DNA Barcoding: Molecular Identification and Phylogenetic Analysis of Pheretimoid Earthworm (Metaphire sp. and Amynthas sp.) Based on Mitochondrial Partial COI Gene from Sialkot, Pakistan

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.

Investigating the impacts of agricultural land use on soil earthworm communities: A case study of northern Zagros Mountains of Iran

Earthworms play a crucial role in the invertebrate community of soil by contributing to the belowground biomass and biogeochemical cycle. Environmental stresses, such as human activities and land use changes, have been found to negatively affect their abundance and diversity. To investigate the impact of agricultural land use and pastures on earthworms' genetic diversity in the Northern Zagros Mountains, we used COI molecular marker and DNA barcoding approaches. We collected earthworm specimens from four farmland sites and six pastures and assessed the abundance and species composition of earthworm communities across the two land uses using quadrat sampling. Using the barcoding method, we identified 13 molecular operational taxonomic units (MOTUs) among the captured earthworms. Our results showed that the number of total MOTUs, density, and earthworm communities differed significantly between the two land uses. We also found that pastures had more abundant earthworms, while farmlands had greater diversity. The diversity of OTUs in the Lumbricidae family was dominant in the agricultural system. Overall, the population of invasive earthworm species in cultivation systems is influenced by chemical inputs and organic materials from plant residues, cover crops, manure, or organic fertilizers. Given the rapid rate of land use change worldwide, especially in Iran, it is crucial to understand the impact of disturbances on earthworms.

A novel strategy to identify the species-specific peptide biomarkers in Pheretima aspergillum (E. Perrier) based on enzymatic digestion followed by LC-MS/MS methods

Guang Dilong [P. aspergillum (E. Perrier)], is an animal-derived traditional Chinese medicine made from the dried body of Pheretima aspergillum (E. Perrier) (TCM). Due to its widely application and high medical values, preparations of P. aspergillum (E. Perrier) may be adulterated by four other species, including three crucial Pheretima species [P. vulgaris (Chen), P. pectinifera (Mkhaeken), and P. guillemi (Michaelsen)] and one considerable adulteration [Metaphire magna (Chen)]. This study developed a novel and effective strategy for analyzing and authenticating Guang Dilong based on enzymatic digestion of protein. The nanoLC-MS/MS technique used to evaluate complete peptidomics profiles of trypsin-digested samples, resulting in the identification of species-specific peptide biomarkers in P. aspergillum (E. Perrier). The significance of different samples and peptides in the target species set was then investigated using mathematical set theory. Consequently, seven peptides were chosen as prospective biomarkers. Finally, five specific peptide biomarkers for differentiating Guang Dilong with other species were confirmed and validated using UFLC-MS/MS and MRM mode. The suggested technique may also be beneficial in evaluating the quality of other animal-derived goods for safety issues in order to avoid misidentification.

Genome-Based Taxa Delimitation (GBTD): A New Approach

Proper taxonomic identification is essential for biological research. Unfortunately, there are no clear guidelines for taxonomic assignment above the species level. Here, we present a novel approach—GBTD—to the use of genetic divergence to evaluate the taxonomic position of certain samples with simultaneous estimation of the current systematics correctness. This approach includes measuring the raw and model-adjusted distances between DNA sequences and attributing them to the lowest taxonomic levels that are common in sample pairs to reveal distance distributions matching different taxonomic levels (species, genus, family etc.). GBTD facilitated the reassessment of the taxonomic position of the samples, whose genetic distances relative to other samples in the dataset did not match their taxonomic divergence. A data set of complete mitochondrial genome sequences of segmented worms was chosen to test this approach. As a result, numerous inconsistencies in the systematics of samples from GenBank were pointed out. These inconsistencies included both the oversplitting and overlumping of individuals into taxa of different levels and clear cases of misidentification. Our approach sparks re-evaluation of the current systematics where traditional methods fail to provide sufficient resolution.

Diversity and Abundance of Delineated Earthworm (Annelida: Clitellata) in Pakistan: A Review

Earthworm, a ubiquitous (but neglected) macro-invertebrate, is found in terrestrial vicinity of Pakistan. Moreover, the occurrence of earthworms is often diverse with fluctuating quantity depending upon abiotic factors and land usage patterns. The aim of this study was to summarize all the reported information related to earthworm diversity in different areas of Pakistan. Almost all the data published from year 2001 to 2021 were collected. Following data organization, total 42 earthworm's species including five families (Acanthodrilidae, Lumbricidae, Moniligastridae, Octochaetidae and Megascolecidae) were reported from various researchers. Among five families, family Acanthodrilidae was found to have only one specie (Ramiella bishambari), Lumbricidae consist of 10 species (Apporactodea rosea, Allolobophora trapezoids, Allolobophora chloroticaa, Aporrectodea longa, A. caliginosa, Bimastus parvus, Eisenia fetida, Helodrilus foetidus, Lumbricus terrestris and L. rubillus), Moniligastridae has two species (Drawida nepalensis and D. pellucida) while Octochaetidae possess only one specie (Eutyphoeus incommodus). The most abundant and diverse family Megascolecidae consist of 28 earthworm species in all habitats of different regions of Pakistan. Among geographical areas, Faisalabad was found as the richest territory with most reported earthworm species (i.e. 28). The current study suggests further in depth research to explore the unidentified and/ missing species of earthworms in Pakistan.