of community associations of plants in a region. Also, a region’s floristic analysis is key not only to investigating their geographical origin(s) but is necessary to their management and protection as a reservoir of greater biodiversity. With an area of 2,250,000 square kilometers, the country of Saudi Arabia covers almost four-fifths of the Arabian Peninsula. Efforts to document information on the flora of Saudi Arabia began in the 1700s and have resulted in several comprehensive publications over the last 25 years. There is no doubt that these studies have helped both the community of scientific researchers as well as the public to gain knowledge about the number of species, types of plants, and their distribution in Saudi Arabia. However, there has been no effort to use digital technology to make the data contained in various Saudi herbarium collections easily accessible online for research and teaching purposes. This research project aims to develop a “virtual flora” portal for the vascular plants of Saudi Arabia. Based on SEINet and the Symbiota software used to power it, a preliminary website portal was established to begin an effort to make information of Saudi Arabia’s flora available on the world- wide web. Data comprising a total of 12,834 specimens representing 175 families were acquired from different organizations and used to create a database for the designed website. After analyzing the data, the Fabaceae family (“legumes”) was identified as a largest family and chosen for further analysis. This study contributes to help scientific researchers, government workers and the general public to have easy, unlimited access to the plant information for a variety of purposes.
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.
This contribution adopts the taxonomic concept annotation and alignment approach. Accordingly, and where indicated, previous and newly inferred meanings of taxonomic names are individuated according to one specific source. Articulations among these concepts and pairwise, logically consistent alignments of original and revisionary classifications are also provided, in addition to conventional nomenclatural provenance information. A phylogenetic revision of the broad-nosed weevil genera Minyomerus Horn, 1876 sec. O’Brien & Wibmer (1982), and Piscatopus Sleeper, 1960 sec. O’Brien & Wibmer (1982) (Curculionidae [non-focal]: Entiminae [non-focal]: Tanymecini [non-focal]) is presented.
Prior to this study, Minyomerus sec. O’Brien & Wibmer (1982) contained seven species, whereas the monotypic Piscatopus sec. O’Brien & Wibmer (1982) was comprised solely of P. griseus Sleeper, 1960 sec. O’Brien & Wibmer (1982). We thoroughly redescribe these recognized species-level entities and furthermore describe ten species as new to science: M. bulbifrons sec. Jansen & Franz (2015) (henceforth: [JF2015]), sp. n., M. aeriballux [JF2015], sp. n., M. cracens [JF2015], sp. n., M. gravivultus [JF2015], sp. n., M. imberbus [JF2015], sp. n., M. reburrus [JF2015], sp. n., M. politus [JF2015], sp. n., M. puticulatus [JF2015], sp. n., M. rutellirostris [JF2015], sp. n., and M. trisetosus [JF2015], sp. n. A cladistic analysis using 46 morphological characters of 22 terminal taxa (5/17 outgroup/ingroup) yielded a single most-parsimonious cladogram (L = 82, CI = 65, RI = 82).
The analysis strongly supports the monophyly of Minyomerus [JF2015] with eight unreversed synapomorphies, and places P. griseus sec. O’Brien & Wibmer (1982) within the genus as sister to M. rutellirostris [JF2015]. Accordingly, Piscatopus sec. Sleeper (1960), syn. n. is changed to junior synonymy of Minyomerus [JF2015], and its sole member P. griseus sec. Sleeper (1960) is moved to Minyomerus [JF2015] as M. griseus [JF2015], comb. n. In addition, the formerly designated type M. innocuus Horn, 1876 sec. Pierce (1913), syn. n. is changed to junior synonymy of M. microps (Say, 1831) [JF2015] which has priority. The genus is widespread throughout western North America, ranging from Canada to Mexico and Baja California. Apparent patterns of interspecific diversity of exterior and genitalic morphology, varying host plant ranges, overlapping and widely extending species distributions, suggest an early origin for Minyomerus [JF2015], with a diversification that likely followed the development of North American desert biomes. Three species in the genus – i.e., M. languidus Horn, 1876 [JF2015], M. microps [JF2015], and M. trisetosus [JF2015] – are putatively considered parthenogenetic.
Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments.
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.
Background: As 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.
Findings: The 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.
Conclusions: A ‘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.
Chapter 2 presents the first formal cladistic analysis on the group to redefine the New World tribes Lechriopini Lacordaire, 1865 and Zygopini, Lacordaire, 1865. An analysis of 75 taxa (65 ingroup) with 75 morphological characters yielded six equally parsimonious trees and synapomorphies that are used to reconstitute the tribes, resulting in the transfer of sixteen genera from the Zygopini to the Lechriopini and four generic transfers out of the Lechriopini to elsewhere in the Conoderinae.
Chapter 3 constitutes a taxonomic revision of the genus Trichodocerus Chevrolat, 1879, the sole genus in the tribe Trichodocerini Champion, 1906, which has had an uncertain phylogenetic placement in the Curculionidae but has most recently been treated in the Conoderinae. In addition to redescriptions of the three previously described species placed in the genus, twenty-four species are newly described and an identification key is provided for all recognized species groups and species.
Chapter 4 quantitatively tests the similarity in color pattern among species hypothesized to belong to several different mimicry complexes. The patterns of 160 species of conoderine weevils were evaluated for 15 categorical and continuous characters. Non-metric multidimensional scaling (NMDS) is used to visualize similarity by the proximity of individual species and clusters of species assigned to a mimicry complex in ordination space with clusters being statistically tested using permutational multivariate analysis of variance (PERMANOVA).