Abstract
Phylogenomic research is accelerating the publication of landmark studies that aim to resolve deep divergences of major organismal groups. Meanwhile, systems for identifying and integrating the products of phylogenomic inference–such as newly supported clade concepts–have not kept pace. However, the ability to verbalize node concept congruence and conflict across multiple, in effect simultaneously endorsed phylogenomic hypotheses, is a prerequisite for building synthetic data environments for biological systematics and other domains impacted by these conflicting inferences. Here we develop a novel solution to the conflict verbalization challenge, based on a logic representation and reasoning approach that utilizes the language of Region Connection Calculus (RCC–5) to produce consistent alignments of node concepts endorsed by incongruent phylogenomic studies. The approach employs clade concept labels to individuate concepts used by each source, even if these carry identical names. Indirect RCC–5 modeling of intensional (property-based) node concept definitions, facilitated by the local relaxation of coverage constraints, allows parent concepts to attain congruence in spite of their differentially sampled children. To demonstrate the feasibility of this approach, we align two recent phylogenomic reconstructions of higher-level avian groups that entail strong conflict in the "neoavian explosion" region. According to our representations, this conflict is constituted by 26 instances of input "whole concept" overlap. These instances are further resolvable in the output labeling schemes and visualizations as "split concepts", which provide the labels and relations needed to build truly synthetic phylogenomic data environments. Because the RCC–5 alignments fundamentally reflect the trained, logic-enabled judgments of systematic experts, future designs for such environments need to promote a culture where experts routinely assess the intensionalities of node concepts published by our peers–even and especially when we are not in agreement with each other.
Highlights
Three years ago, Jarvis et al (2014; 2014.JEA) [1] published a landmark reconstruction of higher-level bird relationships
Synthetic platforms for phylogenomic knowledge tend to manage conflict between different evolutionary reconstructions in the following way: "If we do not agree, it is either our view over yours, or we just collapse all conflicting node concepts into polytomies". We argue that this is not an equitable way to realize synthesis in this domain
We develop a novel system for verbalizing–i.e., consistently identifying and aligning–incongruent node concepts that reflects a more forward-looking attitude: "We may not agree with you, but we understand your phylogenomic inference well enough to express our disagreements in a logic-compatible syntax
Summary
Jarvis et al (2014; 2014.JEA) [1] published a landmark reconstruction of higher-level bird relationships. Within 12 months, another analysis by Prum et al (2015; 2015.PEA) [2] failed to support several of the deep divergences recovered in the preceding study, within the Neoaves sec. After reviewing six phylogenomic studies, Suh [6] concluded that the root region of the Neoaves constitutes a "hard polytomy". Multiple analyses have dissected the impact of differential biases in terminal and genome sampling, as well as evolutionary modeling and analysis constraints, on resolving this complex radiation [7, 8, 9]. Suh [6] argues that a well resolved consensus is not imminent (though see [10]). Brown et al (2017) [11] analyzed nearly 300 avian phylogenies, finding that the most recent studies "continue to contribute new edges"
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
