Taxonomy, Volume 4, Issue 4 (December 2024) – 12 articles

(1) Background: Tabanids are one of the most neglected and difficult-to-identify groups within the order Diptera despite their medical–veterinary importance. Since 2010, DNA barcoding has proved to be a promising method for the identification of horseflies in the Old World, but until now it had explored little with regards to Neotropical species. In Mexico, faunal studies continue to be focused on certain regions of the country, which has limited the generation of taxonomic keys. Here, we employed the DNA barcoding approach to contribute to the knowledge of horsefly species in one of the least explored biogeographic provinces in Mexico, the state of Veracruz. (2) Methods: Tabanids were collected at two localities using Malaise traps during two seasons. With a sampling effort of 300 h per trap per site, a total of 22 specimens were collected and identified using taxonomic keys and partial amplification and sequencing of the mitochondrial gene cytochrome c oxidase subunit 1 (COI). (3) Results: Five species of the Tabanus genus were identified through taxonomic keys, and three of these species were confirmed through molecular analyses: T. oculus, T. commixtus, and T. pungens. (4) Conclusions: This is the first contribution of the sequence data of the Tabanidae family for Mexico and demonstrates that DNA barcoding is a vital tool for the recognition of Neotropical species. Full article

The species Chiton echinatus was first described by Barmes in 1824. Subsequently, it has been allocated to several widely distributed genera (e.g., Acanthopleura, Enoplochiton, Mesotomura) within the subfamily Acanthopleurinae. In order to resolve this species’ taxonomic uncertainty, specimens were collected throughout its entire distribution (i.e. from Peru and Chile) and subjected to a series of morphological and phylogenetic analyses. Scanning electron microscopy was used to improve this species’ morphological description, whereas publicly available sequences were used to infer its phylogenetic position. Morphological and phylogenetic analyses suggest that this species merits its own genus, endemic to the Southeastern Pacific. Of the aforementioned genera, Mesotomura appears to be the most appropriate designation. Therefore, it is proposed that the name Mesotomura echinata be restored, and the range of this species be extended to 39° S. Full article

We describe four new species of the fossil genus Dapalis (Ambassidae), Dapalis absconditus sp. nov., Dapalis octospinus sp. nov., Dapalis parvus sp. nov. and Dapalis quintus sp. nov., based on articulated skeletons with otoliths in situ from a freshwater habitat of the lower Oligocene of Raljin/Strelac (Serbia). Besides in body shape (e.g., body length, body depth, head length, preanal length), the species differ in morphological characters like, e.g., the serration of the preopercle, the length of the first two spines of the first dorsal and the anal fin and the morphology of the sagittal otoliths (e.g., ratio of otolith height to otolith length, ratio of otolith width to otolith length). Together with D. pauciserratus, also described from Raljin, these four species represent the most species-rich assemblage of freshwater Dapalis known so far. The compartmentalization of the internal structure of the spines reveals the close relationship of Dapalis and extant Ambassidae. Additionally, we discuss a new character from the ventral field of the otolith, a ventral depression, only found in species from Raljin. This new character is unique among the European Dapalis species and allows us to separate these five species into two species groups. Full article

Neotropical species of the genus Fannia remain poorly known despite their potential collection as biological evidence in criminal investigations. This is partly due to taxonomic difficulties and a lack of specialists. Identifying neotropical species of Fannia relies mainly on the classical morphological characters of adult males, as females show high similarity between species. Here, landmark-based geometric morphometrics of the wing could constitute an additional tool for associating adult females with conspecifics in this genus. In this study, we used a reference dataset of males belonging to ten putative species of Fannia from Colombia and molecular data to test this hypothesis. We found a strong wing shape sexual dimorphism, resulting in an almost perfect sex assignment based solely on this trait. However, the differences in wing shape between sexes were greater than those between species, making conspecific identification difficult. Our data show that wing shape could only feasibly be used for identifying adult males and females of F. lamosca, and males of F. dorsomaculata and F. pseudoconstricta. Low discrimination scores among remaining species may be partly explained by high intraspecific variation, slight wing shape differences among closely related species, or sampling bias. Although this study provides the first wing size and shape comparison among neotropical Fannia species, more samples and species are needed to validate these findings and identify the potential factors influencing this trait. Furthermore, the wing shape sexual dimorphism across Fannia species suggests different life-history strategies between sexes and possible genetic canalization mechanisms. Full article

This study addresses a critical issue in plant taxonomy and phylogeny: the relationship between archaeological materials and potentially analogous living populations. Given the current limitations in definitively establishing the identity between archaeological and contemporary materials, we propose an intermediate approach. This approach serves as a useful framework while scientific methods advance towards definitively assessing whether an archaeological wheat sample, approximately 5000 years old from Central Europe, belongs to the same species as a modern wheat currently endemic to Central Asia. This approach consolidates the taxonomic validity of both archaeological and living materials, allowing them to be treated as distinct taxa while preserving the possibility of future identification convergence. Triticum vulgare var. antiquorum, an archaeobotanical small-grained, free-threshing wheat, was originally described in 1865. The 1982 discovery of morphologically similar living wheat in Tajikistan raised questions about their taxonomic relationship. Our study reviews the nomenclature of both taxa, designating an illustration from the original description of T. vulgare var. antiquorum as the lectotype to align with the traditional concept of the name. We address the ambiguity surrounding “Triticum antiquorum” as used by Russian agronomists and botanists, proposing a more precise circumscription within the current systematic framework of the genus based on cytogenetic data. Consequently, we describe a new taxon, Triticum sphaerococcum subsp. antiquorum. The holotype, selected from material with available cytogenetic data and grown from Professor Udachin’s original Pamir (Tajikistan) collection, is preserved in the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (WIR) collection. It is deposited at the I.M. Krasnoborov Herbarium of Central Siberian Botanical Garden SB RAS (NS), with an isotype at the WIR. This taxonomic revision and new subspecies designation provide a robust framework for reconciling archaeological and contemporary wheat diversity, advancing our understanding of wheat evolution and agricultural history. Full article

Based on molecular phylogenetic analyses, and also considering morphological characters, four new families are separated from the family Glomeraceae within the order Glomerales and the class Glomeromycetes. The revised family Glomeraceae comprises only four genera: the type genus Glomus, Complexispora, Sclerocarpum and Simiglomus. Septoglomeraceae fam. nov. comprises, besides Septoglomus, Funneliformis, Funneliglomus, Blaszkowskia and Viscospora. Sclerocystaceae fam. nov. is represented by the type genus Sclerocystis but also by Halonatospora, Oehlia, Parvocarpum, Rhizoglomus and Silvaspora. Kamienskiaceae fam. nov. encompasses Kamienskia, Microkamienskia and Epigeocarpum. Finally, Dominikiaceae fam. nov. includes the genera Dominikia, Macrodominikia gen. nov., Microdominikia, Nanoglomus and Orientoglomus. The genera Oehlia and Halonatospora form two other clades well separated from Silvaspora, Sclerocystis and Rhizoglomus and might represent two further families within Glomerales. This deeper separation is, in our opinion, fully supported by molecular phylogeny, but in view of the low numbers of taxa, the separation is not yet proposed at this stage of research progress. Full article

The deep-sea snailfish Careproctus bathycoetus Gilbert et Burke, 1912 was described a century ago from a single specimen caught at a depth of 3292 m in the Kuril Basin (southern Sea of Okhotsk, western North Pacific). Until now, it was known from the holotype only. Therefore, the capture of another specimen is of great interest and provides new data on the morphology and ecology of the species. The second known specimen was collected by the international expedition “SohoBio” (2015) at a depth of 3305 m in the Kuril Basin near the type locality. This study provides a description of a rare fish, which allows us to improve the diagnosis of the species. Differences from other deep-sea snailfishes from the North Pacific Ocean are also given. At a depth of 3292–3305 m, the species lives in extreme conditions: complete darkness, temperature at about 1.9 °C, water pressure about 3300 ton/m², low oxygen concentration, and low biomass of prey. Related Careproctus species can most likely be found in the abyssal depths of the neighboring Kuril–Kamchatka Trench. Full article

Ceratozamia chinantlensis sp. nov., a new cliff-dwelling cycad species from Sierra de La Chinantla, Oaxaca, Mexico, is described and compared with its congeners. The species is morphologically similar to Ceratozamia zoquorum and Ceratozamia santillanii, two geographically distant species, yet it is effortlessly distinguishable from its most proximally geographic congeners. Ceratozamia chinantlensis can be recognized based on several qualitative traits, such as its very coriaceous, long, linear to oblanceolate leaflets. Also, it has bronze-colored emerging leaves and mature leaves with articulations of a light copper color. Compared with C. zoquorum and C. santillanii, C. chinantlensis has significantly longer and wider leaflets. C. chinantlensis should be considered a critically threatened species due to its limited number of populations and individuals. Habitat destruction—historically through the extraction of Dioscorea mexicana and Vanilla planifolia, along with ongoing coffee and corn plantations—is an ongoing threat that narrows its distribution range. Full article

While there are millions of reptile images available online, they are not well organized and not easily findable, accessible, interoperable, or reproducible (FAIR). More importantly, they are not standardized and thus hardly comparable. Here we present a reference database of more than 14,000 standardized images of 1045 reptile species (969 lizard and 76 snake species) that are based on preserved specimens in 20 different collections, including 533 type species of genera and type specimens of 72 species. All images were taken with standardized views, including dorsal and ventral body shots as well as dorsal, ventral, and lateral views of the heads and other body parts. Although only 11 out of the 20 collections are cross-referenced in VertNet, some others are indexed in GBIF, and this fraction will certainly grow in the near future. The utility of this and similar image collections will further grow with additional material and further cross-referencing, e.g., to DNA sequence databases or citizen science projects. The images are searchable and freely available on Morphobank (Project 5121) and on Figshare. Full article

Confusion between the means and ends, specifically between technological achievements and their users, has been evident in taxonomy’s history since the end of the last century. Following a current of thought implicit in Anglo-Saxon culture, this trend aligns with the idea of inevitability. It is inevitable, so it is thought, that what a human organism can do, a machine will be able to do at some point in time. This will ultimately lead to dispensing with the human element for things they do not wish to do themselves. Despite certain misunderstandings about what has become known as the Turing Test, the general idea is to determine whether a machine can analyze data as meaningfully as a human does and make decisions based on that analysis. In the case of taxonomy, the initial aim of using machines was to efficiently replace a researcher for identification purposes. The situation later evolved to include the discovery of new entities in addition to identification. In this essay, I provide a brief overview of some milestones along this trajectory and its current state and discuss the influence of artificial intelligence (AI) in taxonomy. Full article

The genus Dickeya consists of Gram-negative bacteria capable of causing soft rot symptoms in plants, which involves tissue breakdown, particularly in storage organs such as tubers, rhizomes, and bulbs. These bacteria are ranked among the top ten most relevant phytopathogens and seriously threaten economically valuable crops and ornamental plants. This study employs a genomic analysis approach to taxonomically classify and characterize the resistome and virulome of two new strains, CCRMP144 and CCRMP250, identified as Dickeya dadantii. These strains were found to be the causative agents of soft rot symptoms in chili pepper (Capsicum spp.) and lettuce (Lactuca sativa), respectively, in the northeastern region of Brazil. The methodology employed in silico techniques, including tetra correlation search (TCS) and Average Nucleotide Identity (ANI) analysis, in association with a phylogenomic tree inference. TCS and ANI analysis showed that the studied strains belong to the Dickeya dadantii species. The phylogenomic analysis grouped the studied strains in the D. dadantii clade. The genomic characterization demonstrates 68 virulence genes, 54 resistances of biocide and heavy metal genes, and 23 antibiotic resistance genes. As far as we know, this is the first genomic study with Brazilian D. dadantii strains. This study demonstrates the efficacy to taxonomic classification and provides insights into the pathogenesis, host range, and adaptability of these strains which are crucial for the development of more effective management and control strategies for soft rot diseases. Full article

Members of the blowfly family (Calliphoridae) are usually the first insect species to arrive at a corpse, using the body as an oviposition site, and, as such, they are the most important group of insects used to estimate the post-mortem interval (PMI). PMI estimations are based on species-specific developmental timings; therefore, accurate species identification is crucial. Current identification methods are based on morphological characteristics, which are time-consuming and difficult to perform on damaged, immature specimens and closely related species. Advances have led to specimens being identified via a host of molecular techniques, mainly DNA sequencing. Although molecular identification is becoming increasingly more common, there is currently a lack of genetic data regarding UK Calliphoridae species. This study aimed to address this issue. We present the development and validation of an identification assay capable of differentiating six UK species (Calliphora vicina, Calliphora vomitoria, Lucilia sericata, Lucilia illustris, Lucilia caesar, and Protophormia terranovae). The sequencing of six genes, including both nuclear (28S rRNA and Elongation factor 1 alpha) and mitochondrial markers (Cytochrome oxidase I and II, Cytochrome b and 16S rRNA) identified 298 species-specific single nucleotide polymorphisms (SNPs). Fifteen SNPs from six genes were chosen for inclusion in a SNaPshot™ multiplex assay. The developed assay is capable of differentiating the species based on between 4 and 12 SNPs. Validation following guidelines by the International Society of Forensic Genetics (ISFG) demonstrated the assay to be accurate, reproducible, sensitive, and specific. Full article