Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion

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 novel products of phylogenomic inference -such as newly supported clade concepts -have not kept pace. However, the ability to verbalize both node concept congruence and conflict across multiple, (in effect) simultaneously endorsed phylogenomic hypotheses, is a critical prerequisite for building synthetic data environments for biological systematics, thereby also benefitting 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 recently published phylogenomic reconstructions of higher-level avian groups that entail strong conflict in the "neoavian explosion" region. According to our representations, this conflict 14, 2017; 2 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", thereby providing the provenance services 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.International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/233973 doi: bioRxiv preprint first posted online Dec. Author summarySynthetic platforms for phylogenomic knowledge tend to manage conflict between different evolutionary reconstructions in the following way: "If we do not agree, then 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 important biological domain. For instance, it would not be an adequate solution for building a unified data environment where multiple active author teams can endorse and yet also reconcile their diverging perspectives, side by side. Hence, we develop a novel system for verbalizing -i.e., consistently identifying and al...

Phyloreferences: Tree-Native, Reproducible, and Machine-Interpretable Taxon Concepts

“…More recently, Franz et al (2016Franz et al ( , 2019 and Cheng et al (2017) applied this approach to a variety of complex biological use cases, and also extended it to the challenge of reconciling concepts from traditional Linnaean nomenclature with clades in a phylogenetic tree, as well as aligning clade concepts from competing phylogenetic hypotheses. Although evidently useful for the problem of computationally reconciling taxon concepts, for each new input taxonomy or phylogenetic hypothesis to be reconciled, a considerable amount of effort from trained human experts is necessary to create the articulations and constraints, and the resulting assertions still do not disambiguate or make computable the original intensional semantics of a taxon concept.…”

Combining Machine Learning & Reasoning for Biodiversity Data Intelligence

“…However, this approach relies fundamentally on taxonomic insights (referred to as articulations) provided by human experts, which must often be meticulously extracted from the literature (Franz and Peet 2009;Franz, Pier et al 2016;Franz, Musher et al 2019). As we have shown in this paper, primary biodiversity data sources may be leveraged to inform and explain such taxonomic decisions, illuminating the relationship between two (or more) given taxonomic theories.…”

“…This logic is able to represent not only the taxonomies and RCC-5 articulations, but several taxonomically plausible or necessary global constraints: the non-emptiness of taxonomic concepts, siblingdisjointedness (i.e., the disjointedness of child concepts of the same taxonomic parent concept), and, coverage, which denotes the notion that the children denoted by a taxonomic parent concept are completely covered, or included in, that parent (which therefore has no further "extension"). Local, selective relaxation of each constraint allows modeling of a wide variety of systematic use cases (e.g., (Franz, Musher et al 2019)).…”

“…Unfortunately, there is widespread and persistent variation in the ways that scientists represent biodiversity data, e.g. using hierarchical taxonomies, phylogenies reconstructing evolutionary history, and computer ontologies of terms and their relationships (Franz and Sterner 2018;Vaidya, LePage, and Guralnick 2018;Franz, Musher Copyright c 2021, Association for the Advancement of Artificial Intelligence (www.aaai.org). All rights reserved.…”

Morphological and Molecular Perspectives on the Phylogeny, Evolution, and Classification of Weevils (Coleoptera: Curculionoidea): Proceedings from the 2016 International Weevil Meeting

“…In particular, given that weevil phylogenies and classifications are expected to change and conflict with each other for decades to come, he asked how (well) are we keeping up with this change, including in our data repositories? He showed logic-reasoned examples of multi-phylogeny and -classification alignments of different succeeding or simultaneously endorsed arrangements for Belidae (cf., [29,30]). Regarding specimen management, he further introduced the Symbiota Collections of Arthropods (SCAN) as a portal for collaborations involving specimens.…”