Myrmecological diversity (Hymenoptera: Formicidae) in Tamaulipas, México

This investigation involved analyzing 77 publications, 6 national biological collections and an international collection and determining the myrmecological diversity of Tamaulipas, which consists of 195 species that belong to 60 genera, with 410 records in the state. The genera with the highest species richness were Camponotus Mayr (Formicinae), Pheidole Westwood (Myrmicinae) and Neivamyrmex Borgmeier (Dorylinae), with 17, 15 and 12 species, respectively. The ant fauna of Tamaulipas consists of 95% native species and 5% exotic species. The investigation determined that 25 municipalities had been sampled, and Gómez Farías, Victoria and Jaumave stood out with the highest number of ant species records; however, 18 municipalities that provide opportunities to increase the knowledge of Formicidae remain unexplored.

The Wild Silkmoths (Lepidoptera: Bombycoidea: Saturniidae) of Colombia: a database of occurrence points and taxonomic checklist

Based on the review of literature and biological collections, information retrieved from public online databases, and from fieldwork conducted between 2015 and 2020, we provide more than 3500 occurrence records and an updated checklist of Colombian Saturniidae, annotated with distribution data for all species. In the first checklist of Colombian saturniids published two decades ago, a total of 184 species were cited; in the current update the number has risen to 653 species/subspecies classified in 55 genera, representing all six recognized Neotropical subfamilies. The Andean and Pacific regions are the richest, accounting for about three quarters of all species listed herein. We call attention to the fact that for most speciose saturniid genera in the Neotropics, there remains a significant need for further taxonomic and systematic research with objective and integrative approaches. Likewise, it is necessary to continue the study of Saturniidae moths in Colombia, strategically increasing the sampling efforts in specific under-sampled natural regions to further document the diversity of this family in the country.

Fantastic lizards and where to find them: cis-Andean microteiids (Squamata: Alopoglossidae & Gymnophthalmidae) from the Colombian Orinoquia and Amazonia

Although Colombia is perceived as one of the most diverse countries in reptiles, the distribution of many microteiid lizards of the Alopoglossidae and Gymnophthalmidae families is still poorly known. This is particularly true for those species in the cis-Andean regions, in part due to the remoteness or socio-political issues within some of these territories. In order to elucidate the diversity and distribution of the cis-Andean microteiids in Colombia, in this study we present a review based on the examination of specimens deposited in the reptile collection at Instituto de Investigación Alexander von Humboldt, one of the most important Colombian biological collections, and data from the literature. We reported a total of 29 taxa, in which three are new records for Colombia and three are range extensions. Two species were assigned to species complex because their morphological determination was non-conclusive, and three were identified just to genus, since they may correspond to more than one entity or be currently non-described. We found that nine species are distributed in both the Amazonia and Orinoquia regions, nine are currently only present in the Amazonia and seven are in the Orinoquia. Based on our data, we highlight the importance of using local museums to increase the taxonomic and geographic data coverage, we discuss the taxonomic difficulties for some taxa, as well as the potential for future research and their constraints. Finally, we present a taxonomic key for the identification of the microteiids present in the Orinoquia and Amazonia regions of Colombia.

Machine learning approach to support taxonomic species discrimination based on helminth collections data

Background There are more than 300 species of capillariids that parasitize various vertebrate groups worldwide. Species identification is hindered because of the few taxonomically informative structures available, making the task laborious and genus definition controversial. Thus, its taxonomy is one of the most complex among Nematoda. Eggs are the parasitic structures most viewed in coprological analysis in both modern and ancient samples; consequently, their presence is indicative of positive diagnosis for infection. The structure of the egg could play a role in genera or species discrimination. Institutional biological collections are taxonomic repositories of specimens described and strictly identified by systematics specialists. Methods The present work aims to characterize eggs of capillariid species deposited in institutional helminth collections and to process the morphological, morphometric and ecological data using machine learning (ML) as a new approach for taxonomic identification. Specimens of 28 species and 8 genera deposited at Coleção Helmintológica do Instituto Oswaldo Cruz (CHIOC, IOC/FIOCRUZ/Brazil) and Collection de Nématodes Zooparasites du Muséum National d’Histoire Naturelle de Paris (MNHN/France) were examined under light microscopy. In the morphological and morphometric analyses (MM), the total length and width of eggs as well as plugs and shell thickness were considered. In addition, eggshell ornamentations and ecological parameters of the geographical location (GL) and host (H) were included. Results The performance of the logistic model tree (LMT) algorithm showed the highest values in all metrics compared with the other algorithms. Algorithm J48 produced the most reliable decision tree for species identification alongside REPTree. The Majority Voting algorithm showed high metric values, but the combined classifiers did not attenuate the errors revealed in each algorithm alone. The statistical evaluation of the dataset indicated a significant difference between trees, with GL + H + MM and MM only with the best scores. Conclusions The present research proposed a novel procedure for taxonomic species identification, integrating data from centenary biological collections and the logic of artificial intelligence techniques. This study will support future research on taxonomic identification and diagnosis of both modern and archaeological capillariids. Graphical abstract

plantR: An R package and workflow for managing species records from biological collections

Species records from biological collections are becoming increasingly available online. This unprecedented availability of records has largely supported recent studies in taxonomy, bio-geography, macro-ecology, and biodiversity conservation. Biological collections vary in their documentation and notation standards, which have changed through time. For different reasons, neither collections nor data repositories perform the editing, formatting and standardization of the data, leaving these tasks to the final users of the species records (e.g. taxonomists, ecologists and conservationists). These tasks are challenging, particularly when working with millions of records from hundreds of biological collections. To help collection curators and final users to perform those tasks, we introduce plantR an open-source package that provides a comprehensive toolbox to manage species records from biological collections. The package is accompanied by the proposal of a reproducible workflow to manage this type of data in taxonomy, ecology and biodiversity conservation. It is implemented in R and designed to handle relatively large data sets as fast as possible. Initially designed to handle plant species records, many of the plantR features also apply to other groups of organisms, given that the data structure is similar. The plantR workflow includes tools to (1) download records from different data repositories, (2) standardize typical fields associated with species records, (3) validate the locality, geographical coordinates, taxonomic nomenclature and species identifications, including the retrieval of duplicates across collections, and (4) summarize and export records, including the construction of species checklists with vouchers. Other R packages provide tools to tackle some of the workflow steps described above. But in addition to the new features and resources related to the data editing and validation, the greatest strength of plantR is to provide a comprehensive and user-friendly workflow in one single environment, performing all tasks from data retrieval to export. Thus, plantR can help researchers to better assess data quality and avoid data leakage in a wide variety of studies using species records.

Current and Forthcoming Approaches for Benchmarking Genetic and Genomic Diversity

The current attrition of biodiversity extends beyond loss of species and unique populations to steady loss of a vast genomic diversity that remains largely undescribed. Yet the accelerating development of new techniques allows us to survey entire genomes ever faster and cheaper, to obtain robust samples from a diversity of sources including degraded DNA and residual DNA in the environment, and to address conservation efforts in new and innovative ways. Here we review recent studies that highlight the importance of carefully considering where to prioritize collection of genetic samples (e.g., organisms in rapidly changing landscapes or along edges of geographic ranges) and what samples to collect and archive (e.g., from individuals of little-known subspecies or populations, even of species not currently considered endangered). Those decisions will provide the sample infrastructure to detect the disappearance of certain genotypes or gene complexes, increases in inbreeding levels, and loss of genomic diversity as environmental conditions change. Obtaining samples from currently endangered, protected, and rare species can be particularly difficult, thus we also focus on studies that use new, non-invasive ways of obtaining genomic samples and analyzing them in these cases where other sampling options are highly constrained. Finally, biological collections archiving such samples face an inherent contradiction: their main goal is to preserve biological material in good shape so it can be used for scientific research for centuries to come, yet the technologies that can make use of such materials are advancing faster than collections can change their standardized practices. Thus, we also discuss current and potential new practices in biological collections that might bolster their usefulness for future biodiversity conservation research.

Demography reveals populational expansion of a recently extinct Iberian ungulate

Reconstructing the demographic history of endangered taxa is paramount to predict future fluctuations and disentangle the contributing factors. Extinct taxa or populations might also provide key insights in this respect by means of the DNA extracted from museum specimens. Nevertheless, the degraded status of biological material and the limited number of records may pose some constraints. For this reason, identifying all available sources, including private and public biological collections, is a crucial step forward. In this study, we reconstructed the demographic history based on cytochrome-b sequence data of the Pyrenean ibex (Capra pyrenaica pyrenaica), a charismatic taxon of the European wildlife that became extinct in the year 2000. Moreover, we built a database of the museum specimens available in public biological collections worldwide and genotyped a privately owned 140-year-old trophy from the Spanish Pyrenees to confirm its origin. We found that the population of the Pyrenean ibex underwent a recent expansion approximately 20,000 years ago, after which trophy hunting and epizootics triggered a relentless population decline. Our interpretations, based on the genetic information currently available in public repositories, provide a solid basis for more exhaustive analyses relying on all the new sources identified. In particular, the adoption of a genome-wide approach appears a fundamental prerequisite to disentangle the multiple contributing factors associated with low genetic diversity, including inbreeding depression, acting as extinction drivers.