Morphological Phylogenetics in the Genomic Age

Abstract

Evolutionary trees underpin virtually all of biology, and the wealth of new genomic data has enabled us to reconstruct them with increasing detail and confidence. While phenotypic (typically morphological) traits are becoming less important in reconstructing evolutionary trees, they still serve vital and unique roles in phylogenetics, even for living taxa for which vast amounts of genetic information are available. Morphology remains a powerful independent source of evidence for testing molecular clades, and - through fossil phenotypes - the primary means for time-scaling phylogenies. Morphological phylogenetics is therefore vital for transforming undated molecular topologies into dated evolutionary trees. However, if morphology is to be employed to its full potential, biologists need to start scrutinising phenotypes in a more objective fashion, models of phenotypic evolution need to be improved, and approaches for analysing phenotypic traits and fossils together with genomic data need to be refined.

Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction

“…In contrast, a geophilomorph-scolopendromorph clade— the classical Epimorpha—receives morphological support from the perspectives of development, behavior, external morphology and internal anatomy (8 autapomorphies listed by Edgecombe 2011). This ability of morphology to select between rival hypotheses that are each based on vast pools of data affirms the continued relevance of morphological characters in phylogenetics (e.g., Giribet 2015; Lee Michael and Palci 2015; Wanninger 2015) and permits delving into the possible reasons for the discordance between the different analyses.…”

“…Most recent justification for the necessity of morphological data in molecular dating has focused on its indispensability for so-called tip dating or total evidence dating (e.g., Giribet 2015; Lee and Palci 2015; Pyron 2015). However, even in the standard node calibration approach as employed here, the position of fossils can be determined in the context of the precise taxonomic sample used in other parts of the study, rather than cobbling together justifications for node calibrations from external (or possibly mixed) sources.…”

Bayesian estimation of fossil phylogenies and the evolution of early to middle Paleozoic crinoids (Echinodermata)

“…Thus, the construction of a time-calibrated molecular phylogeny requires information on fossil morphologies and their temporal distributions to provide a numerical timescale for testing alternative models of macroevolutionary dynamics (Donoghue and Benton, 2007;dos Reis et al, 2016;Ksepka et al, 2015). Equally illuminating for paleontologists, many probabilistic methods originally developed by molecular phylogeneticists can be modified and applied to paleontologic data (Wagner, 2000a;Wagner and Marcot, 2010;Lee and Palci, 2015; but see Spencer and Wilberg, 2013). For example, Lewis (2001) developed a k-state Markov model for calculating likelihoods of discrete, morphologic characters based on a generalization of the Jukes-Cantor model of molecular sequence evolution.…”

Measuring Stratigraphic Congruence Across Trees, Higher Taxa, and Time

“…A sound understanding of phylogeny is also increasingly important for quantifying macroevolutionary patterns and trends (Steeman et al 2010; Tanja and Folmer 2013), including the selectivity of extinction (Purvis et al 2011; Hardy et al 2012) and the correlation between traits (Betancur et al 2015; Hsiang et al 2015; Soul and Friedman 2015). The stratigraphic distributions of fossils can be used to inform or constrain phylogenetic hypotheses (Wagner 1995a, 1995b, 2000; Fisher 2008), with tip dating (Pyron 2011) and total evidence dating (Ronquist et al 2012) approaches being increasingly implemented (Lee and Palci 2015; O’Reilly et al 2015). However, the majority of cladograms are inferred from the distributions of morphological or molecular character states across taxa alone, and without reference to explicitly temporal data.…”