Exploring Deep-Sea Biodiversity in the Porcupine Bank (NE Atlantic) through Fish Integrative Taxonomy

This study combined morphological and molecular approaches to the species assignment of several rare or poorly known deep-water fishes caught between 549 and 1371 m depth during a Spanish bottom trawl survey in the Porcupine Bank, west of Ireland. The following fish species were identified: Nessorhamphus ingolfianus (Schmidt, 1912), Borostomias antarcticus (Lönnberg 1905), Scopelosaurus lepidus (Krefft and Maul 1955), Bathypterois dubius Vaillant, 1888, Evermannella balbo (Risso, 1820), Antimora rostrata (Günther, 1878), Melanonus zugmayeri Norman, 1930, Lyconus brachycolus Holt and Byrne, 1906; Paraliparis hystrix Merrett, 1983, Neocyttus helgae (Holt and Byrne, 1908); Platyberyx opalescens Zugmayer, 1911; Howella atlantica Post and Quéro, 1991, Lycodes terraenovae Collett, 1896 and Pseudoscopelus altipinnis Parr, 1933. The presence of L. brachycolus, P. opalescens and P. altipinnis is reported for the first time in the Bank. The DNA barcoding results were largely consistent with morphological identification in 10 species but four did not fit the current taxonomy, indicating cases of potential cryptic speciation, misidentification, synonymy or recent diversification. Among them, the results strongly suggest that P. garmani and P. hystrix are conspecific, making P. hystrix a junior synonym of P. garmani.

DNA barcoding of native Caucasus herbal plants: potentials and limitations in complex groups and implications for phylogeographic patterns

DNA barcoding has rapidly become a useful complementary tool in floristic investigations particularly for identifying specimens that lack diagnostic characters. Here, we assess the capability of three DNA barcode markers (chloroplast rpoB, accD and nuclear ITS) for correct species assignment in a floristic survey on the Caucasus. We focused on two herbal groups with potential for ornamental applications, namely orchids and asterids. On these two plant groups, we tested whether our selection of barcode markers allows identification of the “barcoding gap” in sequence identity and to distinguish between monophyletic species when employing distance-based methods. All markers successfully amplified most specimens, but we found that the rate of species-level resolution amongst selected markers largely varied in the two plant groups. Overall, for both lineages, plastid markers had a species-level assignment success rate lower than the nuclear ITS marker. The latter confirmed, in orchids, both the existence of a barcoding gap and that all accessions of the same species clustered together in monophyletic groups. Further, it also allowed the detection of a phylogeographic signal.The ITS marker resulted in its being the best performing barcode for asterids; however, none of the three tested markers showed high discriminatory ability. Even if ITS were revealed as the most promising plant barcode marker, we argue that the ability of this barcode for species assignment is strongly dependent on the evolutionary history of the investigated plant lineage.

Another hitchhiker exposed: Diceratocephala boschmai (Platyhelminthes: Temnocephalida) found associated with ornamental crayfish Cherax spp.

There are known plenty tiny invertebrate species associated with decapod crustaceans. Our contribution documents the first record of New Guinean ornamental Cherax crayfish epibiont, Diceratocephala boschmai (Platyhelminthes: Temnocephalida) found in pet trade in the Czech Republic. Correct species assignment was confirmed by genetic barcoding. The pathway for introductions of organisms unintentionally moved in association with ornamental crayfish via the international trade has been highlighted. Although Cherax species survive in thermal waters in Europe, even potential introduction to these habitats posed threat to native crayfish ectosymbionts (branchiobdellids) thought similar ecological niche.

Common Terns Sterna hirundo incubating a Red-necked Grebe Podiceps grisegena egg

During a study of Red-necked Grebes Podiceps grisegena in Lake Slagsmyren, Sweden, a pair of Common Terns Sterna hirundo were observed to have placed their two eggs on a deserted, floating nest of a Red-necked Grebe. Prior to this, the grebes had laid one egg of their own in the nest and this egg was included by the terns in their clutch and incubated by them. The species assignment of the odd egg was confirmed with DNA sequencing. A lack of natural nest sites for the terns to use at the lake could have caused this somewhat unusual choice of a nest site. I discuss possible explanations for adopting a foreign egg, including the adaptive behavioural response to roll an egg into the nest bowl to salvage lost eggs, the incubation stimulus that foreign eggs or egg-like objects potentially provide, and the limited egg discrimination abilities of Common Terns. The incubation of a foreign egg may reasonably be assumed to cost energy but to be of little benefit, if any, to the incubator.

Taxonomical evaluation of plant genetic markers by Bayesian Classifier

DNA barcodes are standardized sequences that range between 400-800 bp, vary at different taxonomic levels, and make it possible to identify individuals of species that have been previously assigned taxonomically. Several barcodes have been identified in different groups in the tree of life. However, there are groups that lack an accurate DNA marker, and even more so, accurate strategies that enable verification of their taxonomic affiliation. Several DNA barcodes have been postulated for plants, nonetheless, their classification potential has not been evaluated for metabarcoding, and as a result, it would appear as no one of them excels above the others in this area. One tool that has recently gained traction is Naïve Bayesian Classifiers; this type of classifier is based on the independence of attributes and the allocation of categories in each context. The present study aims at evaluating the classification power of several plant genetic markers that have been proposed as barcodes (trnL, rpoB, rbcL, matK, psbA-trnH and psbK) using a Naïve Bayesian Classifier, in order to determine the markers with higher performance at different taxonomic levels for metabarcoding analysis and to identify problematic genera at the time of species assignment. We propose matK and trnL as potential candidates up to the genus assignment. Some problematic genera (Aegilops, Gueldenstaedtia, Helianthus, Oryza, Shorea, Thysananthus and Triticum) within certain families in a sample could lead to misclassification no matter which marker is used. Finally, we propose recommendations when performing taxonomic identification analysis of plants in samples with multiple individuals.

Learning from beautiful monsters: phylogenetic and morphogenetic implications of left-right asymmetry in ammonoid shells

Background Many pathologies that modify the shell geometry and ornamentation of ammonoids are known from the fossil record. Since they may reflect the developmental response of the organism to a perturbation (usually a sublethal injury), their study is essential for exploring the developmental mechanisms of these extinct animals. Ammonoid pathologies are also useful to assess the value of some morphological characters used in taxonomy, as well as to improve phylogenetic reconstructions and evolutionary scenarios. Results We report on the discovery of an enigmatic pathological middle Toarcian (Lower Jurassic) ammonoid specimen from southern France, characterized by a pronounced left-right asymmetry in both ornamentation and suture lines. For each side independently, the taxonomic interpretations of ornamentation and suture lines are congruent, suggesting a Hildoceras semipolitum species assignment for the left side and a Brodieia primaria species assignment for the right side. The former exhibits a lateral groove whereas the second displays sinuous ribs. This specimen, together with the few analogous cases reported in the literature, lead us to erect a new forma-type pathology herein called “forma janusa” for specimens displaying a left-right asymmetry in the absence of any clear evidence of injury or parasitism, whereby the two sides match with the regular morphology of two distinct, known species. Conclusions Since “forma janusa” specimens reflect the underlying developmental plasticity of the ammonoid taxa, we hypothesize that such specimens may also indicate unsuspected phylogenetic closeness between the two displayed taxa and may even reveal a direct ancestor-descendant relationship. This hypothesis is not, as yet, contradicted by the stratigraphical data at hand: in all studied cases the two distinct taxa correspond to contemporaneous or sub-contemporaneous taxa. More generally, the newly described specimen suggests that a hitherto unidentified developmental link may exist between sinuous ribs and lateral grooves. Overall, we recommend an integrative approach for revisiting aberrant individuals that illustrate the intricate links among shell morphogenesis, developmental plasticity and phylogeny.