Assumption 0 analysis: comparative phylogenetic studies in the age of complexity

Darwin's panoramic view of biology encompassed two metaphors: the phylogenetic tree, pointing to relatively linear (and divergent) complexity, and the tangled bank, pointing to reticulated (and convergent) complexity. The emergence of phylogenetic systematics half a century ago made it possible to investigate linear complexity in biology. Assumption 0, first proposed in 1986, is not needed for cases of simple evolutionary patterns, but must be invoked when there are complex evolutionary patterns whose hallmark is reticulated relationships. A corollary of Assumption 0, the duplication convention, was proposed in 1990, permitting standard phylogenetic systematic ontology to be used in discovering reticulated evolutionary histories. In 2004, a new algorithm, phylogenetic analysis for comparing trees (PACT), was developed specifically for use in analyses invoking Assumption 0. PACT can help discern complex evolutionary explanations for historical biogeographical, coevolutionary, phylogenetic, and tokogenetic processe

Modelling Biodiversity Linked Data: Pragmatism May Narrow Future Opportunities

International audienceAs the biodiversity community increasingly adopts Semantic Web (SW) standards to represent taxonomic registers, trait banks or museum collections, some questions come up relentlessly: How to model the data? For what goals? Can the same model fulfill different goals?So far, the community has mostly considered the SW standards through their most salient manifestation: the Web of Linked Data (Heath and Bizer 2011). Indeed, the 5-star Linked Data principles are geared towards the building of a large, distributed knowledge graph that may successfully fulfill biodiversity’s need for interoperability and data integration. However, the SW addresses a much broader set of problems involving automatic reasoning. For instance, reasoners can exploit ontological knowledge to improve query answering, leverage class definitions to infer class subsumption relationships, or classify individuals i.e. compute instance relationships between individuals and classes by applying reasoning techniques on class definitions and instance descriptions (Shearer et al. 2008).Whether a "thing" should be modelled as a class or a class instance has been debated at length in the SW community, and the answer is often a matter of perspective. In the context of taxonomic registers for example, the NCBI Organismal Classification (Federhen 2012) and Vertebrate Taxonomy Ontology (Midford et al. 2013) represent taxa as classes in the Ontology Web Language (OWL). By contrast, other initiatives represent taxa as instances of various classes, e.g. the SKOS Concept class (skos:Concept) in the AGROVOC thesaurus (Caracciolo et al. 2013) (we speak of the instances as SKOS concepts), the Darwin Core taxon class (dwc:Taxon) in Encyclopedia of Life (Parr et al. 2016), or classes depicting taxonomic ranks in GeoSpecies, DBpedia and the BBC Wildlife Ontology. Such modelling discrepancies impede linking congruent taxa throughout taxonomic registers. Indeed, one can state the equivalence between two classes (with owl:equivalentClass) or two class instances (with owl:sameAs, skos:exactMatch, etc.), but good practices discourage the alignment of classes with class instances (Baader et al. 2003).Recently, Darwin Core's popularity has fostered the modeling of taxa as instances of class dwc:Taxon (Senderov et al. 2018, Parr et al. 2016). In this context, pragmatism may incline a Linked Data provider to comply with this majority trend to ensure maximum interlinking. Although technically and conceptually valid, this choice entails certain drawbacks. First, considering a taxon only as a an instance misses the fact that it is a set of biological individuals with common characteristics. An OWL class exactly captures this semantics through the set of necessary and sufficient conditions that an individual must meet to be a class member. In turn, an OWL reasoner can leverage this knowledge to perform query answering, compute subsumption or instance relationships. By contrast, taxa depicted by class instances are not defined but described by stating their properties. Hence the second drawback: unless we develop bespoke reasoners, there is not much a standard OWL reasoner can deduce from instances.Yet, some works have demonstrated the effectiveness of logic representation and reasoning capabilities, e.g. computing the alignments of two primate classifications (Franz et al. 2016) using generic reasoners that nevertheless require proprietary input formats. OWL reasoners are typically designed to solve such classification problems. They may leverage taxonomic ontologies to compute alignments with other ontologies or apply reasoning to individuals' properties to infer their species. Hence, pragmatically following the instance-based approach may indeed maximize interlinking in the short term, but bears the risk of denying ourselves potentially desirable use cases in the longer term. We believe that developing class-based ontologies for biodiversity should help leverage the SW’s extensive theoretical and practical works to tackle a variety of use cases that so far have been addressed with bespoke solutions

Alternatives to Realist Consensus in Bio-Ontologies: Taxonomic Classification as a Basis for Data Discovery and Integration

Big data is opening new angles on old questions about scientific progress. Is scientific knowledge cumulative? If yes, how does it make progress? In the life sciences, what we call the Consensus Principle has dominated the design of data discovery and integration tools: the design of a formal classificatory system for expressing a body of data should be grounded in consensus. Based on current approaches in biomedicine and systematic biology, we formulate and compare three types of the Consensus Principle: realist, contextual-best, and coordinative. Contrasted with the realist program of the Open Biomedical Ontologies Foundry, we argue that historical practices in systematic biology provide an important and overlooked alternative based on coordinative consensus. Systematists have developed a robust system for referring to taxonomic entities that can deliver high quality data discovery and integration without invoking consensus about reality or “settled” science

Agreeing to disagree: reconciling conflicting taxonomic views using a logic-based approach

Taxonomy alignment is a way to integrate two or more taxonomies. Semantic interoperability between datasets, information systems, and knowledge bases is facilitated by combining the different input taxonomies into merged taxonomies that reconcile apparent differences or conflicts. We show how alignment problems can be solved with a logic-based region connection calculus (RCC-5) approach, using five base relations to compare concepts: congruence, inclusion, inverse inclusion, overlap, and disjointness. To illustrate this method, we use different “geo-taxonomies”, which organize the United States into several, apparently conflicting, geospatial hierarchies. For example, we align T(CEN), a taxonomy derived from the Census Bureau’s regions map, with T(NDC), from the National Diversity Council (NDC), and with T(TZ), a taxonomy capturing the U.S. time zones. Using these case studies, we show how this logic-based approach can reconcile conflicts between taxonomies. We have implemented these case studies with an open source tool called Euler/X which has been applied primarily for solving complex alignment problems in biological classification. In this paper, we demonstrate the feasibility and broad applicability of this approach to other domains and alignment problems in support of semantic interoperability.DEB- 1155984DBI-1342595DBI-1643002Ope

Three new species of entimine weevils in Early Miocene amber from the Dominican Republic (Coleoptera: Curculionidae)

abstract: Background Using syntactic and semantic conventions of the taxonomic concept approach (Franz et al. 2015), we describe three newly recognized fossil broad-nosed weevils (Coleoptera: Curculionidae: Entiminae) preserved in Early Miocene amber (ca. 20.4-16.0 mya) from the Dominican Republic: Scelianoma compacta sp. n. sec. Franz & Zhang (2017) (henceforth abbreviated as [FZ2017]), Tropirhinus palpebratus sp. n. [FZ2017], and Diaprepes anticus sp. n. [FZ2017]. The taxonomic assignment of the amber inclusions is grounded in a preceding phylogenetic analysis by Franz (2012). As many as 88 of the 143 therein identified characters were coded for the fossils, whose traits are largely congruent with those present in extant congeners while also differing in ways that justify their new nomenclatural and taxonomic status. New information We present detailed images, descriptions, and phylogenetically informed diagnoses for the three new species-level entities, along with logically consistent Region Connection Calculus (RCC-5) alignments of the amended genus-level classifications for Scelianoma Franz and Girón 2009 [FZ2017], Tropirhinus Schoenherr 1823 [FZ2017], and Diaprepes Schoenherr 1823 [FZ2017] - in relation to 2-4 preceding classifications published in 1982-2012. The description of Scelianoma compacta [FZ2017] from Hispaniola is indicative of a more widespread historical range of Scelianoma [FZ2017] than reflected in the extant, southwestern Puerto Rican Scelianoma elydimorpha Franz and Girón 2009 sec. Franz and Girón (2009). The presence of Diaprepes anticus [FZ2017] in Hispaniola during the Early Miocene suggests an eastward directed process of island colonization and likely speciation of members of Diaprepes [FZ2017], given that most extant relatives occur throughout the Lesser Antilles. The herein presented data will facilitate more reliable reconstructions of historical biographic processes thought to have played a prominent role in the diversification of the West Indian and Neotropical mainland broad-nosed weevil lineages.The final version of this article, as published in Biodiversity Data Journal, can be viewed online at: https://bdj.pensoft.net/articles.php?id=1046

An oak is an oak, or not? Understanding and dealing with confusion and disagreement in biological classification

Human interaction with the living world, in science and beyond, always involves classification. While it has been a long-standing scientific goal to produce a single all-purpose taxonomy of life to cater for this need, classificatory practice is often subject to confusion and disagreement, and many philosophers have advocated forms of classificatory pluralism. This entails that multiple classifications should be allowed to coexist, and that whichever classification is best, is context-dependent. In this paper, we discuss some practical consequences of classificatory pluralism, in particular with regard to how one is supposed to find the best classification for a given context. We do so by means of a case study concerning oaks, in particular the pedunculate oak (Quercus robur L.) and the sessile oak (Quercus petraea (Matt.) Liebl.), two important putative species that present several classificatory challenges; and by applying one recent philosophical framework conceptualizing classification, the so-called Grounded Functionality Account (GFA) of (natural) kinds. We show how the GFA elucidates several issues related to oak classification and gives directions to optimize classificatory practices, and discuss some implications for scientific taxonomy

Alternatives to Realist Consensus in Bio-Ontologies: Taxonomic Classification as a Basis for Data Discovery and Integration

Big data is opening new angles on old questions about scientific progress. Is scientific knowledge cumulative? If yes, how does it make progress? In the life sciences, what we call the Consensus Principle has dominated the design of data discovery and integration tools: the design of a formal classificatory system for expressing a body of data should be grounded in consensus. Based on current approaches in biomedicine and systematic biology, we formulate and compare three types of the Consensus Principle: realist, contextual-best, and coordinative. Contrasted with the realist program of the Open Biomedical Ontologies Foundry, we argue that historical practices in systematic biology provide an important and overlooked alternative based on coordinative consensus. Systematists have developed a robust system for referring to taxonomic entities that can deliver high quality data discovery and integration without invoking consensus about reality or “settled” science

Problematising Civil Society- on What Terrain Does Xenophobia Flourish

Is there a need to reconceptualise civil society organisations (CSOs) given the fragmented, uneven, varied and sometimes contradictory responses of CSOs to the May 2008 violence