Underground evolution: new roots for the old tree of lumbricid earthworms

Comparison of complete mitochondrial genome sequences in the Aporrectodeacaliginosa species group (Annelida, Crassiclitellata, Lumbricidae)

We present for the first time the complete mitochondrial genomes (mt genomes) of the earthworms Aporrectodeacaliginosa and Ap.trapezoides (Clitellata, Megadrili) collected in Hungary and Korea, respectively. The complete mt genome of Ap.trapezoides comprised 15,014 base pairs. Lengths of the three complete Ap.caliginosa mt genomes varied between 15,090 and 15,123 bp. All four mt genomes contained 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and one major non-coding control region. These mt genome arrangements are identical to those observed in the mt genomes of most earthworms, and all the 37 genes are transcribed from the same directional strand. All 13 PCGs had the same ATG start codon. Most of the PCGs end with TAA or TAG, whereas the remaining end with an incomplete stop codon, T. Stop codons were consistent in the PCGs throughout the mt genomes, except Ap.caliginosa 5, which contains a TAG stop codon in ND5 instead of the TAA found in the other samples. Both species' genomes showed biased base composition, with 63.5% AT and 36.4% GC content in Ap.trapezoides and 62.8% and 37.2% in Ap.caliginosa. Phylogenetic analysis of the mt genomes corroborated the monophyly of the family Lumbricidae and the close relationship between Ap.trapezoides and Ap.caliginosa species pairs. The available Ap.tuberculata sequences were embedded between the Ap.caliginosa samples, thereby supporting the synonymy of the two names.

Clarification of the controversy around the problematic species "Eophila gestroi" (Cognetti, 1905) in the Balkan

The taxonomy and phylogeny of the Southern Alpine species Eophila gestroi (Cognetti, 1905) can be confusing. The main reason for this is the morphological similarity of this species with the Vardar endemic species Cernosvitovia strumicae (Šapkarev, 1973). The confirmation of the identification of our findings based on morphological characters, previous molecular phylogenetic analyses, and biogeographical analysis revealed the misidentification of C. strumicae in earlier studies. Identifying this species is essential in clarifying earthworms' confusing taxonomic and phylogenetic position on the Balkan Peninsula.

Checklist of earthworms of North Macedonia (Clitellata: Megadrili)

In this paper, we have summarized the current knowledge of earthworm fauna in North Macedonia. This list presents earthworm diversity, general ecology, distribution, and zoogeographical types for the first time. The complete list of earthworm taxa of North Macedonia comprises 59 species and subspecies, of which 57 taxa belong to the family Lumbricidae and one taxon each of the families Acanthodrilidae and Criodrilidae. Dendrobaena is the most speciose genus (18 taxa). The family Lumbricidae of North Macedonia is characterized by a large number of narrow range Balkanic endemics (9 taxa = 15.3%), together with the occurrence of broad range Balkanic endemic (7 taxa = 11.8%) and Vardar endemic species (5 taxa = 8.47%). A high representation of endemic species (35.6%) indicates a high degree of autochthonous earthworm fauna.

Catch-All No More: Integrative Systematic Revision of the Genus Allolobophora Eisen, 1874 (Crassiclitellata, Lumbricidae) with the Description of Two New Relict Earthworm Genera

The taxonomy of earthworms has been riddled by instability, lack of systematically useful characters, and lax diagnoses of some genera. This has led to the use of some genera such as Allolobophora Eisen, 1874 as taxonomic wastebaskets, blurring their evolution and biogeographical history. The implementation of molecular techniques has revolutionized the systematics of the genus; however, some of its species have not been previously included in molecular phylogenetic analyses. Thus, the molecular markers COI, 16S, ND1, 12S, and 28S were sequenced for six endemic species including several taxa of Allolobophora and Aporrectodea Örely, 1885 (another related catch-all genus). Phylogenetic relationships determined by Bayesian inference and maximum likelihood analyses support the status of two of the six taxa examined (Allolobophora burgondiae Bouché, 1972 and Aporrectodea icterica Savigny, 1826) as part of Allolobophora sensu stricto and a presumed synonymy between Allolobophora and Heraclescolex Qiu and Bouché, 1998. Branch lengths and average pairwise genetic distances support the transfer of Allolobophora satchelli Bouché, 1972 to the genus Panoniona Mršić and Šapkarev, 1988 and the emergence of two new genera, Heraultia gen. nov. and Vosgesia gen. nov., endemic to France, hosting Allolobophora tiginosa Bouché, 1972 and Allolobophora zicsii Bouché, 1972, respectively. The aforementioned changes of status and the diagnosis for Heraultia and Vosgesia are presented. These results provided more evolutionarily and biogeographically coherent earthworm groups and highlighted that the Maghreb and the area around the Alps are potential key locations for the diversification of Allolobophora and several lineages of Lumbricidae.

First molecular evidence of hybridization in endosymbiotic ciliates (Protista, Ciliophora)

Hybridization is an important evolutionary process that can fuel diversification via formation of hybrid species or can lead to fusion of previously separated lineages by forming highly diverse species complexes. We provide here the first molecular evidence of hybridization in wild populations of ciliates, a highly diverse group of free-living and symbiotic eukaryotic microbes. The impact of hybridization was studied on the model of Plagiotoma, an obligate endosymbiont of the digestive tube of earthworms, using split decomposition analyses and species networks, 2D modeling of the nuclear rRNA molecules and compensatory base change analyses as well as multidimensional morphometrics. Gene flow slowed down and eventually hampered the diversification of Lumbricus-dwelling plagiotomids, which collapsed into a single highly variable biological entity, the P. lumbrici complex. Disruption of the species boundaries was suggested also by the continuum of morphological variability in the phenotypic space. On the other hand, hybridization conspicuously increased diversity in the nuclear rDNA cistron and somewhat weakened the host structural specificity of the P. lumbrici complex, whose members colonize a variety of phylogenetically closely related anecic and epigeic earthworms. By contrast, another recorded species, P. aporrectodeae sp. n., showed no signs of introgression, no variability in the rDNA cistron, and very high host specificity. These contrasting eco-evolutionary patterns indicate that hybridization might decrease the alpha-diversity by dissolving species boundaries, weaken the structural host specificity by broadening ecological amplitudes, and increase the nuclear rDNA variability by overcoming concerted evolution within the P. lumbrici species complex.

Guess who? Taxonomic problems in the genus Eiseniella revisited by integrated approach

Eiseniella neapolitana is a semi-aquatic, diploid earthworm that for many years was related to the cosmopolitan species Eiseniella tetraedra and even considered a subspecies of it. Norealidys andaluciana was described in Spain and is usually synonymized with E. neapolitana. We collected 69 specimens from Italy, Spain, and Cyprus and studied five molecular markers (COI, 16S, 28S, 12S, and ND1) and their morphology to solve this taxonomic problem. Phylogenetic analyses reveal the possible existence of two separate genera confounded under the name Eiseniella, but the study of more molecular markers and species of the genus would be necessary to confirm this. Therefore, the synonymy between Eiseniella and Norealidys is maintained. Various genetic analyses, including species delimitation, confirm the separation between E. neapolitana and E. andaluciana (= N. andaluciana) and excluded that E. neapolitana is a subspecies of E. tetraedra. The resemblance in external appearance despite clear genetic differences of the three species could be explained by convergent adaptation to the aquatic habitat. Despite the expected low haplotype diversity based on the 28S gene, we found a surprisingly high variability in the E. andaluciana (= N. andaluciana) population in Spain. However, its stable predicted secondary structure and its high content of G + C reject the presence of a pseudogene.

Three in one: molecular phylogeny of the genus Helodrilus (Crassiclitellata: Lumbricidae) with a description of two new genera and two new species

The earthworm genus Helodrilus comprises about 20 species with distributions ranging from the Iberian Peninsula to the Caucasus, through Central Europe, the Balkans, Anatolia and the Levant. The species prefer moist habitats and are often found in the mud of river banks, in swamps or in caves. Although a high degree of morphological variability is observed in the taxonomic characters, the genus shares a common feature: the absence of nephridial bladders. In this study, we clarify the phylogeny and taxonomy of the genus Helodrilus using an integrated approach including a multilocus molecular phylogenetic analysis and thorough morphological examination of several species across the putative Helodrilus area of distribution. The findings of this study have led to the genus Helodrilus being split and to the description of two new genera and two new species: Coventina Szederjesi, Sarbu & Csuzdi gen. nov. and Imetescolex movilensis Szederjesi, Sarbu & Csuzdi gen. & sp. nov. The highly homoplasic nature of the absence of nephridial bladders was also revealed.

Host taxonomy determines the composition, structure, and diversity of the earthworm cast microbiome under homogenous feeding conditions

Host evolutionary history is a key factor shaping the earthworm cast microbiome, although its effect can be shadowed by the earthworm's diet. To untangle dietary from taxon effects, we raised nine earthworm species on a uniform diet of cow manure and compared cast microbiome across species while controlling for diet. Our results showed that, under controlled laboratory conditions, earthworm microbiomes are species-specific, more diverse than that of the controlled diet, and mainly comprised of native bacteria (i.e., not acquired from the diet). Furthermore, diet has a medium to large convergence effect on microbiome composition since earthworms shared 16 to 74% of their bacterial amplicon sequence variants (ASV). The inter-species core microbiome included 10 ASVs, while their intra-species core microbiomes were larger and varied in ASV richness (24-48%) and sequence abundance across earthworm species. This specificity in core microbiomes and variable degree of similarity in bacterial composition suggest that phylosymbiosis could determine earthworm microbiome assembly. However, lack of congruence between the earthworm phylogeny and the microbiome dendrogram suggests that a consistent diet fed over several generations may have weakened potential phylosymbiotic effects. Thus, cast microbiome assembly in earthworms seem to be the result of an interplay among host phylogeny and diet.

The complete mitochondrial DNA sequences of two sibling species of lumbricid earthworms, Eiseniafetida (Savigny, 1826) and Eiseniaandrei (Bouché, 1972) (Annelida, Crassiclitellata): comparison of mitogenomes and phylogenetic positioning

Composting earthworms of the genus Eisenia play an important role in soil ecosystems. However, taxonomic classification of this genus, especially the sibling species Eiseniafetida and Eiseniaandrei, is complicated because of their morphological similarity. In this study, we assessed the utility of the complete mitochondrial genome (mitogenome) for identification and differentiation of the two species. The complete mitogenomes of E.andrei and E.fetida were 15,714 and 16,560 bp, respectively. They contained 37 genes, comprising 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and a putative non-coding region, as observed in other earthworms. Sequence comparisons based on the complete nucleotide sequences excluding the non-coding region showed 85.8% similarity, whereas the predicted amino acid sequences of the 13 PCGs were 92.7% similar between the two species. In particular, distinct features were found in the non-coding regions of the mitogenomes. They include a control region associated with putative mitogenome replication and an extended sequence. The extended sequence showed significant differences between the two species and other known earthworm species, suggesting its potential as a feasible molecular marker for species identification. Phylogenetic analysis of the 36 mitogenomes of earthworm species corroborated the monophyly of the genus Eisenia and the taxonomic distinctness of the sibling species pair, E.fetida and E.andrei.

Molecular analysis of five controversial Balkanic species of Allolobophora (sensu lato) Eisen, 1873 (Lumbricidae, Clitellata) with emendation of the genus Cernosvitovia Omodeo, 1956

Allolobophora (sensu lato) is one of the most controversial genera in the taxonomy of Lumbricidae. Due to its poor definition, this genus is plagued by extensive taxonomic confusion, and its generic composition and internal relationships have remained uncertain, especially in species of the Balkan Peninsula. In this study, we have combined the study of morphological data and molecular phylogenetics based on five genetic markers, regions of the nuclear 28S rRNA and mitochondrial 16S rRNA, 12S rRNA, NADH dehydrogenase (ND1) and cytochrome oxidase C subunit 1 (COI), to delimit the taxonomic status of five controversial Balkanic endemic species, Allolobophora (s.l.) dofleini, Allolobophora (s.l.) serbica, Allolobophora (s.l.) strumicae, Allolobophora (s.l.) paratuleskovi and Allolobophora (s.l.) treskavicensis, sampled in the Kopaonik Mountain. Phylogenetic analyses based on our sampling of these five species recovered a well-supported clade containing the species Allolobophora (s.l.) robusta, Allolobophora (s.l.) mehadiensis mehadiensis, Allolobophora (s.l.) sturanyi dacica, Cernosvitovia rebeli and Cernosvitovia dudichi. Based on these results and previous evidence, the aforementioned Balkanic species are transferred to a redefined Cernosvitovia. We further present a revised list of all species currently included in Cernosvitovia., which includes now 21 species and subspecies taxa, 13 of them newly combined here. Serbiona Mršić & Šapkarev, 1988 is considered a junior synonym of Cernosvitovia Omodeo, 1956.  

Establishment of the upstream processing for renewable production of hydrogen using vermicomposting-tea and molasses as substrate

This study aimed to establish the optimal operational conditions for hydrogen production using vermicomposting-tea and sugarcane molasses as substrate. The experiments were carried out by triplicate in 110 ml serological bottles, a Box-Behnken design of experiments was performed in anaerobic dark conditions. The maximal hydrogen production (HP), hydrogen production rate (HPR), and hydrogen yield (HY) attained were 1021.0 mlL^-1, 5.32 mlL^-1h^-1, and 60.3 mlL_H2^-1/g_TCC, respectively. The statistical model showed that the optimal operational conditions for pH, molasses concentration, and temperature were 6.5; 30 % (v/v) and 25 °C. The bioreactor run showed 17.202 L of hydrogen, 0.58 Lh^-1, and 77.2 ml_H2g_TCC^-1 For HP, HPR, and HY. Chemometric analysis for the volatile fatty acids obtained at the fermentation showed that only two principal components are required to explain 90 % of the variance. The representative pathways for hydrogen production were acetic and butyric acids. This study established the operational conditions for the upstream processing amenable to pilot and industrial-scale operations. Our results add value to molasses within the circular economy for hydrogen production using a novel consortium from vermicompost.

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

The extremely difficult and challenging process is identifying pheretimoid species, genus Metaphire and Amynthas involving increased homoplasy in various morphological characteristics. The molecular identification, phylogenetic relationships, and evolutionary divergence time of earthworms belonging to the pheretimoid complex were investigated in this study using partial mitochondrial COI (cytochrome C oxidase subunit I) gene sequences ranging from 550-680 bp. Results revealed that 86 pheretimoid earthworms were morphologically different from a total of 342 mature worms. Moreover, 11 pheretimoid species were molecularly identified, including Metaphire posthuma (02), M. anomala (01), M. houlleti (02), M. californica (01), M. birmanica (02), Amynthas minimus (01), A. morrisi (01), and M. bununa (01). A phylogenetic tree was constructed with bootstrap values of 95%, which supported a monophyletic lineage of two well-supported clades formed by 12 partial COI sequences and 48 GenBank sequences using Hirudo medicinalis as an outgroup. The monophyly of these obtained genera indicated overall similarity at species level. Today, species like Amynthas, Metaphire and Pheretima have worm diversity in the form of pheretimoid earthworms, which dates to the Late Miocene (11.2-5.3 Mya) and the Pliocene (5.3-2.4 Mya). Compared to all relevant pheretimoid species, genetic p-distance values ranged from 0.0% to 0.57% (less than 1%). These low range values demonstrated that both genera Metaphire and Amynthas, supported the theory, which states that there are shared similarities among the species, despite different morphology. The current study is the first attempt in Pakistan to identify earthworms through DNA barcoding thus providing a genomic stamp. The work explored the significance of COI gene sequences to construct molecular tools that will be useful to overcome the different obstacles in morphologically similar earthworm identification and their phylogenetic study.

Sokefun, Yadav S. Disentangling earthworm taxonomic stumbling blocks using molecular markers

Taxonomic classification of earthworms based on anatomical features has created several challenges for systematics and population genetics. This study examines the application of molecular markers, in particular mitochondrial cytochrome oxidase (COI), to facilitate discrimination of closely related earthworm species. Molecular markers have also provided insights into population genetics by aiding assessment of genetic diversity, lineage sorting, and genealogical distributions of populations for several species. Phylogeography—a study that evaluates the geographical distribution of these genealogical lineages and the role of historical processes in shaping their distribution—has also provided insights into ecology and biodiversity. Such studies are also essential to understand the distribution patterns of invasive earthworm species that have been introduced in non-native ecosystems globally. The negative consequences of these invasions on native species include competition for food resources and altered ecosystems. We anticipate that molecular markers such as COI and DNA barcoding offer potential solutions to disentangling taxonomic impediments in earthworms and advancing their systematics and population genetics. 

Multiple independent losses of cell mouth in phylogenetically distant endosymbiotic lineages of oligohymenophorean ciliates: A lesson from Clausilocola

The cell mouth is a property of the vast majority of free-living and endosymbiotic/epibiotic ciliates of the class Oligohymenophorea. Cytostome, however, naturally absents in the whole endosymbiotic subclass Astomatia and was naturally or experimentally lost in a few members of the subclass Hymenostomatia. This poses a question of how homoplastic might be the lack of oral structures in the oligohymenophorean evolution. To address this question, we used two mitochondrial genes, five nuclear markers, and detailed morphological data from an enigmatic mouthless ciliate, Clausilocola apostropha, which we re-discovered after more than half of a century. According to the present phylogenetic analyses, astomy evolved at least three times independently and in different time frames of the oligohymenophorean phylogeny, ranging from the Paleozoic to the Cenozoic period. Mouthless endosymbionts inhabiting mollusks (represented by Clausilocola), planarians (Haptophrya), and annelids ('core' astomes) never clustered together. Haptophrya grouped with the scuticociliate genus Conchophthirus, 'core' astomes were placed in a sister position to the scuticociliate orders Philasterida and Pleuronematida, and Clausilocola was robustly nested within the hymenostome family Tetrahymenidae. The tetrahymenid origin of Clausilocola is further corroborated by the existence of mouthless Tetrahymena mutants and the huge phenotypic plasticity in the cytostome size in tetrahymenids.

Systematic revision of Gatesona (Crassiclitellata, Lumbricidae), an endemic earthworm genus from the Massif Central (France)

The Massif Central in France could potentially harbor numerous ancient endemic lineages owing to its long history of continuous geological stability. Several endemic earthworm species inhabit the area, with Allolobophora (Gatesona) chaetophora, Helodrilus (Acystodrilus) and Avelona ligra showing hints of a common evolutionary origin. However, the phylogenetic relationships and taxonomic status of the species remain to be studied through integrative molecular and morphological methods. To this end, eight species including most of the known species and subspecies of All. (Gatesona), Helodrilus (Acystodrilus) musicus, and Avelona ligra were sequenced for a set of five molecular markers. The species were grouped on the basis of the molecular findings in a phylogenetic framework. All. (Gatesona) was included within the same clade as Helodrilus (Acystodrilus) and Avelona, separated from Allolobophora sensu stricto, supporting its status as a good genus. Branch lengths and average pairwise genetic distances suggested the subspecies of All. (Gatesona) chaetophora examined should be considered species-level taxa. Thus, a generic diagnosis for Gatesona stat. nov. is provided, along with redescriptions of Gatesona chaetophora comb. nov., Gatesona rutena comb. nov. stat. nov., Gatesona lablacherensis comb. nov. stat. nov. and Gatesona serninensis comb. nov. stat. nov. The study findings highlight the need for further sampling of earthworm diversity in the Massif Central (and Southern France), in addition to an increased focus on the Eastern European species of Helodrilus.

Sorry atlanticus, you are not my type: molecular assessment splits Zophoscolex (Lumbricidae: Crassiclitellata) into French and Iberian genera

Molecular phylogenetics contributes to making important advances in the challenging field of earthworm taxonomy. Use of this type of analysis has enabled clarification of the phylogenetic relationships between early-branching genera of Lumbricidae within the highly diverse Franco-Iberian realm. However, molecular phylogenetic studies of the genus Zophoscolex are scarce and have led to taxonomic uncertainty due to insufficient sampling and the absence of the type species, Z. atlanticus, from such studies. The present study investigated 11 species of Zophoscolex (including Z. atlanticus), and the phylogenetic relationships were deduced from seven molecular markers (COI, COII, 16S, tRNAs, ND1, 12S, 28S) by Bayesian and maximum likelihood inference. The findings show that species of Zophoscolex did not belong to a single clade. Zophoscolex atlanticus was placed in a clade with Z. micellus, Z. graffi and Ethnodrilus zajonci. Other species of the genus were found to belong to the genera Cataladrilus and Compostelandrilus. Finally, most of the Iberian species form a distinct clade, which was formally described as the revised genus Castellodrilus. Based on these findings, Zophoscolex is restricted to French representatives. These results highlight the importance of incorporating type species in molecular phylogenetic analyses in order to reconcile taxonomy and systematics.

Diversity and Eco-Evolutionary Associations of Endosymbiotic Astome Ciliates With Their Lumbricid Earthworm Hosts

Coevolution of endosymbionts with their hosts plays an important role in the processes of speciation and is among the most fascinating topics in evolutionary biology. Astome ciliates represent an interesting model for coevolutionary studies because they are so tightly associated with their host organisms that they completely lost the cell oral apparatus. In the present study, we used five nuclear markers (18S rRNA gene, ITS1-5.8S-ITS2 region, and 28S rRNA gene) and two mitochondrial genes (16S rRNA gene and cytochrome c oxidase subunit I) to explore the diversity of astomes inhabiting the digestive tract of lumbricid earthworms at temperate latitudes in Central Europe and to cast more light on their host specificity and coevolution events that shaped their diversification. The present coevolutionary and phylogenetic interaction-adjusted similarity analyses suggested that almost every host switch leads to speciation and firm association with the new host. Nevertheless, the suggested high structural host specificity of astomes needs to be tested with increased earthworm sampling, as only 52 out of 735 lumbricid earthworms (7.07%) were inhabited by ciliates. On the other hand, the diversification of astomes associated with megascolecid and glossoscolecid earthworms might have been driven by duplication events without host switching.

Delimitation of five astome ciliate species isolated from the digestive tube of three ecologically different groups of lumbricid earthworms, using the internal transcribed spacer region and the hypervariable D1/D2 region of the 28S rRNA gene

Background

Various ecological groups of earthworms very likely constitute sharply isolated niches that might permit speciation of their symbiotic ciliates, even though no distinct morphological features appear to be recognizable among ciliates originating from different host groups. The nuclear highly variable ITS1–5.8S-ITS2 region and the hypervariable D1/D2 region of the 28S rRNA gene have proven to be useful tools for the delimitation of species boundaries in closely related free-living ciliate taxa. In the present study, the power of these molecular markers as well as of the secondary structure of the ITS2 molecule were tested for the first time in order to discriminate the species of endosymbiotic ciliates that were isolated from the gastrointestinal tract of three ecologically different groups of lumbricid earthworms.

Results

Nineteen new ITS1–5.8S-ITS2 region and D1/D2-28S rRNA gene sequences were obtained from five astome species (Anoplophrya lumbrici, A. vulgaris, Metaradiophrya lumbrici, M. varians, and Subanoplophrya nodulata comb. n.), which were living in the digestive tube of three ecological groups of earthworms. Phylogenetic analyses of the rRNA locus and secondary structure analyses of the ITS2 molecule robustly resolved their phylogenetic relationships and supported the distinctness of all five species, although previous multivariate morphometric analyses were not able to separate congeners in the genera Anoplophrya and Metaradiophrya. The occurrence of all five taxa, as delimited by molecular analyses, was perfectly correlated with the ecological groups of their host earthworms.

Conclusions

The present study indicates that morphology-based taxonomy of astome ciliates needs to be tested in the light of molecular and ecological data as well. The use of morphological identification alone is likely to miss species that are well delimited based on molecular markers and ecological traits and can lead to the underestimation of diversity and overestimation of host range. An integrative approach along with distinctly increased taxon sampling would be helpful to assess the consistency of the eco-evolutionary trend in astome ciliates.

Population Genetic Structure Reveals Two Lineages of Amynthas triastriatus (Oligochaeta: Megascolecidae) in China, with Notes on a New Subspecies of Amynthas triastriatus

Amynthas triastriatus (Oligochaete: Megascolecidae) is a widely distributed endemic species in Southern China. To shed light on the population genetic diversity and to elucidate the population differentiation and dispersal of A. triastriatus, a population genetic structure study was undertaken based on samples from 35 locations collected from 2010 to 2016. Two exclusive lineages within A. triastriatus-lineage A and lineage B-were revealed. Lineage A was mainly distributed at high altitudes while lineage B was mainly distributed at low altitudes in Southeast China. The genetic diversity indices indicated that the populations of A. triastriatus had a strong genetic structure and distinct dispersal histories underlying the haplogroups observed in this study. Combined with morphological differences, these results indicated a new cryptic subspecies of A. triastriatus. Lineage A was almost degenerated to parthenogenesis and lineage B had a trend to parthenogenesis, which suggested that parthenogenesis could be an internal factor that influenced the differentiation and dispersal of A. triastriatus. The divergence time estimates showed that A. triastriatus originated around Guangxi and Guangdong provinces and generated into two main lineages 2.97 Ma (95%: 2.17-3.15 Ma) at the time of Quaternary glaciation (2.58 Ma), which suggested that the Quaternary glaciation may have been one of main factors that promoted the colonization of A. triastriatus.

Evolutionary Origin and Host Range of Plagiotoma lumbrici (Ciliophora, Hypotrichia), an Obligate Gut Symbiont of Lumbricid Earthworms

Four common earthworm species, the anecic Lumbricus terrestris, the endogeic Octolasion tyrteum as well as the epigeic Eisenia fetida and Dendrobaena veneta, were examined for the presence of the microbial gut symbiont Plagiotoma lumbrici. The evolutionary origin of this endobiotic microbe was reconstructed, using the 18S rRNA gene, the ITS1-5.8S-ITS2 region, and the first two domains of the 28S rRNA gene. Plagiotoma lumbrici was exclusively detected in the anecic Lumbricus terrestris. Multigene analyses and the ITS2 secondary structure robustly determined the phylogenetic home of Plagiotoma lumbrici populations within the oxytrichid Dorsomarginalia (Spirotrichea: Hypotrichia) as a sister taxon of the free-living Hemiurosomoida longa. This indicates that earthworms obtained their gut endosymbiont by ingesting soil/leaf litter containing oxytrichine ciliates that became adapted to the intestinal tract of earthworms. Interestingly, according to the literature data, Plagiotoma lumbrici was detected in multiple anecic and some epigeic but never in endogeic earthworms. These observations suggest that Plagiotoma lumbrici might be adapted to certain gut conditions and the lifestyle of anecic Lumbricidae, such as Lumbricus, Aporrectodea, and Scherotheca, as well as of some co-occurring epigeic Lumbricus species.

A multigene timescale and diversification dynamics of Ciliophora evolution

Ciliophora is one of the most diverse lineages of unicellular eukaryotes. Nevertheless, a robust timescale including all main lineages and employing properly identified ciliate fossils as primary calibrations is lacking. Here, we inferred a time-calibrated multigene phylogeny of Ciliophora evolution, and we used this timetree to investigate the rates and patterns of lineage diversification through time. We implemented a two-step analytical approach that favored both gene and taxon sampling, reducing the uncertainty of time estimates and yielding narrower credibility intervals on the ribosomal-derived chronogram. We estimate the origin of Ciliophora at 1143 Ma, which is substantially younger than previously proposed ages, and the huge diversity explosion occurred during the Paleozoic. Among the current groups recognized as classes, Spirotrichea diverged earlier, its origin was dated at ca. 850 Ma, and Protocruziea was the younger class, with crown age estimated at 56 Ma. Macroevolutionary analysis detected a significant rate shift in diversification dynamics in the spirotrichean clade Hypotrichia + Oligotrichia + Choreotrichia, which had accelerated speciation rate ca. 570 Ma, during the Ediacaran-Cambrian transition. For all crown lineages investigated, speciation rates declined through time, whereas extinction rates remained low and relatively constant throughout the evolutionary history of ciliates.

Transcriptomic analysis confirms differences among nuclear genomes of cryptic earthworm lineages living in sympatry

BACKGROUND

Many earthworm species demonstrate significant cryptic diversity, with several highly diverged mitochondrial lineages found within most of the taxa studied to date. The status of differences between these lineages on the nuclear level is still unclear. Because of widespread polyploidy in earthworms, most studies were limited to two nuclear loci, the ribosomal and the histone clusters. Here we attempted to elucidate the status of a set of genetic lineages within Eisenia nordenskioldi nordenskioldi, an earthworm species from Northern Asia with high intraspecific diversity. We performed RNA-seq on an IonTorrent platform for five specimens of this species belonging to five genetic lineages, as well as two outgroups from the family Lumbricidae, the congenetic E. andrei, and Lumbricus rubellus.

RESULTS

We de novo assembled transcriptomes and constructed datasets of genes present in all seven specimens using broad (ProteinOrtho; 809 genes) and narrow (HaMStR; 203 genes) ortholog assignment. The majority of orthologs had identical amino acid sequences in all studied specimens, which we believe was due to strong bias towards the most conserved genes. However, for the rest of genes the differences among the lineages were lower than those between them and the congeneric E. andrei. Both datasets yielded phylogenetic trees with the same topology. E. n. nordenskioldi was found to be monophyletic. The differences on the genetic level had no concordance with geography, implying complex history of dispersal.

CONCLUSIONS

We found that genetic lineages of E. n. nordenskioldi are genetically distinct on nuclear level and probably diverged long ago. Current data implies that they might even represent distinct species within the E. nordenskioldi species complex.

Multigene phylogeny reveals a new Iranian earthworm genus (Lumbricidae: Philomontanus) with three new species

Lumbricidae taxonomy is vastly restricted by the morphological simplicity of earthworms and their lack of complex appendices. This has led to confusing results in the Lumbricidae classifications, which in turn, has hindered our ability to identify and assign new and cryptic species to the family. Here we propose the addition of a new Lumbricidae genus from the Zagros and Elburz Mountains of Iran, i.e. Philomontanus gen. nov, including three new species. Our taxonomic inferences were based on the phylogenetic analysis of two nuclear gene regions (28S rDNA and 18S rDNA) and 11 mitochondrial gene regions (16S rDNA, 12S rDNA, NADH dehydrogenase I, cytochrome oxidase subunits I and II and tRNAs Asn, Asp, Val, Leu, Ala and Ser). Philomontanus gen. nov comprises the earthworm species Philomontanus sarii sp. nov., Philomontanus mahmoudi sp. nov. and Philomontanus baloutchi sp. nov. These three species are morphologically similar to each other with only a few characters separating them (e.g. size, pigmentation and position of clitellum). Our findings support the adoption of an integrative approach including molecular information (e.g., DNA sequences) to aid earthworm classification and develop a robust taxonomy.

Dawn of astome ciliates in light of morphology and time-calibrated phylogeny of Haptophrya planariarum, an obligate endosymbiont of freshwater turbellarians

Morphology, systematic position and time-calibrated phylogeny of Haptophrya planariarum were investigated. This endosymbiont of freshwater turbellarians is characterized by: (i) a length of about 200-900 μm; (ii) a campanulate to truncate claviform body carrying an anterior adhesive sucker; (iii) an ellipsoidal macronucleus localized in the rear body end; (iv) a contractile canal extending along the dorsal margin; and (v) usually more than 150 meridional ciliary rows, a horseshoe-shaped suture line along the sucker, and two inconspicuous secant systems at lateral ends of the suture line. In 18S rRNA gene phylogenies, astomes were depicted as a non-monophyletic group within the scuticociliate clade, whereby H. planariarum clustered with the loxocephalid genus Dexiotricha. After considering morphological evidence, statistical tree topology tests and evolutionary distances, we find astomes as a distinct group that evolved from a free-living scuticociliate ancestor in the early Paleozoic. Molecular clock analyses indicated that astomes living in annelids diverged from those inhabiting turbellarians within about 50 Ma during the Late Cambrian and the Upper Ordovician. This comparatively short time span might have not sufficed for fixation of molecular synapomorphies in the 18S rRNA gene and/or they might have been erased by substitutions during the almost 500 Ma-long evolutionary history of astomes.

Evolution of a key trait greatly affects underground community assembly process through habitat adaptation in earthworms

Underground community assemblies have not been studied well compared with aboveground communities, despite their importance for our understanding of whole ecosystems. To investigate underground community assembly over evolutionary timescales, we examined terrestrial earthworm communities (Oligochaeta: Haplotaxida) in conserved mountainous primary forests in Japan as a model system. We collected 553 earthworms mostly from two dominant families, the Megascolecidae and the Lumbricidae, from 12 sites. We constructed a molecular taxonomic unit tree based on the analysis of three genes to examine the effects of a biogeographic factor (dispersal ability) and an evolutionary factor (habitat adaptation) on the earthworm community assembly process. The phylogenetic distance of the earthworm communities among sites was positively correlated with geographic distance when intraspecific variation was included, indicating that the divergence within species was affected by biogeographic factors. The community assembly process in the Megascolecidae has also been affected by environmental conditions in relation to an evolutionary relationship between habitat environment and intestinal cecum type, a trait closely related to habitat depth and diet, whereas that in the Lumbricidae has not been affected as such. Intestinal cecum type showed a pattern of niche conservatism in the Megascolecidae lineage. Our results suggest that investigating the evolution of a key trait related to life history can lead to the clear description of community assembly process over a long timescale and that the community assembly process can differ greatly among related lineages even though they live sympatrically.

Integrative systematic revision of a Mediterranean earthworm family: Hormogastridae (Annelida, Oligochaeta)

The problem of reconciling earthworm taxonomy and phylogeny has shown advances with the application of molecular techniques, yet they have proven insufficient. Integrative systematics could solve this by combining multiple sources of evolutionary information. Relatively low diversity, restricted range and low nomenclatural conflict make Hormogastridae Michaelsen, 1900 a desirable target for an integrative systematics approach. The main systematic conflicts within this family are the polyphyly of the species Hormogaster pretiosa Michaelsen, 1899, the widespread presence of cryptic lineages, the lack of resolution of supraspecific relationships and the paraphyly of the genus Hormogaster Rosa, 1877 (found to be composed of four well-supported genus-level clades by molecular phylogenetic inference). This work integrates all the existing information by performing phylogenetic inference based on morphological, molecular and total evidence datasets, comparing their performance with the topology obtained by phylogenomic analyses. It also includes a comparative study of representatives of the main clades based on microcomputed tomography (µCT) reconstructions. The addition of morphological characters improved the resolution of the Hormogastridae tree; ancestral state reconstruction displayed the evolution of character states and provided morphological diagnoses for the genera within a new system, which incorporates information about ecological niches and biogeography.

Integrated taxonomy reveals multiple species in the Dendrobaena byblica (Rosa, 1893) complex (Oligochaeta: Lumbricidae)

Dendrobaena byblica (Rosa, 1893) is a Circum-Mediterranean species complex composed of at least 17 nominal taxa. Regarding the most important species characters (clitellum and tubercles) the worms belonging to the genus Fitzingeria Zicsi, 1978 seem to be very close to the D. byblica species group. Here we provide the first molecular phylogenetic analysis of the byblica species group and the Fitzingeria species, and show that the genus Fitzingeria is polyphyletic and groups together with the Carpathian and Balkanic deeply pigmented byblica forms. The other main clade consists of the ‘classical’ byblica species. The morphological characteristics also support these results. On the basis of the molecular and morphological characters the species of the former Fitzingeria were relegated to Dendrobaena and four new species were described together with a new replacement name Dendrobaena carpathomontana nom. nov. for F. platyura montana (Černosvitov, 1932).

Molecular phylogeny and systematics of native North American lumbricid earthworms (Clitellata: Megadrili)

The family Lumbricidae is arguably the most well-known and well-studied earthworm group due to its dominance in the European earthworm fauna and its invasion in temperate regions worldwide. However, its North American members, especially the genus Bimastos Moore, 1893, are poorly understood. We revised the systematics of the genus Bimastos and tested the hypothesis of the monophyly of North American lumbricids using morphological characters and eight molecular markers. Phylogenetic analyses based on our extensive sampling of Bimastos and inclusion of Dendrodrilus and Allolobophoridella indicated a well-supported clade containing Bimastos and Eisenoides Gates, 1969, and provided the first evidence supporting that North American lumbricids are monophyletic. Assuming the available divergence time estimations and dating of land bridges are correct, it would suggest that the ancestor of this clade arrived North America through Beringia or the De Geer route during Late Cretaceous, and since then the clade has diverged from its Eurasian sister group, Eisenia. The peregrine genera Dendrodrilus and Allolobophoridella are nested within the Bimastos clade; we propose to treat them as junior synonyms of the genus Bimastos, and, contradictory to the commonly held belief of being European, they are indeed part of the indigenous North American earthworm fauna. Morphological characters, such as red-violet pigmentation, proclinate U-shaped nephridial bladders and calciferous diverticula in segment 10 further support this placement. The East Mediterranean–Levantine Spermophorodrilus Bouché, 1975 and Healyella Omodeo & Rota, 1989 are nested within the Dendrobaena sensu lato clade; therefore their close relationship with the North American Bimastos is refuted. Species fit the revised diagnosis of Bimastos are reviewed and keyed, and a new species, Bimastos schwerti sp. nov., is described.

Phylogenetic evaluation of Amynthas earthworms from South China reveals the initial ancestral state of spermathecae

Our knowledge of the phylogeny of the earthworm genus Amynthas under the family Megascolecidae, which is comprised of a huge number of species, is very limited compared to the better-known and much smaller family Lumbricidae. In order to investigate the phylogenetic relationships among the species within the genus Amynthas, which is the largest genus of the Megascolecidae family, nuclear and mitochondrial DNA sequences of 77 species, including 76 in-group Amynthas species collected from South China and 1 out-group species, were analyzed. A 5402bp segments composed of whole nuclear 18S rDNA and the mitochondrial genes COI, COII, ND1, 12S, and 16S was assembled from 77 species. Maximum Likelihood and Bayesian analyses of the concatenated sequences were performed. The results revealed evolution of two geographically independent lineages, both showing the ancestral state of two pairs of spermatheca (Sp.p 7/8/9). We found the species groups described by Sims and Easton (1972) to be non-monophyletic, and the origin of the parthenogenetic species group to likely be a quadthecal ancestor. These results provide modest evidence in support of an Indochinese peninsula origin of the Chinese Amynthas species and divergence of the genus once it had spread to mainland China. The findings of this study are consistent with a divergence scenario that resulted in at least one branch spreading to the Southeast of China and another branch spreading to the Southwest of China, but further research is required to confirm this interpretation of the Amynthas phylogeny.

Phylogenomic analyses of Crassiclitellata support major Northern and Southern Hemisphere clades and a Pangaean origin for earthworms

BACKGROUND

Earthworms (Crassiclitellata) are a diverse group of annelids of substantial ecological and economic importance. Earthworms are primarily terrestrial infaunal animals, and as such are probably rather poor natural dispersers. Therefore, the near global distribution of earthworms reflects an old and likely complex evolutionary history. Despite a long-standing interest in Crassiclitellata, relationships among and within major clades remain unresolved.

METHODS

In this study, we evaluate crassiclitellate phylogenetic relationships using 38 new transcriptomes in combination with publicly available transcriptome data. Our data include representatives of nearly all extant earthworm families and a representative of Moniligastridae, another terrestrial annelid group thought to be closely related to Crassiclitellata. We use a series of differentially filtered data matrices and analyses to examine the effects of data partitioning, missing data, compositional and branch-length heterogeneity, and outgroup inclusion.

RESULTS AND DISCUSSION

We recover a consistent, strongly supported ingroup topology irrespective of differences in methodology. The topology supports two major earthworm clades, each of which consists of a Northern Hemisphere subclade and a Southern Hemisphere subclade. Divergence time analysis results are concordant with the hypothesis that these north-south splits are the result of the breakup of the supercontinent Pangaea.

CONCLUSIONS

These results support several recently proposed revisions to the classical understanding of earthworm phylogeny, reveal two major clades that seem to reflect Pangaean distributions, and raise new questions about earthworm evolutionary relationships.

Pinpointing cryptic borders: Fine-scale phylogeography and genetic landscape analysis of the Hormogaster elisae complex (Oligochaeta, Hormogastridae)

Spatial and temporal aspects of the evolution of cryptic species complexes have received less attention than species delimitation within them. The phylogeography of the cryptic complex Hormogaster elisae (Oligochaeta, Hormogastridae) lacks knowledge on several aspects, including the small-scale distribution of its lineages or the palaeogeographic context of their diversification. To shed light on these topics, a dense specimen collection was performed in the center of the Iberian Peninsula - resulting in 28 new H. elisae collecting points, some of them as close as 760m from each other- for a higher resolution of the distribution of the cryptic lineages and the relationships between the populations. Seven molecular regions were amplified: mitochondrial subunit 1 of cytochrome c oxidase (COI), 16S rRNA and tRNA Leu, Ala, and Ser (16S t-RNAs), one nuclear ribosomal gene (a fragment of 28S rRNA) and one nuclear protein-encoding gene (histone H3) in order to infer their phylogenetic relationships. Different representation methods of the pairwise divergence in the cytochrome oxidase I sequence (heatmap and genetic landscape graphs) were used to visualize the genetic structure of H. elisae. A nested approach sensu Mairal et al. (2015) (connecting the evolutionary rates of two datasets of different taxonomic coverage) was used to obtain one approximation to a time-calibrated phylogenetic tree based on external Clitellata fossils and a wide molecular dataset. Our results indicate that limited active dispersal ability and ecological or biotic barriers could explain the isolation of the different cryptic lineages, which never co-occur. Rare events of long distance dispersal through hydrochory appear as one of the possible causes of range expansion.

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.

Fauna Europaea: Annelida - Terrestrial Oligochaeta (Enchytraeidae and Megadrili), Aphanoneura and Polychaeta

Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. This paper provides updated information on the taxonomic composition and distribution of the Annelida - terrestrial Oligochaeta (Megadrili and Enchytraeidae), Aphanoneura and Polychaeta, recorded in Europe. Data on 18 families, 11 autochthonous and 7 allochthonous, represented in our continent by a total of 800 species, are reviewed, beginning from their distinctness, phylogenetic status, diversity and global distribution, and following with major recent developments in taxonomic and faunistic research in Europe. A rich list of relevant references is appended. The Fauna Europaea Annelida - terrestrial Oligochaeta data-set, as completed in 2004, will be updated accordingly.

Evolution of the tripartite symbiosis between earthworms, Verminephrobacter and Flexibacter-like bacteria

Nephridial (excretory organ) symbionts are widespread in lumbricid earthworms and the complexity of the nephridial symbiont communities varies greatly between earthworm species. The two most common symbionts are the well-described Verminephrobacter and less well-known Flexibacter-like bacteria. Verminephrobacter are present in almost all lumbricid earthworms, they are species-specific, vertically transmitted, and have presumably been associated with their hosts since the origin of lumbricids. Flexibacter-like symbionts have been reported from about half the investigated earthworms; they are also vertically transmitted. To investigate the evolution of this tri-partite symbiosis, phylogenies for 18 lumbricid earthworm species were constructed based on two mitochondrial genes, NADH dehydrogenase subunit 2 (ND2) and cytochrome c oxidase subunit I (COI), and compared to their symbiont phylogenies based on RNA polymerase subunit B (rpoB) and 16S rRNA genes. The two nephridial symbionts showed markedly different evolutionary histories with their hosts. For Verminephrobacter, clear signs of long-term host-symbiont co-evolution with rare host switching events confirmed its ancient association with lumbricid earthworms, likely dating back to their last common ancestor about 100 million years (MY) ago. In contrast, phylogenies for the Flexibacter-like symbionts suggested an ability to switch to new hosts, to which they adapted and subsequently became species-specific. Putative co-speciation events were only observed with closely related host species; on that basis, this secondary symbiosis was estimated to be minimum 45 MY old. Based on the monophyletic clustering of the Flexibacter-like symbionts, the low 16S rRNA gene sequence similarity to the nearest described species (<92%) and environmental sequences (<94.2%), and the specific habitat in the earthworm nephridia, we propose a new candidate genus for this group, Candidatus Nephrothrix.