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

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.

Two Influential Primate Classifications Logically Aligned.

Classifications and phylogenies of perceived natural entities change in the light of new evidence. Taxonomic changes, translated into Code-compliant names, frequently lead to name:meaning dissociations across succeeding treatments. Classification standards such as the Mammal Species of the World (MSW) may experience significant levels of taxonomic change from one edition to the next, with potential costs to long-term, large-scale information integration. This circumstance challenges the biodiversity and phylogenetic data communities to express taxonomic congruence and incongruence in ways that both humans and machines can process, that is, to logically represent taxonomic alignments across multiple classifications. We demonstrate that such alignments are feasible for two classifications of primates corresponding to the second and third MSW editions. Our approach has three main components: (i) use of taxonomic concept labels, that is name sec. author (where sec. means according to), to assemble each concept hierarchy separately via parent/child relationships; (ii) articulation of select concepts across the two hierarchies with user-provided Region Connection Calculus (RCC-5) relationships; and (iii) the use of an Answer Set Programming toolkit to infer and visualize logically consistent alignments of these input constraints. Our use case entails the Primates sec. Groves (1993; MSW2-317 taxonomic concepts; 233 at the species level) and Primates sec. Groves (2005; MSW3-483 taxonomic concepts; 376 at the species level). Using 402 RCC-5 input articulations, the reasoning process yields a single, consistent alignment and 153,111 Maximally Informative Relations that constitute a comprehensive meaning resolution map for every concept pair in the Primates sec. MSW2/MSW3. The complete alignment, and various partitions thereof, facilitate quantitative analyses of name:meaning dissociation, revealing that nearly one in three taxonomic names are not reliable across treatments-in the sense of the same name identifying congruent taxonomic meanings. The RCC-5 alignment approach is potentially widely applicable in systematics and can achieve scalable, precise resolution of semantically evolving name usages in synthetic, next-generation biodiversity, and phylogeny data platforms.

Reasoning over taxonomic change: exploring alignments for the Perelleschus use case.

Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations.