Abstract
Phylogenetic trees underpin reconstructions of evolutionary history and tests of evolutionary hypotheses. They are inferred from both molecular and morphological data, yet the relative value of morphology has been questioned in this context due to perceived homoplasy, developmental linkage, and nonindependence of characters. Nevertheless, fossil data are limited to incomplete subsets of preserved morphology, and different regions are treated as equivalent. Through meta-analysis of 40 data sets, we show here that the dental and osteological characters of mammals convey significantly different phylogenetic signals, and that osteological characters are significantly more compatible with molecular trees. Furthermore, the application of simplified paleontological filters (retaining only dental data) results in significantly greater loss of phylogenetic signal than random character ablation. Although the mammal fossil record is largely comprised of teeth, dental data alone are generally found to be less reliable for phylogenetic reconstruction given their incongruence with osteological and molecular data. These findings highlight the need for rigorous meta-analyses of distributions of homoplasy in morphological data. These tests, and consequent refinements to phylogenetic analyses that they permit, promise to improve the quality of all macroevolutionary studies that hinge on accurate trees. [Homoplasy; Mammalia; morphology; osteology; phylogeny; teeth
Highlights
SYSTEMATIC BIOLOGY found similar levels of homoplasy in some cases (e.g., Sánchez-Villagra and Williams 1998; Mounce et al 2016)
This raises a number of questions: Why is there an apparent discordance between developmental studies and empirical morphological data regarding the relative phylogenetic informativeness of tooth morphology? Are there differences between the phylogenetic signals contained within dental and osteological morphology? Can dental data alone be used reliably to reconstruct the evolutionary history of mammals? To answer these questions we compiled morphological data sets comprising dental and osteological characters for a broad range of mammal clades, both extant and extinct
Use a meta-analytical approach to address the following three questions: (1) Do morphological partitions of dental and osteological characters convey a homogenous phylogenetic signal? we test the null hypothesis that the partitions do not exhibit significant partition heterogeneity according to the incongruence length difference test (ILD: Farris et al 1995a, 1995b) and incongruence relationships difference test (IRD: Mounce et al 2016)
Summary
SYSTEMATIC BIOLOGY found similar levels of homoplasy in some cases (e.g., Sánchez-Villagra and Williams 1998; Mounce et al 2016). 451) [see O’Leary et al (2003) and Naylor and Adams (2001) for further discussion] This raises a number of questions: Why is there an apparent discordance between developmental studies and empirical morphological data regarding the relative phylogenetic informativeness of tooth morphology? It is impossible to know the evolutionary history of empirical taxa with certainty, but congruence between trees inferred from different sources of data offers a means for cross-validation. In this context, we used trees derived from molecular data to assess the congruence of different classes of morphological data. (2) Are dental and osteological partitions of morphological data sets consistent with trees derived from independent molecular sequence data? The specific null hypothesis is that dental and osteological partitions do not retain different levels of relative homoplasy as assessed by the ensemble retention index (RI: Farris 1989). (3) Do the generalized taphonomic filters that occur during fossilization (i.e., loss of osteological data, retention of dental data) degrade the phylogentic signal any more or less than equivalent random filters? are a similar number of nodes recovered by matrices missing osteological characters compared with matrices missing identical amounts of random characters (as assessed by the node recovery test Sansom and Wills 2013)
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