Molecular identification and morphological characteristics of native and invasive Asian brush-clawed crabs (Crustacea: Brachyura) from Japanese and German coasts: Hemigrapsus penicillatus (De Haan, 1835) versus Hemigrapsus takanoi Asakura & Watanabe 2005

A new species of the genus Ptychognathus Stimpson, 1858 (Crustacea: Brachyura: Varunidae) from Vanuatu

Ptychognathus Stimpson, 1858 is a speciose genus in the family Varunidae, widely distributed in the Indo-West Pacific. Although species of Ptychognathus are common in estuaries with low salinity, some species are difficult to be identified correctly because of their small body size and similar morphology. This study describes one new species, Ptychognathus amikee sp. nov., from Vanuatu based on the morphological differences and the genetic data from mitochondrial cytochrome c oxidase subunit 1 (COI). This new species can be distinguished from the other congeners by the characters of the carapace, male chelipeds, and ambulatory legs.

A universal tool for marine metazoan species identification: towards best practices in proteomic fingerprinting

Proteomic fingerprinting using MALDI-TOF mass spectrometry is a well-established tool for identifying microorganisms and has shown promising results for identification of animal species, particularly disease vectors and marine organisms. And thus can be a vital tool for biodiversity assessments in ecological studies. However, few studies have tested species identification across different orders and classes. In this study, we collected data from 1246 specimens and 198 species to test species identification in a diverse dataset. We also evaluated different specimen preparation and data processing approaches for machine learning and developed a workflow to optimize classification using random forest. Our results showed high success rates of over 90%, but we also found that the size of the reference library affects classification error. Additionally, we demonstrated the ability of the method to differentiate marine cryptic-species complexes and to distinguish sexes within species.

An environmental gradient dominates ecological and genetic differentiation of marine invertebrates between the North and Baltic Sea

Environmental gradients have emerged as important barriers to structuring populations and species distributions. We set out to test whether the strong salinity gradient from the marine North Sea to the brackish Baltic Sea in northern Europe represents an ecological and genetic break, and to identify life history traits that correlate with the strength of this break. We accumulated mitochondrial cytochrome oxidase subunit 1 sequence data, and data on the distribution, salinity tolerance, and life history for 28 species belonging to the Cnidaria, Crustacea, Echinodermata, Mollusca, Polychaeta, and Gastrotricha. We included seven non‐native species covering a broad range of times since introduction, in order to gain insight into the pace of adaptation and differentiation. We calculated measures of genetic diversity and differentiation across the environmental gradient, coalescent times, and migration rates between North and Baltic Sea populations, and analyzed correlations between genetic and life history data. The majority of investigated species is either genetically differentiated and/or adapted to the lower salinity conditions of the Baltic Sea. Species exhibiting population structure have a range of patterns of genetic diversity in comparison with the North Sea, from lower in the Baltic Sea to higher in the Baltic Sea, or equally diverse in North and Baltic Sea. Two of the non‐native species showed signs of genetic differentiation, their times since introduction to the Baltic Sea being about 80 and >700 years, respectively. Our results indicate that the transition from North Sea to Baltic Sea represents a genetic and ecological break: The diversity of genetic patterns points toward independent trajectories in the Baltic compared with the North Sea, and ecological differences with regard to salinity tolerance are common. The North Sea–Baltic Sea region provides a unique setting to study evolutionary adaptation during colonization processes at different stages by jointly considering native and non‐native species.

The Entire Mitochondrial Genome of Macrophthalmus abbreviatus Reveals Insights into the Phylogeny and Gene Rearrangements of Brachyura

Brachyuran crabs comprise the most species-rich clades among extant Decapoda and are divided into several major superfamilies. However, the phylogeny of Brachyuran remains controversial, comprehensive analysis of the overall phylogeny is still lacking. Complete mitochondrial genome (mitogenome) can indicate phylogenetic relationships, as well as useful information for gene rearrangement mechanisms and molecular evolution. In this study, we firstly sequenced and annotated the complete mitogenome of Macrophthalmus abbreviatus (Brachyura; Macrophthalmidae). The mitogenome length of M. abbreviatus is 16,322 bp, containing the entire set of 37 genes and a control region typically observed in Brachyuran mitogenomes. The genome composition of M. abbreviatus was highly A+T biased 76.3% showing positive AT-skew (0.033) and negative GC-skew (- 0.351). In M. abbreviatus mitogenome, most tRNA genes were folded into the clover-leaf secondary structure except trnH, trnS1 and trnC, which was similar to the other species in Macrophthalmidae. Phylogenetic analysis showed that all families form a monophyletic, and Varunidae and Macrophthalmidae clustered into a monophyletic clade as sister groups. Comparative analyses of rearrangement among Brachyura revealed that Varunidae (Grapsoidea) and Macrophthalmidae (Ocypodoidea) had the same gene order, which reinforced the result of phylogeny. The combined results of two aspects revealed that the polyphyly of Ocypodoidea and Grapsoidea were well supported. In general, the results obtained in this research will contribute to further studies on molecular based for the classification and gene rearrangements of Macrophthalmidae or even Brachyura.

How dense is dense? Toward a harmonized approach to characterizing reefs of non-native Pacific oysters – with consideration of native mussels

Pacific oysters Crassostrea (Magallana) gigas have been successfully invading ecosystems worldwide. As an ecosystem engineer, they have the potential to substantially impact on other species and on functional processes of invaded ecosystems. Engineering strength depends on oyster density in space and time. Density has not yet been studied on the extent of reef structural dynamics. This study assessed abundance of naturalized Pacific oysters by shell length (SL) of live individuals and post-mortem shells at six sites over six consecutive years during post-establishment. Individual biomass, i.e. live wet mass (LWM), flesh mass (FM) and live shell mass (SM LIVE), were determined from a total of 1.935 live oysters in order to estimate areal biomass. The generic term density attribute was used for SL-related population categories and the biomass variables LWM, FM, SM LIVE and SM. As the oyster invasion modulated resident Mytilus edulis beds, the study was supplemented by contemporaneously assessed data of mussels and corresponding analyses.

Interrelations of abundance and areal biomass revealed distinct linkages between specific density attributes. Most importantly, large individuals were identified as intrinsic drivers for the determination of areal biomass. Additionally, allometry of large oysters differed from small oysters by attenuated scaling relations. This effect was enhanced by oyster density as results showed that crowding forced large individuals into an increasing slender shape. The significant relationship between the density attributes large oyster and biomass enabled a classification of reef types by large oyster abundance. Reef type (simple or complex reef) and oyster size (small or large) were considered by implementing a novel concept of weighted twin functions (TF) for the relationship between SL and individual biomass. This study demonstrates that the interplay of scaling parameters (scalar, exponent) is highly sensitive to the estimation of individual biomass (shape) and that putative similar scaling parameters can exceedingly affect the estimation of areal biomass.

For the first time, this study documents the crucial relevance of areal reference, i.e. cluster density (CD) or reef density (RD), when comparing density. RD considers reef areas devoid of oysters and results from CD reduced by reef coverage (RC) as the relative reef area occupied by oysters. A compilation of density attributes at simple and complex reefs shall serve as a density guide. Irrespective of areal reference, oyster structural density attributes were significantly higher at complex than at simple reefs. In contrast, areal reference was of vital importance when evaluating the impact of engineering strength at ecosystem-level. While mussel CD was similar at both reef types, RD at complex reefs supported significantly more large mussels and higher mussel biomass than at simple reefs. Although mussels dominated both reef types by abundance of large individuals, oysters were the keystone engineers by dominating biomass.

The prominent status of large oysters for both allometric scaling and density, presumably characteristic for Pacific oyster populations worldwide, should be considered when conducting future investigations. The effort of monitoring will substantially be reduced as only large oysters have to be counted for an empirical characterization of Pacific oyster reefs. The large oyster concept is independent of sampling season, assessment method or ecosystem, and is also applicable to old data sets. Harmonization on the proposed density attributes with a clear specification of areal reference will allow trans-regional comparisons of Pacific oyster reefs and will facilitate evaluations of engineering strength, reef performance and invasional impacts at ecosystem-level.

Metabarcoding of marine environmental DNA based on mitochondrial and nuclear genes

We establish the new approach of environmental DNA (eDNA) analyses for the North Sea. Our study uses a multigene approach, including the mitochondrial cytochrome-c-oxidase subunit I (COI) gene for analyzing species composition and the nuclear hypervariable region V8 of 18S rDNA for analyzing supraspecific biodiversity. A new minibarcode primer (124 bp) was created on the basis of a metazoan COI barcode library with 506 species and tested in silico, in vitro, and in situ. We applied high throughput sequencing to filtrates of 23 near-bottom water samples taken at three seasons from 14 stations. The set of COI primers allowed amplification of mitochondrial minibarcodes for diverse metazoan phyla and the differentiation at the species level for more than 99% of the specimens in the dataset. Our results revealed that the number of sequences is not consistent with proportions in the given DNA mixture. Altogether, environmental sequences could be assigned to 114 species and to 12 metazoan phyla. A spatial distribution of taxa recovered by eDNA was congruent with known distributions. Finally, the successful detection of species and biodiversity depends on a comprehensive sequence reference database. Our study offers a powerful tool for future biodiversity research, including the detection of nonnative species.

The Application of DNA Barcodes for the Identification of Marine Crustaceans from the North Sea and Adjacent Regions

During the last years DNA barcoding has become a popular method of choice for molecular specimen identification. Here we present a comprehensive DNA barcode library of various crustacean taxa found in the North Sea, one of the most extensively studied marine regions of the world. Our data set includes 1,332 barcodes covering 205 species, including taxa of the Amphipoda, Copepoda, Decapoda, Isopoda, Thecostraca, and others. This dataset represents the most extensive DNA barcode library of the Crustacea in terms of species number to date. By using the Barcode of Life Data Systems (BOLD), unique BINs were identified for 198 (96.6%) of the analyzed species. Six species were characterized by two BINs (2.9%), and three BINs were found for the amphipod species Gammarus salinus Spooner, 1947 (0.4%). Intraspecific distances with values higher than 2.2% were revealed for 13 species (6.3%). Exceptionally high distances of up to 14.87% between two distinct but monophyletic clusters were found for the parasitic copepod Caligus elongatus Nordmann, 1832, supporting the results of previous studies that indicated the existence of an overlooked sea louse species. In contrast to these high distances, haplotype-sharing was observed for two decapod spider crab species, Macropodia parva Van Noort & Adema, 1985 and Macropodia rostrata (Linnaeus, 1761), underlining the need for a taxonomic revision of both species. Summarizing the results, our study confirms the application of DNA barcodes as highly effective identification system for the analyzed marine crustaceans of the North Sea and represents an important milestone for modern biodiversity assessment studies using barcode sequences.