Genetic variation in the popular lab worm Lumbriculus variegatus (Annelida: Clitellata: Lumbriculidae) reveals cryptic speciation

The inhibitory effect of nicotine on Lumbriculus variegatus stereotypical movements and locomotor activity

Nicotine has been shown to induce profound physiological and behavioural responses in invertebrate model organisms such as Caenorhabditis elegans and Drosophila melanogaster. Lumbriculus variegatus is an aquatic oligochaete worm which we have previously demonstrated has application within pharmacological research. Herein, we demonstrate the presence of endogenous acetylcholine and cholinesterase activity within L. variegatus and show the time-dependent effects on the sensitivity of L. variegatus to nicotine. We describe the effects of a broad range of concentrations of nicotine (1 μM - 1 mM) on L. variegatus response to tactile stimulation and locomotor activity following acute (10-min) and chronic (24-h) exposure. Here, we show that 10 min of exposure to ≥0.1 mM nicotine reversibly reduces the ability of tactile stimulation to elicit stereotypical movements of body reversal and helical swimming, and locomotor activity in L. variegatus. We also demonstrate that exposure to ≥0.1 mM nicotine for 24 h was toxic to L. variegatus. Chronic low-dose nicotine ≥25 μM similarly inhibits L. variegatus behaviours with 50 μM causing irreversible inhibition of movement. Thus, L. variegatus presents a model for studying the effects of nicotine and further demonstrates the application of the in vivo model L. variegatus for behavioural pharmacology research.

Distribution and in situ bioaccumulation test of radioecologically relevant metals in boreal freshwater sediments

Sediments act as important sinks for metals and their radionuclides in aquatic environments and play a crucial role in their transfer and uptake to aquatic organisms. Traditional radioecological models use radionuclide concentrations in water to predict concentrations in aquatic organisms. In this study, we investigated the distribution of radioecologically important metals (Ba, Co, Ni, Sr, U) among sediment, porewater and hypolimnion over seasons. We also studied the uptake of these metals to benthic organisms and importance of sediment as an uptake source by conducting a 28-day in situ bioaccumulation experiment with oligochaete worms (Lumbriculus variegatus). The studied metals were chosen based on common occurrence of their radioactive isotopes in nuclear fuel cycle. Measurements of total elemental concentration were used as proxies to study the behavior of specific radionuclides. Sediment and water samples were collected from two small lakes connected to a former uranium mine in Eastern Finland, and from a nearby reference lake connected to a different drainage area. Environmental characteristics and concentrations measured from sediment, porewater and overlying water indicated only minor changes between seasons. Measured metals were highly associated with sediment particles, rather than porewater or hypolimnion. Both the distribution of metals and in situ experiment indicated the importance of sediment as the main source of bioaccumulation. Significant differences in Ba, Ni and U concentrations between treatments containing contaminated sediment and reference sediment were noted, regardless of water concentrations. Additionally, as U contaminated lakes lacked seasonal overturn during our monitoring period, metal distribution and environmental conditions remained unchanged in deeper parts of those lakes. Lastly, the results of this in situ bioaccumulation experiment are in line with the findings of our previous laboratory study using sediments from these same lakes.

Concentration- and time-dependent behavioural effects of ethanol on Lumbriculus variegatus

Ethanol is one of the most widely used drugs in the world. Ethanol induces profound physiological and behavioural responses in invertebrate model organisms, such as Caenorhabditis elegans and Drosophila melanogaster. Lumbriculus variegatus (Annelida, Oligochaete) is an aquatic worm which shows behavioural responses to common drugs and thus is potentially useful in pharmacological research. The effects of ethanol are unknown in this organism. In this study, we examine the effects of acute exposure to ethanol (0-500 mM) on the stereotypical movements and locomotor activity of L. variegatus and examine the concentration- (0-500 mM) and time-dependent (0-210 min) effects of ethanol in L. variegatus. We show that ≥250 mM ethanol reversibly reduced the ability of tactile stimulation to elicit stereotypical movements, namely body reversal and helical swimming and locomotor activity (p < 0.05, N = 8). We also found that 2 min of exposure to ≥250 mM ethanol rapidly induces steady-state hypokinesis (p < 0.05, N = 11) and confirm ethanol absorption into L. variegatus tissues. Additionally, we also observed acute ethanol tolerance after 150 min of exposure to 500 mM ethanol (p < 0.05, N = 24). This study is the first to report the behavioural effects of ethanol in L. variegatus. Our results show that this is a model organism for use in ethanol studies, providing further evidence for its utility in pharmacological research.

Cryptic Species in Ecotoxicology

The advent of genetic methods has led to the discovery of an increasing number of species that previously could not be distinguished from each other on the basis of morphological characteristics. Even though there has been an exponential growth of publications on cryptic species, such species are rarely considered in ecotoxicology. Thus, the particular question of ecological differentiation and the sensitivity of closely related cryptic species is rarely addressed. Tackling this question, however, is of key importance for evolutionary ecology, conservation biology, and, in particular, regulatory ecotoxicology. At the same time, the use of species with (known or unknown) cryptic diversity might be a reason for the lack of reproducibility of ecotoxicological experiments and implies a false extrapolation of the findings. Our critical review includes a database and literature search through which we investigated how many of the species most frequently used in ecotoxicological assessments show evidence of cryptic diversity. We found a high proportion of reports indicating overlooked species diversity, especially in invertebrates. In terrestrial and aquatic realms, at least 67% and 54% of commonly used species, respectively, were identified as cryptic species complexes. The issue is less prominent in vertebrates, in which we found evidence for cryptic species complexes in 27% of aquatic and 6.7% of terrestrial vertebrates. We further exemplified why different evolutionary histories may significantly determine cryptic species' ecology and sensitivity to pollutants. This in turn may have a major impact on the results of ecotoxicological tests and, consequently, the outcome of environmental risk assessments. Finally, we provide a brief guideline on how to deal practically with cryptic diversity in ecotoxicological studies in general and its implementation in risk assessment procedures in particular. Environ Toxicol Chem 2023;42:1889-1914. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

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.

Genetic Variation and Phylogeography of Lumbriculus variegatus (Annelida: Clitellata: Lumbriculidae) Based on Mitochondrial Genes

Lumbriculus variegatus is a typical cold-water worm and is mainly distributed in the Tibetan Plateau and Northeast in China. The current study aimed to explore the genetic diversity and phylogeography of L. variegatus sampled from different geographical regions based on concatenated (COI + 16S rRNA, 879 bp) genes. Among 63 L. variegatus specimens, 29 haplotypes were identified with high haplotype diversity (h = 0.923) and nucleotide diversity (π = 0.062). The Bayesian phylogenetic analysis and Median-joining haplotype network revealed two lineages, or species, of L. variegatus. Taxa belonging to lineage I was mainly distributed in the Tibetan Plateau of China, North America, and Sweden, while lineage II composed taxa from Northeast China, southern China, and Sweden. The analysis of molecular variance indicated that the genetic difference was mainly due to differences between lineages. Neutrality tests showed that the overall L. variegatus have a stable population since the time of origin. Divergence time analysis suggested that L. variegatus originated from the Triassic period of Mesozoic in 235 MYA (95%HPD: 199–252 MYA), and the divergence between different lineages of L. variegatus began from the next 170 million years.

DNA barcoding of Naididae (Annelida, Oligochaeta), based on cytochrome C oxidase gene and ITS2 region in China

Exploring the effectiveness of DNA barcoding in species identification is a prerequisite for biodiversity conservation and environmental monitoring. Aquatic oligochaetes could serve as excellent indicators in aquatic monitoring programmes. However, few studies have examined the effectiveness of DNA barcoding in these specific organisms. The mitochondrial cytochrome C oxidase (COI) gene of 83 specimens belonging to 40 species of 18 genera were sequenced in this study. The results showed that there was a barcode gap between species of Naididae and the intraspecific genetic distances of each species were smaller than interspecific genetic distances. The classification results of ABGD (Automatic Barcode Gap Discovery) were consistent with those of morphological identification, except for Tubifextubifex and Lumbriculusvariegatus. All species were successfully distinguished in the phylogenetic tree, based on the ITS2 region, which was coincident with the morphological result. Our results provided evidence that DNA barcoding can be used as an effective and convenient tool for species identification of the family Naididae and even for other aquatic oligochaetes.

It Cuts Both Ways: An Annelid Model System for the Study of Regeneration in the Laboratory and in the Classroom

The mechanisms supporting regeneration and successful recovery of function have fascinated scientists and the general public for quite some time, with the earliest description of regeneration occurring in the 8th century BC through the Greek mythological story of Prometheus. While most animals demonstrate the capacity for wound-healing, the ability to initiate a developmental process that leads to a partial or complete replacement of a lost structure varies widely among animal taxa. Variation also occurs within single species based on the nature and location of the wound and the developmental stage or age of the individual. Comparative studies of cellular and molecular changes that occur both during, and following, wound healing may point to conserved genomic pathways among animals of different regenerative capacity. Such insights could revolutionize studies within the field of regenerative medicine. In this review, we focus on several closely related species of Lumbriculus (Clitellata: Lumbriculidae), as we present a case for revisiting the use of an annelid model system for the study of regeneration. We hope that this review will provide a primer to Lumbriculus biology not only for regeneration researchers but also for STEM teachers and their students.

Lumbriculus variegatus: A novel organism for in vivo pharmacology education

Pharmacology graduates require an understanding of both in vitro and in vivo drug responses but there has been a decline in animal use in pharmacology education over the last 30 years. To address this, we present the novel invertebrate model, Lumbriculus variegatus, for in vivo testing of drugs in a teaching environment. We have developed two novel behavioral assays: the stereotypical movement assay, which measures the effect of drugs on the ability of L. variegatus to perform stereotypical movements following tactile stimulation, and the free locomotion assay, which measures drug effects on unstimulated movement. We report the effects of compounds with diverse pharmacodynamic properties on L. variegatus using these assays. The ryanodine receptor antagonist, dantrolene, altered the unstimulated movement of L. variegatus at 5 μM, whereas stimulated movement was inhibited at ≥25 μM. Lidocaine, a voltage-gated sodium channel blocker, and quinine, a nonselective sodium and potassium channel blocker, reduced both stimulated and unstimulated L. variegatus movement at ≥0.5 mM. Inhibitory effects of quinine persisted for up to 24 h after drug removal, whereas lidocaine effects were reduced 10 min after drug removal. Herein, we provide proof-of-concept utilization of L. variegatus as an organism for use in in vivo pharmacology education but without regulatory constraints or the need for specialized equipment and training.

Lumbriculus variegatus (Müller, 1774) (Oligochaeta, Lumbriculidae) in Campos do Jordão State Park, São Paulo, Brazil

The aim of this paper was recording the occurrence of the species Lumbriculus variegatus (Müller, 1774) (Oligochaeta, Lumbriculidae) in lotic systems of the State of São Paulo. Specimens were collected in Sapucaí River, located in Campos do Jordão State Park. The mapping of geographical distribution of this species is of interest to public health since L. variegatus may be an intermediate host of Dioctophyme renale (Goeze, 1782) (Nematoda, Dioctophymatidae), a parasite of recognized zoonotic potential. Distribution data serves as a basis for environmental monitoring and evaluation, being essential to map possible cases of the disease (Dioctophimosis) and provide information to health professionals.

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

Methods for species delimitation using molecular data have developed greatly and have become a staple in systematic studies of clitellate worms. Here we give a historical overview of the data and methods used to delimit clitellates from the mid-1970s to today. We also discuss the taxonomical treatment of the cryptic species, including the recommendation that cryptic species, as far as possible, should be described and named. Finally, we discuss the prospects and further development of the field.

DNA barcoding reveals cryptic diversity in the underestimated genus Triplophysa (Cypriniformes: Cobitidae, Nemacheilinae) from the northeastern Qinghai-Tibet Plateau

Background

The northeastern part of the Qinghai-Tibet Plateau (QTP) presents a high number of plateau loach species. As one of the three major groups of fishes distributed on the QTP, plateau loach has high ecological value. However, the taxonomy and systematics of these fish are still controversial, and a large number of new species have been reported. The reason for this phenomenon is that the degree of morphological variation is low, the phylogenetic information provided by morphological and anatomical features used for species identification is relatively poor, and many cryptic species are observed. Based on the high-density sampling points from the biodiversity hotspots surveyed, this study aims to evaluate the biodiversity of plateau loach in the northeastern part of the QTP and reveal the hidden diversity by comparing morphological species with molecular operational taxonomic units (MOTUs).

Results

After careful identification and comparison of the morphology and DNA barcoding of 1630 specimens, 22 species were identified, with 20 considered valid local species and two identified as new species that had not been previously described. Based on the combination of morphological and molecular methods, a total of 24 native species were found, two of which were cryptic species: Triplophysa robusta sp1 and Triplophysa minxianensis sp1. Fourteen of the 24 species form clusters of barcodes that allow them to be reliably identified. The remaining cases involved 10 closely related species, including rapidly differentiated species and species that seemed to have experienced incomplete lineage sorting or showed introgressions.

Conclusions

The results highlight the need to combine traditional taxonomies with molecular methods to correctly identify species, especially closely related species, such as the plateau loach. This study provides a basis for protecting the biodiversity of plateau loach.

High-throughput DNA barcoding of oligochaetes for abundance-based indices to assess the biological quality of sediments in streams and lakes

Aquatic oligochaete communities are valuable indicators of the biological quality of sediments in streams and lakes, but identification of specimens to the species level based on morphological features requires solid expertise in taxonomy and is possible only for a fraction of specimens present in a sample. The identification of aquatic oligochaetes using DNA barcodes would facilitate their use in biomonitoring and allow a wider use of this taxonomic group for ecological diagnoses. Previous approaches based on DNA metabarcoding of samples composed of total sediments or pools of specimens have been proposed for assessing the biological quality of ecosystems, but such methods do not provide precise information on species abundance, which limits the value of resulting ecological diagnoses. Here, we tested how a DNA barcoding approach based on high-throughput sequencing of sorted and genetically tagged specimens performed to assess oligochaete species diversity and abundance and the biological quality of sediments in streams and lakes. We applied both molecular and morphological approaches at 13 sites in Swiss streams and at 7 sites in Lake Geneva. We genetically identified 33 or 66 specimens per site. For both approaches, we used the same index calculations. We found that the ecological diagnoses derived from the genetic approach matched well with those of the morphological approach and that the genetic identification of only 33 specimens per site provided enough ecological information for correctly estimating the biological quality of sediments in streams and lakes.

Genetic variation, pseudocryptic diversity, and phylogeny of Erpobdella (Annelida: Hirudinida: Erpobdelliformes), with emphasis on Canadian species

Leeches of the family Erpobdellidae are important members of benthic freshwater environments, where they are voracious predators of other invertebrates and an important source of nutrition for several species of vertebrates. Beset by a lack of reliable diagnostic morphological characters and destructive identification processes, molecular approaches have, in recent years, been employed to illuminate the relationships within this family, and DNA barcoding has been employed for identification purposes. However, an understanding of the levels of genetic variation across the geographic distributions of members of the genus is still lacking. Herein, we sequence the mitochondrial COI locus for 249 newly collected North American individuals, representing 5 species, as well as mitochondrial 12S rDNA, nuclear 18S rDNA, and nuclear 28S rDNA for a select subset of these. Our COI dataset was leveraged to detect potential cryptic species, and to calculate genetic distances as a proxy for the degree of gene flow between populations. Augmented by numerous sequences from GenBank, the multilocus dataset was used to reconstruct a phylogenetic hypothesis for worldwide members of the genus. Beyond corroborating previous overarching phylogenetic frameworks, our results show that an undescribed species that is morphologically and genetically similar to Erpobdella punctata exists in sympatry with this species - the new species has likely been overlooked in previous studies due to its morphological similarity with Erpobdella punctata. Erpobdella bucera is reported from Canada for the first time; and Erpobdella microstoma is newly reported from Saskatchewan and placed in a phylogeny for the first time. Finally, we find evidence for genetic structure in both E. cf. punctata and Erpobdella obscura that is correlated with major river drainage basin boundaries in North America.

Cytochrome c oxidase barcodes for aquatic oligochaete identification: development of a Swiss reference database

Introduction

Aquatic oligochaetes represent valuable indicators of the quality of sediments of watercourses and lakes, but their difficult identification based on morphological criteria compromises their more common use for eco-diagnostic analyses. This issue could be overcome by using DNA barcodes for species identification. A 10% threshold of cytochrome c oxidase (COI) divergence was proposed for differentiating between oligochaete species based on molecular and morphological data. A Swiss database of COI sequences of aquatic oligochaetes was initiated in 2012. The aim of this study is to complement the Swiss oligochaete database of COI sequences and to confirm the relevance of this threshold for species delimitation.

Methods

We sequenced the COI sequence of 216 specimens collected in different regions of Switzerland and ITS2 region of some lineages whose delimitation with COI data was doubtful.

Results

We distinguished 53 lineages, among which 34 were new for Switzerland and 17 sequenced for the first time. All the lineages were separated by more than 10% of COI variation, with the exception of some species within Nais and Uncinais. In these two genera, the threshold was lowered to 8% to be congruent with the morphological analysis. The total number of lineages reported so far for Switzerland is 75, including 59 morphospecies or unidentified species and 16 cryptic species.

Discussion

Our study shows that the threshold of 10% of COI divergence is generally appropriate to distinguish aquatic oligochaete lineages, but that it must be adjusted for some species. The database reported here will be complemented in the future in parallel to the development of genetic oligochaete indices.

The effect of lead contamination on bioturbation by Lumbriculus variegatus in a freshwater microcosm

The present study investigated the effect of lead (Pb) on bioturbation by the oligochaete worm Lumbriculus variegatus, using freshwater microcosms. The experiment used lead at "0", 140, 700, and 3500 μg/g in sediment, and used two different laboratory populations of L. variegatus. A molecular genetic analysis and bioassays were conducted to determine if the two populations differed genetically and whether they differed in Pb-sensitivity. The bioturbation of L. variegatus was estimated using luminophores placed at the sediment-water interface at the beginning of the experiment. After the 14 d experiment the luminophore profiles in sediment were used to estimate the biodiffusion and bioadvection coefficients, using the diffusion-advection model. The results showed that the biodiffusion and bioadvection coefficients were generally negatively related to the Pb concentrations in the sediment. Lead at 700 and 3500 μg/g reduced both coefficients, while Pb at 140 μg/g did not. Luminophore profiles in the "0" and 140 μg/g treatments were indicative of a non-local transport, while a diffusive transport was observed at the higher Pb levels. The two laboratory populations of L. variegatus used in the experiment differed in their sensitivity to Pb when mortality was used as the endpoint, but they did not differ in sediment bioturbation or the Pb-sensitivity of this process. Moreover, the genetic analysis did not detect any genetic differences between the populations. This study demonstrated that elevated levels of Pb can impact ecosystem functioning by decreasing the bioturbation activity of benthic organisms such as L. variegatus.

Next-Generation Sequencing of Aquatic Oligochaetes: Comparison of Experimental Communities

Aquatic oligochaetes are a common group of freshwater benthic invertebrates known to be very sensitive to environmental changes and currently used as bioindicators in some countries. However, more extensive application of oligochaetes for assessing the ecological quality of sediments in watercourses and lakes would require overcoming the difficulties related to morphology-based identification of oligochaetes species. This study tested the Next-Generation Sequencing (NGS) of a standard cytochrome c oxydase I (COI) barcode as a tool for the rapid assessment of oligochaete diversity in environmental samples, based on mixed specimen samples. To know the composition of each sample we Sanger sequenced every specimen present in these samples. Our study showed that a large majority of OTUs (Operational Taxonomic Unit) could be detected by NGS analyses. We also observed congruence between the NGS and specimen abundance data for several but not all OTUs. Because the differences in sequence abundance data were consistent across samples, we exploited these variations to empirically design correction factors. We showed that such factors increased the congruence between the values of oligochaetes-based indices inferred from the NGS and the Sanger-sequenced specimen data. The validation of these correction factors by further experimental studies will be needed for the adaptation and use of NGS technology in biomonitoring studies based on oligochaete communities.

Barcoding gap, but no support for cryptic speciation in the earthworm Aporrectodea longa (Clitellata: Lumbricidae)

DNA-barcoding, using the mitochondrial marker COI, has been found successful for the identification of specimens in many animal groups, but may not be suited for species discovery and delimitation if used alone. In this study, we investigate whether two observed COI haplogroups in the earthworm Aporrectodea longa correspond to two cryptic species or if the variation is intraspecific. This is done by complementing COI with two nuclear markers, ITS2 and Histone 3. The variation is studied using distance methods, parsimony networks and Bayesian coalescent trees, and the statistical distinctness of the groups is tested on gene trees using the genealogical sorting index, Rosenberg's P_AB and Rodrigo et al.'s P_(RD). We also applied multilocus species delimitation based on the multispecies coalescence model. The two haplogroups were found in COI, and all tests except P_(RD) found them to be significantly distinct. However, in ITS2, the same groups were not recovered in any analyses or tests. H3 was invariable in A. longa, and was, therefore, included only in the multilocus analysis, which preferred a model treating A. longa as one species over a model splitting it into two. We also compared two measurements of size, body length, and no. of segments between the groups. No difference in body length was found, and although a significant difference in no. of segments was noted the haplogroup with the lower mean showed both the highest and the lowest value. When combined, these results led us to the conclusion that there is no support for the separation of A. longa into two cryptic species. This study again highlights the importance of complementing mitochondrial barcodes with more data when establishing species boundaries.

Gonad establishment during asexual reproduction in the annelid Pristina leidyi

Animals that can reproduce by both asexual agametic reproduction and sexual reproduction must transmit or re-establish their germ line post-embryonically. Although such a dual reproductive mode has evolved repeatedly among animals, how asexually produced individuals establish their germ line remains poorly understood in most groups. We investigated germ line development in the annelid Pristina leidyi, a species that typically reproduces asexually by paratomic fission, intercalating a new tail and head in the middle of the body followed by splitting. We found that in fissioning individuals, gonads occur in anterior segments in the anterior-most individual as well as in new heads forming within fission zones. Homologs of the germ line/multipotency genes piwi, vasa, and nanos are expressed in the gonads, as well as in proliferative tissues including the posterior growth zone, fission zone, and regeneration blastema. In fissioning animals, certain cells on the ventral nerve cord express a homolog of piwi, are abundant near fission zones, and sometimes make contact with gonads. Such cells are typically undetectable near the blastema and posterior growth zone. Time-lapse imaging provides direct evidence that cells on the ventral nerve cord migrate preferentially towards fission zones. Our findings indicate that gonads form routinely in fissioning individuals, that a population of piwi-positive cells on the ventral nerve cord is associated with fission and gonads, and that cells resembling these piwi-positive cells migrate along the ventral nerve cord. We suggest that the piwi-positive ventral cells are germ cells that transmit the germ line across asexually produced individuals via migration along the ventral nerve cord.

Molecular barcoding of aquatic oligochaetes: implications for biomonitoring

Aquatic oligochaetes are well recognized bioindicators of quality of sediments and water in watercourses and lakes. However, the difficult taxonomic determination based on morphological features compromises their more common use in eco-diagnostic analyses. To overcome this limitation, we investigated molecular barcodes as identification tool for broad range of taxa of aquatic oligochaetes. We report 185 COI and 52 ITS2 rDNA sequences for specimens collected in Switzerland and belonging to the families Naididae, Lumbriculidae, Enchytraeidae and Lumbricidae. Phylogenetic analyses allowed distinguishing 41 lineages separated by more than 10 % divergence in COI sequences. The lineage distinction was confirmed by Automatic Barcode Gap Discovery (ABGD) method and by ITS2 data. Our results showed that morphological identification underestimates the oligochaete diversity. Only 26 of the lineages could be assigned to morphospecies, of which seven were sequenced for the first time. Several cryptic species were detected within common morphospecies. Many juvenile specimens that could not be assigned morphologically have found their home after genetic analysis. Our study showed that COI barcodes performed very well as species identifiers in aquatic oligochaetes. Their easy amplification and good taxonomic resolution might help promoting aquatic oligochaetes as bioindicators for next generation environmental DNA biomonitoring of aquatic ecosystems.

Alike but different: the evolution of the Tubifex tubifex species complex (Annelida, Clitellata) through polyploidization

BACKGROUND

Tubifex tubifex is a widespread annelid characterized by considerable variability in its taxonomic characteristics and by a mixed reproductive strategy, with both parthenogenesis and biparental reproduction. In a molecular phylogenetic analysis, we detected substantial genetic variability among sympatric Tubifex spp. from the Lambro River (Milano, Italy), which we suggested comprise several cryptic species. To gain insights into the evolutionary events that generated this differentiation, we performed a cytogenetic analysis in parallel with a molecular assay. Approximately 80 cocoons of T. tubifex and T. blanchardi were collected and dissected. For each cocoon, we sequenced a fragment of the 16S rRNA from half of the sibling embryos and karyotyped the other half. To generate a robust phylogeny enabling the reconstruction of the evolutionary processes shaping the diversity of these sympatric lineages, we complemented our original 16S rRNA gene sequences with additional COI sequences.

RESULTS

The chromosome number distribution was consistent with the presence of at least six sympatric euploid chromosome complements (one diploid, one triploid, three tetraploids and one hexaploid), as confirmed by a FISH assay performed with an homologous 18S rDNA probe. All the worms with 2n = 50 chromosomes belonged to an already identified sibling species of T. tubifex, T. blanchardi. The six euploid sets were coherently arranged in the phylogeny, with each lineage grouping specimens with the same chromosome complement.

CONCLUSIONS

These results are compatible with the hypothesis that multiple polyploidization events, possibly enhanced by parthenogenesis, may have driven the evolution of the T. tubifex species complex.

Inhibition of pyrene biotransformation by piperonyl butoxide and identification of two pyrene derivatives in Lumbriculus variegatus (Oligochaeta)

Using the freshwater annelid Lumbriculus variegatus (Oligochaeta), the presence of cytochrome P450 (CYP) isozymes was investigated by analyzing metabolites of the polycyclic aromatic hydrocarbon (PAH) pyrene in treatments with and without the CYP inhibitor piperonyl butoxide (PBO). The results show a low biotransformation capability of L. variegatus (7% of total pyrene body burden as metabolites at 168 h). Addition of PBO resulted in a significant reduction of metabolites, suggesting the presence of a CYP in L. variegatus. Besides 1-hydroxypyrene, three peaks representing unknown metabolites were detected in LC-FLD (liquid chromatography with fluorescence detection) chromatograms of L. variegatus. Deconjugations showed that sulfonation and glucosidation are involved in the formation of these unknowns. Further studies with the time of flight mass analyzer provided the identification of the glucose-sulfate conjugate of 1-hydroxypyrene. The same metabolites were detected in the solvent-nonextractable fraction by incubation of the tissue residues with proteinase K, suggesting that part of these metabolites are bound to proteins. Overall, the slow biotransformation of pyrene by L. variegatus (involving CYP) supports the use of this species in standard bioaccumulation tests; however, the tissue-bound metabolite fraction described in the current study deserves further investigation for its toxicity and availability to upper trophic levels through diet.

Phylogenetic analysis of oligochaete Tubificinae (Annelida:Clitellata) based on mitochondrial sequence data

Partial sequences of the mitochondrial genes 16S rRNA and cytochrome c oxidase subunit I (COI) were used (1) to resolve the internal relationships of the subfamily Tubificinae (Annelida : Clitellata) and (2) to test the existence of cryptic species within the stygobiont oligochaete Troglodrilus galarzai (Giani & Rodriguez, 1988). Phylogenies were estimated using maximum likelihood, Bayesian inference and parsimony. Although trees were incompletely resolved at intergeneric level, a close relationship between Heterochaeta Claparède, 1863 and Troglodrilus Juget, des Châtelliers & Rodriguez was revealed, and the separation of Lophochaeta ignota Štolc, 1886 and Heterochaeta costata Claparède, 1863 from Tubifex Lamarck, 1816 was corroborated by mitochondrial molecular data. Maximum genetic divergence between allopatric populations of T. galarzai was 18% for COI (uncorrected pairwise distance), suggesting cryptic speciation within this nominal species.

Genetic variation and phylogeny of the cosmopolitan marine genus Tubificoides (Annelida: Clitellata: Naididae: Tubificinae)

Prior attempts to resolve the phylogenetic relationships of the cosmopolitan, marine clitellate genus Tubificoides, using only morphology, resulted in unresolved trees. In this study, three mitochondrial and three nuclear loci (5912 aligned sites) were analyzed, representing 14 morphologically separate species. Genetic distances within and between these forms on the basis of the mitochondrial genes (COI, 16S and 12S) revealed that 18 distinct mitochondrial lineages were represented in the data set. After analyzing also nuclear data (28S, 18S and ITS) we conclude that 17 separately evolving lineages (i.e., phylogenetic species) were represented, including three new, cryptic species closely related to T. pseudogaster, T. amplivasatus and T. insularis, respectively. Special emphasis was put on the DNA barcoding gene (COI), which was subject to haplotype diversity analysis and, for four species, diagnostic position (as determined by the Characteristic Attribute Organization System [CAOS]) screening. Typically, the intralineage variation was 1-2 orders of magnitude smaller than the interlineage divergence, making COI useful for identification of species within Tubificoides. The genetic data corroborate that many of the morphospecies are coherent but widely distributed metapopulations. Monophyly of the genus is supported and the evolutionary history of parts of the genus is revealed by phylogenetic analysis of the combined data set. A northern hemisphere origin of the genus is suggested, and most of the widely distributed species are members of one particular clade. Two morphological characters previously emphasized in Tubificoides taxonomy (hair chaetae and cuticular papillation) were optimized on the phylogenetic tree, revealing considerable homoplasy, belying the utility of these features as phylogenetic markers.

Using population genetic theory and DNA sequences for species detection and identification in asexual organisms

Background

It is widely agreed that species are fundamental units of biology, but there is little agreement on a definition of species or on an operational criterion for delimiting species that is applicable to all organisms.

Methodology/Principal Findings

We focus on asexual eukaryotes as the simplest case for investigating species and speciation. We describe a model of speciation in asexual organisms based on basic principles of population and evolutionary genetics. The resulting species are independently evolving populations as described by the evolutionary species concept or the general lineage species concept. Based on this model, we describe a procedure for using gene sequences from small samples of individuals to assign them to the same or different species. Using this method of species delimitation, we demonstrate the existence of species as independent evolutionary units in seven groups of invertebrates, fungi, and protists that reproduce asexually most or all of the time.

Conclusions/Significance

This wide evolutionary sampling establishes the general existence of species and speciation in asexual organisms. The method is well suited for measuring species diversity when phenotypic data are insufficient to distinguish species, or are not available, as in DNA barcoding and environmental sequencing. We argue that it is also widely applicable to sexual organisms.