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Molecular tools have revolutionized the exploration of biodiversity, especially in organisms for which traditional taxonomy is difficult, such as for microscopic animals (meiofauna). Environmental (eDNA) metabarcode surveys of DNA extracted from sediment samples are increasingly popular for surveying biodiversity. Most eDNA surveys use the nuclear gene-encoding small-subunit rDNA gene (18S) as a marker; however, different markers and metrics used for delimiting species have not yet been evaluated against each other or against morphologically defined species (morphospecies). We assessed more than 12,000 meiofaunal sequences of 18S and of the main alternatively used marker [Cytochrome c oxidase subunit I (COI) mtDNA] belonging to 55 datasets covering three taxonomic ranks. Our results show that 18S reduced diversity estimates by a factor of 0.4 relative to morphospecies, whereas COI increased diversity estimates by a factor of 7.6. Moreover, estimates of species richness using COI were robust among three of four commonly used delimitation metrics, whereas estimates using 18S varied widely with the different metrics. We show that meiofaunal diversity has been greatly underestimated by 18S eDNA surveys and that the use of COI provides a better estimate of diversity. The suitability of COI is supported by cross-mating experiments in the literature and evolutionary analyses of discreteness in patterns of genetic variation. Furthermore its splitting of morphospecies is expected from documented levels of cryptic taxa in exemplar meiofauna. We recommend against using 18S as a marker for biodiversity surveys and suggest that use of COI for eDNA surveys could provide more accurate estimates of species richness in the future.

Meiofauna represent one of the most abundant and diverse communities in marine benthic ecosystems. However, an accurate assessment of diversity at the level of species has been and remains challenging for these microscopic organisms. Therefore, for many taxa, especially the soft body forms such as nemerteans, which often lack clear diagnostic morphological traits, DNA taxonomy is an effective means to assess species diversity. Morphological taxonomy of Nemertea is well documented as complicated by scarcity of unambiguous character states and compromised by diagnoses of a majority of species (and higher clades) being inadequate or based on ambiguous characters and character states. Therefore, recent studies have advocated for the primacy of molecular tools to solve the taxonomy of this group. DNA taxonomy uncovers possible hidden cryptic species, provides a coherent means to systematize taxa in definite clades, and also reveals possible biogeographic patterns. Here, we analyze diversity of nemertean species by considering the barcode region of the mitochondrial gene Cytochrome Oxidase subunit I (COI) and different species delineation approaches in order to infer evolutionarily significant units. In the aim to uncover actual diversity of meiofaunal nemerteans across different sites in Central America, COI sequences were obtained for specimens assigned here to the genera Cephalothrix, Ototyphlonemertes, and Tetrastemma-like worms, each commonly encountered in our sampling. Additional genetic, taxonomic, and geographic data of other specimens belonging to these genera were added from GenBank. Results are consistent across different DNA taxonomy approaches, and revealed (i) the presence of several hidden cryptic species and (ii) numerous potential misidentifications due to traditional taxonomy. (iii) We additionally test a possible biogeographic pattern of taxonomic units revealed by this study, and, except for a few cases, the putative species seem not to be widely distributed, in contrast to what traditional taxonomy would suggest for the recognized morphotypes.

Understanding patterns and processes in biological diversity is a critical task given current and rapid environmental change. Such knowledge is even more essential when the taxa under consideration are important ecological and evolutionary models. One of these cases is the monogonont rotifer cryptic species complex Brachionus plicatilis , which is by far the most extensively studied group of rotifers, is widely used in aquaculture, and is known to host a large amount of unresolved diversity. Here we collate a dataset of previously available and newly generated sequences of COI and ITS1 for 1273 isolates of the B. plicatilis complex and apply three approaches in DNA taxonomy (i.e. ABGD, PTP, and GMYC) to identify and provide support for the existence of 15 species within the complex. We used these results to explore phylogenetic signal in morphometric and ecological traits, and to understand correlation among the traits using phylogenetic comparative models. Our results support niche conservatism for some traits (e.g. body length) and phylogenetic plasticity for others (e.g. genome size).

Gastrotricha systematics is in a state of flux mainly due to the conflicts between cladistic studies base on molecular markers and the classical systematisation based on morphological traits. In sandy samples from Thailand, we found numerous macrodasyidan gastrotrichs belonging to an undescribed species of difficult taxonomic affiliation. The abundance and original nature of the specimens prompted us to undertake a deep survey of both morphological and molecular traits aiming at a reliable systematisation of the new taxon. Using several microscopical techniques we investigated the external and internal anatomy, including the muscular and nervous systems of the new species. Additional specimens were used to obtain the 18S rRNA gene sequence; molecular data was analysed cladistically in conjunction with data from additional species belonging to the near complete Macrodasyida taxonomic spectrum. Specimens are vermiform, up to 806 μm in total length, and show a well-defined head equipped with peculiar leaf-like sensorial organs and a single-lobed posterior end. The adhesive apparatus includes anterior, ventrolateral, dorsal and posterior tubes. Pharynx is about 1/4 of the total length and shows pores at its posterior 3/4. Adult specimens exhibit maturing eggs and a bulky, muscular caudal organ, but do not show sperm nor the frontal organ. Musculature and nervous system organisation resemble the usual macrodasyidan plan; however, the somatic circular muscles of the intestinal region surround all other muscular components and a third FMRFamide-IR commissure ventral to the pharyngo-intestinal junction appear to be an autoapomorphic traits of the new species. While the anatomical characteristics of the Asian specimens appear so unique to grant the establishment of a new taxon, for which the name Thaidasys tongiorgii gen. et sp. nov. is proposed, the result of phylogenetic analyses based on the 18S rRNA gene unites the new genus with the family Macrodasyidae.

Gastrotrichs are highly diverse and abundant in all aquatic ecosystems; however, they are often overlooked. During a biodiversity survey in Sardinia (Italy), a new species of gastrotrich herein described was discovered. Specimens of Urodasys bifidostylis sp. nov. were found in sandy sediments from two submarine caves. Using an integrative approach of traditional light (DIC) and high-resolution (CLSM) microscopies, we herein reveal, for the first time, the fine structure and function of the reproductive organ in an Urodasys representative. This is particularly relevant considering the complex reproductive organs and strategies of this group. Results allow comparisons between the reproductive apparatus and sperm transfer modalities in Urodasys and the closely related genus Macrodasys. One similarity is that both groups transfer male gametes in packets, suggesting the production of spermatophores to be a common phenomenon in Gastrotricha. Unique to Urodasys is the ability of multiple and consecutive copulations and sperm transfers and, differently than Macrodasys, the transfer of sperms unlikely occurs simultaneously between the two hermaphroditic partners. These findings provide new insights into the reproductive strategies of Urodasys and are expected to advance future studies on the evolution of reproductive strategies and the rise of interspecific reproductive barriers in interstitial meiofauna.

Biogeographical and macroecological principles are derived from patterns of distribution in large organisms, whereas microscopic ones have often been considered uninteresting, because of their supposed wide distribution. Here, after reporting the results of an intensive faunistic survey of marine microscopic animals (meiofauna) in Northern Sardinia, we test for the effect of body size, dispersal ability, and habitat features on the patterns of distribution of several groups. As a dataset we use the results of a workshop held at La Maddalena (Sardinia, Italy) in September 2010, aimed at studying selected taxa of soft-bodied meiofauna (Acoela, Annelida, Gastrotricha, Nemertodermatida, Platyhelminthes and Rotifera), in conjunction with data on the same taxa obtained during a previous workshop hosted at Tjärnö (Western Sweden) in September 2007. Using linear mixed effects models and model averaging while accounting for sampling bias and potential pseudoreplication, we found evidence that: (1) meiofaunal groups with more restricted distribution are the ones with low dispersal potential; (2) meiofaunal groups with higher probability of finding new species for science are the ones with low dispersal potential; (3) the proportion of the global species pool of each meiofaunal group present in each area at the regional scale is negatively related to body size, and positively related to their occurrence in the endobenthic habitat. Our macroecological analysis of meiofauna, in the framework of the ubiquity hypothesis for microscopic organisms, indicates that not only body size but mostly dispersal ability and also occurrence in the endobenthic habitat are important correlates of diversity for these understudied animals, with different importance at different spatial scales. Furthermore, since the Western Mediterranean is one of the best-studied areas in the world, the large number of undescribed species (37%) highlights that the census of marine meiofauna is still very far from being complete.

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.

Phylosymbiosis, the association between the phylogenetic relatedness of hosts and the composition of their microbial communities, is a widespread phenomenon in diverse animal taxa. However, the generality of the existence of such a pattern has been questioned in many animals across the tree of life, including small‐sized aquatic invertebrates. This study aims to investigate the microbial communities associated with poorly known marine interstitial nemerteans to uncover their microbiota diversity and assess the occurrence of phylosymbiosis. Specimens from various Central American sites were analyzed using morphology‐based taxonomy and molecular techniques targeting the host 18S rRNA gene whereas their microbial association was analyzed by targeting the prokaryotic 16S rRNA gene. Phylogenetic and statistical analyses were conducted to examine the potential effects of host nemertean taxa and sampling locations on the host‐associated microbial communities. The results provide compelling evidence of phylosymbiosis in meiofaunal nemertean species, highlighting the significant impact of host genetic relatedness on microbiome diversity in small‐sized animals. This finding supports previous studies that demonstrate how certain nemertean species harbor distinct microbial communities with functional and ecological implications. Given the remarkable diversity of meiofaunal animals—spanning numerous phyla with varying lifestyles and co‐existing in the same habitat—combined with advancements in multi‐omics approaches, there is a promising opportunity to deepen our understanding of the evolutionary and ecological interactions between hosts and their microbiota throughout the animal tree of life. This study explores phylosymbiosis, the connection between host phylogenetic relatedness and microbial community composition, in marine interstitial nemerteans. The research reveals compelling evidence of phylosymbiosis in these small aquatic animals, emphasizing the influence of host genetic relatedness on microbiome diversity.

This study shows the results of a rotifer faunistic survey in thalassic waters from 26 sites located in northeastern U.S. states and one in California. A total of 44 taxa belonging to 21 genera and 14 families were identified, in addition to a group of unidentifiable bdelloids. Of the fully identified species, 17 are the first thalassic records for the U.S., including Encentrum melonei sp. nov. and Synchaeta grossa sp. nov., which are new to science, and Colurella unicauda Eriksen, 1968, which is new to the Nearctic region. Moreover, a refined description of Encentrum rousseleti (Lie-Pettersen, 1905) is presented. During the survey, we characterized samples by different salinity values and ecosystems and compared species composition across communities to test for possible ecological correlations. Results indicate that both salinities and ecosystems are a significant predictor of rotifer diversity, supporting that biodiversity estimates of small species provide fundamental information for biomonitoring. Finally, we provide a comprehensive review of the diversity and distribution of thalassic rotifers in the United States. The results of the present study increase the thalassic rotifer record for the U.S. from about 105 (87 at species level) to 124 (106 at species level) taxa.

Oceanic islands, characterized by high levels of endemism and distinct faunas when compared to neighbouring continents, represent natural evolutionary laboratories for biologists to understand ecological and evolutionary processes. However, most studies on oceanic islands have focused on terrestrial and marine macrofaunal organisms, and ignored microscopic animals. We present here an inventory of all soft-bodied meiofaunal organisms collected during a 2-week workshop on the oceanic island of Lanzarote, Canary Islands. Our checklist included 239 species, with 88 of them endemic to the archipelago. The number of endemic species was lower in groups with a higher proportion of parthenogenetic species, while it was not significantly affected by body size and percentage of species with dispersal stages. A higher percentage of endemic species was found in isolated habitats and environments, with only annelids showing significantly higher number of endemic species in anchialine caves. Our results might be biased by the high number of indeterminate species found in our samples and the lack of knowledge of the meiofauna of the African coast. Our findings, however, provide the first insight of patterns of diversity of soft-bodied meiofauna in Atlantic oceanic islands, suggesting that island endemic species might also exist amongst microscopic animals.