DeSignate: detecting signature characters in gene sequence alignments for taxon diagnoses

Ocean Species Discoveries 1-12 - A primer for accelerating marine invertebrate taxonomy

Background

Discoveries of new species often depend on one or a few specimens, leading to delays as researchers wait for additional context, sometimes for decades. There is currently little professional incentive for a single expert to publish a stand-alone species description. Additionally, while many journals accept taxonomic descriptions, even specialist journals expect insights beyond the descriptive work itself. The combination of these factors exacerbates the issue that only a small fraction of marine species are known and new discoveries are described at a slow pace, while they face increasing threats from accelerating global change. To tackle this challenge, this first compilation of Ocean Species Discoveries (OSD) presents a new collaborative framework to accelerate the description and naming of marine invertebrate taxa that can be extended across all phyla. Through a mode of publication that can be speedy, taxonomy-focused and generate higher citation rates, OSD aims to create an attractive home for single species descriptions. This Senckenberg Ocean Species Alliance (SOSA) approach emphasises thorough, but compact species descriptions and diagnoses, with supporting illustrations and with molecular data when available. Even basic species descriptions carry key data for distributions and ecological interactions (e.g., host-parasite relationships) besides universally valid species names; these are essential for downstream uses, such as conservation assessments and communicating biodiversity to the broader public.

New information

This paper presents thirteen marine invertebrate taxa, comprising one new genus, eleven new species and one re-description and reinstatement, covering wide taxonomic, geographic, bathymetric and ecological ranges. The taxa addressed herein span three phyla (Mollusca, Arthropoda, Echinodermata), five classes, eight orders and twelve families. Apart from the new genus, an updated generic diagnosis is provided for four other genera. The newly-described species of the phylum Mollusca are Placiphorellamethanophila Vončina, sp. nov. (Polyplacophora, Mopaliidae), Lepetodrilusmarianae Chen, Watanabe & Tsuda, sp. nov. (Gastropoda, Lepetodrilidae), Shinkailepasgigas Chen, Watanabe & Tsuda, sp. nov. (Gastropoda, Phenacolepadidae) and Lyonsiellaillaesa Machado & Sigwart, sp. nov. (Bivalvia, Lyonsiellidae). The new taxa of the phylum Arthropoda are all members of the subphylum Crustacea: Lepechinellanaces Lörz & Engel, sp. nov. (Amphipoda, Lepechinellidae), Cuniculomaeragrata Tandberg & Jażdżewska, gen. et sp. nov. (Amphipoda, Maeridae), Pseudionellapumulaensis Williams & Landschoff, sp. nov. (Isopoda, Bopyridae), Mastigoniscusminimus Wenz, Knauber & Riehl, sp. nov. (Isopoda, Haploniscidae), Macrostylispapandreas Jonannsen, Riehl & Brandt, sp. nov. (Isopoda, Macrostylidae), Austroniscusindobathyasellus Kaiser, Kniesz & Kihara, sp. nov. (Isopoda, Nannoniscidae) and Apseudopsisdaria Esquete & Tato, sp. nov. (Tanaidacea, Apseudidae). In the phylum Echinodermata, the reinstated species is Psychropotesbuglossa E. Perrier, 1886 (Holothuroidea, Psychropotidae).The study areas span the North and Central Atlantic Ocean, the Indian Ocean and the North, East and West Pacific Ocean and depths from 5.2 m to 7081 m. Specimens of eleven free-living and one parasite species were collected from habitats ranging from an estuary to deep-sea trenches. The species were illustrated with photographs, line drawings, micro-computed tomography, confocal laser scanning microscopy and scanning electron microscopy images. Molecular data are included for nine species and four species include a molecular diagnosis in addition to their morphological diagnosis.The five new geographic and bathymetric distribution records comprise Lepechinellanaces Lörz & Engel, sp. nov., Cuniculomaeragrata Tandberg & Jażdżewska, sp. nov., Pseudionellapumulaensis Williams & Landschoff, sp. nov., Austroniscusindobathyasellus Kaiser, Kniesz & Kihara, sp. nov. and Psychropotesbuglossa E. Perrier, 1886, with the novelty spanning from the species to the family level. The new parasite record is Pseudionellapumulaensis Williams & Landschoff, sp. nov., found in association with the hermit crab Pagurusfraserorum Landschoff & Komai, 2018.

Validation and redescription of Acanthamoeba terricola Pussard, 1964 (Amoebozoa: Acanthamoebidae)

Acanthamoeba castellanii (Douglas, 1930) Page, 1967 is the type species of a widespread genus of free-living amoebae, potentially pathogenic for humans and animals. The Neff strain is one of the most widely used in biological research, serving as a model for both A. castellanii and the whole genus in general. The Neff strain, isolated in California, closely resembles another strain found in France and originally described as a separate species, Acanthamoeba terricola Pussard, 1964, but both were successively synonymized with A. castellanii. Molecular sequence analysis has largely replaced morphological diagnosis for species identification in Acanthamoeba, and rDNA phylogenies show that the Neff strain forms a distinct lineage from that of the type strain of A. castellanii. In this study, we compared the type strain of A. terricola with the Neff strain and A. castellanii, and analysed the available molecular data including new sequences obtained from A. terricola. Here we provide molecular evidence to validate the species A. terricola. The Neff strain is therefore transferred to A. terricola and should no longer be considered as belonging to A. castellanii.

A morphological and molecular study of Ligia exotica Roux, 1828 (Crustacea: Isopoda: Ligiidae) from Japan, with descriptions of two new species

Ligia exotica Roux, 1828 was originally described based on specimens collected on a ship that came from Cayenne in French Guiana, and has been known to be widely distributed in the world. In Japan this species is the most common in Ligia, and two forms of L. exotica inhabit Osaka Bay, central Japan. To reveal the accurate scientific names of the two forms, we examined not only the detailed morphology but also 16S rRNA and NaK nucleotide sequences, together with L. exotica from another Japanese locality and the related species, L. shinjiensis Tsuge, 2008. As a result, three species, Ligia exotica, L. furcata sp. nov. and L. laticarpa sp. nov., are recognized in four localities, and L. shinjiensis is synonymized with L. exotica. Ligia exotica is characterized by the dentate lacinia mobilis on the right mandible and the appendix masculina lacking a projection. Ligia furcata and L. laticarpa are also characterized by the furcate propodus of the male pereopod 1 and the appendix masculina with an angular projection, and the swollen carpus of the male pereopod 1 and the appendix masculina with a rounded projection, respectively. The three species are distinguishable from one another mainly based on the shapes of pereopods 1-3 in both sexes and the appendix masculina of male. The 16S rRNA analysis confirms the results of the morphological study, and reveals that L. exotica and L. laticarpa also inhabit all over the world (e.g., East Asia, Southeast Asia, India, Africa, the Americas and Hawaii), and China and South Korea, respectively.

DNA barcodes reliably differentiate between nivicolous species of Diderma (Myxomycetes, Amoebozoa) and reveal regional differences within Eurasia

The nivicolous species of the genus Diderma are challenging to identify, and there are several competing views on their delimitation. We analyzed 102 accessions of nivicolous Diderma spp. that were sequenced for two or three unlinked genes to determine which of the current taxonomic treatments is better supported by molecular species delimitation methods. The results of a haplotype web analysis, Bayesian species delimitation under a multispecies coalescent model, and phylogenetic analyses on concatenated alignments support a splitting approach that distinguishes six taxa: Diderma alpinum, D. europaeum, D. kamchaticum, D. meyerae, D. microcarpum and D. niveum. The first two approaches also support the separation of Diderma alpinum into two species with allopatric distribution. An extended dataset of 800 specimens (mainly from Europe) that were barcoded with 18S rDNA revealed only barcode variants similar to those in the species characterized by the first data set, and showed an uneven distribution of these species in the Northern Hemisphere: Diderma microcarpum and D. alpinum were the only species found in all seven intensively sampled mountain regions. Partial 18S rDNA sequences serving as DNA barcodes provided clear signatures that allowed for unambiguous identification of the nivicolous Diderma spp., including two putative species in D. alpinum.

DNA Barcodes in Taxonomic Descriptions

This chapter discusses methods for incorporating DNA barcode information into formal taxonomic descriptions. We first review what a formal description entails and then discuss previous attempts to incorporate barcode information into taxonomic descriptions. Several computer programs are listed that extract diagnostics from DNA barcode data. Finally, we examine a test case (Astraptes taxonomy).

DNA Barcode-Based Species Diagnosis with MolD

Rapid biodiversity loss sets new requirements for taxonomic research, prompting updating some long-established practices to maximize timely documentation of species before they have gone extinct. One of the crucial procedures associated with the description of new taxa in Linnean taxonomy is assigning them a diagnosis, which is an account of the specific features of the taxon, differentiating it from already described species. Traditionally, diagnostic characters have been morphological, but especially in the case of morphologically cryptic species, molecular diagnoses become increasingly important. In this chapter, we provide detailed protocols for molecular taxon diagnosis with the bioinformatic tool MolD which is available as open-source Python code, command-line driven binary, GUI-driven executable for Windows and Mac, and Galaxy implementation. MolD identifies diagnostic combinations of nucleotides (DNCs) in addition to single (pure) diagnostic sites, enabling users to base DNA diagnoses on a minimal number of diagnostic sites necessary for reliable differentiation of taxa.

Tightening the requirements for species diagnoses would help integrate DNA-based descriptions in taxonomic practice

Modern advances in DNA sequencing hold the promise of facilitating descriptions of new organisms at ever finer precision but have come with challenges as the major Codes of bionomenclature contain poorly defined requirements for species and subspecies diagnoses (henceforth, species diagnoses), which is particularly problematic for DNA-based taxonomy. We, the commissioners of the International Commission on Zoological Nomenclature, advocate a tightening of the definition of "species diagnosis" in future editions of Codes of bionomenclature, for example, through the introduction of requirements for specific information on the character states of differentiating traits in comparison with similar species. Such new provisions would enhance taxonomic standards and ensure that all diagnoses, including DNA-based ones, contain adequate taxonomic context. Our recommendations are intended to spur discussion among biologists, as broad community consensus is critical ahead of the implementation of new editions of the International Code of Zoological Nomenclature and other Codes of bionomenclature.

DNA Barcoding of Moon Jellyfish (Cnidaria, Scyphozoa, Ulmaridae, Aurelia): Two Cryptic Species from the Azores (NE Atlantic, Macaronesia), and Evaluation of the Non-Indigenous Species (NIS)

Moon jellies are some of the most popular, widely distributed, and best-studied marine jellyfish. By the end of the past century only two or three Aurelia species were recognized, but with the rise of DNA barcoding studies, around thirty Aurelia species are presently accepted. Most of the species are morphologically indistinguishable and have restricted biogeography. We reveal, with COI, 16S, and ITS1-5.8S sequence data, two (pseudo-)cryptic species of Aurelia, potentially endemic to the Azores ecoregion, herein provisionally classified as A. “cf. pseudosolida” and A. “misteriosa”. These species are closely related to the Mediterranean lineages of A. pseudosolida and A. persea, respectively. In the Azores, the shape of the campanula and oral arms readily distinguishes the two species: the former with folded oral arms and globose campanula, and the latter with flattened campanula and thick and long oral arms. Previous reports of A. solida and A. aurita in the Azores should generally correspond to A. “misteriosa” and A. cf. pseudosolida, respectively. The phylogenetic (re-)examination of the available DNA barcodes of Aurelia only evidenced human-mediated dispersal for A. coerulea, A. relicta, and A. aurita. Aurelia solida cannot be yet considered NIS in the Mediterranean. More jellyfish DNA (meta)barcoding should reveal further cryptic diversity, biological invasions, and phylogeographic inferences.

The importance of molecular characters when morphological variability hinders diagnosability: systematics of the moon jellyfish genus Aurelia (Cnidaria: Scyphozoa)

Cryptic species have been detected across Metazoa, and while no apparent morphological features distinguish them, it should not impede taxonomists from formal descriptions. We accepted this challenge for the jellyfish genus Aurelia, which has a long and confusing taxonomic history. We demonstrate that morphological variability in Aurelia medusae overlaps across very distant geographic localities. Even though some morphological features seem responsible for most of the variation, regional geographic patterns of dissimilarities are lacking. This is further emphasized by morphological differences found when comparing lab-cultured Aurelia coerulea medusae with the diagnostic features in its recent redescription. Previous studies have also highlighted the difficulties in distinguishing Aurelia polyps and ephyrae, and their morphological plasticity. Therefore, mostly based on genetic data, we recognize 28 species of Aurelia, of which seven were already described, 10 are formally described herein, four are resurrected and seven remain undescribed. We present diagnostic genetic characters for all species and designate type materials for newly described and some resurrected species. Recognizing moon jellyfish diversity with formal names is vital for conservation efforts and other studies. This work clarifies the practical implications of molecular genetic data as diagnostic characters, and sheds light on the patterns and processes that generate crypsis.

Describing the hidden species diversity of Chaetozone (Annelida, Cirratulidae) in the Norwegian Sea using morphological and molecular diagnostics

Using molecular markers and species delimitation analyses, a high diversity of bi-tentaculate Cirratulidae was discovered from the North-East Atlantic. Five new species are described: Chaetozone pseudosetosa sp. nov., Chaetozone quinta sp. nov., Chaetozone barentsensis sp. nov., Chaetozone monteverdii sp. nov., and Chaetozone chambersae sp. nov. Several morphogroups are also described, even though the presence of cryptic diversity prevented naming of individual species. For each species presented, a molecular diagnostic is given from the universal barcode COI and, when available, the D1-D2 domains of the 28S rRNA. This increases the number of species in Chaetozone in northern European waters from ten to at least 17 species, the exact number of species remaining uncertain as taxonomic issues with older names remain unresolved.

Morphology and ontogenesis of two new Hemiholosticha species (Ciliophora, Hypotrichia, Hemiholostichidae nov. fam.)

The morphology and ontogenesis of two new hypotrich ciliates, Hemiholosticha solitaria and Hemiholosticha germanica, were studied using live observation, protargol impregnation, and scanning electron microscopy. Both species share a medium-sized, almost globular body with a short anterior projection; two macronuclear nodules with a single micronucleus in between; a central contractile vacuole; three or four ventral, one postoral, one right and one left marginal cirral row; and three dorsal kineties extending along ribs. However, H. germanica is distinguished from congeners by a higher number of cirri in ventral rows R1 and R2 (3-6 vs. 2 cirri in each row). Hemiholosticha solitaria differs from congeners by having four (vs. three) ventral cirral rows and by the lack (vs. presence) of intracellular green algae. The ontogenesis of H. solitaria follows the H. pantanalensis mode in that (i) the oral primordium develops in a deep pouch and generates the first two cirral streaks in addition to adoral membranelles and undulating membranes, (ii) the undulating membrane anlage does not produce any cirri, and (iii) the longitudinal ventral cirral row R3 originates from two anlagen. The ontogenetic peculiarities along with the 18S rRNA gene phylogenies suggest classification of Hemiholosticha, Psilotrichides, and Urospinula into a new family, Hemiholostichidae.

Colpodean ciliate phylogeny and reference alignments for phylogenetic placements

The Colpodea form a major clade of ciliates that are often found in environmental DNA sequencing studies. They are united by similar somatic ciliature, but differentiated by complex oral structures. Although there are four well supported colpodean subclades, there is disagreement in molecular phylogenetic inferences about their branching order. Using available nuclear SSU-rRNA sequences, we evaluated if the bursariomorphids or the platyophryids are sister to the remaining colpodeans. We inferred the "platyophryids-early" topologies using different alignment and masking methods, but constrained analyses could not reject the "bursariomorphids-early" topology. Both bursariomorphids and platyophryids clades have a similar number of nucleotide positions shared with the outgroup, and both are interconnected with the outgroup in phylogenetic networks. Based on these discordant results, it is hard to determine which clade branched off first, although the "platyophryids-early topology" is also supported by mitochondrial SSU-rRNA data. We also offer different reference alignments that can be used to phylogenetically place short- and long-read data from environmental DNA sequencing studies, and we propose some tentative evolutionary and ecological interpretations of those placements.