If the goal of an analysis is to provide the best estimate of genealogy afforded by the available character evidence, then taxonomic congruence is substantially more arbitrary than a total evidence approach. The theoretical advantages of phylogenetic estimates based on total evidence are argued in the present study and are illustrated with an example of amniote relationships. We report conflicting results from total evidence and taxonomic congruence approaches, with analyses of previously reported data from both fossil and living amniotes and from both morphology and molecules, the latter including available 18S rRNA, 28S rRNA, and protein sequences. We conclude that a more highly resolved and robust phylogenetic hypothesis of amniotes, the traditional one, emerges when a total evidence approach is employed.

Generic circumscriptions in <I>Geoglossomycetes</I>

“…Effective sample size (ESS) was estimated using Tracer v. 1.5 (Rambaut & Drummond 2009). Individual datasets of ITS, LSU, MCM7 and RPB1 were examined for potential conflict before concatenated into a single dataset for total evidence analysis (Kluge 1989, Eernisse & Kluge 1993). Individual gene phylogenies were considered to be incongruent if clades with significant ML BS and BPP (≥ 70 % BS and/or ≥ 95 % BPP) were conflicting in the individual tree topologies (Wiens 1998, Alfaro et al 2003, Lutzoni et al 2004).…”

The Head and Neck Anatomy of Sea Turtles (Cryptodira: Chelonioidea) and Skull Shape in Testudines

“…[79], [90]–[92]). Combined morphological-molecular studies to date, appear to mainly support an anapsid origin [70], [73]. Evidence from embryological data suggests an origin from outside Sauria (Lepidosauria+Archosauria) [42].…”

“…Although this interpretation is often labelled the “traditional” hypothesis (e.g. [59], [70]–[74]), there are several examples of pre-cladistic and premolecular studies that instead argued in favour of a closer affinity between turtles and diapsids based on morphological data (e.g. [45]–[47], [75]–[79]).…”

Extensive introgression in a malaria vector species complex revealed by phylogenomics

“…The total evidence approach to phylogenetic reconstruction ( 24 ) is premised on the notion that the best estimate of species relationships arises from character congruence when all available data are considered simultaneously. Alternative approaches seek taxonomic congruence between different data sets or data partitions, analyzed separately ( 25 ).…”