Nico M. Franz

Finding Our Way through Phenotypes

Imagine if we could compute across phenotype data as easily as genomic data; this article calls for efforts to realize this vision and discusses the potential benefits.

On The Use Of Taxonomic Concepts In Support Of Biodiversity Research And Taxonomy

Future biodiversity research will make increased use of distributed data networks, scientific workflows, and powerful mechanisms for resolving a broad spectrum of primary data. This paper outlines the anatomy of an ecological niche modeling workflow and concomitant needs for taxonomic resolution. Contemporary Linnaean names and synonymy relationships are shown to be too imprecise too support these needs. Taxonomic concepts (i.e., the meanings of names as specified in a particular source) and a new vocabulary for expressing their semantic interrelationships are introduced as a more reliable long-term solution. The concept approach has so far been implemented with success in select taxonomic databases and regional floristic treatments. Quantitative analyses have added further weight to the claim that taxonomic concepts are suitable to overcome the problem of name/meaning disjunction inherent in conventional nomenclature. Therefore, full documentation of the taxonomic process will depend on a wider adoption of concept taxonomy. The concept approach will improve communication about nature without compromising any of the useful properties of the Linnaean system.

Towards a language for mapping relationships among taxonomic concepts

Abstract Taxonomic concepts (sensu Berendsohn) embody the underlying meanings of scientific names as stated in a particular publication, thus offering a new way to resolve semantic ambiguities that result from multiple revisions of a taxonomic name. This paper presents a comprehensive and powerful language for representing the relationships among taxonomic concepts. The language features terms and symbols for concept relationships within a single taxonomic hierarchy, or between two related but independently published hierarchies. Taxonomic concepts pertaining to a single hierarchy are characterised by parent/child relationships, whereas those pertaining to two independent hierarchies may have the following basic relationships: congruence, inclusion (non‐symmetrical, relative to the side of comparison), overlap, and exclusion. The relationships are asserted by specialists who have the option to add or subtract concepts on one or both sides of a relationship equation in order to reconcile differences between non‐congruent taxonomic perspectives. The terms ‘and’, ‘or’ and ‘not’ are available, respectively, to connect multiple simultaneously or alternatively valid relationship assessments, or to explicitly negate the validity of a relationship. The language also permits the decomposition of a relationship according to the intensional (property referencing) and ostensive (member pointing) aspects of the compared taxonomic concepts. Adopting the concept relationship language will facilitate a more precise documentation of similarities and differences in multiple succeeding taxonomic perspectives, thereby preparing the stage for an ontology‐based integration of taxonomic and related biological information.

On the lack of good scientific reasons for the growing phylogeny/classification gap

An increasing number of phylogenetic analyses is no longer translated into classifications. The resulting phylogeny/classification gap is undesirable because the precise transmission of phylogenetic insights depends on the frequent revision of Linnaean names. The move away from classifying has numerous correlates. These include: an expanded pool of researchers who are able to produce phylogenetic estimates, a mismatch between the properties of molecular phylogenies and the requirements for verbal Linnaean definitions, the emphasis of statistical representations over the creation and evaluation of scientific terms, and a partial disconnect between the processes of nomenclature and taxonomy. The “taxonomic concept” approach allows systematists to express their varying perspectives with a high precision and can therefore help reduce the aforementioned gap. The phylogeny/classification link must persist in order to ensure community‐wide access to, and continued testing of, the products of systematic research.

Symbiota – A virtual platform for creating voucher-based biodiversity information communities

Abstract We review the Symbiota software platform for creating voucher-based biodiversity information portals and communities. Symbiota was originally conceived to promote small- to medium-sized, regionally and/or taxonomically themed collaborations of natural history collections. Over the past eight years the taxonomically diverse portals have grown into an important resource in North America and beyond for mobilizing, integrating, and using specimen- and observation-based occurrence records and derivative biodiversity information products. Designed to mirror the conceptual structure of traditional floras and faunas, Symbiota is exclusively web-based and employs a novel data model, information linking, and algorithms to provide highly dynamic customization. The themed portals enable meaningful access to biodiversity data for anyone from specialist to high school student. Symbiota emulates functionality of modern Content Management Systems, providing highly sophisticated yet intuitive user interfaces for data entry, batch processes, and editing. Each kind of content provision may be selectively accessed by authenticated information providers. Occupying a fairly specific niche in the biodiversity informatics arena, Symbiota provides extensive data exchange facilities and collaborates with other development projects to incorporate and not duplicate functionality as appropriate.

Scientific names of organisms: attribution, rights, and licensing

BackgroundAs biological disciplines extend into the ‘big data’ world, they will need a names-based infrastructure to index and interconnect distributed data. The infrastructure must have access to all names of all organisms if it is to manage all information. Those who compile lists of species hold different views as to the intellectual property rights that apply to the lists. This creates uncertainty that impedes the development of a much-needed infrastructure for sharing biological data in the digital world.FindingsThe laws in the United States of America and European Union are consistent with the position that scientific names of organisms and their compilation in checklists, classifications or taxonomic revisions are not subject to copyright. Compilations of names, such as classifications or checklists, are not creative in the sense of copyright law. Many content providers desire credit for their efforts.ConclusionsA ‘blue list’ identifies elements of checklists, classifications and monographs to which intellectual property rights do not apply. To promote sharing, authors of taxonomic content, compilers, intermediaries, and aggregators should receive citable recognition for their contributions, with the greatest recognition being given to the originating authors. Mechanisms for achieving this are discussed.

Mating behaviour of Staminodeus vectoris (Coleoptera: Curculionidae), and the value of systematics in behavioural studies

The mating behaviour of Staminodeus vectoris Franz (Curculionidae: Curculioninae: Derelomini) is described and discussed in light of a phylogeny of Staminodeus Franz. At La Selva, Costa Rica, S. vectoris is associated with the staminodes of the inflorescences of Asplundia uncinata Harling and several other species of Cyclanthaceae. The males have a row of 6–10 teeth along the margin of the protibia, whereas the females have a small, curved spine on the frons. The adults arrive in numbers at the inflorescences during the pistillate phase of the anthesis of A. uncinata, feeding on the staminodes. Eventually, a female detaches a staminode with her mandibles, falls to the ground, and transports it to the site of oviposition in the leaf litter. First, she crawls underneath the staminode, then moves it posteriorly with her legs, and finally returns to its distal end before repeating the process. The female turns on her back and maintains her original position during the movement of the staminode, using her frontal spine as a point of resistance against the substrate. Meanwhile, a male associates with the staminode. The males fight with their prothoracic legs, executing fast blows until their protibial teeth cling and dislodge competitors from the staminode. The positive and negative allometries of the lengths of the male protibia and female spine, are consistent with their functions in the contexts of sexual and natural selection, respectively. The phylogeny of all seven species of Staminodeus hypothesises that female transporting behaviour evolved before male fighting behaviour.

Description of two new species and phylogenetic reassessment of Perelleschus O’Brien & Wibmer, 1986 (Coleoptera: Curculionidae), with a complete taxonomic concept history of Perelleschus sec. Franz & Cardona-Duque, 2013

The weevil genus Perelleschus O’Brien & Wibmer, 1986, is revised; including the description of P. salpinflexus Cardona-Duque & Franz sp. nov. sec. Franz & Cardona-Duque (2013) from Colombia and P. spinothylax Cardona-Duque & Franz sp. nov. sec. Franz & Cardona-Duque (2013) from Colombia and Venezuela. This study furthermore demonstrates the feasibility and utility of the taxonomic concept approach as laid out in Franz & Peet (2009). In particular, we establish and consistently practice a convention where (1) the taxonomic name sec. author annotation is used in all instances where a specific meaning of a name is intended; (2) just the taxonomic name is used to refer to the cumulative nomenclatural and taxonomic legacy associated with that name; and (3) the term [non-focal] is added to a taxonomic name to signal that specifying or redefining its meaning is outside of the scope of this study. We reproduce six classifications and 54 constituent taxonomic concepts that represent a complete taxonomic history of the entities classified in Perelleschus sec. Franz & Cardona-Duque (2013). We provide tabular summaries in which (1) each of the 54 concepts is uniquely identified, (2) the six concept groups are arranged via parent/child relationships into their respective classifications, (3) 76 articulations are asserted to semantically integrate concepts across classifications, and (4) the textual circumscription of each concept is reproduced. These data reveal that the taxonomic history of Perelleschus sec. Franz & Cardona-Duque (2013) has been rather stable at the species level and more complicated at higher levels, where 49 out of 54 articulations are not unambiguously congruent and 37 articulations use the intensional/ostensive annotation. This cumulative information presents a novel use case suitable for representation and reasoning about taxonomic classifications and classification provenance in computational logic. We discuss the merits of this approach and provide recommendations for a wider implementation.

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.

Anatomy of a cladistic analysis

The sequential stages culminating in the publication of a morphological cladistic analysis of weevils in the Exophthalmus genus complex (Coleoptera: Curculionidae: Entiminae) are reviewed, with an emphasis on how early‐stage homology assessments were gradually evaluated and refined in light of intermittent phylogenetic insights. In all, 60 incremental versions of the evolving character matrix were congealed and analysed, starting with an assembly of 52 taxa and ten traditionally deployed diagnostic characters, and ending with 90 taxa and 143 characters that reflect significantly more narrow assessments of phylogenetic similarity and scope. Standard matrix properties and analytical tree statistics were traced throughout the analytical process, and series of incongruence length indifference tests were used to identify critical points of topology change among succeeding matrix versions. This kind of parsimony‐contingent rescoping is generally representative of the inferential process of character individuation within individual and across multiple cladistic analyses. The expected long‐term outcome is a maturing observational terminology in which precise inferences of homology are parsimony‐contingent, and the notions of homology and parsimony are inextricably linked. This contingent view of cladistic character individuation is contrasted with current approaches to developing phenotype ontologies based on homology‐neutral structural equivalence expressions. Recommendations are made to transparently embrace the parsimony‐contingent nature of cladistic homology.