A new species of cave crab, Stygothelphusa antu new species, is described from limestone formations in Temurang, Sarawak, Malaysia. The new species is the most highly adapted to a cavericolous lifestyle among the four known species of Stygothelphusa, having a pale body pigmentation, reduced eyes and elongated pereopods. In contrast, the other three species have normal eyes that almost completely fill the orbits. The new species also differs from its congeners by a number of carapace, pereopod and gonopod characters.
The identity of the common lowland freshwater crab in western Sarawak, Borneo, East Malaysia, Parathelphusa oxygona Nobili, 1901 (family Gecarcinucidae), is clarified. The species is redescribed and figured, and its taxonomy discussed. Specimens from western Kalimantan, Borneo, Indonesia, which have been referred to P. oxygona are here referred to a new species, Parathelphusa nobilii. The new species can be differentiated from congeners by its relatively more swollen branchial regions of the carapace, wider and lower external orbital tooth, relatively more slender male abdomen and a straight male first gonopod.
The male of Hexapinus latipes (De Haan, 1835), so far known only from female specimens, is described based on the material reported by De Man (1888) as "Hexapus sexpes". Material referred to "Hexapus sexpes" by Tesch (1918) is shown instead to belong to Hexapinus simplex Rahayu & Ng, 2014, and Hexapinus latus Rahayu & Ng, 2014, while his "Hexaplax megalops Doflein, 1904" belongs to Hexaplax aurantium Rahayu & Ng, 2014. A new species, Mariaplax aspera n. sp., is described from a female collected in Lombok, Indonesia. This new species most closely resembles M. narusei Rahayu & Ng, 2014, described from Japan, but differs by its relatively narrower carapace, shorter ambulatory legs, tuberculated third maxillipeds, and shorter telson.
Despite recent advances in sequencing technology, a complete mitogenome assembly is still unavailable for the gecarcinid land crabs that include the iconic Christmas Island red crab (Gecarcoidea natalis) which is known for its high population density, annual mass breeding migration and ecological significance in maintaining rainforest structure. Using sequences generated from Nanopore and Illumina platforms, we assembled the complete mitogenome for G. natalis, the first for the genus and only second for the family Gecarcinidae. Nine Nanopore long reads representing 0.15% of the sequencing output from an overnight MinION Nanopore run were aligned to the mitogenome. Two of them were >10 kb and combined are sufficient to span the entire G. natalis mitogenome. The use of Illumina genome skimming data only resulted in a fragmented assembly that can be attributed to low to zero sequencing coverage in multiple high AT-regions including the mitochondrial protein-coding genes (NAD4 and NAD5), 16S ribosomal rRNA and non-coding control region. Supplementing the mitogenome assembly with previously acquired transcriptome dataset containing high abundance of mitochondrial transcripts improved mitogenome sequence coverage and assembly reliability. We then inferred the phylogeny of the Eubrachyura using Maximum Likelihood and Bayesian approaches, confirming the phylogenetic placement of G. natalis within the family Gecarcinidae based on whole mitogenome alignment. Given the substantial impact of AT-content on mitogenome assembly and the value of complete mitogenomes in phylogenetic and comparative studies, we recommend that future mitogenome sequencing projects consider generating a modest amount of Nanopore long reads to facilitate the closing of problematic and fragmented mitogenome assemblies.
A new species of terrestrial sesarmid crab, Scandarma raymondi, is described from Sabah, Malaysia. This is the third species in the genus; others are from Taiwan, Japan and Sarawak, Borneo. The new species differs from congeners in the live coloration, proportions of the carapace and ambulatory legs and morphologies of the male abdomen, chela and male first gonopod.
A new species of gecarcinucid freshwater crab of the genus Parathelphusa H. Milne Edwards, 1853, is described from freshwater swamp habitats in Pekanbaru, Riau Province, in central-eastern Sumatra, Indonesia. Parathelphusa pardus sp. nov., has a very distinctive colour pattern, and in this respect, resembles P. maindroni (Rathbun, 1902) from Sumatra and Peninsular Malaysia; P. batamensis Ng, 1992, from Batam Island, Indonesia; P. reticulata Ng, 1990, from Singapore; and P. oxygona Nobili, 1901, from western Sarawak. It can be distinguished from these species and congeners by a suite of carapace, ambulatory leg, thoracic sternal and most importantly, male first gonopod characters.
The infraorder Anomura consists of a morphologically and ecologically heterogeneous group of decapod crustaceans, and has attracted interest from taxonomists for decades attempting to find some order out of the seemingly chaotic diversity within the group. Species-level diversity within the Anomura runs the gamut from the "hairy" spindly-legged yeti crab found in deep-sea hydrothermal vent environments to the largest known terrestrial invertebrate, the robust coconut or robber crab. Owing to a well-developed capacity for parallel evolution, as evidenced by the occurrence of multiple independent carcinization events, Anomura has long tested the patience and skill of both taxonomists attempting to find order, and phylogeneticists trying to establish stable hypotheses of evolutionary inter-relationships. In this study, we performed genome skimming to recover the mitogenome sequences of 12 anomuran species including the world's largest extant invertebrate, the robber crab (Birgus latro), thereby over doubling these resources for this group, together with 8 new brachyuran mitogenomes. Maximum-likelihood (ML) and Bayesian-inferred (BI) phylogenetic reconstructions based on amino acid sequences from mitogenome protein-coding genes provided strong support for the monophyly of the Anomura and Brachyura and their sister relationship, consistent with previous studies. The majority of relationships within families were supported and were largely consistent with current taxonomic classifications, whereas many relationships at higher taxonomic levels were unresolved. Nevertheless, we have strong support for a polyphyletic Paguroidea and recovered a well-supported clade of a subset of paguroids (Diogenidae + Coenobitidae) basal to all other anomurans, though this requires further testing with greater taxonomic sampling. We also introduce a new feature to the MitoPhAST bioinformatics pipeline (https://github.com/mht85/MitoPhAST) that enables the extraction of mitochondrial gene order (MGO) information directly from GenBank files and clusters groups based on common MGOs. Using this tool, we compared MGOs across the Anomura and Brachyura, identifying Anomura as a taxonomic "hot spot" with high variability in MGOs among congeneric species from multiple families while noting the broad association of highly-rearranged MGOs with several anomuran lineages inhabiting extreme niches. We also demonstrate the value of MGOs as a source of novel synapomorphies for independently reinforcing tree-based relationships and for shedding light on relationships among challenging groups such as the Aegloidea and Lomisoidea that were unresolved in phylogenetic reconstructions. Overall, this study contributes a substantial amount of new genetic material for Anomura and attempts to further resolve anomuran evolutionary relationships where possible based on a combination of sequence and MGO information. The new feature in MitoPhAST adds to the relatively limited number of bioinformatics tools available for MGO analyses, which can be utilized widely across animal groups.