Cryptic Clitellata: Molecular Species Delimitation of Clitellate Worms (Annelida): An Overview

Toxicity evaluation of neonicotinoids to earthworm (Eisenia fetida) behaviors by a novel locomotion tracking assay

Pesticides are substances used for controlling, preventing, and repelling pests in agriculture. Among them, neonicotinoids have become the fastest-growing class of insecticides because of their efficiency in targeting pests. They work by strongly binding to nicotinic acetylcholine receptors (nAChRs) in the central nervous system of insects, leading to receptor blockage, paralysis, and death. Despite their selectivity for insects, these substances may be hazardous to non-target creatures, including earthworms. Although earthworms may be invasive in some regions like north America, they contribute to the development of soil structure, water management, nutrient cycling, pollution remediation, and cultural services, positively impacting the environment, particularly in the soil ecosystem. Thus, this study aimed to develop a novel earthworm behavior assay since behavior is a sensitive marker for toxicity assay, and demonstrated its application in evaluating the toxicity of various neonicotinoids. Here, we exposed Eisenia fetida to 1 and 10 ppb of eight neonicotinoids (acetamiprid, clothianidin, dinotefuran, imidacloprid, nitenpyram pestanal, thiacloprid, thiametoxam, and sulfoxaflor) for 3 days to observe their behavior toxicities. Overall, all of the neonicotinoids decreased their locomotion, showed by a reduction of average speed by 24.94-68.63% and increment in freezing time movement ratio by 1.51-4.25 times, and altered their movement orientation and complexity, indicated by the decrement in the fractal dimension value by 24-70%. Moreover, some of the neonicotinoids, which were acetamiprid, dinotefuran, imidacloprid, nitenpyram, and sulfoxaflor, could even alter their exploratory behaviors, which was shown by the increment in the time spent in the center area value by 6.94-12.99 times. Furthermore, based on the PCA and heatmap clustering results, thiametoxam was found as the neonicotinoid that possessed the least pronounced behavior toxicity effects among the tested pesticides since these neonicotinoid-treated groups in both concentrations were grouped in the same major cluster with the control group. Finally, molecular docking was also conducted to examine neonicotinoids' possible binding mechanism to Acetylcholine Binding Protein (AChBP), which is responsible for neurotransmission. The molecular docking result confirmed that each of the neonicotinoids has a relatively high binding energy with AChBP, with the lowest binding energy was possessed by thiametoxam, which consistent with its relatively low behavior toxicities. Thus, these molecular docking results might hint at the possible mechanism behind the observed behavior alterations. To sum up, the present study demonstrated that all of the neonicotinoids altered the earthworm behaviors which might be due to their ability to bind with some specific neurotransmitters and the current findings give insights into the toxicities of neonicotinoids to the environment, especially animals in a soil ecosystem.

Exploring Barbronia species diversity and phylogenetic relationship within Suborder Erpobdelliformes (Clitellata: Annelida)

Background

Barbronia, a genus of freshwater macrophagous leeches, belongs to Erpobdelliformes (Salifidae: Clitellata: Annelida), and B. weberi, a well-known leech within this genus, has a worldwide distribution. However, the systematics of Barbronia have not yet been adequately investigated, primarily due to a few molecular markers, and only 20 Barbronia sequences available in the GenBank database. This gap significantly limits our understanding of the Barbronia species identification, as well as the phylogenetic placement of the genus Barbronia within Salifidae.

Methods

Next-generation sequencing (NGS) was used to simultaneously capture the entire mitochondrial genome and the full-length 18S/28S rDNA sequences. The species boundary of Barbronia species was estimated using bGMYC and bPTP methods, based on all available Barbronia COI sequences. Uncorrected COI p-distance was calculated in MEGA. A molecular data matrix consisting of four loci (COI, 12S, 18S, and 28S rDNA) for outgroups (three Haemopis leeches) and 49 erpobdellid leeches, representing eight genera within the Suborder Erpobdelliformes was aligned using MAFFT and LocARNA. This matrix was used to reconstruct the phylogenetic relationship of Barbronia via Bayesian inference (BI) and the maximum likelihood (ML) method.

Results

The full lengths of the mitochondrial genome, 18S and 28S rDNAs of B. cf. gwalagwalensis, are 14847 bp, 1876 bp 1876 bp, and 2863 bp, respectively. Both bGMYC and bPTP results based on COI data are generally congruent, suggesting that the previously proposed taxa (B. arcana, B. weberi formosana, and B. wuttkei or Erpobdella wuttkei) are synonyms of B. weberi. The specimens listed in the B. gwalagwalensis group, however, are split into at least two Primary Species Hypotheses (PSHs). The p-distance of the first PSH is less than 1.3% but increased to 4.5% when including the secondary PSH (i.e., B. cf. gwalagwalensis). In comparison, the interspecific p-distance between the B. weberi group and the B. gwalagwalensis group ranged from 6.4% to 8.7%, and the intraspecific p-distance within the B. weberi group is less than 0.8%. Considering the species delimitation results and the sufficient large p-distance, the specimen sampled in China is treated as B. cf. gwalagwalensis. The monophyly of the four Erpobdelliformes families Salifidae, Orobdellidae, Gastrostomobdellidae sensu stricto and Erpobdellidae is well supported in ML and BI analysis based on a data of four markers. Within the Salifidae, a well-supported Barbronia is closely related to a clade containing Odontobdella and Mimobdella, and these three genera are sister to a clade consisted of Salifa and Linta. According to the results of this study, the strategy of simultaneous obtaining both whole mitochondria and nuclear markers from extensively sampled Salifids species using NGS is expected to fathom both the species diversity of B. gwalagwalensis and the evolutionary relationship of Salifidae.

Global species delimitation of the cosmopolitan marine littoral earthworm Pontodrilus litoralis (Grube, 1855)

The marine littoral earthworm Pontodrilus litoralis (Grube, 1855) is widely distributed and is reported as a single species. This study utilized an integrative taxonomic approach based upon morphological examination, phylogenetic reconstruction, and molecular species delimitation, to test whether the taxon is a single species or a species complex. For this, a total of 114 P. litoralis specimens collected from North America, Africa, Australia and Oceania, Europe and Asia were used. The phylogenetic analyses revealed deeply divergent mitochondrial lineages and a high level of genetic diversity among P. litoralis populations. Both single and multi-locus species delimitation analyses yielded several molecular operational taxonomic units. Therefore, due to the homogeneity of morphological characteristics, it is likely that the morphospecies P. litoralis is a complex of four or more cryptic species, suggesting that more sampling is required and that the population structure genetic data and gene flow need to be investigated.

Cryptic carnivores: Intercontinental sampling reveals extensive novel diversity in a genus of freshwater annelids

Freshwater annelids are globally widespread in aquatic ecosystems, but their diversity is severely underestimated. Obvious morphological features to define taxa are sparse, and molecular phylogenetic analyses regularly discover cryptic diversity within taxa. Despite considerable phylogenetic work on certain clades, many groups of freshwater annelids remain poorly understood. Included among these are water nymph worms of the genus Chaetogaster (Clitellata: Tubificida: Naididae: Naidinae). These worms have diverged from the detritivorous diet of most oligochaetes to become more predatory and exist as omnivores, generalist predators, parasites, or symbionts on other invertebrates. Despite their unusual trophic ecology, the true diversity of Chaetogaster and the phylogenetic relationships within the genus are uncertain. Only three species are commonly referenced in the literature (Chaetogaster diaphanus, Chaetogaster limnaei, and Chaetogaster diastrophus), but additional species have been described and prior molecular data suggests that there is cryptic diversity within named species. To clarify the phylogenetic diversity of Chaetogaster, we generated the first molecular phylogeny of the genus using mitochondrial and nuclear sequence data from 128 worms collected primarily across North America and Europe. Our phylogenetic analyses suggest that the three commonly referenced species are a complex of 24 mostly cryptic species. In our dataset, Chaetogaster "diaphanus" is represented by two species, C. "limnaei" is represented by three species, and C. "diastrophus" is represented by 19 species. North American and European sequences are largely interspersed across the phylogeny, with four pairs of clades involving distinct North American and European sister groupings. Overall, our study demonstrates that the species diversity of Chaetogaster has been underestimated and that carnivory has evolved at least twice in the genus. Chaetogaster is being used as a model for symbiotic evolution and the loss of regenerative ability, and our study indicates that researchers must be careful to identify which species of Chaetogaster they are working with in future studies.

Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis)

In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden cryptic species diversity. Typically, phylogenetic structure and distance-based approaches are used to demonstrate the distinctness of clades and justify the recognition of new cryptic species. However, this approach does not account for gene flow, spatial, and environmental processes that can obfuscate phylogenetic inference and bias species delimitation. As a case study, we sequenced genome-wide exons and introns to evince the processes that underlie the diversification of Philippine Puddle Frogs-a group that is widespread, phenotypically conserved, and exhibits high levels of geographically-based genetic structure. We showed that widely adopted tree- and distance-based approaches inferred up to 20 species, compared to genomic analyses that inferred an optimal number of five distinct genetic groups. Using a suite of clustering, admixture, and phylogenetic network analyses, we demonstrate extensive admixture among the five groups and elucidate two specific ways in which gene flow can cause overestimations of species diversity: (1) admixed populations can be inferred as distinct lineages characterized by long branches in phylograms; and (2) admixed lineages can appear to be genetically divergent, even from their parental populations when simple measures of genetic distance are used. We demonstrate that the relationship between mitochondrial and genome-wide nuclear p-distances is decoupled in admixed clades, leading to erroneous estimates of genetic distances and, consequently, species diversity. Additionally, genetic distance was also biased by spatial and environmental processes. Overall, we showed that high levels of genetic diversity in Philippine Puddle Frogs predominantly comprise metapopulation lineages that arose through complex patterns of admixture, isolation-by-distance, and isolation-by-environment as opposed to species divergence. Our findings suggest that speciation may not be the major process underlying the high levels of hidden diversity observed in many taxonomic groups and that widely-adopted tree- and distance-based methods overestimate species diversity in the presence of gene flow.

Still Digging: Advances and Perspectives in the Study of the Diversity of Several Sedentarian Annelid Families

Sedentarian annelids are a diverse and heterogeneous group of marine worms representing more than 8600 species gathered in ca. 43 families. The attention brought to these organisms is unevenly distributed among these families, and the knowledge about them sometimes scarce. We review here the current knowledge about the families Acrocirridae, Cirratulidae (including Ctenodrilidae), Cossuridae, Longosomatidae, Paraonidae, and Sternaspidae in terms of biodiversity as well as the evolution of the taxonomy and systematics of each group. We present the challenges faced when studying these organisms and compare methodologies across groups and perspectives in future research.

Annelid Diversity: Historical Overview and Future Perspectives

Annelida is a ubiquitous, common and diverse group of organisms, found in terrestrial, fresh waters and marine environments. Despite the large efforts put into resolving the evolutionary relationships of these and other Lophotrochozoa, and the delineation of the basal nodes within the group, these are still unanswered. Annelida holds an enormous diversity of forms and biological strategies alongside a large number of species, following Arthropoda, Mollusca, Vertebrata and perhaps Platyhelminthes, among the species most rich in phyla within Metazoa. The number of currently accepted annelid species changes rapidly when taxonomic groups are revised due to synonymies and descriptions of a new species. The group is also experiencing a recent increase in species numbers as a consequence of the use of molecular taxonomy methods, which allows the delineation of the entities within species complexes. This review aims at succinctly reviewing the state-of-the-art of annelid diversity and summarizing the main systematic revisions carried out in the group. Moreover, it should be considered as the introduction to the papers that form this Special Issue on Systematics and Biodiversity of Annelids.