DOI: 10.5061/dryad.8206227
title: Data from: Verbalizing phylogenomic conflict: representation of node congruence across competing reconstructions of the neoavian explosion

description: 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.
description: S1A-Psittaciformes-Coverage-AppliedS1A Text. Reasoner input constraints for the 2015./2014.Psittaciformes alignment, with coverage globally applied. Includes information on run commands; and 0 instances of "no coverage". File format: .txt.S1B-Psittaciformes-Coverage-AppliedS1B Fig. Input visualization for the 2015./2014.Psittaciformes alignment, with coverage globally applied. File format: .pdf.S2A-Psittaciformes-Coverage-Applied-0-mnpwS2A Fig. Alignment visualization for the 2015./2014.Psittaciformes alignment, with coverage globally applied. File format: .pdf.S2B-Psittaciformes-Coverage-Applied-mirS2B File. Set of Maximally Informative Relations (MIR) inferred for the 2015./2014.Psittaciformes alignment, with coverage globally applied. Total = 108 MIR. File format: .csv.S3A-Psittaciformes-Coverage-RelaxedS3A Text. Reasoner input constraints for the 2015./2014.Psittaciformes alignment, with coverage locally relaxed. Includes information on run commands; and 4 instances of "no coverage". File format: .txt.S3B-Psittaciformes-Coverage-RelaxedS3B Fig. Input visualization for the 2015./2014.Psittaciformes alignment, with coverage locally relaxed. File format: .pdf.S4A-Psittaciformes-Coverage-Relaxed-0-mnpwS4A Fig. Alignment visualization for the 2015./2014.Psittaciformes alignment, with coverage locally relaxed. File format: .pdf.S4B-Psittaciformes-Coverage-Relaxed-mirS4B File. Set of Maximally Informative Relations (MIR) inferred for the 2015./2014.Psittaciformes alignment, with coverage locally relaxed. Total = 160 MIR. File format: .csv.S5A-Eurylaimidae-ParaphyleticS5A Text. Reasoner input constraints for the alignment of passeriform clade concepts ("Phylo2015") sec. 2015.PEA with the corresponding classification concepts ("Class2015") sec. Gill & Donsker (2015); including the (paraphyletic) Class2015.Eurylaimidae. Includes information on run commands; and 0 instances of "no coverage". File format: .txt.S5B-Eurylaimidae-ParaphyleticS5B Fig. Input visualization for the alignment of passeriform clade concepts ("Phylo2015") sec. 2015.PEA with the corresponding classification concepts ("Class2015") sec. Gill & Donsker (2015); including the (paraphyletic) Class2015.Eurylaimidae. File format: .pdf.S6A-Eurylaimidae-Paraphyletic-0-mnpwS6A Fig. Alignment visualization for the alignment of passeriform clade concepts ("Phylo2015") sec. 2015.PEA with the corresponding classification concepts ("Class2015") sec. Gill & Donsker (2015); including the (paraphyletic) Class2015.Eurylaimidae. File format: .pdf.S6B-Eurylaimidae-Paraphyletic-mirS6B File. Set of Maximally Informative Relations (MIR) inferred for the alignment of passeriform clade concepts ("Phylo2015") sec. 2015.PEA with the corresponding classification concepts ("Class2015") sec. Gill & Donsker (2015); including the (paraphyletic) Class2015.Eurylaimidae. Total = 63 MIR. File format: .csv.S7A-Tityridae-ParaphyleticS7A Text. Reasoner input constraints for the alignment of tyrannoid clade concepts ("Phylo2015") sec. 2015.PEA with the corresponding classification concepts ("Class2015") sec. Gill & Donsker (2015); including the (paraphyletic) Class2015.Tityridae. Includes information on run commands; and 0 instances of "no coverage". File format: .txt.S7B-Tityridae-ParaphyleticS7B Fig. Input visualization for the alignment of tyrannoid clade concepts ("Phylo2015") sec. 2015.PEA with the corresponding classification concepts ("Class2015") sec. Gill & Donsker (2015); including the (paraphyletic) Class2015.Tityridae. File format: .pdf.S7C-Tityridae-Paraphyletic-0-mnpwS7C Fig. Alignment visualization for the alignment of tyrannoid clade concepts ("Phylo2015") sec. 2015.PEA with the corresponding classification concepts ("Class2015") sec. Gill & Donsker (2015); including the (paraphyletic) Class2015.Tityridae. File format: .pdf.S7D-Tityridae-Paraphyletic-mirS7D File. Set of Maximally Informative Relations (MIR) inferred for the alignment of tyrannoid clade concepts ("Phylo2015") sec. 2015.PEA with the corresponding classification concepts ("Class2015") sec. Gill & Donsker (2015); including the (paraphyletic) Class2015.Tityridae. Total = 140 MIR. File format: .csv.S8A-Hydrobatidae-Procellariidae-ParaphyleticS8A Text. Reasoner input constraints for the alignment of procellariiform clade concepts ("Phylo2015") sec. 2015.PEA with the corresponding classification concepts ("Class2015") sec. Gill & Donsker (2015); including the (paraphyletic) Class2015.Hydrobatidae and Class2015.Procellariidae. Includes information on run commands; and 0 instances of "no coverage". File format: .txt.S8B-Hydrobatidae-Procellariidae-ParaphyleticS8B Fig. Input visualization for the alignment of procellariiform clade concepts ("Phylo2015") sec. 2015.PEA with the corresponding classification concepts ("Class2015") sec. Gill & Donsker (2015); including the (paraphyletic) Class2015.Hydrobatidae and Class2015.Procellariidae. File format: .pdf.S8C-Hydrobatidae-Procellariidae-Paraphyletic-0-mnpwS8C Fig. Alignment visualization for the alignment of procellariiform clade concepts ("Phylo2015") sec. 2015.PEA with the corresponding classification concepts ("Class2015") sec. Gill & Donsker (2015); including the (paraphyletic) Class2015.Hydrobatidae and Class2015.Procellariidae. File format: .pdf.S8D-Hydrobatidae-Procellariidae-Paraphyletic-mirS8D File. Set of Maximally Informative Relations (MIR) inferred for the alignment of procellariiform clade concepts ("Phylo2015") sec. 2015.PEA with the corresponding classification concepts ("Class2015") sec. Gill & Donsker (2015); including the (paraphyletic) Class2015.Hydrobatidae and Class2015.Procellariidae. Total = 221 MIR. File format: .csv.S9A-Caprimulgiformes-ParaphyleticS9A Text. Reasoner input constraints for the alignment of caprimulgiform clade concepts ("Phylo2015") sec. 2015.PEA with the corresponding classification concepts ("Class2015") sec. Gill & Donsker (2015); including the (paraphyletic) Class2015.Caprimulgiformes. Includes information on run commands; and 0 instances of "no coverage". File format: .txt.S9B-Caprimulgiformes-ParaphyleticS9B Fig. Input visualization for the alignment of caprimulgiform clade concepts ("Phylo2015") sec. 2015.PEA with the corresponding classification concepts ("Class2015") sec. Gill & Donsker (2015); including the (paraphyletic) Class2015.Caprimulgiformes. File format: .pdf.S9C-Caprimulgiformes-Paraphyletic-0-mnpwS9C Fig. Alignment visualization for the alignment of caprimulgiform clade concepts ("Phylo2015") sec. 2015.PEA with the corresponding classification concepts ("Class2015") sec. Gill & Donsker (2015); including the (paraphyletic) Class2015.Caprimulgiformes. File format: .pdf.S9D-Caprimulgiformes-Paraphyletic-mirS9D File. Set of Maximally Informative Relations (MIR) inferred for the alignment of caprimulgiform clade concepts ("Phylo2015") sec. 2015.PEA with the corresponding classification concepts ("Class2015") sec. Gill & Donsker (2015); including the (paraphyletic) Class2015.Caprimulgiformes. Total = 672 MIR. File format: .csv.S10A-Neornithes-Excepting-TelluravesS10A Text. Reasoner input constraints for the 2015./2014.Neornithes alignment (excepting 2015./2014.Telluraves), with coverage locally relaxed. Includes information on run commands; and 58 instances of "no coverage". File format: .txt.S10B-Neornithes-Excepting-TelluravesS10B Fig. Input visualization for the 2015./2014.Neornithes alignment (excepting 2015./2014.Telluraves), with coverage locally relaxed. File format: .pdf.S10C-Neornithes-Excepting-Telluraves-0-mnpwS10C Fig. Alignment visualization for the 2015./2014.Neornithes alignment (excepting 2015./2014.Telluraves), with coverage locally relaxed. File format: .pdf.S10D-Neornithes-Excepting-Telluraves-mirS10D File. Set of Maximally Informative Relations (MIR) inferred for the 2015./2014.Neornithes alignment (excepting 2015./2014.Telluraves), with coverage locally relaxed. Total = 68,208 MIR. File format: .csv.S11A-TelluravesS11A Text. Reasoner input constraints for the 2015./2014.Telluraves alignment, with coverage locally relaxed. Includes information on run commands; and 37 instances of "no coverage". File format: .txt.S11B-TelluravesS11B Fig. Input visualization for the 2015./2014.Telluraves alignment, with coverage locally relaxed. File format: .pdf.S11C-Telluraves-0-mnpwS11C Fig. Alignment visualization for the 2015./2014.Telluraves alignment, with coverage locally relaxed. File format: .pdf.S11D-Telluraves-mirS11D File. Set of Maximally Informative Relations (MIR) inferred for the 2015./2014.Telluraves alignment, with coverage locally relaxed. Total = 32,864 MIR. File format: .csv.S12A-Pelecanimorphae-OverlapS12A Text. Reasoner input constraints for the 2015./2014.Pelecanimorphae alignment, with coverage locally relaxed. Includes information on run commands; and 2 instances of "no coverage". File format: .txt.S12B-Pelecanimorphae-OverlapS12B Fig. Input visualization for the 2015./2014.Pelecanimorphae alignment, with coverage locally relaxed. File format: .pdf.S12C-Pelecanimorphae-Overlap-0-mnpwS12C Fig. Alignment visualization for the 2015./2014.Pelecanimorphae alignment, with coverage locally relaxed. File format: .pdf.S12D-Pelecanimorphae-Overlap-mirS12D File. Set of Maximally Informative Relations (MIR) inferred for the 2015./2014.Pelecanimorphae alignment, with coverage locally relaxed. Total = 200 MIR. File format: .csv.S13A-Passeri-OverlapS13A Text. Reasoner input constraints for the 2015.Passeri/2014.Passeriformes_Clade2 alignment, with coverage locally relaxed. Includes information on run commands; and 1 instance of "no coverage". File format: .txt.S13B-Passeri-OverlapS13B Fig. Input visualization for the 2015.Passeri/2014.Passeriformes_Clade2 alignment, with coverage locally relaxed. File format: .pdf.S13C-Passeri-Overlap-0-mnpwS13C Fig. Alignment visualization for the 2015.Passeri/2014.Passeriformes_Clade2 alignment, with coverage locally relaxed. File format: .pdf.S13D-Passeri-Overlap-mirS13D File. Set of Maximally Informative Relations (MIR) inferred for the 2015.Passeri/2014.Passeriformes_Clade2 alignment, with coverage locally relaxed. Total = 140 MIR. File format: .csv.S14A-Telluraves-Overlap-Whole-Concept-ResolutionS14A Text. Reasoner input constraints for the 2015./2014.Telluraves alignment (higher-level subset), under whole-concept resolution. Includes information on run commands; and 0 instances of "no coverage". File format: .txt.S14B-Telluraves-Overlap-Whole-Concept-ResolutionS14B Fig. Input visualization for the 2015./2014.Telluraves alignment (higher-level subset), under whole-concept resolution. File format: .pdf.S14C-Telluraves-Overlap-Whole-Concept-Resolution-0-mnpwS14C Fig. Alignment visualization for the 2015./2014.Telluraves alignment (higher-level subset), under whole-concept resolution. File format: .pdf.S14D-Telluraves-Overlap-Whole-Concept-Resolution-mirS14D File. Set of Maximally Informative Relations (MIR) inferred for the 2015./2014.Telluraves alignment (higher-level subset), under whole-concept resolution. Total = 81 MIR. File format: .csv.S15A-Telluraves-Overlap-Split-Concept-ResolutionS15A Text. Reasoner input constraints for the 2015./2014.Telluraves alignment (higher-level subset), under split-concept resolution. Includes information on run commands; and 0 instances of "no coverage". File format: .txt.S15B-Telluraves-Overlap-Split-Concept-ResolutionS15B Fig. Input visualization for the 2015./2014.Telluraves alignment (higher-level subset), under split-concept resolution. File format: .pdf.S15C-Telluraves-Overlap-Split-Concept-Resolution-0-mncbS15C Fig. Alignment visualization for the 2015./2014.Telluraves alignment (higher-level subset), under split-concept resolution. File format: .pdf.S15D-Telluraves-Overlap-Split-Concept-Resolution-mirS15D File. Set of Maximally Informative Relations (MIR) inferred for the 2015./2014.Telluraves alignment (higher-level subset), under split-concept resolution. Total = 81 MIR. File format: .csv.S16A-Neornithes-Higher-Level-OverlapS16A Text. Reasoner input constraints for the 2015./2014.Neornithes alignment, under whole-concept resolution, ranging from the root to the ordinal level (with exceptions where needed). Includes information on run commands; and 4 instances of "no coverage". File format: .txt.S16B-Neornithes-Higher-Level-OverlapS16B Fig. Input visualization for the 2015./2014.Neornithes alignment, under whole-concept resolution, ranging from the root to the ordinal level (with exceptions where needed). File format: .pdf.S16C-Neornithes-Higher-Level-Overlap-0-mnpwS16C Fig. Alignment visualization for the 2015./2014.Neornithes alignment, under whole-concept resolution, ranging from the root to the ordinal level (with exceptions where needed). File format: .pdf.S16D-Neornithes-Higher-Level-Overlap-mirS16D File. Set of Maximally Informative Relations (MIR) inferred for the 2015./2014.Neornithes alignment, under whole-concept resolution, ranging from the root to the ordinal level (with exceptions where needed). Total = 8,051 MIR. File format: .csv.S17A-Neoaves-Conflict-Region-Overlap-Whole-Concept-ResolutionS17A Text. Reasoner input constraints for the 2015./2014.Neoaves alignment, under whole-concept resolution, limited to the main conflict region. Includes information on run commands; and 0 instances of "no coverage". File format: .txt.S17B-Neoaves-Conflict-Region-Overlap-Whole-Concept-ResolutionS17B Fig. Input visualization for the 2015./2014.Neoaves alignment, under whole-concept resolution, limited to the main conflict region. File format: .pdf.S17C-Neoaves-Conflict-Region-Overlap-Whole-Concept-Resolution-0-mnpwS17C Fig. Alignment visualization for the 2015./2014.Neoaves alignment, under whole-concept resolution, limited to the main conflict region. File format: .pdf.S17D-Neoaves-Conflict-Region-Overlap-Whole-Concept-Resolution-mirS17D File. Set of Maximally Informative Relations (MIR) inferred for the 2015./2014.Neoaves alignment, under whole-concept resolution, limited to the main conflict region. Total = 441 MIR. File format: .csv.S18A-Neoaves-Conflict-Region-Overlap-Split-Concept-ResolutionS18A Text. Reasoner input constraints for the 2015./2014.Neoaves alignment, under split-concept resolution, limited to the main conflict region. Includes information on run commands; and 0 instances of "no coverage". File format: .txt.S18B-Neoaves-Conflict-Region-Overlap-Split-Concept-ResolutionS18B Fig. Input visualization for the 2015./2014.Neoaves alignment, under split-concept resolution, limited to the main conflict region. File format: .pdf.S18C-Neoaves-Conflict-Region-Overlap-Split-Concept-Resolution-0-mncbS18C Fig. Alignment visualization for the 2015./2014.Neoaves alignment, under split-concept resolution, limited to the main conflict region. File format: .pdf.S18D-Neoaves-Conflict-Region-Overlap-Split-Concept-Resolution-mirS18D File. Set of Maximally Informative Relations (MIR) inferred for the 2015./2014.Neoaves alignment, under split-concept resolution, limited to the main conflict region. Total = 441 MIR. File format: .csv.S19-OToL_Visualization_2015.PEA_Conflict_On_2014.JEAS19 File. Output tree file (visualized using FigTree) of the OToL conflict visualization method, with 2014.JEA as the primary source phylogeny and 2015.PEA as the alternative. File format: .tre.S20-OToL_Visualization_2014.JEA_Conflict_On_2015.PEAS20 File. Output tree file (visualized using FigTree) of the OToL conflict visualization method, with 2015.PEA as the primary source phylogeny and 2014.JEA as the alternative. File format: .tre.