Systematic analysis of the caridean shrimp superfamily Pandaloidea (Crustacea: Decapoda) based on molecular and morphological evidence.

One of the systematically controversial superfamilies in Caridea is the predominately deep-sea or cold water Pandaloidea, largely because this species-rich group of nearly 200 species in 25 genera exhibits a very high diversity of body forms and ecology. Although the relationships amongst the taxa within Pandaloidea have been repeatedly discussed based on morphology, no comprehensive molecular phylogeny exists. In this study, we present the first molecular phylogeny of the group, based on a combined dataset of two mitochondrial (12S and 16S rRNA) and six nuclear (ATP synthase ß-subunit, enolase, glyceraldehyde-3-phosphate dehydrogenase, histone 3, phosphoenolpyruvate carboxykinase and sodium-potassium ATPase α-subunit) markers, based on 62 species (about 1/3 of known biodiversity) in 22 genera (88% of genera) of two pandaloid families (Pandalidae, Thalassocarididae) and outgroups from seven other caridean families. With generally high support, the relationships within the clade are fully resolved. Pandalidae is shown to be paraphyletic with Thalassocarididae deeply nested within as a monophyletic group, and the latter is herein considered to be a synonym of Pandalidae. Five major clades are recovered, with the shallow water genera Anachlorocurtis, Chlorocurtis, Chlorotocella and Miropandalus forming a sister clade to the remaining genera. At the genus level, the phylogeny indicates Plesionika, Heterocarpus and Pandalus to be not monophyletic. The validity of Pandalopsis, Stylopandalus and Calipandalus is challenged and these genera are considered herein to be junior synonyms of Pandalus (Pandalopsis) and Plesionika (Stylopandalus and Calipandalus). Although not fully resolved, some evidence potentially considers Nothocaris to be a valid genus. Ancestral State Reconstruction successfully recovered 15 synapomorphies for the major clades, with 11 of them reported to be of systematic significance for the first time.

Paradoxium irvingi n.gen. n.sp. (Microsporidia) infecting the musculature of European pink shrimp Pandalus montagui.

This paper utilises histological, ultrastructure and molecular phylogenetic data to describe a novel genus and species (Paradoxium irvingi n.gen., n.sp.) within clade 5 of the phylum Microsporidia. The parasite infects the musculature of the pink shrimp Pandalus montagui captured from United Kingdom waters. The novel microsporidium is morphologically and phylogenetically dissimilar to its nearest phylogenetic branch relative Thelohania butleri infecting the sister shrimp taxon Pandalus jordani. Furthermore, it is morphologically distinct from the type species of the genus Thelohania, Thelohania giardi infecting European brown shrimp Crangon crangon. Since phylogenetic data pertaining to type T. giardi is not currently available, our discovery places some doubt on the likelihood that T. butleri represents the proposed surrogate for the type taxon. Further it demonstrates potential for significant morphological plasticity in this clade of muscle-infecting microsporidians of crustaceans which contains the genera Myospora, Cucumispora, Thelohania, and now Paradoxium. Since it cannot be stated with certainty that T. butleri (or other taxa within the clade) represent true close relatives of T. giardi, clarity on this issue will only occur with re-discovery and genotyping of type T. giardi infecting C. crangon from European waters.

Sequence comparison of the mitochondrial genomes of Plesionika species (Caridea: Pandalidae), gene rearrangement and phylogenetic relationships of Caridea.

Background: Despite the Caridean shrimps' vast species richness and ecological diversity, controversies persist in their molecular classification. Within Caridea, the Pandalidae family exemplifies significant taxonomic diversity. As of June 25, 2023, GenBank hosts only nine complete mitochondrial genomes (mitogenomes) for this family. The Plesionika genus within Pandalidae is recognized as polyphyletic. To improve our understanding of the mitogenome evolution and phylogenetic relationships of Caridea, this study introduces three novel mitogenome sequences from the Plesionika genus: P.  ortmanni, P. izumiae and P. lophotes. Methods: The complete mitochondrial genomes of three Plesionika species were sequenced utilizing Illumina's next-generation sequencing (NGS) technology. After assembling and annotating the mitogenomes, we conducted structural analyses to examine circular maps, sequence structure characteristics, base composition, amino acid content, and synonymous codon usage frequency. Additionally, phylogenetic analysis was performed by integrating existing mitogenome sequences of true shrimp available in GenBank. Results: The complete mitogenomes of the three Plesionika species encompass 37 canonical genes, comprising 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR). The lengths of these mitogenomes are as follows: 15,908 bp for P. ortmanni, 16,074 bp for P. izumiae and 15,933 bp for P. lophotes. Our analyses extended to their genomic features and structural functions, detailing base composition, gene arrangement, and codon usage. Additionally, we performed selection pressure analysis on the PCGs of all Pandalidae species available in Genbank, indicating evolutionary purification selection acted on the PCGs across Pandalidae species. Compared with the ancestral Caridea, translocation of two tRNA genes, i.e., trnP or trnT, were found in the two newly sequenced Plesionika species-P. izumiae and P. lophotes. We constructed a phylogenetic tree of Caridea using the sequences of 13 PCGs in mitogenomes. The results revealed that family Pandalidae exhibited robust monophyly, while genus Plesionika appeared to be a polyphyletic group. Conclusions: Gene rearrangements within the Pandalidae family were observed for the first time. Furthermore, a significant correlation was discovered between phylogenetics of the Caridea clade and arrangement of mitochondrial genes. Our findings offer a detailed exploration of Plesionika mitogenomes, laying a crucial groundwork for subsequent investigations into genetic diversity, phylogenetic evolution, and selective breeding within this genus.

Complete mitochondrial genome of green shrimp, Chlorotocus crassicornis (Crustacea: Decapoda: Pandalidae) in Korean water.

The complete mitochondrial genome of green shrimp, Chlorotocus crassicornis (Costa, 1871) was generated by the combination of next-generation sequencing platform and long PCR technique. The mitochondrial genome of C. crassicornis was 16,500 bp, in which 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and a putative control region was encoded. Based on the 13 protein-coding genes region, the phylogenetic tree was clearly demonstrated that C. crassicornis is closest to Pandalopsis japonica and Pandalus borealis with 77% identity. This mitogenome information will be helpful for the further studies of deep-sea fisheries resources management strategies in Korea including C. crassicornis species.

New records of six deep-sea caridean shrimps (Crustacea: Decapoda) from the Ryukyu Islands and its adjacent waters, southwestern Japan.

Six species of caridean shrimps from four families are recorded from Japanese waters for the first time on the basis of material from the Ryukyu Islands and its adjacent waters, collected during research cruises of the T/RV "Toyoshio-maru" of Faculty of Applied Biological Science, Hiroshima University: two species of Crangonidae, Lissosabinea unispinosa Komai, 2006 and Pseudopontophilus serratus Komai, 2004; one species of Oplophoridae, Systellaspis pellucida (Filhol, 1885); one species of Pandalidae, Calipandalus elachys Komai Chan, 2003; and two species of Pasiphaeidae, Pasiphaea debitusae Hayashi, 1999 and P. gracilis Hayashi, 1999. Of them, L. unispinosa, Pseudopontophilus serratus, Pasiphaea debitusae and P. gracilis are heretofore known from the South-West Pacific localities, and then the geographical ranges of these four species are greatly extended to the north and west. Illustrations and/or colour images are provided for each species to supplement previous descriptions and to give evidence for identification.

First zoeal stage of Plesionika crosnieri Chan Yu, 1991, P. ortmanni Doflein, 1902, and P. semilaevis Bate, 1888, with remarks on the early larvae of Plesionika Bate, 1888 (Crustacea, Decapoda).

The morphology of first stage zoea larvae of three pandalid shrimps Plesionika crosnieri Chan Yu, 1991, P. ortmanni Doflein, 1902, and P. semilaevis Bate, 1888 are described for the first time from larvae obtained in laboratory culture. The zoea I is compared amongst those species of the genus Plesionika with larval morphology known. It is found that the length of the rostrum, the number of anteroventral denticles on the carapace, presence of exopodal setae in the maxillule, and setation pattern of the peduncle of antennule, endopod of antenna, and coxa/basis of maxillipeds are useful characters in distinguishing these larvae.

Larval development to the first eighth zoeal stages in the deep-sea caridean shrimp Plesionika grandis Doflein, 1902 (Crustacea, Decapoda, Pandalidae).

The larvae of the deep-sea pandalid shrimp Plesionika grandis Doflein, 1902 were successfully reared in the laboratory for the first time. The larvae reached the eighth zoeal stage in 36 days, both of which are longest records for the genus. Early larval stages of P. grandis bear the general characters of pandalid shrimps and differ from the other two species of Plesionika with larval morphology known in the number of spines on the anteroventral margin of carapace, number of tubercles on antennule, endopod segmentation in antenna, and third maxilliped setation. Although members in Plesionika are often separated into species groups, members of the same species group do not necessarily have similar early larval morphology. Since the zoea VIII of P. grandis still lacks pleopods and fifth pereiopod, this shrimp likely has at least 12 zoeal stages and a larval development of 120 days.

A new species of shrimp of the genus Anachlorocurtis Hayashi, 1975 from the Red Sea, with range extension of A. commensalis Hayashi, 1975 (Crustacea, Decapoda, Pandalidae).

A new species of pandalid shrimp Anachlorocurtis occidentalis sp. n., associated with antipatharian corals, is described and illustrated from the north-eastern Red Sea. This new species is closely related to Anachlorocurtis commensalis Hayashi, 1975, the only other species in the genus, and can be distinguished by the more slender body and appendages; the carapace with 3 large, and one small, subtriangular lobes in the middorsal line; a flattened dorsal outline of the third abdominal segment; the sixth abdominal segment twice as long as fifth one; propodi of the ambulatory pereiopods bearing only a single posterior spinule; and harbouring 3-5 pairs of dorsolateral spines on the telson. A revised generic diagnosis is provided here to accommodate the present new species. The genetic divergence of mitochondrial gene cytochrome c oxidase subunit I (COI) between Anachlorocurtis occidentalis sp. n., and A. commensalis is 15.2-15.4%. Molecular analysis also confirmed a sister position of the genus Anachlorocurtis to Miropandalus. The present records of A. commensalis from Taiwan constitute an extension of the known range of the species.