Distinct genetic differentiation and species diversification within two marine nematodes with different habitat preference in Antarctic sediments

A New Species of Free-Living Nematodes (Desmodorida, Desmodoridae) in the Romanian Black Sea Waters

The paper reports the record of Pseudochromadora gomoi sp.n. in circalittoral habitats (at depths of 47–59 m) of the Romanian Black Sea waters. The species is characterized by a unispiral amphidial fovea, the presence of lateral alae stretching from the posterior end of the cardia to the level of the cloacal opening, but also shows unique features found in other Desmodorida genera (i.e., the presence of a precloacal ventral ala in males similar to several Desmodora or Echinodesmodora species and eight subcephalic setae on the head capsule). The presence of a constrictor cuticle ring and orange elongated ducts in the anterior body part as in Pseudodesmodora lacrima, Leduc and Wharton, 2010, were also noted. The morphometric measurements of our species differ from most of the Pseudochromadora species reported in specialty literature. We extracted and counted all desmodorid individuals from 9 meiobenthic samples collected in June 2020, and performed a detailed morphological analysis of 12 individuals (5 females and 7 males) belonging to our species, also highlighting the dissimilarities with the related desmodorid species.

New Distribution and Molecular Diversity of the Reniform Nematode Rotylenchulus macrosoma (Nematoda: Rotylenchulinae) in Europe

Reniform nematodes of the genus Rotylenchulus are semi-endoparasites of numerous herbaceous and woody plant species roots and occur largely in regions with temperate, subtropical, and tropical climates. In this study, we provide new records of the nematode Rotylenchulus macrosoma in eight European countries (Czech Republic, France, Germany, Hungary, Italy, Romania, Serbia, and Portugal), in addition to the six Mediterranean countries (Greece, Israel, Jordan, Spain, Syria, and Turkey) where the nematode was previously reported. Four new host species (corn, pea, wheat, and an almond-peach hybrid rootstock) are added to the recorded host species (bean, chickpea, hazelnut, peanut, soybean, and wild and cultivated olive). Molecular analyses based on the cytochrome c oxidase subunit coxI and D2-D3 segments of 28S RNA markers showed high diversity and pronounced genetic structure among populations of Rotylenchulus macrosoma. However, the complexity of phylogeographic patterns in plant-parasitic nematodes may be related to the intrinsic heterogeneity in the distribution of soil organisms, a rare occurrence of a species, or the potential human impact associated with agricultural practices.

Analyzing drivers of speciation in the Southern Ocean using the sea spider species complex Colossendeis megalonyx as a test case

Colossendeis megalonyx Hoek, 1881 has the broadest distribution of all sea spiders in the Southern Ocean. Previous studies have detected several evolutionarily young lineages within this taxon and interpreted them as a result of allopatric speciation in a few shelf refuges during glacial maxima. However, alternative scenarios such as ecological speciation in sympatry have rarely been considered or tested. Here, we generated the most extensive genomic and morphometric data set on the C. megalonyx species complex to (i) comprehensively describe species diversity, (ii) explore intraspecific connectivity between populations located around Antarctica, and (iii) systematically test for positive selection indicative of adaptive speciation. We successfully applied a target hybrid enrichment approach and recovered all 1607 genes targeted. Phylogenomic analysis was consistent with previous findings and, moreover, increased the resolution of branching within lineages. We found specimens of phylogenetically well-separated lineages occurring in sympatry to be genetically distinct from each other and gene flow between geographically separated populations of the same lineages to be restricted. Evidence for positive selection was found for four genes associated with structural and neuronal functions. Hence, there is an indication for positive selection in the C. megalonyx species complex, yet its specific contribution to the speciation process remains to be explored further. Finally, morphometric analyses revealed multiple significant differences between lineages, but a clear separation proved difficult. Our study highlights the relevance of positive selection as a potential driver for speciation in the Southern Ocean.

DNA Barcoding for Delimitation of Putative Mexican Marine Nematodes Species

Nematode biodiversity is mostly unknown; while about 20,000 nematode species have been described, estimates for species diversity range from 0.1 to 100 million. The study of nematode diversity, like that of meiofaunal organisms in general, has been mostly based on morphology-based taxonomy, a time-consuming and costly task that requires well-trained specialists. This work represents the first study on the taxonomy of Mexican nematodes that integrates morphological and molecular data. We added eleven new records to the Mexican Caribbean nematode species list: Anticomidae sp.1, Catanema sp.1, Enoploides gryphus, Eurystomina sp.1, Haliplectus bickneri, Metachromadora sp.1, Odontophora bermudensis, Oncholaimus sp.1, Onyx litorale, Proplatycoma fleurdelis, and Pontonema cf. simile. We improved the COI database with 57 new sequences from 20 morphotypes. All COI sequences obtained in this work are new entries for the international genetic databases GenBank and BOLD. Among the studied sites, we report the most extensive species record (12 species) at Cozumel. DNA barcoding and species delineation methods supported the occurrence of 20 evolutionary independent entities and confirmed the high taxonomic resolution of the COI gene. Different approaches provided consistent results: ABGD and mPTP methods disentangled 20 entities, whereas Barcode Index Numbers (BINs) recovered 22 genetic species. Results support DNA barcoding being an efficient, fast, and low-cost method to integrate into morphological observations in order to address taxonomical shortfalls in meiofaunal organisms.

Just the once will not hurt: DNA suggests species lumping over two oceans in deep-sea snails (Cryptogemma)

The practice of species delimitation using molecular data commonly leads to the revealing of species complexes and an increase in the number of delimited species. In a few instances, however, DNA-based taxonomy has led to lumping together of previously described species. Here, we delimit species in the genus Cryptogemma (Gastropoda: Conoidea: Turridae), a group of deep-sea snails with a wide geographical distribution, primarily by using the mitochondrial COI gene. Three approaches of species delimitation (ABGD, mPTP and GMYC) were applied to define species partitions. All approaches resulted in eight species. According to previous taxonomic studies and shell morphology, 23 available names potentially apply to the eight Cryptogemma species that were recognized herein. Shell morphometrics, radular characters and geographical and bathymetric distributions were used to link type specimens to these delimited species. In all, 23 of these available names are here attributed to seven species, resulting in 16 synonymizations, and one species is described as new: Cryptogemma powelli sp. nov. We discuss the possible reasons underlying the apparent overdescription of species within Cryptogemma, which is shown here to constitute a rare case of DNA-based species lumping in the hyper-diversified superfamily Conoidea.

Multilocus data reveal cryptic species in the Atlantic seabob shrimp Xiphopenaeus kroyeri (Crustacea: Decapoda)

The recognition of cryptic biodiversity provides valuable insights for the management of exploited species. The Atlantic seabob shrimp (Xiphopenaeus kroyeri) is a commercially important fishery resource in the Guianan ecoregion, South America. Previous research in Brazil suggested the presence of cryptic species within the genus. Here, we confirm this presence and delimit the species by applying a multilocus approach based on two mitochondrial (COI and cytb) and two nuclear (PEPCK and NaK) genes. Species boundaries were tested using BPP, GMYC and bPTP delimitation algorithms. These analyses provided strong support for three clades within the genus Xiphopenaeus, including one undescribed clade, which occurs sympatrically with X. kroyeri in the Western Atlantic. Unexpectedly, this undescribed clade is more closely related to the Pacific Xiphopenaeus riveti than to their Atlantic congener. Our DNA-based species delimitation was further supported by new ecological information on habitat and morphology (colour). We also expand the known distribution range of the cryptic species, currently restricted to Brazil, to include French Guiana, Suriname and Colombia. Our findings have important consequences for the management of the species, in terms of both biodiversity management and fisheries management.

Phylogeny of the Echinoderes coulli-group (Kinorhyncha : Cyclorhagida : Echinoderidae) – a cosmopolitan species group trapped in the intertidal

Kinorhyncha is a phylum of microscopic, benthic marine invertebrates found throughout the world, from the Arctic to Antarctica and from the intertidal zone to the deep sea. Within the most species-rich genus, Echinoderes, we find a putatively monophyletic species group, the so-called Echinoderes coulli-group. The remarkable morphological similarities of the E. coulli-group species and the fact that the group has a global distribution even though most of the species are restricted to intertidal habitats, has led to the hypothesis that dispersal and speciation within the group has been driven by the process of continental drift. However, this has never been confirmed empirically. With morphology and two molecular loci, COI and 18S, we calculated phylogenetic trees by analysing datasets separately and in combination using Maximum Parsimony, Maximum Likelihood and Bayesian Inference. Using different models of evolution in combination with different statistical approaches, we show that two major clade divergences were consistent with historic drifting of continents, suggesting that vicariance has played an important role for the speciation within the E. coulli-group. Furthermore, we found that reconstructions of past tectonic drifting since the Devonian (416–359 million years ago) were able to explain present species distributions, and suggest that the group originated in a supposedly vast shallow marine environment in north-eastern Gondwana by the mid-late Silurian, 426–416 million years ago.

Phylogenetic analysis of Spirocerca lupi and Spirocerca vulpis reveal high genetic diversity and intra-individual variation

Background

Spirocerca lupi is a parasitic nematode of canids that can lead to a severe and potentially fatal disease. Recently, a new species, Spirocerca vulpis, was described from red foxes in Europe, suggesting a high genetic diversity of the Spirocerca spp. infecting canids. The genetic variation and phylogenetic relationships of S. lupi collected from naturally-infected domestic dogs from Australia, Hungary, Israel, Italy, India and South Africa, and S. vulpis from red foxes from Bosnia and Herzegovina, Italy and Spain, was studied using mitochondrial and rDNA markers.

Results

A high intra-individual variation was found in the first internal transcribed spacer (ITS1) locus in all Spirocerca spp., ranging between 0.37–2.84%, with up to six haplotypes per specimen. In addition, a combination of phylogenetic and haplotype analyses revealed a large variability between S. lupi specimens collected from different geographical locations using the ITS1 (0.37–9.33%) and the cytochrome c oxidase subunit 1 (cox1) gene (1.42–6.74%). This genetic diversity led to the identification of two S. lupi genotypes circulating among dogs (PTP support > 0.829), including genotype 1 found in S. lupi from Australia, India, Israel and South Africa, and genotype 2 represented by specimens from Hungary and Italy. These genotypes presented pairwise nucleotide distances of 0.14%, 8.06% and 6.48 ± 0.28% in the small rDNA subunit (18S), ITS1 and cox1 loci, respectively. Additionally, Nei’s genetic distance in the ITS1 showed a further subdivision of genotype 1 worms into 1A (Israel and South Africa) and 1B (Australia and India). A morphological analysis of the anterior and posterior extremities of genotype 1 and genotype 2 worms using scanning electron microscopy did not show any differences between the specimens, contrary to the morphological differences between S. lupi and S. vulpis.

Conclusions

These findings demonstrate the high genetic variability among Spirocerca spp. from different geographical locations, thereby expanding our understanding of the epidemiology, evolution and phylogenetic variability within the genus.

Electronic supplementary material

The online version of this article (10.1186/s13071-018-3202-0) contains supplementary material, which is available to authorized users.

Population genetic structure in Sabatieria (Nematoda) reveals intermediary gene flow and admixture between distant cold seeps from the Mediterranean Sea

BACKGROUND

There is a general lack of information on the dispersal and genetic structuring for populations of small-sized deep-water taxa, including free-living nematodes which inhabit and dominate the seafloor sediments. This is also true for unique and scattered deep-sea habitats such as cold seeps. Given the limited dispersal capacity of marine nematodes, genetic differentiation between such geographically isolated habitat patches is expected to be high. Against this background, we examined genetic variation in both mitochondrial (COI) and nuclear (18S and 28S ribosomal) DNA markers of 333 individuals of the genus Sabatieria, abundantly present in reduced cold-seep sediments. Samples originated from four Eastern Mediterranean cold seeps, separated by hundreds of kilometers, and one seep in the Southeast Atlantic.

RESULTS

Individuals from the Mediterranean and Atlantic were divided into two separate but closely-related species clades. Within the Eastern Mediterranean, all specimens belonged to a single species, but with a strong population genetic structure (ΦST = 0.149). The haplotype network of COI contained 19 haplotypes with the most abundant haplotype (52% of the specimens) shared between all four seeps. The number of private haplotypes was high (15), but the number of mutations between haplotypes was low (1-8). These results indicate intermediary gene flow among the Mediterranean Sabatieria populations with no evidence of long-term barriers to gene flow.

CONCLUSIONS

The presence of shared haplotypes and multiple admixture events indicate that Sabatieria populations from disjunct cold seeps are not completely isolated, with gene flow most likely facilitated through water current transportation of individuals and/or eggs. Genetic structure and molecular diversity indices are comparable to those of epiphytic shallow-water marine nematodes, while no evidence of sympatric cryptic species was found for the cold-seep Sabatieria.