Biology subjects

Nico Franz

Publications and source records attributed to Nico Franz.

3 recordsLinked to original sources

bioRxiv2016

A logic approach to modeling nomenclatural change

We utilize an Answer Set Programming (ASP) approach to show that the principles of nomenclature are tractable in computational logic. To this end we design a hypothetical, 20 nomenclatural taxon use case with starting conditions that embody several overarching principles of the International Code of Zoological Nomenclature; including Binomial Nomenclature, Priority, Coordination, Homonymy, Typification, and the structural requirement of Gender Agreement. The use case ending conditions are triggered by the reinterpretation of the diagnostic features of one of 12 type specimens anchoring the corresponding species-level names. Permutations of this child-to-parent reassignment action lead to 36 alternative scenarios, where each scenario requires 1-14 logically contingent nomenclatural emendations. We show that an ASP transition system approach can correctly infer the Code-mandated changes for each scenario, and visually output the ending conditions. The results provide a foundation for further developing logic-based nomenclatural change optimization and compliance verification services, which could be applied in globally coordinated nomenclatural registries. More generally, logic explorations of nomenclatural and taxonomic change scenarios provide a novel means of assessing design biases inherent in the principles of nomenclature, and thus may inform the design of future, big data-compatible identifier systems for systematic products that recognize and mitigate these constraints.

Evolutionary Biology↗

bioRxiv2016

Model selection in statistical historical biogeography of Neotropical insects-the Exophthalmus genus complex (Curculionidae: Entiminae)

Statistical historical biogeographical methods rely on the use of models that assume various biogeographic processes. Until recently model selection remains an explored topic and the impacts of using different models on inferring biogeographic history are poorly understood. Focusing on the Neotropical weevils in the Exophthalmus genus complex (Insecta: Curculionidae: Entiminae), we compare three commonly used biogeographic models - DIVA (Dispersal-Vicariance Analysis), DEC (Dispersal-Extinction-Cladogenesis) and BayArea (Bayesian Analysis of Biogeography), and examine the impact of modeling founder-event jump dispersal on biogeographic history estimation. We also investigate the biogeographic events that have shaped patterns of distributions, diversification, and endemism in this group of weevils. We sample representatives of 65 species of the Exophthalmus genus complex and 26 outgroup terminals from the Neotropics including Caribbean islands and mainland. We reconstruct a molecular phylogeny based on six genes and performed molecular dating using a relaxed clock with three fossil calibration points. We conduct biogeographic history estimations and compare alternative biogeographic models with the R package BioGeoBEARS. Model selection strongly favors biogeographic models that include founder-event jump dispersal. Without modeling jump dispersal, estimations based on the three biogeographic models are dramatically different, especially at early diverging nodes. When jump dispersal is modeled, however, the three biogeographic models perform similarly. Accordingly, we show that the Neotropical mainland was colonized by Caribbean species in the early Miocene, and that in situ diversification accounts for a majority (~75%) of the biogeographic events in the Exophthalmus genus complex. Our study highlights the need for testing for wide-ranging historical biogeographic processes in the study of Caribbean biogeography and the importance of comparing and selecting the best-fitting model in statistical biogeographic inferences. We demonstrate that modeling founder-event jump dispersal significantly improves the fit of the biogeographic history estimation of Caribbean and Neotropical mainland weevils. We establish that in situ diversification acts as a dominant biogeographic force in the evolution of the Exophthalmus genus complex. The colonization of the Neotropical mainland from Caribbean islands reinforces the notion that islands can be an important source of continental diversity.

Evolutionary Biology↗

bioRxiv2015

Taxonomy - for Computers

We explore solutions for identifying and reconciling taxonomic concepts that take advantage of the powers of computational representation and reasoning without compromising the suitability of the Linnaean system of nomenclature for human communication. Using the model of the semiotic triangle, we show that taxonomic names must variously achieve reference to nomenclatural types, taxonomic concepts (human-created theories of taxonomic identities), and taxa (evolutionary entities in nature). Expansion of the reference models into temporally transitioning systems shows that the elements of each triangle, and provenance among elements across triangles, are only identifiable if taxonomic names and concepts are precisely contextualized. The Codes of nomenclature, by mandating identifier (name) reuse but not requiring concept-specific identifier granularity, leave the challenge of framing and aligning the symbol/reference instances to human communicators who have superior cognitive abilities in this regard. Computers, in turn, can process greater volumes of narrowly framed and logically aligned data. Comparative, taxonomically referenced biological data are becoming increasingly networked and reutilized in analyses that expand their original context of generation. If we expect our virtual comparative information environments to provide logically enabled taxonomic concept provenance services, then we must improve the syntax and semantics of human taxonomy making - for computers.

Evolutionary Biology↗