Another plea for ‘best practice’ in molecular approaches to trematode systematics: Diplostomum sp. clade Q identified as Diplostomum baeri Dubois, 1937 in Europe

DNA sequence data became an integral part of species characterization and identification. Still, specimens associated with a particular DNA sequence must be identified by the use of traditional morphology-based analysis and correct linking of sequence and identification must be ensured. Only a small part of DNA sequences of the genus Diplostomum (Diplostomidae) is based on adult isolates which are essential for accurate identification. In this study, we provide species identification with an aid of morphological and molecular (cox1, ITS-5.8S-ITS2 and 28S) characterization of adults of Diplostomum baeri Dubois, 1937 from naturally infected Larus canus Linnaeus in Karelia, Russia. Furthermore, we reveal that the DNA sequences of our isolates of D. baeri are identical with those of the lineage Diplostomum sp. clade Q , while other sequences labelled as the ‘D. baeri’ complex do not represent lineages of D. baeri. Our new material of cercariae from Radix balthica (Linnaeus) in Ireland is also linked to Diplostomum sp. clade Q. We reveal that D. baeri is widely distributed in Europe; as first intermediate hosts lymnaeid snails (Radix auricularia (Linnaeus), R. balthica) are used; metacercariae occur in eye lens of cyprinid fishes. In light of the convoluted taxonomy of D. baeri and other Diplostomum spp., we extend the recommendations of Blasco-Costa et al. (2016, Systematic Parasitology 93, 295–306) for the ‘best practice’ in molecular approaches to trematode systematics. The current study is another step in elucidating the species spectrum of Diplostomum based on integrative taxonomy with well-described morphology of adults linked to sequences.

Description of Aurelia pseudosolida sp. nov. (Scyphozoa, Ulmaridae) from the Adriatic Sea

Until 2021, the genus Aurelia contained eleven described species (WoRMS, 2020), with many genetic species still awaiting a formal description. In 2021, ten new species of Aurelia were described almost solely from genetic data in a novel attempt to use genetic characters as diagnostic characters for species descriptions, leaving seven genetic species still undescribed. Here we present the description of a new Aurelia species from the Adriatic Sea using an integrative taxonomy approach, i.e., employing molecular as well as morphological characteristics in order to describe this new Aurelia species. The species is described based on a single medusa sampled from the town of Rovinj (Croatia), North Adriatic, amidst combined blooms of the ctenophore Mnemiopsis leidy and cnidarian Aurelia solida in the summer of 2020. Based on genetic data, the newly described Aurelia pseudosolida sp. nov. has never been sequenced in any of the previous investigations of the molecular diversity of Aurelia. This is the second species belonging to Discomedusae described from the North Adriatic in little more than half a decade, which could be yet another indication of the susceptibility of the North Adriatic to proliferation of non-indigenous gelatinous species, especially if we take into account historical as well as recent blooms of suspected non-indigenous gelatinous species such as Muggiaea atlantica, Aurelia solida, Mawia benovici and Mnemiopsis leidy.

Herzog Vindicated: Integrative Taxonomy Reveals that Trichostomum brachydontium (Pottiaceae, Bryophyta) Comprises Several Species

The morphologically variable moss Trichostomum brachydontium is very common in south and west Europe, particularly under Mediterranean and Atlantic climates. A morphological study was conducted alongside a molecular phylogenetic study based on nr ITS and cp rbcL regions in order to assess if T. brachydontium is an exceptionally polymorphic species as evidenced by the number of described infraspecific taxa from the last century or, alternatively, if it includes more than one species, and if so, to find the valid name for them. Phylogenetic analyses of both nuclear and chloroplast datasets show that there are four well-supported clades. While the ITS based tree is in good agreement with the morphological data, there are a few inconsistencies with reference to the rbcL tree; this may be explained by incomplete lineage sorting or by hybridization. The morphological survey revealed well-defined discriminate differences between the four phylogenetic lineages. The taxonomic conclusions include the recognition of four species: T. brachydontium s.s., T. herzogii (a new name proposed for var. cuspidatum), T. littorale and T. meridionale (a new name proposed for var. densum). Lectotypes are designated for T. brachydontium and T. littorale. Our results underline the ongoing need of integrative studies to examine further the underestimated diversity of the T. brachydontium complex in other regions.

Desoria calderonis sp. nov., a new species of alpine cryophilic springtail (Collembola: Isotomidae) from the Apennines (Italy), with phylogenetic and ecological considerations

We describe and delimit with integrative taxonomy the new springtail species Desoria calderonis sp. nov. (Collembola: Isotomidae). This cryophilic species is strictly linked to the supraglacial stony debris of the isolated Calderone glacier (Central Apennines, Italy), one of the southernmost glaciers of Europe. Desoria calderonis sp. nov. could belong to the nivalis-complex, a group of European mountain species included in the violacea-group. Genetic analysis (COI mtDNA barcoding) confirms the morphological attribution to the genus Desoria Nicolet in Desor, 1841, but highlights that the genus, in its current definition, is polyphyletic. We specify the peculiar micro-habitat preferences and highlight the threat of extinction for this cryophilic species in the context of the ongoing climate change and subsequent risk of complete disappearance of the glacier.

Postulating the Modality of Integrative Taxonomy in Describing the Cryptic Congener Pampus griseus (Cuvier) and Systematics of the Genus Pampus (Perciformes: Stromateidae)

Pomfrets (genus Pampus), a highly commercial fishery resource distributed in the Indo-Western Pacific that includes Lessepsian migrants, have witnessed a series of systematic reforms. In this study, based on comprehensive sampling spanning type localities and coevals in the Northern Indian Ocean, the cryptic and valid species Stromateus griseus is resurrected from the synonymy and re-described as Pampus griseus (New Combination) based on 35 specimens from the Bay of Bengal, corroborated by a molecular analysis, which indicated a confined distribution of the species. The Bayesian phylogeny of the genus was reconstructed, incorporating redressed barcodes (582 nucleotides) and concatenated mitochondrial gene sequence data (1,822 nucleotides) generated from the recorded species P. candidus, P. chinensis and the neophyte along with sequences from GenBank entrusting the latest literature. The phylograms differed in topology as for seven valid species, and the one predicated on the concatenated data erected a highly supported polytomous clade for the P. cinereus complex (P. griseus, P. cinereus, and P. candidus) which shares synapomorphies. Pampus argenteus and P. minor, together, formed a sister clade to the rest. Climate-driven vicariant events during glacial epochs and the Indo-Pacific Barrier effect can be the drivers behind the Indian and Pacific Ocean sister lineages in P. chinensis. A multivariate analysis isolated the cryptic species from its congeners. This article portrays the systematics revision of genus Pampus with an integrative taxonomic approach compiling distinctive molecular, morphological, and anatomical features, revised key for species identification, taxonomic archives of Indian stromateids, and winds up with specific remarks.

Dead man’s fingers point towards new species: A taxonomic revision of Alcyonium aurantiacum with statistical discrimination methods and a survey of integrative taxonomy in Octocorallia

<p><b>Octocorals are a diverse group of sessile, colonial, filter-feeding anthozoan cnidarians, which form significant components of benthic marine communities worldwide. Globally, the most critical hurdle to the effective management of octocorals in the face of increasing anthropogenic pressure is the poor state of their species-level taxonomy, which hinders understanding of their biodiversity. New Zealand’s octocoral assemblage is among the most diverse of any country and is characterised by high levels of endemism, yet over half of its octocoral species remain undescribed. While progress is being made, this has focussed almost exclusively on protected deep-sea gorgonian octocorals.</b></p> <p>Unprotected coastal soft corals are less studied in New Zealand. This includes the endemic Alcyonium aurantiacum Quoy and Gaimard, 1833. Multiple, morphologically diverse forms have been attributed to this species. Here, the taxonomic status of A. aurantiacum is reviewed, and its phylogenetic relationships are examined using molecular data (nuclear 28S and mitochondrial MutS genes), which is compared to morphology in an integrative approach. As a result, evidence for two new, endemic genera and ten new species is presented. Alcyonium aurantiacum is referred to Kotatea gen. n. (as K. aurantiaca comb. n.), which contains seven additional new species. A second genus, Ushanaia gen. n., contains three new species.</p> <p>Of the new taxa described herein, K. aurantiaca and K. lobata sp. n. are the most commonly encountered and widespread, yet little is known regarding their biology. Both species co-occur in their natural habitat, could not be differentiated genetically with the tools used here, and can be difficult to distinguish without microscopic sclerite examinations. To facilitate the identification of these two similar species by non-taxonomists, a statistical model was developed that can discriminate them with up to 90% accuracy using easily obtainable measurements of gross colony morphology. Relationships between colony morphology and depth are also examined.</p> <p>Considering the difficulties associated with species discrimination among octocorals, a literature survey was conducted to review the use of integrative taxonomy in this group since the start of the 21st century, focusing particularly on morpho-molecular data comparisons. This revealed that, while description rates at family, genus, and species levels over the last twenty-one years rank among the highest ever, integrative techniques have been applied unevenly across taxonomic groups and geographic regions and overall remain a minority compared to taxonomic research based solely on morphology. Implementation of the integrative approach is increasing, however, as are the per-annum number of taxonomic publications and the total pool of authors associated with these publications.</p> <p>It is hoped that the research presented herein can contribute to ongoing global efforts of revising octocoral systematics and that the examination of integrative practices in octocoral taxonomy will serve as a baseline against which future taxonomic progress can be compared and promoted. For New Zealand specifically, elucidating the taxonomy and variability of these endemic taxa will enable aspects such as their contribution to ecosystem functioning and management needs to be examined accurately for the first time, which in turn may lead to their recognition as organisms worthy of legal protection.</p>

Dead man’s fingers point towards new species: A taxonomic revision of Alcyonium aurantiacum with statistical discrimination methods and a survey of integrative taxonomy in Octocorallia

<p><b>Octocorals are a diverse group of sessile, colonial, filter-feeding anthozoan cnidarians, which form significant components of benthic marine communities worldwide. Globally, the most critical hurdle to the effective management of octocorals in the face of increasing anthropogenic pressure is the poor state of their species-level taxonomy, which hinders understanding of their biodiversity. New Zealand’s octocoral assemblage is among the most diverse of any country and is characterised by high levels of endemism, yet over half of its octocoral species remain undescribed. While progress is being made, this has focussed almost exclusively on protected deep-sea gorgonian octocorals.</b></p> <p>Unprotected coastal soft corals are less studied in New Zealand. This includes the endemic Alcyonium aurantiacum Quoy and Gaimard, 1833. Multiple, morphologically diverse forms have been attributed to this species. Here, the taxonomic status of A. aurantiacum is reviewed, and its phylogenetic relationships are examined using molecular data (nuclear 28S and mitochondrial MutS genes), which is compared to morphology in an integrative approach. As a result, evidence for two new, endemic genera and ten new species is presented. Alcyonium aurantiacum is referred to Kotatea gen. n. (as K. aurantiaca comb. n.), which contains seven additional new species. A second genus, Ushanaia gen. n., contains three new species.</p> <p>Of the new taxa described herein, K. aurantiaca and K. lobata sp. n. are the most commonly encountered and widespread, yet little is known regarding their biology. Both species co-occur in their natural habitat, could not be differentiated genetically with the tools used here, and can be difficult to distinguish without microscopic sclerite examinations. To facilitate the identification of these two similar species by non-taxonomists, a statistical model was developed that can discriminate them with up to 90% accuracy using easily obtainable measurements of gross colony morphology. Relationships between colony morphology and depth are also examined.</p> <p>Considering the difficulties associated with species discrimination among octocorals, a literature survey was conducted to review the use of integrative taxonomy in this group since the start of the 21st century, focusing particularly on morpho-molecular data comparisons. This revealed that, while description rates at family, genus, and species levels over the last twenty-one years rank among the highest ever, integrative techniques have been applied unevenly across taxonomic groups and geographic regions and overall remain a minority compared to taxonomic research based solely on morphology. Implementation of the integrative approach is increasing, however, as are the per-annum number of taxonomic publications and the total pool of authors associated with these publications.</p> <p>It is hoped that the research presented herein can contribute to ongoing global efforts of revising octocoral systematics and that the examination of integrative practices in octocoral taxonomy will serve as a baseline against which future taxonomic progress can be compared and promoted. For New Zealand specifically, elucidating the taxonomy and variability of these endemic taxa will enable aspects such as their contribution to ecosystem functioning and management needs to be examined accurately for the first time, which in turn may lead to their recognition as organisms worthy of legal protection.</p>

Trends in Taxonomy of Chagas Disease Vectors (Hemiptera, Reduviidae, Triatominae): From Linnaean to Integrative Taxonomy

Chagas disease is a neglected tropical disease caused by the protozoan Trypanosoma cruzi and transmitted mainly by members of the subfamily Triatominae. There are currently 157 species, grouped into 18 genera and five tribes. Most descriptions of triatomine species are based on classical taxonomy. Facing evolutionary (cryptic speciation and phenotypic plasticity) and taxonomic (more than 190 synonymizations) problems, it is evident that integrative taxonomy studies are an important and necessary trend for this group of vectors. Almost two-and-a-half centuries after the description of the first species, we present for the first time the state-of-the-art taxonomy of the whole subfamily, covering from the initial classic studies to the use of integrative taxonomy.

Integrative Taxonomy of Two Peruvian Strains of Brachionus plicatilis Complex with Potential in Aquaculture

Two Peruvian strains of the genus Brachionus were isolated from impacted coastal wetlands. With an integrative taxonomic view, we described their taxonomic status, morphological characters, productive parameters, and phylogenetic position. In the case of both strains, the relationship between biometrics and productive parameters obtained with Principal Components Analysis indicated that the lorica length was associated with longevity, progeny, egg production, and reproductive age, while the lorica width and aperture were associated with the maximum number of eggs carried. Maximum Likelihood and Bayesian Inference analysis carried out with mtDNA COI gene and rDNA ITS1 region showed that both strains were clustered in two clades with distinct phylogenetic positioning from what is currently known for Brachionus plicatilis s.l. One of the strains, Z010-VL, is proposed to be a subspecies of L4 (B. paranguensis), and the other strain, Z018-SD, is proposed as a sub species of SM2 (B. koreanus). In addition, 33 and 31 aquaculture production lineages are proposed, delimited by COI and concatenated COI+ITS1 sequences, respectively. Finally, this study provides new tools that enhance the traceability of the origin of each sub-species throughout the world.

Integrative taxonomy of two thrush complexes (Aves: Turdidae) reveals introgression across sister species

The classification of some Turdus species, such as the Naumann’s and dusky thrush complexes and the red-throated and black-throated thrush complexes, is controversial. Herein, we used molecular data (mitochondrial genes and microsatellite loci) and morphological characters to review the taxonomy of these thrush complexes and analyze the genetic differentiation between them. Our phylogenetic analysis based on mitochondrial genes indicated that all haplotypes could be divided into two reciprocally monophyletic sister clades corresponding to these two thrush complexes. The same results were revealed by coalescence-based species delimitation. Therefore, these two thrush complexes should be divided into two separate species (T. naumanni and T. ruficollis) and include two subspecies per species according to combined characters from morphological analyses and multilocus approaches. The above classifications were also supported by an analysis of genetic differentiation between T. naumanni and T. ruficollis and within each species. Moreover, there was significant mixing between these two thrush species in the neighbor-joining (NJ) tree and the cluster analysis of microsatellite loci. This led to a pattern of nuclear-mitochondrial discordance between the two species. This could be the result of extensive nuclear introgression between these two sister species. We also provide a potential explanation for the mechanism of gene introgression and nuclear-mitochondrial discordance between the two bird species.