Bionumeric Codes for Amphibians and Reptiles of the World. I. Salamanders

BackgroundIn order to designate the various concepts of taxa in biology, evolution and paleontology, scientists have developed various rules on how to create unique names for taxa. Different Codes of Nomenclature have been developed for animals, plants, fungi, bacteria etc., with standard sets of Rules that govern the formation, publication and application of the nomina of extant and extinct species. These Codes are the result of decades of discussions, workshops, publications and revisions. The structure and complexity of these Codes have been criticized many times by zoologists. This project aims, using the International Code of Zoological Nomenclature as a case study, to show that the structure of these Codes is better reflected and understood as networks.MethodsThe majority of the text of the Code has been divided into hundreds of Nodes of different types, connected to each other with different types of Edges to form a network. The various mathematical descriptors of the entire system, as well as for the elements of the network, have been conceptually framed to help describing and understanding the Code as a network.ResultsThe network of the Code comprises 1,379 Nodes, which are connected with 11,276 Edges. The structure of the Code can be accurately described as a network, a mathematical structure that is better suited than any kind of linear text publication to reflect its structure.DiscussionThinking of the Code as a network allows a better, in-depth understanding of the Code itself, as the user can navigate in a more efficient way, as well as to depict and analyze all the implied connections between the various parts of the Code that are not visible immediately. The network of the Code is an open access tool that could also help teaching, using and disseminating the Code. More importantly, this network is a powerful tool that allows identifying a priori the parts of the Code that could be potentially affected by upcoming amendment and revisions. This kind of analysis is not limited to nomenclature, as it could be applied to other fields that use complex textbooks with long editing history, such as Law, Medicine and Linguistics.

ABSTRACTA small lot of fossil whale barnacles from the Upper Pleistocene of California and the Middle Pleistocene (Chibanian) of Oregon (United States West Coast), described in a 1972 unpublished MA thesis, are formally described and illustrated herein. In that thesis, a new genus and species name were proposed; however, according to the International Code of Zoological Nomenclature, they have no taxonomic standing and are thus unavailable. Based on our reappraisal, two specimens in this lot belong to a new, extinct species that can be assigned to the purportedly extant genus Cetopirus. Cetopirus polysyrinx sp. nov. differs from congeners in that its secondary T-shaped flanges are multitubiferous internally, that is, they are perforated by a high number of irregularly-sized and irregularly-spaced tubules that result in a spongy aspect in transverse section. Whether or not this peculiar condition had any adaptive significance is difficult to determine. Considering that Cetopirus is currently known as an obligate epibiont of right whales (including the North Pacific form Eubalaena japonica (Lacépède 1818)), the host of C. polysyrinx sp. nov. was E. japonica or some other species of Eubalaena. The Plio-Pleistocene deposits of the Pacific coast of North America have yielded a rather idiosyncratic fossil whale barnacle fauna, inclusive of the genera Cetolepas, Cryptolepas and now Cetopirus, which seemingly contrasts with all other coeval assemblages worldwide, the latter being in turn dominated by Coronula spp.

Background. Regardless using a rank-based or a phylogenetic nomenclature code, the use of Latinized binomens to describe the extant and extinct species has been essential. Ever since the times of Linnaeus, the use of Latinized Greek names has been a common practice both for neontologists and paleontologists. Methods. I critically analyzed the most common Greek words used as taxa names in the chelonian literature to establish their etymology and check whether the transliteration process has been done correctly. I also compared the current guidelines for the latinisation of Greek words recommended by the International Code of Zoological Nomenclature, with other alternative systems for the transformation of names formed in the Greek alphabet into Latin-based languages. Results. The preliminary results show that some Greek words (e.g. Chelone, Emys) dominate the chelonian nomenclature, but the history of the application of many of those names is intriguing. The use of Greek words is quite common in turtle taxa names when the name describes physical properties of the animal (size, shape, colour). However, several unfortunate examples exist, as some quite successful and famous names contain misspellings or poor choice of words that resulted in meanings opposite from the ones intended by the authors. Discussion. Naming species is an integral part of the research of both neontologists and palaeontologists, but the application of Greek words to life sciences is even far more extensive, applied to numerous terminologies as well. Forming a proper name for a taxon could aid significantly to the communication and interpretation of the scientific results. Publishing a new name requires a sense of responsibility as well, as the formation of a taxon name is a unique linguistic procedure. But in the end, to add a taxonomic side to the old shakespearean question, is not the name that is important, but the information it conveys. That which we call a turtle by any other name would be as unique.

As we have seen in Chapter 4, many invalid European Pleistocene amphibian and reptile species were named on the basis of insufficient and inadequately described fossils (e.g., Estes, 1981, 1983; Rage, 1984c; Sanchiz, in press). Some of these forms have been synonymized with modern species, but others are in taxonomic limbo because of the international rules of zoological nomenclature. We now turn to a consideration of the few European Pleistocene fossil herpetological species that have been recognized as valid in recent years. These taxa fit into three catagories: (1) an extinct Pliocene anuran taxon that extended into the Pleistocene, (2) large Lacerta species that lived on oceanic islands, and (3) Pleistocene species that are probably morphological variants of living forms. All of the following taxa are addressed in Chapter 4. No extinct species of Pleistocene salamanders are currently recognized in Britain or Europe. The genus * Pliobatrachus from the Pliocene of eastern Europe extended into the Lower Pleistocene of Poland and the Middle Pleistocene of Germany in the form of * Pliobatrachus cf. Pliobatrachus langhae. The *Palaeobatrachidae, the only family in the history of the Anura that became totally extinct (Roček, 1995), represents the only extinct herpetological family known in the Pleistocene of Britain and Europe, and *Pliobalrachus represents the only extinct herpetologcal genus known in the Pleistocene of the region. Rocck (1995) suggested that the *Palaeobatrachidae did not survive the Pleistocene cooling because of their prevailingly aquatic mode of life, unlike, for instance, the Ranidac and Bufonidae that were able to withdraw from iceobliterated areas and return when climatic conditions improved. *Lacerta goliath is a Pleistocene or Holocene species that is known only from two localities in the Canary islands (see Chapters 4 and 5). It is twice the size of Lacerta lepida, the largest modern European Lacerta. *Lacerta maxima is another very large Pleistocene or Holocene Lacerta that is endemic to the Canary Islands. This species is known from a single fossil locality (see Chapters 4 and 5) and is differentiated from * Lacerta goliath on the basis of several trenchant osteological characters.

Our knowledge of global biodiversity remains incomplete and beset by knowledge shortfalls affecting both the census of species (i.e. the Linnean shortfall) and our understanding of their distributions (i.e. the Wallacean shortfall; Hortal et al. 2015). While alarming rates of species extinction have been reported in most groups of organisms, our capacity to assess extinction threats is limited by these shortfalls and it has become imperative to optimize our use of existing information for the analyses of biodiversity data. There are two major challenges when integrating biodiversity data from heterogeneous sources to ultimately analyzing them: The frequent disparity in taxon names used to refer to the same organisms; Geographical inconsistencies on specimen information. The frequent disparity in taxon names used to refer to the same organisms; Geographical inconsistencies on specimen information. The first refers to disagreements about the taxon concepts attached to names alongside the different interpretations and applications (e.g. gender agreement in taxonomic names) of the existing nomenclatural rules that ensure universality and stability of scientific names. The development of new methods for species delineation, and in particular with the growing integration of genetic data in the practice of taxonomy (e.g. DNA barcoding; Ratnasingham and Hebert 2013), has increased our ability to discriminate closely related species. This enhances the resolution level at which biodiversity is documented, described and analyzed(Goldstein and DeSalle 2011). One frequent outcome is the redefinition of species boundaries; either through merging (synonymy) or splitting of previously recognized species. In understudied groups such as insects, the resulting inflation of names, sometimes provisional, further defies the reconciliation of names used by different sources. The second challenge refers to the completeness and accuracy of geographical information. Specimen records in biodiversity databases often lack GPS coordinates. Consequently we need to accurately infer the latitude and longitude from place names. Other frequent inaccuracies include erroneous georeferencing, imprecision and/or error in the location of a record (Soberón and Peterson 2004). Integration of data on the basis of taxon names and their geographic information is a major challenge that either results in excluding a significant number of records, or in merging incompatible records, leading to erroneous outcomes. Therefore, we have developed WF.ACTIAS, a computational workflow that gathers data from several sources and provides the user with tools to make objective and reproducible decisions to assign records to a consensus species name, while detecting and correcting geographical inconsistencies. Its main objective is to automate a process that can integrate information about nomenclature, taxon concepts and geographical information to reconcile taxon names from different sources. Here, we present the WF.ACTIAS workflow in the context of the analysis of diversity in two sister families of moths – the Saturniidae and Sphingidae. Species boundaries in these insects have been thoroughly and comprehensively revisited through the integration of DNA barcodes and we are tackling the reconciliation of taxon names in ca. 282 000 records of which more than 77 000 have DNA barcodes. The outcome of this data integration is essential to study patterns of biodiversity and distributions and sets the ground to extend this process to other groups of organisms.

The Dodo and its extinct sister species, the Solitaire, are iconic exemplars of the destructive capabilities of humanity. These secondarily terrestrial columbids became extinct within a century of their first encounter with humanity. Their rapid extinction, with little material retained in natural history collections, led 18th and some early 19th century naturalists to believe that these aberrant birds were mythological. This meant that the nomenclatural publications in which their scientific nomina were established were based on accounts written before the species became extinct. As such, no type specimens were designated for either the Dodo or the Solitaire. Our in-depth historical overview of both species and associated family-group nomina found that the nominal authority of the Dodo-based family group is not what is reported in the literature. Moreover, our detailed review of the family-group nomina based on columbid genera ensures that the current columbid family-group systematization is valid. Changing nomenclatural norms between the 19th and 20th centuries had a profound impact on Dodo nomenclature; so much so that the Dodo is an example of how pervasive nomenclatural ‘ripples’ can be and a warning for our current world of multiple nomenclatural codes.

OF THESIS EFFECTS OF MOUNTAINTOP REMOVAL MINING ON POPULATION DYNAMICS OF STREAM SALAMANDERS Mountaintop removal mining (MTR) is a notorious stressor of stream ecosystems in the Central Appalachians. Valley fills (VF) lead to reduced occupancy, abundance, and species richness of stream salamanders. Multiple factors may be responsible for these reductions, but specifically habitat fragmentation and degradation may reduce colonization rates and increase local extinction rates. From 2013-2015, repeated counts of salamanders were conducted in stream reaches impacted by MTR/VF and compared to counts in reference reaches to answer the question: do stream salamander population dynamics differ between stream reaches impacted by MTR/VF and reference stream reaches? I also investigated dynamics of stream habitat using measures relevant to stream salamander persistence. Accordingly, I examined number of cover objects, percent detritus, hydroperiod, and specific conductance. From the salamander capture data, colonization and survival probabilities were lower in MTR/VF reaches than reference reaches. MTR/VF reaches also had fewer cover objects, higher percent detritus, constant stream flow, and elevated specific conductance. Although specific conductance was increased in MTR/VF reaches, it was not strongly correlated with colonization and survival. I suggest reduced rates of colonization and survival in MTR/VF stream reaches are driven by inhibited dispersal and reduced individual survival due to degraded terrestrial and aquatic environments.

Whether hybridization generates or erodes species diversity has long been debated, but to date most studies have been conducted at small taxonomic scales. Salamanders (order Caudata) represent a taxonomic order in which hybridization plays a prevalent ecological and evolutionary role. We employed a recently developed model of trait-dependent diversification to test the hypothesis that hybridization impacts the diversification dynamics of species that are currently hybridizing. We find strong evidence supporting this hypothesis, showing that hybridizing salamander lineages have significantly greater net-diversification rates than non-hybridizing lineages. This pattern is driven by concurrently increased speciation rates and decreased extinction rates in hybridizing lineages. Our results support the hypothesis that hybridization can act as a generative force in macroevolutionary diversification.