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[dinosaur] Continuous characters outperform binary characters in morphological phylogenetics (free pdf)
A new preprint that may be of interest to the list:Parins-Fukuchi C 2017 Continuous characters outperform binary discrete characters in phylogenetic inference. bioRxiv doi:10.1101/121343http://biorxiv.org/content/biorxiv/early/2017/03/28/121343.full.pdf
The recent surge in enthusiasm for simultaneously inferring relationships from extinct and extant species has reinvigorated interest in statistical approaches for modelling morphological evolution. Current statistical methods use the Mk model to describe substitutions between discrete character states. Although representing a significant step forward, the Mk model presents challenges in biological interpretation, and its adequacy in modelling character evolution has not been well explored. Another major hurdle toward increasing objectivity and reproducibility in morphological phylogenetics is the often subjective process of character coding of discrete characters. Assignment of discrete characters by different researchers can often yield discordant phylogenetic hypotheses. One potential solution to issues may be the employment of continuous measurements to infer phylogenies. Although not widely used in the inference of topology, models describing the evolution of continuous characters have been well examined, and their statistical behaviour is well understood. Also, continuous measurements avoid the substantial ambiguity often associated with the assignment of discrete characters to states. I present a set of simulations to determine whether use of continuous characters is a feasible alternative to discrete for inferring phylogeny. I compare relative reconstruction accuracy by inferring phylogenies from continuous characters simulated under unbounded Brownian motion and discrete characters simulated under the Mk model of morphological evolution. These tests demonstrate significant promise for continuous traits by demonstrating their higher overall accuracy as compared to reconstruction from discrete characters under Mk. Continuous characters also perform reasonably well in the presence of covariance between sites. This study provides the first step toward recognition of the potential utility of continuous characters in phylogenetic inference through use of Brownian motion and related Gaussian models.