Molecular taxonomy and description of a new species of Limnodrilus (Naididae, Clitellata, Annelida) in China

The freshwater annelid worm genus Limnodrilus, including the widely distributed L. claparedianus Ratzel, 1868, is common in Chinese freshwater ecosystems. One species, previously recognized as morphologically intermediate between L. claparedianus and the North American taxon L. cervix Brinkhurst, 1963, is here described as a new species, L. paraclaparedianus Zhou & Cui n. sp., using both molecular and traditional taxonomy. Comparisons of sequences of the Cytochrome Oxidase subunit I (COI) mtDNA in a sample of Limnodrilus species showed that the distances between species were generally higher than the divergences within them. Phylogenetic analysis of COI as well as 16S mtDNA and Internal Transcribed Spacer 2 (ITS2) nDNA confirmed that the new species is an independent lineage. Moreover, morphological differences in the prostomium, characteristics of the chaetae and internal genitalia support the separation of the species.

BALLAST WATER: A POLYPHASIC APPROACH IN THE EVALUATION OF POTENTIAL PHYTOPLANKTONIC BIOINVASION

The main transport vector for exotic-invasive species around the world is ballast water in merchant ships, crossing natural biogeographic barriers. This is one of the main factors responsible for the reduction and homogenization of the global biota. As phytoplankton is the main group transported by these vessels, this study assesses the risk of bioinvasion in the port complex of Itajaí and Navegantes (southern Brazil), using a polyphasic approach, mixing classical taxonomy with molecular biology. Ballast water collections were carried out to analyze the traditional taxonomy and for clonal cultivation in the laboratory. A successful cultivation of 12 local strains and 10-ballast water was successful. In the latter case, some fresh water, contrary to the statement by the commanders of the exchange of water in the deep ocean (> 200 m). Molecular identification was performed by sequencing the complete ITS region, confirming the presence of Thalassiosira minuscula Krasske, 1941, harmful and of public health interest, previously not mentioned for the region. The species Pleurosigma W. Smith, 1852; Asterionellopsis glacialis (Castracane) Round, 1990; Trieres mobiliensis (Bailey) Ashworth and E.C. Theriot, 2013; Thalassiosira minima Gaarder, 1951; Skeletonema pseudocostatum Medlin, 1991; Pectinodesmus holtmannii E. Hegewald, C. Bock and Krienitz, 2013; Neodesmus Hindák, 1976; and Pseudopediastrum boryanum (Turpin) E. Hegewald, 2005, were identified. The results indicate the possibility of growth of the species found in the ballast environment, which may negatively alter the disposal environment. Keywords: exotic species, molecular identification, marine phytoplankton, port complex of Itajaí and Navegantes.

mproved Stereo Matching Algorithm based on Census Transform and Dynamic Histogram Cost Computation

Stereo matching is a significant subject in the stereo vision algorithm. Traditional taxonomy composition consists of several issues in the stereo correspondences process such as radiometric distortion, discontinuity, and low accuracy at the low texture regions. This new taxonomy improves the local method of stereo matching algorithm based on the dynamic cost computation for disparity map measurement. This method utilised modified dynamic cost computation in the matching cost stage. A modified Census Transform with dynamic histogram is used to provide the cost volume. An adaptive bilateral filtering is applied to retain the image depth and edge information in the cost aggregation stage. A Winner Takes All (WTA) optimisation is applied in the disparity selection and a left-right check with an adaptive bilateral median filtering are employed for final refinement. Based on the dataset of standard Middlebury, the taxonomy has better accuracy and outperformed several other state-ofthe-art algorithms. Keywords—Stereo matching, disparity map, dynamic cost, census transform, local method

The First Age of Reptiles? Comparing Reptile and Synapsid Diversity, and the Influence of Lagerstätten, During the Carboniferous and Early Permian

Terrestrial ecosystems during the Pennsylvanian (late Carboniferous) and Cisuralian (early Permian) are usually described in the literature as being dominated by synapsids, the mammal-line amniotes. The pelycosaurs (a paraphyletic grouping of synapsid families) have been considered more speciose, abundant, and ecologically diverse than contemporary reptile-line amniotes. However, this dominance has never been subjected to quantitative testing accounting for sampling bias. Moreover, in recent years the amniote phylogeny has undergone numerous revisions, with suggestions that varanopids and recumbirostran microsaurs fall within reptiles, and that diadectomorphs may be pelycosaurian-grade synapsids. An examination of local species richness (alpha diversity) of synapsids and reptiles during the Pennsylvanian and Cisuralian at different spatial scales shows that these taxonomic revisions have substantial impacts on relative diversity patterns of synapsids and reptiles. Synapsids are only found to be consistently more diverse through the early Permian when using the “traditional” taxonomy. The recent taxonomic updates produce diversity estimates where reptile diversity is consistent with, or in some cases higher than that of synapsids. Moreover, biases in preservation may affect patterns. Where preservation favors smaller vertebrates, e.g., Richards Spur, South Grandfield, reptiles overwhelmingly dominate. If smaller vertebrates are expected to make up the bulk of amniote diversity, as they do in the present day, such lagerstätten may be more representative of true diversity patterns. Therefore, the dominance of pelycosaurs during this interval should be reconsidered, and this interval may be considered the First Age of Reptiles.

Combining Traditional Taxonomy and Metabarcoding: Assemblage Structure of Nematodes in the Shelf Sediments of the Eastern Antarctic Peninsula

This study provides a snapshot of the largely understudied meiobenthic and nematode communities in the Prince Gustav Channel (PGC) and Duse Bay (DB). We compared five stations sampled at different water depths along the shelf and investigated their meiobenthic community structure. We approached nematode biodiversity combining traditional taxonomic identification and high throughput sequencing (HTS), with the use of Amplicon Sequence Variants (ASVs). Additionally, we characterized the environment by primary production proxies, grain size and seasonal ice conditions. Our results suggest that the availability of organic matter and its freshness are responsible for the high densities found at all depths. However, potential factors influencing the high local and regional variability of meiofauna density and biodiversity are less clear. A bathymetric transect consisting of three stations in DB (200, 500, and 1,000 m depth) showed increasing pigment concentrations in the first centimeters of the sediment vertical profile with increasing water depth, whereas the meiofauna densities showed the opposite trend. The deepest station of DB seems to function as a sink for fine material as supported by the higher silt fraction and higher organic matter concentrations. When comparing the two basins in the PGC (1,000 and 1,250 m) and the one in DB (1,000 m), differences in terms of environmental variables, meiofaunal densities, and composition were observed. The deepest basin in PGC is located further South (closer to the highly unstable Larsen area), and marked differences with the other basins suggest that it might be experiencing different conditions as a result of its presence near the summer ice margin and its more elongated topography. Both, the shallowest and the deepest stations showed the highest number of unique sequences, suggesting a more biodiverse nematode assemblage. The morphological identification did not show significant differences in the biodiversity of all stations, differently from the ASVs approach. However, the lack of reference sequences in online databases and the thickness of nematode’s cuticule are still important issues to consider as they potentially lead to underestimations of biodiversity and functional traits.

The speciation continuum and species relations between populations: in search of agreement between the theory and practice of systematics

From an evolutionary point of view, the achievement of species status by a group of populations is an ongoing process (except for rare cases of instantaneous speciation), during which isolated populations acquire traits and adaptations that minimize gene flow between them. However, depending on the group, the ways and timing of the gaining of reproductive isolation may be different. In such a complex group for systematics as small vipers (genus Vipera, subgenus Pelias), there are a number of problematic situations for species delimitation: the ability to form hybrids and hybrid populations between species, adaptive hybridization and hybrid speciation, and possible traces of reversed speciation, which indicate that complete and irreversible reproductive isolation may not be achieved at all. The effectiveness of reproductive isolation largely depends on external factors, mostly related to the range spatial structure, ecology of species in areas of sympatry, as well as climatic conditions and their changes, landscape dynamics, etc. The only species concept that allows to describe new species in the absence of reproductive isolation, recognizes the possibility of hybrid and reverse speciation — de Queiroz unified species concept — is practically unsuitable due to the need to consider as species a large number of isolated populations. Therefore, the solution is a conservative approach in practical taxonomy, which takes into account as a species criterion the ecological divergence of species, the possibility of their sympatric existence, which is usually achieved at 5% divergence of the mitochondrial cytochrome b gene. Stabilized hybrid populations occupying distinct ecological niche different from those of parental species also deserve recognition as species of hybrid origin. Not only species deserves to be protected, but also a distinguishable and diverged group of populations — Evolutionary Significant Unit (ESU) or subspecies in traditional taxonomy.

Caste-specific phenotypic plasticity of Asian weaver ants: Revealing the allometric and non-allometric component of female caste system of Oecophylla smaragdina (Hymenoptera: Formicidae) by using geometric morphometrics

In eusocial insects, particularly in ants, caste differentiation is extremely complicated when we rely on traditional taxonomy. In most species, the worker caste does not display any distinct morphological characters neither the caste’s central division according to their morphological size variations. We used a landmark-based geometric morphometric approach to quantify the morphological characteristics of female caste systems (queen, major and minor worker ant) of Oecophylla smaragdina. Our findings suggested that each caste has its unique shape and size. Especially in the worker caste, apart from the size variations, we can use the shape as a prominent tool for distinguishing between them. The O. smaragdina exhibits a triphasic allometry pattern. Studying the allometry and non-allometry components of each caste system revealed a highly complex size and shape relationship in the female caste systems. From the allometric and non-allometric analysis, we concluded that the major worker ants showed a closer relationship with the queen than the minor worker ant. This outcome demonstrated that Asian weaver ant exhibits complex shape variations related to size and is correlated to their functional modular characters. This research sheds new light on caste systems’ taxonomic uncertainties for eusocial hymenopteran groups, especially ants.

Hybridization and cryptic speciation in the Tropical Eastern Pacific octocoral genus Pacifigorgia

The shallow waters of the Tropical Eastern Pacific (TEP) harbor a species-rich octocoral fauna, with seven genera and 124 octocoral species described to date for the region. Of these lineages, Pacifigorgia, with 35 species, is by far the most speciose and abundant shallow-water octocoral occurring in the region. The speciation mechanisms resulting in this remarkable diversity remain speculative, despite the extensive taxonomic and molecular systematic research conducted so far in the TEP. Using genome-wide SNP markers, we provide evidence for hybridization and extensive cryptic speciation in Pacifigorgia, suggesting that the genus’ diversity has been underestimated by traditional and molecular systematic research. Our study highlights the difficulties faced by both traditional taxonomy and single-marker based molecular approaches to characterize octocoral diversity and evolution, and the role genome-wide molecular studies coupled to morphological research play to advance our understanding of this group.

DNA barcoding reveals an unknown Chironomidae diversity from the freshwater biodiversity hot-spot: comparison between local and the European datasets

In the present study, we developed and evaluated the first reference barcode library for non-biting midges (Diptera: Chironomidae) as flagship taxa of freshwater ecology from Skadar Lake system (Montenegro and Albania), a well-known hotspot of freshwater biodiversity composed by the young lake Skadar (originated 1200 before present) and by its old system of springs (originated during Pliocene). Using an expanded reference library and records deposited in Barcode of Life Database (BOLD), we estimated DNA barcoding efficiency for the European Chironomidae. Study provides COI barcodes for 770 Chironomidae individuals assigned, based on morphology, to 77 species collected in the Skadar Lake basin. Molecular analyses assigned sequences to 100 BINs and 104 OTUs (all records from this area are new for online repositories) and confirms the usefulness of DNA barcoding for the identification of non-biting midges. Additionally, we explored chironomid species distribution patterns in Europe using universal Barcode Index Number (BIN) with a discussion of problematic species groups, both for traditional taxonomy and DNA barcoding. The results of our study provide the first insight into the factual chironomid species diversity of the Lake Skadar basin, in comparison with chironomid fauna at the European scale. The results fill a significant gap in knowledge of biodiversity in the Balkan region. Based on the results of Chironomidae fauna investigation, we conclude that the Skadar Lake basin is now well sampled and such a high representation of species from various sampling sites provides reliable estimation of the non-biting midges fauna.

Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)

The ant genus Syscia Roger, 1861 is part of the cryptic ant fauna inhabiting leaf litter and rotten wood in the Asian and American tropics. It is a distinct clade within the Dorylinae, the subfamily from which army ants arose. Prior to this work, the genus comprised seven species, each known from a single or very few collections. Extensive collecting in Middle America revealed an unexpected and challenging diversity of morphological forms. Locally distinct forms could be identified at many sites, but assignment of specimens to species spanning multiple sites was problematic. To improve species delimitation, Ultra-Conserved Element (UCE) phylogenomic data were sequenced for all forms, both within and among sites, and a phylogeny was inferred. Informed by phylogeny, species delimitation was based on monophyly, absence of within-clade sympatry, and a subjective degree of morphological uniformity. UCE phylogenomic results for 130 specimens were complemented by analysis of mitochondrial COI (DNA barcode) data for an expanded taxon set. The resulting taxonomy augments the number of known species in the New World from 3 to 57. We describe and name 31 new species, and 23 species are assigned morphospecies codes pending improved specimen coverage. Queens may be fully alate or brachypterous, and there is a wide variety of intercaste female forms. Identification based on morphology alone is very difficult due to continuous character variation and high similarity of phylogenetically distant species. An identification aid is provided in the form of a set of distribution maps and standard views, with species ordered by size.